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CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
ANTISENSE MODULATION OF Navl.3 EXPRESSION
The present application claims priority under Title 35, United States Code,
~ 119 to United States Provisional application Serial No. 60/403,416, filed
August 14, 2002, which is incorporated by reference in its entirety as if
written herein.
FIELD OF THE INVENTION
[001] The present invention provides compositions and methods for
modulating the expression of Type III sodium channel (Navl.3). In
particular, this invention relates to antisense compounds, particularly
oligonucleotides, specifically hybridizable with nucleic acids encoding Type
III sodium channel (Navl.3). Such oligonucleotides have been shown to
modulate the expression of Type III sodium channel (Navl.3).
BACKGROUND OF THE INVENTION
.. [002] Voltage-dependent sodium channels play a fundamental role in
controlling neuronal membrane excitability. They are responsible for the
upstroke of the action potential in neurons. Neuropathic pain is considered
to be the result of injured and/or remodeled neurons, which exhibit an
increase in excitability in both primary afferent fibers and synaptic contacts
within the central pain processing pathway. Thus it is not surprising that
three of the four drugs of choice used in the treatment of neuropathic pain
syndromes are sodium channel blockers. These include carbamazepine,
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lamotrigine, and phenytoin. In addition, lidocaine, another sodium channel
Mocker, was recently approved for treatment of certain types of neuropathic
pain. However, although sodium channel blockers are currently the
treatment of choice for neuropathic pain, they have been only moderately
successful in treating these conditions. A primary factor in the weak
efficacy of these compounds is their lack of selectivity and low affinity for
the various sodium channels resulting in numerous side effects including
emesis, dizziness, ataxia, and cardiotoxicity.
[003] Many recent efforts have been focused on defining and
describing which sodium channels are actively involved in the development
and maintenance of neuropathic pain. The alpha subunit is the pore forming
subunit and to date, 11 alpha subunits have been identified including 7
neuronal, 2 glial, 1 muscular, 1 cardiac subunit. The alpha subunits can be
divided into three classes based on their sensitivity to tetrodotoxin (TTX):
TTX sensitive (TTXs), TTX resistant (TTXr), and TTX insensitive (TTXi).
TTXs channels are sensitive to TTX in the nanomolar range, have a low
threshold for activation and rapid inactivation kinetics. These channels
include the skeletal muscle channel, two channels that are found primarily in
peripheral neurons and all brain type channels described thus far.
[004] Recent reports have suggested that the type III sodium channel
(Navl.3) may also be involved in neuropathic pain development and
maintenance. This particular channel is found in brain, peripheral nerve
and, neuroendocrine cells. Critically, it is absent from heart and many other
peripheral organs. The mRNA for Navl .3 increases in small and large DRG
neurons following axotomy in animal models (Dib-Hajj S, et al.,
2
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Proc.Natl.Acad.Sci. 1996; 93:14950-14954), suggesting its involvement in
neuropathic pain. It has recently been demonstrated that peripheral nerve
damage produced a large increase in the expression of a tetrodotoxin (TTX)-
sensitive Navl .3 sodium channel (Boucher TJ, et al., Science 2000;
290:124-127) They also replicated past experiments from several labs
establishing that the development of neuropathic pain is linked to increased
spontaneous activity following nerve damage and that this ectopic activity is
sensitive to TTX. Finally, the study from Wood's group also found that
glial-derived neurotrophic factor (GDNF) prevented the induction of
Navl.3, reduced the spontaneous activity of the injured nerve, thus
preventing the resulting neuropathic pain. These studies implicated TTX-
sensitive sodium channels, and in particular Navl.3, as having a role in the
development and maintenance of neuropathic pain that follows nerve
damage.
[005] Despite the variety of sodium channel inhibitors disclosed in the
art, there still remains a need for therapeutic agents capable of effectively
and specifically inhibiting the function of the Type III sodium channel
(Navl.3). Furthermore, antisense technology could specifically target
neonatal vs. adult forms of Navl .3. Exon 6 of the Navl .3 gene is
alternatively spliced in humans (Lu C-M, Brown GB. J. Mol. Neu~osci.
1988; 10:67-70) and rodents (Gustafson TA, et al.. J. Biol. Claena. 1993;
268:18648-53). The two alternative exon 6 sequences are very similar,
differing by only a single amino acid at the protein level, but they could be
targeted individually by sequence-specific antisense oligonucleotides. This
3
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could be useful in the treatment of certain pediatric disorders, such as
neonatal, infantile, or childhood epilepsies.
[006] Antisense technology is emerging as an effective means for
reducing the expression of specific gene products and may therefore prove
to be uniquely useful in a number of therapeutic, diagnostic, and research
applications for the modulation of Navl.3 expression.
SUMMARY OF THE INVENTION
[007] The present invention is directed to antisense compounds,
particularly oligonucleotides, which are targeted to a nucleic acid encoding
Navl.3, and which modulate the expression of Navl.3. Pharmaceutical and
other compositions comprising the antisense compounds of the invention are
also provided. Further provided are methods of modulating the expression
of Navl .3 in cells or tissues comprising contacting said cells or tissues
with
one or more of the antisense compounds or compositions of the invention.
Further provided are methods of treating an animal, particularly a human,
suspected of having or being prone to a disease or condition associated with
expression of Navl .3 by administering a therapeutically or prophylactically
effective amount of one or more of the antisense compounds or
compositions of the invention.
DETAILED DESCRIPTION OF THE INVENTION
[008] The present invention employs oligomeric antisense compounds,
particularly oligonucleotides, for use in modulating the function of nucleic
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acid molecules encoding Navl.3, ultimately modulating the amount of
Navl .3 produced. This is accomplished by providing antisense compounds,
which specifically hybridize with one or more nucleic acids encoding
Navl.3. As used herein, the terms "target nucleic acid" and "nucleic acid
encoding Navl.3" encompass DNA encoding Navl.3, RNA (including pre-
mRNA and mRNA) transcribed from such DNA, and also cDNA derived
from such RNA. The specific hybridization of an oligomeric compound
with its target nucleic acid interferes with the normal function of the
nucleic
acid. This modulation of function of a target nucleic acid by compounds,
which specifically hybridize to it, is generally referred to as "antisense".
The
functions of DNA to be interfered with include replication and transcription.
The functions of RNA to be interfered with include all vital functions such
as, for example, translocation of the RNA to the site of protein translation,
translation of protein from the RNA, splicing of the RNA to yield one or
more mRNA species, and catalytic activity which may be engaged in or
facilitated by the RNA. The overall effect of such interference with target
nucleic acid function is modulation of the expression of Navl .3. In the
context of the present invention, "modulation" means either an increase
(stimulation) or a decrease (inhibition) in the expression of a gene. In the
context of the present invention, inhibition is the preferred form of
modulation, of gene expression and mRNA is a preferred target.
[009] It is preferred to target specific nucleic acids for antisense.
"Targeting" an antisense compound to a particular nucleic acid, in the
context of this invention, is a multistep process. The process usually begins
with the identification of a nucleic acid sequence whose function is to be
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modulated. This may be, for example, a cellular gene (or mRNA transcribed
from the gene) whose expression is associated with a particular disorder or
disease state, or a nucleic acid molecule from an infectious agent. In the
present invention, the target is a nucleic acid molecule encoding Navl.3.
The targeting process also includes determination of a site or sites within
this gene for the antisense interaction to occur such that the desired effect,
e.g., detection or modulation of expression of the protein, will result.
Within
the context of the present invention, a preferred intragenic site is the
region
encompassing the translation initiation or termination codon of the open
reading frame (ORF) of the gene. Since, as is known in the art, the
translation initiation codon is typically 5'-AUG (in transcribed mRNA
molecules; 5'-ATG in the corresponding DNA molecule), the translation
initiation codon is also referred to as the "AUG codon," the "start codon" or
the "AUG start codon". A minority of genes have a translation initiation
codon having the RNA sequence 5'-GUG, 5'-UUG or 5'-CUG, and 5'-
AUA, 5'-ACG and 5'-CUG have been shown to function in vivo. Thus, the
terms "translation initiation codon" and "start codon" can encompass many
codon sequences, even though the initiator amino acid in each instance is
typically methionine (in eukaryotes) or fonnylmethionine (in prokaryotes).
It is also known in the art that eukaryotic and prokaryotic genes may have
two or more alternative start codons, any one of which may be preferentially
utilized for translation initiation in a particular cell type or tissue, or
under a
particular set of conditions. In the context of the invention, "start codon"
and
"translation initiation codon" refer to the codon or codons that are used in
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vivo to initiate translation of an mRNA molecule transcribed from a gene
encoding Navl .3, regardless of the sequences) of such colons.
[0010] It is also known in the art that a translation termination colon (or
"stop colon") of a gene may have one of three sequences, i.e. 5'-UAA, 5'-
UAG and 5'-UGA (the corresponding DNA sequences are 5'-TAA, 5'-TAG
and 5'-TGA, respectively). The terms "start colon region" and "translation
initiation colon region "refer to a portion of such an mRNA or gene that
encompasses from about 25 to about 50 contiguous nucleotides in either
direction (i.e., 5' or 3') from a translation initiation colon. Similarly, the
terms "stop colon region" and "translation termination colon region "refer
to a portion of such an mRNA or gene that encompasses from about 25 to
about 50 contiguous nucleotides in either direction (i.e., 5' or 3') from a
translation termination colon.
[0011] The open reading frame (ORF) or "coding region," which is
known in the art to refer to the region between the translation initiation
colon and the translation termination colon, is also a region which may be
targeted effectively. Other target regions include the 5' untranslated region
(5'UTR), known in the art to refer to the portion of an mRNA in the 5'
direction from the translation initiation colon, and thus including
nucleotides between the 5' cap site and the txanslation initiation colon of an
mRNA or corresponding nucleotides on the gene, and the 3' untranslated
region (3'UTR), known in the art to refer to the portion of an mRNA in the
3' direction from the translation termination colon, and thus including
nucleotides between the translation termination colon and 3' end of an
mRNA or corresponding nucleotides on the gene. The 5' cap of an mRNA
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comprises an N7-methylated guanosine residue joined to the 5'-most residue
of the mRNA via a 5'-5' triphosphate linlcage. The 5' cap region of an
mRNA is considered to include the 5' cap structure itself as well as the first
SO nucleotides adjacent to the cap. The 5' cap region may also be a
preferred target region.
[0012] Although some eulcaryotic mRNA transcripts are directly
translated, many contain one or more regions, known as "introns," which are
excised from a transcript before it is translated. The remaining (and
therefore translated) regions are known as "exons" and are spliced together
to form a continuous mRNA sequence. mRNA splice sites, i.e., intron-exon
junctions, may also be preferred target regions, and are particularly useful
in
situations where aberrant splicing is implicated in disease, or where an
overproduction of a particular mRNA splice product is implicated in
disease. Aberrant fusion junctions due to rearrangements or deletions are
also preferred targets. It has also been found that introns can also be
effective, and therefore preferred, target regions for antisense compounds
targeted, for example, to DNA or pre-mRNA.
[0013] Once one or more target sites have been identified,
oligonucleotides axe chosen which are sufficiently complementary to the
target, i.e., hybridize sufficiently well and with sufficient specificity, to
give
the desired effect.
[0014] In the context of this invention, "hybridization" means hydrogen
bonding, which may be Watson-Crick, Hoogsteen or rever sed Hoogsteen
hydrogen bonding, between complementary nucleoside or nucleotide bases.
For example, adenine and thymine are complementary nucleobases, which
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pair through the formation of hydrogen bonds. "Complementary," as used
herein, refers to the capacity for precise pairing between two nucleotides.
For example, if a nucleotide at a certain position of an oligonucleotide is
capable of hydrogen bonding with a nucleotide at the same position of a
DNA or RNA molecule, then the oligonucleotide and the DNA or RNA are
considered to be complementary to each other at that position. The
oligonucleotide and the DNA or RNA are complementary to each other
when a sufficient number of corresponding positions in each molecule are
occupied by nucleotides which can hydrogen bond with each other. Thus,
"specifically hybridizable" and "complementary" are terms which are used
to indicate a sufficient degree of complementarity or precise pairing such
that stable and specific binding occurs between the oligonucleotide and the
DNA or RNA target. It is understood in the art that the sequence of an
antisense compound need not be 100% complementary to that of its target
nucleic acid to be specifically hybridizable. An antisense compound is
specifically hybridizable when binding of the compound to the target DNA
or RNA molecule interferes with the normal function of the target DNA or
RNA to cause a loss of utility, and there is a sufficient degree of
complementarity to avoid non-specific binding of the antisense compound
to non-target sequences under conditions in which specific binding is
desired, i.e., under physiological conditions in the case of in vivo assays or
therapeutic treatment, and in the case of in vitro assays, under conditions in
which the assays are performed.
[0015] Antisense compounds are commonly used as research reagents
and diagnostics. For example, antisense oligonucleotides, which are able to
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inhibit gene expression with exquisite specificity, are often used by those of
ordinary skill to elucidate the function of particular genes. Antisense
compounds are also used, for example, to distinguish between functions of
various members of a biological pathway. Antisense modulation has,
therefore, been harnessed for research use.
[0016] The specificity and sensitivity of antisense is also harnessed by
those of skill in the art for therapeutic uses. Antisense oligonucleotides
have
been employed as therapeutic moieties in the treatment of disease states in
animals and man. Antisense oligonucleotides have been safely and
effectively administered to humans and numerous clinical trials are
presently underway. It is thus established that oligonucleotides can be useful
therapeutic modalities that can be configured to be useful in treatment
regimes for treatment of cells, tissues and animals, especially humans. In the
context of this invention, the term "oligonucleotide" refers to an oligomer or
polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) or
mimetics thereof. This term includes oligonucleotides composed of
naturally occurring nucleobases, sugars and covalent internucleoside
(backbone) linkages as well as oligonucleotides having non-naturally
occurring portions which function similarly. Such modified or substituted
oligonucleotides are often preferred over native forms because of desirable
properties such as, for example, enhanced cellular uptake, enhanced affinity
for nucleic acid target and increased stability in the presence of nucleases.
[0017] While antisense oligonucleotides are a preferred form of
antisense compound, the present invention comprehends other oligomeric
antisense compounds, including but not limited to oligonucleotide mimetics
io
comprises an N7-m
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such as are described below. The antisense compounds in accordance with
this invention preferably comprise from about 8 to about 30 nucleobases
{i.e. from about 8 to about 30 linced nucleo sides). Particularly preferred
antisense compounds are antisense oligonucleotides, even more preferably
those comprising from about 12 to about 25 nucleobases. As is known in the
art, a nucleoside is a base-sugar combination. The base portion of the
nucleoside is normally a heterocyclic base. The two most common classes
of such heterocyclic bases are the purines and the pyrimidines. Nucleotides
are nucleosides that further include a phosphate group covalently linked to
the sugar portion of the nucleoside. For those nucleosides that include a
pentofuranosyl sugar, the phosphate group can be linked to either the 2', 3'
or 5' hydroxyl moiety of the sugar. In forming oligonucleotides, the
phosphate groups covalently link adjacent nucleosides to one another to
form a linear polymeric compound. In turn the respective ends of this linear
polymeric structure can be further joined to form a circular structure,
however, open linear structures are generally preferred. Within the
oligonucleotide structure, the phosphate groups are commonly referred to as
forming the internucleoside backbone of the oligonucleotide. The normal I
linkage or backbone of RNA and DNA is a 3' to 5' phosphodiester linkage.
[0018] Specific examples of preferred antisense compounds useful in
this invention include oligonucleotides containing modified backbones or
non-natural internucleoside linkages. As defined in this specification,
oligonucleotides having modified backbones include those that retain a
phosphorus atom in the backbone and those that do not have a phosphorus
2S atom in the backbone. For the purposes of this specification, and as
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sometimes referenced in the art, modif ed oligonucleotides that do not have
a phosphorus atom in their intemucleoside backbone can also be considered
to be oligonucleosides.
[0019) Preferred modified oligonucleotide backbones include, for
example, phosphorothioates, chiral phosphorothioates, phosphorodithioates,~,
phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl
phosphonates including 3'alkylene phosphonates and chiral phosphonates,
phosphinates, phosphoramidates including 3'-amino phosphoramidate and
aminoalkylphosphoramidates, thionophosphoramidates,
thionoalkylphosphonates, thionoalkylphosphotricstcrs, and
boranophosphates having normal 3'-S' linkages, 2'-5' linked analogs of
these, and those having inverted polarity wherein the adjacent pairs of
nucleoside units are linked 3'-5' to S'-3' or 2'-S' to S'-2'. Various salts,
mixed salts and free acid forms are also included.
IS [0020] Representative United States patents that teach the preparation of
the above phosphorus-containing linkages include, but are not limited to,
U.S. 3,687,808; 4,469,863; 4,4?6,301; 5,023,243; 5,177,196; 5,188,89?;
5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676;
S,40S,939; S,4S3,496; S,4S5,233; 5,466,677; 5,476,925; 5,519,126;
5,536,821; 5,541,306; S,SS0,111; 5,563,253; 5,571,799; 5,587,361; and
S,62S,050 .
[0021] Preferred modified oligonucleotide backbones that do not
include a phosphorus atom therein have backbones that are formed by a~hort
chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and
2S alkyl or cycloalkyl intemucleoside linkages, or one or more short chain
TZ
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heteroatomic or heterocyclic internucleoside linkages. These include those
having morpholino linkages (formed in part from the sugar portion of a
nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones;
for~nacetyl and thiofoxmacetyl backbones; methylene formacetyl and
thioformaeetyl backbanes; alkene containing backbones; sulfamate
backbones; methyleneimino and methylenehydrazino backbones; sulfonate
and sulfonamide backbones; amide backbones; and others having mixed N,
O, S and CHz component parts.
[0022] Representative United States patents that teach the preparatioai of
~ 0 . the above oligonucleosides include, but are not limited to, U.S.
5,034,506;
5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562;
5,264,564;5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677;
5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289; 5,602,240;
5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360;
5,677,437; and 5,677,439 .
[0023j In other preferred oligonucleotide mimetics, both the sugar and
the internucleoside linkage, i.e., the backbone, of the nucleotide units are
replaced with novel groups. The base units are maintained for hybridization
with an appropriate nucleic acid target compound. One such oligomerie
compound, an oligonucleotide mimetic that has been shown to have
excellent hybridization properties, is referred to as a peptide nucleic acid
(PNA). In PNA compounds, the sugar backbone of an oligonucleotide is
replaced with an amide containing backbone, in particular an
aminoethylglycine backbone. The nucleobases are retained and are bound
13
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directly or indirectly to aza nitrogen atoms of the amide portion of the
backbone. Representative United States patents that teach the preparation of
PNA compounds include, but are not limited to, U.S. 5,539,082; 5,714,331;
and 5,719,262. Further
teaching ofPNA compounds can be found in Nielsen et al., Science, 1991,
254, 1497-1500.
[0024] Most preferred embodiments of the invention are
oligonucleotides with phosphorothioate backbones and oligonucleosides
with heteroatom backbones, and in particular -CH2 NH-O-CHZ-, -CHI-N
(CH3) -O-CHZ- [Irnown as a methylene (methylimino) or MMI backbone] , -
CH2-O-N (CH3) -CHZ-, -CH2N(CH3)-N(CH~)-CHI- and -O-N(CH3)-CHZ-
CHZ- jwherein the native phosphodiester backbone is represented as -O-P-
O-CHZ-] of the above referenced U.S. patent 5,489,677, and the amide
backbones of the above referenced U.S. patent 5,602,240. Also preferred are
oligonucleotides having rnorpholino backbone structures of the above-
referenced U.S. patent 5,034,506.
[0025] Modified oligonucleotides may also contain one or more
substituted sugar moieties. Preferred oligonucleotides comprise one of the
following at the 2' position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl;
O-, S- or N-aikynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and
alkynyl may be substituted or unsubstituted Cl to Clo alkyl or C2 to Coo
allcenyl and alkynyl. Particularly preferred are O[(CH2~0]mCH3,
O(CH2~",OCH3, O(CHZ)"NHz, O(CHZh,CH3, O(CHz)"ONH2, and
O(CHZ"ON[(CH2)"CH3)]Z where n and m are from 1 to about 10. Other
preferred oligonucleotides comprise one of the following at the 2' position:
14
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CI to Coo, ( lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-
allcaryl
or O-aralkyl, SH, SCH3, OCN, Cl, Br, CN, CF3, OCF3, SOCH3, SOZCH3,
ONOz, N02, N3, NH2, heterocycloalkyl, heterocycloalkaryl,
aminoalkylamino, polyallcylamino, substituted silyl, an RNA cleaving
group, a reporter group, an intercalator, a group for improving the
pharmacokinetic properties of an oligonucleotide, or a group for improving
the pharmacodynamic properties of an oligonucleotide, and other
substituents having similar properties. A preferred modification includes 2'
-methoxyethoxy (2' -O-CH2CH20CH3, also known as 2'-O- (2-
methoxyethyl) or 2'-MOE) (Martin et al., Helv. Chim. Acta, 1995, 78, 486-
504) i.e., an alkoxyalkoxy group. A further preferred modification includes
2'-dimethylaminooxyethoxy, i.e., a O(CH2)20N(CH3)2 group, also known as
2'-DMAOE, as described in examples herein below, and 2'-
dimethylaminoethoxyethoxy (also known in the art as 2'-O-
dimethylaminoethoxyethyl or 2'-DMAEOE), i.e., 2'-O-CHZ-O-CH2-N
(CH2)z, also described in examples herein below.
[0026] Other preferred modifications include 2'-methoxy (2'-O CH3),
2'-aminopropoxy (2'-O CH2 CHZ CHZNH2) and 2'-fluoro (2'-F). Similar
modifications may also be made at other positions on the oligonucleotide,
particularly the 3' position of the sugar on the 3' terminal nucleotide or in
2'-5' linked oligonucleotides and the 5' position of 5' terminal nucleotide.
Oligonucleotides may also have sugar rnimetics such as cyclobutyl moieties
in place of the pentofuranosyl sugar. Representative United States patents
that teach the preparation of such modified sugar structures include, but are
not limited to, U.S. 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878;
Is
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5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427;
5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265;
5,658,873; 5,670,633; and 5,700,920 .
[002?] Oligonucleotides may also include nucleobase (often referred tp
in the art simply as "base") modifications or substitutions. As used herein,
"unmodified" or "natural" nucleobases include the purine bases adenine (A)
and guanine (G), and the pyrimidine bases thymine ('I~, cytosine (C) and
uracil (f~. Modified nucleobases include other synthetic and natural
nucleobases such as 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine,
xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl
derivatives of adenine and guanine, 2 propyl and other alkyl derivatives of
adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-
halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil,
cytosine and thymine, S-uracil (pseudouraeil), 4-thiouracil, 8-halo, 3-amino,
8-ihiol, 8-thioallcyl, 8 hydroxyl and other 8-substituted adenines and
guanines, 5-halo particularly 5 bromo, 5-trifluoromethyl and other 5-
substituted uracils and cytosines, 7-methylquanine and 7 methyladenino, 8-
azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaaderiine and 3-
deazaguanine and 3-deazaadenine. Further nucleobases include those
disclosed in Unitcd States Patent No. 3,687,808, those disclosed in The
Concise Encyclopedia Of Polymer Science And Engineering, pages 858-
859, Kroschwitz, J.L, ed. John Wilcy & Sons, 1990, those disclosed by
Englisch et al., Angewandte Chemie, International Edition,1991, 30, 613,
and those disclosed by Sanghvi, Y.S:, Chapter 15, Antisense Research and
16
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Applications, pages 289-302, Crooke, S.T. and Lebleu, B. ed., CRC Press,
1993. Certain of these nucleobases are particularly useful for increasing the
binding affinity of the oligomeric compounds of the invention. These
include S-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6
S substituted purines, including 2-aminopropyladenine, S propynyluracil and
S-propyriylcytosine. 5-methylcytosine substitutions have bees shown to
increase nucleic acid duplex atabdity by 0.6-1.2°C (Sanghvi, Y.S.,
Crooke,
S.T. and Ixbleu, B., eds, Antisense Research and Applications, CRC Press,
Boca Raton, 1993, pp. 276.-278) and are presently preferred base
substitutions, even more particularly when combined with 2'-O-
methoxyethyl sugar modifications.
[0028] Representative United States patents that teach the preparation of
certain of the above noted modified nucleobases as well as other modi$ed
nucleobases include, but are not limited to, the above noted U.S. 3,687,808,
1S as well as U.S. 4,845,205; 5,134,302; 5,134,066; 5,175,273; 5,367,066;
5,432,272; 5,457,187; 5,459,255; 5,484908; 5,502,177; S,S25,711;
S,SS2,S40; 5;587,469; 5,594,121, S,S96,091; 5,614,617; S,7S0,692; and
5,681,941.
[0029j Another modificaxion of the oligonucleotides of the invention
involves chemically linking to the oligonucleotide one or more moieties or
conjugates, which enhance the activity, cellular distribution or cellular
uptake of the oligonucleotide. Such moieties include but are not limited to
lipid moieties such as a cholesterol moiety (Ixtsinger et al., Proc. Natl.
Aced. Sci. USA,1989, 86, 6553-6556), cholic acid (Manoharan et al.,
2S Bioorg: Med Chem. Let., 1994, 4,1053-1060), a thioether, e.g., hexyl-S-
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WO 2004/016754 PCT/US2003/025465
tritylthiol (Manoharan et al., Ann. N Y. Acad. Sci., 1992, 660, 306-309;
Manoharan et al., Bioosg. Med. Claena. Let., 1993, 3, 2765-2770), a
thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20, 533-538), an
aliphatic chain, e.g., dodecandiol or undecyl residues (Saison-Behmoaras et
al., EMBO J., 1991, 10, 1111-1118; Kabanov et al., FEBS Lett., 1990, 259,
327-330; Svinarchuk et al., Bioclainaie, 1993, 75, 49-54), a phospholipid,
e.g., di-hexadecyl-rac-glycerol or triethylammonium 1,2-di-O-hexadecyl-
rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995,
36, 3651-3654; Shea et al., Nucl. Acids Res., 1990, 18, 3777-3783), a
polyamine or a polyethylene glycol chain (Mancharan et al., Nucleosides ~
Nucleotides, 1995, 14, 969-973), or adamantane acetic acid (Manoharan et
al., Tetrahedron Lett., 1995, 36, 365'-3654), a palmityl moiety (Mishra et
al., Biochim. Biophys. Acta, 1995, 1264, 229-237), or an octadecylamine or
hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Plaarmacol.
Exp. Tlaer., 1996, 277, 923-937).
[0030] Representative United States patents that teach the preparation of
such oligonucleotide conjugates include, but are not limited to, U.S.
4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730;
5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124;
5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718;
5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737;
4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830;
5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022;
5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098;
5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667;
18
Applications, pages 289
CA 02495398 2005-02-10
5106'7-55
S,SI4,?8S; S,S6S,SS2; S,S67,810; 5,574,142; S,S8S,481; S,S87,371;
S,S9S,726; 5,597,696; S,S99,923; 5,599,928 and S,b88,941.
[0031) It is not necessary for all positions in a given compound to be
S uniformly modified, and in fact more than one of the aforementioned ,
modifications may be incorporated in a single compound or even at a single
nucleoside withia an oligonucleotide. The present invention also includes
antise~nse compounds, which are chimerio compounds. "Chimerie" antisense
compounds ox "chimeras," in the context of this invention, are amisense
compounds, particularly oligonucleotides, which contain two or more
chemically distinct regions, each made up of at least one monomer unit, i.e.,
a nucleotide in the case of an oligonucleotide compound. These
oligonucleotides typically contain at least one region wherein the
oligonucleotide is modified so as to confer upon the oligonucleotide
increased resistrince to nuclease degradation, increased cellular uptake,
and/or increased binding affinity for the target nucleic acid. An additional
region of the oligonucleotide may serve as a substrate for enzymes capable
of cleaving RNA:DNA or RNA:RNA hybrids. By way of example, RNase
H is a cellular endonuclease, which cleaves the RNA strand of RNA:DNA
duplex. Activation of RNase H, therefore, results in cleavage of the RNA,
target, thereby greatly enhancing the efficiency of oligonucleotide
inlu'bitioa
of gene expression. Consequently, comparable results can often be obtained
with shorter oligonucleotides when chimeric oligonucleotides are used,
compared to phosphorothioate deoxyoligonucleotides hybridizing to the
2S same target region. Cleavage of the RNA target can be routinely detected by
19
5106'7-55
CA 02495398 2005-02-10
gel electrophoresis and, if necessary, associated nucleic acid hybridization
techniques known in the art.
[0032] Chimeric antisense compounds of the invention may be formed
as composite structures of two or more oligonucleotides, modified
oligonucleotides, oligonucleosides and/or oligonucleotide mimetics as
descn'lxd above. Such compounds have also been refernd to in the art as
hybrids or gapmers. Representative United States pates that teach the
preparation of such hybrid structures include, but are not limited to, U.S.
5,013,830; 5,149,797; 5,220,007; 5,256,775; 5,366,878; 5,403,711;
5,491,133; 5,565,350; 5,623,065; 5,652,355; 5,652,356; and 5,700,922 .
[0033] The antisense compounds used in accordance with this invention
may be conveniently, and routinely made through the well-known technique
of solid phase synthesis. Equipment for such synthesis is sold by several
vendors including, for example, Applied Biosystems (Foster City, CA). Any
other means for such synthesis known in the art may additionally or
alternatively be employed. It is well known to use similar techniques to
prepare oligonucleotides such as the phosphorothioates and alkylated
derivatives.
[0034] The antisense compounds of the invention are synthesized in
vitro and do not include antisense compositions of biological origin, or
genetic vector constructs designed to direct the in vivo synthesis of
antisense molecules. The compounds of the invention may also be admixed,
encapsulated, conjugated or otherwise associated with other molecules,
molecule structures or mixtures of compounds, as for example, liposomes,
51067-55
CA 02495398 2005-02-10
receptor targeted molecules, oral, rectal, topical or other formulations, for
assisting in uptake, distn'bution and/or absorption. Representative United
States patents that teach the preparation of such uptake, distribution and/or
absorption assisting formulations include, but are not limited to, U.S.
5,108,921; 5,354,844; 5,416,016; 5,459,127; 5,521,291; 5,543,158;
5,547,932; 5,583,020; 5,591,721; 4,426,330; 4,534,899; 5,013,556;
5,108,921; 5,213,804; 5,227,170; 5,264,221; 5,356;633; 5,395,619;
5,416,016; 5,417,978; 5,462,854; 5,469,854; 5,512,295; 5,527,528;
5,534;259; 5,543,152; 5,556,948; 5,580,575; and 5,595,756 .
[0035] The antisense compounds of the invention encompass any
pharmaceutically acceptable salts, esters, or salts of such esters, or any
other
compound which, upon administration to an animal including a human, is
capable of providing (directly or indirectly) the biologically active
metabolite or residue thereof. Accordingly, for example, the disclosure is
also drawn to prodrugs and pharmaceutically acceptable salts of the
compounds of the invention, pharmaceutically acceptable salts of such
prodrugs, and other bioequivalents.
[0036] The term "prodrug" indicates a therapeutic agent that is prepared
in an inactive form that is converted to an active form (i.e., drug) within
the
body or cells thereof by the action of endogenous enzymes or other
chemicals and/or conditions. In particular, prodrug versions of the
oligonucleotides of the invention are prepared as SATE [(S-acetyl-2-
thioethyl) phosphate] derivatives according to the methods disclosed in WO
2~
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WO 2004/016754 PCT/US2003/025465
93/24510 to Gosselin et al., published December 9, 1993 or in WO
94/26764 to Imbach et al.
[0037] The term "pharmaceutically acceptable salts" refers to
physiologically and pharmaceutically acceptable salts of the compounds of
the invention: i.e., salts that retain the desired biological activity of the
parent compound and do not impart undesired toxicological effects thereto.
[0038] Pharmaceutically acceptable base addition salts are formed with
metals or amines, such as alkali and alkaline earth metals or organic amines.
Examples of metals used as cations are sodium, potassium, magnesium,
calcium, and the like. Examples of suitable amines are N, N'-
dibenzylethylenediamine, chloroprocaine, choline, diethanolamine,
dicyclohexylamine, ethylenediamine, N-methylglucamine, and procaine
(see, for example, Berge et al., "Pharmaceutical Salts," J. of Phaf°jna
Sci.,
1977, 66, 119). The base addition salts of said acidic compounds are
prepared by contacting the free acid form with a sufficient amount of the
desired base to produce the salt in the conventional manner. The free acid
form may be regenerated by contacting the salt form with an acid and
isolating the free acid in the conventional manner. The free acid forms differ
from their respective salt forms somewhat in certain physical properties
such as solubility in polar solvents, but otherwise the salts are equivalent
to
their respective free acid for purposes of the present invention. As used
herein, a "pharmaceutical addition salt" includes a pharmaceutically
acceptable salt of an acid form of one of the components of the
compositions of the invention. These include organic or inorganic acid salts
2S of the amines. Preferred acid salts are the hydrochlorides, acetates,
22
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WO 2004/016754 PCT/US2003/025465
salicylates, nitrates and phosphates. Other suitable pharmaceutically
acceptable salts are well known to those skilled in the art and include basic
salts of a variety of inorganic and organic acids, such as, for example, with
inorganic acids, such as fox example hydrochloric acid, hydrobromic acid,
sulfuric acid or phosphoric acid; with organic carboxylic, sulfonic, sulfo or
phospho acids or N-substituted sulfamic acids, for example acetic acid,
propionic acid, glycolic acid, succinic acid, malefic acid, hydroxymaleic
acid, methylmaleic acid, fumaric acid, malic acid, tartaric acid, lactic acid,
oxalic acid, gluconic acid, glucaric acid, glucuronic acid, citric acid,
benzoic
acid, cinnamic acid, mandelic acid, salicylic acid, 4-aminosalicylic acid, 2-
phenoxybenzoic acid, 2-acetoxybenzoic acid, embonic acid, nicotinic acid
or isonicotinic acid; and with amino acids, such as the 20 alpha-amino acids
involved in the synthesis of proteins in nature, for example glutamic acid or
aspartic acid, and also with phenylacetic acid, methanesulfonic acid,
ethanesulfonic acid, 2-hydroxyethanesulfonic acid, ethane-1,2-disulfonic
acid, benzenesulfonic acid, 4-methylbenzenesulfaic acid, naphthalene-2-
sulfonic acid, naphthalene-1,5-disulfonic acid, 2- or 3-phosphoglycerate,
glucose-6-phosphate, N-cyclohexylsulfamic acid (with the formation of
cyclamates), or with other acid organic compounds, such as ascorbic acid.
Pharmaceutically acceptable salts of compounds may also be prepared with
a pharmaceutically acceptable cation. Suitable pharmaceutically acceptable
canons are well known to those skilled in the art and include alkaline,
alkaline earth, ammonium and quaternary ammonium cations. Carbonates or
hydrogen carbonates are also possible.
23
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WO 2004/016754 PCT/US2003/025465
[0039] For oligonucleotides, preferred examples of pharmaceutically
acceptable salts include but are not limited to (a) salts formed with cations
such as sodium, potassium, ammonium, magnesium, calcium, polyamines
such as spennine and spermidine, etc.; (b) acid addition salts formed with
inorganic acids, for example hydrochloric acid, hydrobromic acid, sulfuric
acid, phosphoric acid, nitric acid and the like; (c) salts formed with organic
acids such as, for example, acetic acid, oxalic acid, tartaric acid, succinic
acid, malefic acid, fumaric acid, gluconic acid, citric acid, malic acid,
ascorbic acid, benzoic acid, tannic acid, palmitic acid, alginic acid,
polyglutamic acid, naphthalenesulfonic acid, methanesulfonic acid, p-
toluenesulfonic acid, naphthalenedisulfonie acid, polygalacturonic acid, and
the like; and (d) salts formed from elemental anions such as chlorine,
bromine, and iodine.
[0040] The antisense compounds of the present invention can be utilized
for diagnostics, therapeutics, prophylaxis, and as research reagents and kits.
For therapeutics, an animal, preferably a human, suspected of having a
disease or disorder, which can be treated by modulating the expression of
Navl .3, is treated by administering antisense compounds in accordance with
this invention. The compounds of the invention can be utilized in
pharmaceutical compositions by adding an effective amount of an antisense
compound to a suitable pharmaceutically acceptable diluent or carrier. Use
of the antisense compounds and methods of the invention may also be useful
prophylactically, e.g., to prevent or delay infection, inflammation or tumor
formation, fox example.
24
CA 02495398 2005-02-10
5106'7-55
[0041] The antiscnse compounds of the invention are useful for research
and diagnostics; because these compounds hybridize to nucleic acids
encoding Navl.3, enabling sandwich and other assays to easily be
constructed to exploit this fact. Hybi~dization of the antisense
oligonucleotides of the invention with a nucleic acid encodiag Navl.3 can ;
be detected by means known in the atrt. Such means may include
conjugation of an enzyme to the oligonucleotide, radiolalxlling of the
oligonucleotidc or any other suitable detection weans. Kits using such
detection means for detecting the level of Navl .3 in a sample may also be
prepared.
[0042] The present invention also includes pharmaceutical compositions
and formulations, which include the antisense compounds of the invention.
The pharmaceutical compositions of the present invention may be
administered in a number of ways depending upon whether local or
1 ~ systemic treatment is desired and upon the area to be treated
Administration
may be topical (including ophthalmic and to mucous membranes including
vaginal and rectal delivery), pulmonary, e.g., by inhalation or insufflation
of
powders or aerosols, including by nebulizer; intratracheal, intranasal,
epiderraal and transdermal), oral or parenteral. Parenteral administration
includes intravenous, intraarterial, subcutaneous, intraperitoneal or
intramuscular injection or infusion; or intracranial, e.g., intrathecal or
intraventricular, administration. Oligonucleotides with at least one 2'-O-
methoxyethyl modification are believed to be particularly useful for oral
administration. The present invention also includes commercial packages
comprising compounds as described herein together with instructions for use.
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WO 2004/016754 PCT/US2003/025465
[0043] Intraventricular drug administration, for the direct delivery of drug
to the
brain of a patient, may be desired for the treatment of patients with diseases
or
conditions afflicting the brain. To effect this mode of oligonucleotide
administration, a silicon catheter is surgically introduced into a ventricle
of the
brain of a human patient, and is connected to a subcutaneous infusion pump
(SynchroMed 0 and IsoMee infusion systems, Medtronic Inc., Minneapolis, Minn.)
that has been surgically implanted in the abdominal region (Zinnu et al.,
Cancef°
Reseaf~ch, 1984, 44, 1698. The pump is used to inject the oligonucleotides and
allows precise dosage adjustments and variation in dosage schedules with the
aid of
an external programming device. The reservoir capacity of the pump is 18-20 mL
and infusion rates may range from 0.1 mL/h to 1 mL/h. Depending on the
frequency
of administration, ranging from daily to monthly, and the dose of drug to he
administered, ranging from 0.01 micro g to I00 g per kg of body weight, the
pump
reservoir may be refilled at 3 -10 week intervals. Refilling of the pump is
accomplished by percutaneous puncture of the self sealing septum of the pump.
[0044] Intrathecal Epidural, Subdural, drug administration, for the
introduction
of a drug into the spinal column of a patient may be desired for the treatment
of
patients with diseases of the central nervous system. To effect this route of
oligonucleotides administration, a silicon catheter is surgically implanted
subarachnoid spinal interspace of a human patient for example implantation
into the
L3-4 lumbar cord would target the legs), and is connected to a subcutaneous
infusion pump which has been surgically implanted in the upper abdominal
region
(Leer and Hatton, The Annals of Plaas°macotlae~°apy, 1993, 27,
912; Ettinger et al.,
1978, Cancef°, 41, 1270, 1978; Yaida et al., Regul. Pept., 1995, 59,
193). The pump
is used to inject the oligonucleotides and allows precise dosage adjustments
and
26
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
variations in dose schedules with the aid of an external programming device.
The
reservoir capacity of the pump is 1 S-20 mL, and infusion rates may vary from
0. 1
mL/h to 1 mL& Depending on the frequency of drug administration, ranging from
daily to monthly, and dosage of drug to be administered, ranging from 0.01
micro g
to 100 g per kg of body weight, the pump reservoir may be refilled at 3 -10
week
intervals. Refilling of the pump is accomplished by a single percutaneous
puncture
to the self sealing septum of the pump. The distribution, stability and
pharmacokinetics of oligonucleotides within the central nervous system may be
followed according to known methods. Subdural administration is also
envisioned
other by a pump mechanism or direct injection.
[0045] To effect delivery of oligonucleotides to areas other than the brain or
spinal column via this method, the silicon catheter is configured to connect
the
subcutaneous infusion pump to, e.g., the hepatic artery, for delivery to the
liver.
Infusion pumps may also be used to effect systemic delivery of
oligonucleotides
1 S (Ewel et al., Ca~eer° Research, 1992, 52, 3005; Rubenstein et al.,
J. Surg. Oncol.,
1996, 62, 194).
[0046] Pharmaceutical compositions and formulations for topical
administration may include transdermal patches, ointments, lotions, creams,
gels, drops, suppositories, sprays, liquids and powders. Conventional
pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the
like may be necessary or desirable. Coated condoms, gloves and the like
may also be useful.
[0047] Compositions and formulations for oral administration include
powders or granules, suspensions or solutions in water or non-aqueous
27
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WO 2004/016754 PCT/US2003/025465
media, capsules, sachets or tablets. Thickeners, flavoring agents, diluents,
emulsifiers, dispersing aids or binders may be desirable.
[0048] Compositions and formulations for parenteral, intrathecal or
intraventxicular administration may include sterile aqueous solutions, which
may also contain buffers, diluents and other suitable additives such as, but
not limited to, penetration enhancers, carrier compounds and other
pharmaceutically acceptable carriers or excipients.
[0049] Pharmaceutical compositions of the present invention include,
but are not limited to, solutions, emulsions, and liposome-containing
formulations. These compositions may be generated from a variety of
components that include, but are not limited to, preformed liquids, self
emulsifying solids and self emulsifying semisolids.
[0050] The pharmaceutical formulations of the present invention, which
may conveniently be presented in unit dosage form, may be prepared
according to conventional techniques well known in the pharmaceutical
industry. Such techniques include the step of bringing into association the
active ingredients with the pharmaceutical carri.er(s) or excipient(s). In
general the formulations are prepared by uniformly and intimately bringing
into association the active ingredients with liquid carriers or finely divided
solid carriers or both, and then, if necessary, shaping the product.
[0051] The compositions of the present invention may be formulated
into any of many possible dosage forms such as, but not limited to, tablets,
capsules, liquid syrups, soft gels, suppositories, and enemas. The
compositions of the present invention may also be formulated as
2S suspensions in aqueous, non-aqueous or mixed media. Aqueous suspensions
28
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WO 2004/016754 PCT/US2003/025465
may further contain substances, which increase the viscosity of the
suspension including, for example, sodium carboxymethylcellulose, sorbitol
and/or dextran. The suspension may also contain stabilizers.
[0052] In one embodiment of the present invention the pharmaceutical
compositions may be formulated and used as foams. Pharmaceutical foams
include formulations such as, but not limited to, emulsions, microemulsions,
creams, jellies and liposomes. While basically similar in nature these
formulations vary in the components and the consistency of the final
product. The preparation of such compositions and formulations is generally
known to those skilled in the pharmaceutical and formulation arts and may
be applied to the formulation of the compositions of the present invention.
Emulsions
[0053] The compositions of the present invention may be prepared and
formulated as emulsions. Emulsions are typically heterogenous systems of
one liquid dispersed in another in the form of droplets usually exceeding 0.1
~,m in diameter. (Idson, in Pharmaceutical Dosage Forms, Lieberman,
Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y.,
volume 1, p. 199; Rosoff, in Pharn2aceutical Dosage Forms, Lieberman,
Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y.,
Volume 1, p. 245; Block in Pharmaceutical Dosage For°rns,
Lieberman,
Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y.,
volume 2, p. 335; Higuchi et al., in Rernington's Pharmacezatical Sciences,
Mack Publishing Co., Easton, PA, 1985, p. 301). Emulsions.are often
biphasic systems comprising of two immiscible liquid phases intimately
mixed and dispersed with each other. In general, emulsions may be either
29
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
water-in-oil (w/o) or of the oil-in-water (o/w) variety. When an aqueous
phase is finely divided into and dispersed as minute droplets into a bulk oily
phase the resulting composition is called a water-in-oil (w/o) emulsion.
Alternatively, when an oily phase is finely divided into and dispersed as
S minute droplets into a bulk aqueous phase the resulting composition is
called an oil-in-water (o/w) emulsion. Emulsions may contain additional
components in addition to the dispersed phases and the active drug, which
may be present as a solution in either the aqueous phase, oily phase or itself
as a separate phase. Pharmaceutical excipients such as emulsifiers,
stabilizers, dyes, and anti-oxidants may also be present in emulsions as
needed. Pharmaceutical emulsions may also be multiple emulsions that are
comprised of more than two phases such as, for example, in the case of oil-
in-water-in-oil (o/w/o) and water-in-oil-in-water (w/o/w) emulsions. Such
complex formulations often provide certain advantages that simple binary
1 S emulsions do not. Multiple emulsions in which individual oil droplets of
an
o/w emulsion enclose small water droplets constitute a w/o/w emulsion.
Likewise a system of oil droplets enclosed in globules of water stabilized in
an oily continuous provides an o/w/o emulsion.
[0054] Emulsions are characterized by little or no thermodynamic
stability. Often, the dispersed or discontinuous phase of the emulsion is well
dispersed into the external or continuous phase and maintained in this form
through the means of emulsifiers or the viscosity of the formulation. Either
of the phases of the emulsion may be a semisolid or a solid, as is the case of
emulsion-style ointment bases and creams. Other means of stabilizing
2S emulsions entail the use of emulsifiers that may be incorporated into
either
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
phase of the emulsion. Emulsifiers may broadly be classified into four
categories: synthetic surfactants, naturally occurring emulsifiers, absorption
bases, and finely dispersed solids (Idson, in Pharmaceutical Dosage Fof~ms,
Lieberman, Rieger and Baz~lcer (Eds.), 1988, Marcel Dekker, Inc., New
Yorlc, N.Y., volume 1, p. 199).
[0055] Synthetic surfactants, also known as surface active agents, have
found wide applicability in the formulation of emulsions and have been
reviewed in the literature (Rieger, in Pharmaceutical Dosage Forms,
Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New
York, N.Y., volume 1, p. 285; Idson, in Pharmaceutical Dosage Forrns,
Lieberman, Rieger and Banker (Eds.), Marcel Dekker, Inc., New York,
N.Y., 1988, volume 1, p. 199). Surfactants are typically amphiphilic and
comprise a hydrophilic and a hydrophobic portion. The ratio of the
hydrophilic to the hydrophobic nature of the surfactant has been termed the
hydrophile/lipophile balance (HLB) and is a valuable tool in categorizing
and selecting surfactants in the preparation of formulations. Surfactants may
be classified into different classes based on the nature of the hydrophilic
group: nonionic, anionic, cationic and amphoteric (Rieger, in
Pharmaceutical Dosage Fof°ms, Lieberman, Rieger and Banker (Eds.),
1988, Marcel Dekker, Inc., New York, N.Y., volume l, p. 285).
[0056] Naturally occurring emulsifiers used in emulsion formulations
include lanolin, beeswax, phosphatides, lecithin and acacia. Absorption
bases possess hydrophilic properties such that they can soak.up water to
form w/o emulsions yet retain their semisolid consistencies, such as
2S anhydrous lanolin and hydrophilic petrolatum. Finely divided solids have
31
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
also been used as good emulsifiers especially in combination with
surfactants and in viscous preparations., These include polar inorganic
solids, such as heavy metal hydroxides, nanswelling clays such as bentonite,
attapulgite, hectorite, kaolin, montmorillonite, colloidal aluminum silicate
and colloidal magnesium aluminum silicate, pigments and nonpolar solids
such as carbon or glyceryl tristearate.
[0057) A large variety of non-emulsifying materials are also included in
emulsion formulations and contribute to the properties of emulsions. These
include fats, oils, waxes, fatty acids, fatty alcohols, fatty esters,
humectants,
hydrophilic colloids, preservatives, and antioxidants (Block, in
Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.),
1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335; Idson, in
Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.),
1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).
[005] Hydrophilic colloids or hydrocolloids include naturally occurring
gums and synthetic polymers such as polysaccharides (for example, acacia,
agar, alginic acid, carrageenan, guar gum, karaya gum, and tragacanth),
cellulose derivatives (for example, carboxymethylcellulose and
carboxypropylcellulose), and synthetic polymers (for example, carbomers,
cellulose ethers, and carboxyvinyl polymers). These disperse or swell in
water to form colloidal solutions that stabilize emulsions by forming strong
interfacial films around the dispersed phase droplets and by increasing the
viscosity of the external phase.
[0059] Since emulsions often contain a number of ingredients such as
carbohydrates, proteins, sterols and phosphatides that may readily support
32
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WO 2004/016754 PCT/US2003/025465
the growth of microbes, these formulations often incorporate preservatives.
Commonly used preservatives included in emulsion formulations include
methyl paraben, propyl paraben, quaternary ammonium salts, benzalkonium
chloride, esters of p-hydroxybenzoic acid, and boric acid. Antioxidants axe
also commonly added to emulsion formulations to prevent deterioration of
the formulation. Antioxidants used may be free radical scavengers such as
tocopherols, alkyl gallates, butylated hydroxyanisole, butylated
hydroxytoluene, or reducing agents such as ascorbic acid and sodium
metabisulfite, and antioxidant synergists such as citric acid, tartaric acid,
and lecithin.
[0060] The application of emulsion forinulations via dennatological,
oral, and parenteral routes and methods for their manufacture have been
reviewed in the literature (Idson, in Plaanmaceutical Dosage Foy~rns,
Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New
York, N.Y., volume 1, p. 199). Emulsion formulations for oral delivery have
been very widely used because of reasons of ease of formulation, efficacy
from an absorption and bioavailability standpoint. (Rosoff, in
Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.),
1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245; Idson, in
Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.),
1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199). Mineral-oil
base laxatives, oil-soluble vitamins and high fat nutritive preparations are
among the materials that have commonly been administered. orally as o/w
emulsions.
33
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[0061] In one embodiment of the present invention, the compositions of
oligonucleotides and nucleic acids are formulated as microemulsions. A
microemulsion may be defined as a system of water, oil and amphiphile,
which is a single optically isotropic, and thermodynamically stable liquid
solution (Rosoff, in Pharmaceutical Dosage Fog°nZS, Lieberman, Rieger
and
Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume l, p.
245). Typically microemulsions are systems that are prepared by first
dispersing an oil in an aqueous surfactant solution and then adding a
sufficient amount of a fourth component, generally an intermediate chain-
length alcohol to form a transparent system. Therefore, microemulsions
have also been described as thermodynamically stable, isotropically clear
dispersions of two immiscible liquids that are stabilized by interfacial films
of surface-active molecules (Leung and Shah, in: Cont~°olled Release of
D~~ugs: Polymer s and Aggf~egate Systems, Rosoff, M., Ed., 1989, VCH
Publishers, New York, pages 1852-5). Microemulsions commonly are
prepared via a combination of three to five components that include oil,
water, surfactant, cosurfactant and electrolyte. Whether the microemulsion
is of the water-in-oil (w/o) or an oil-in-water (o/w) type is dependent on the
properties of the oil and surfactant used and on the structure and geometric
packing of the polar heads and hydrocarbon tails of the surfactant molecules
(Schott, in Remington's Pharmaceutical Sciences, Mack Publishing Co.,
Easton, PA, 1985, p. 271).
[0062] The phenomenological approach utilizing phase diagrams has
been extensively studied and has yielded a comprehensive knowledge, to
one skilled in the art, of how to formulate microemulsions (Rosoff, in
34
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Pharmaceutical Dosage Forrns, Lieberman, Rieger and Banker (Eds.),
1988, Marcel Dekker, Inc., New Yorlc, N.Y., volume 1, p. 245; Block, in
Pharmaceutical Dosage Fornas, Lieberman, Rieger and Banker (Eds.),
1988, Marcel Deklcer, Inc., New Yorlc, N.Y., volume 1, p. 335). Compared
to conventional emulsions, microemulsions offer the advantage of
solubilizing water-insoluble drugs in a formulation of thermodynamically
stable droplets that are formed spontaneously.
[0063] Surfactants used in the preparation of microemulsions include,
but are not limited to, ionic surfactants, non-ionic surfactants, Brij 96,
polyoxyethylene oleyl ethers, polyglycerol fatty acid esters, tetraglycerol
monolaurate (ML310), tetraglycerol monooleate (M0310), hexaglycerol
monooleate (PO310), hexaglycerol pentaoleate (PO500), decaglycerol
monocaprate (MCA750), decaglycerol monooleate (M0750),,decaglycerol
sequioleate (50750), decaglycerol decaoleate (DA0750), alone or in
combination with cosurfactants. The cosurfactant, usually a short-chain
alcohol such as ethanol, 1-propanol, and 1-butanol, serves to increase the
interfacial fluidity by penetrating into the surfactant film and consequently
creating a disordered film because of the void space generated among
surfactant molecules. Microemulsions may, however, be prepared without
the use of cosurfactants and alcohol-free self emulsifying microemulsion
systems are known in the art. The aqueous phase may typically be, but is not
limited to, water, an aqueous solution of the drug, glycerol, PEG300,
PEG400, polyglycerols, propylene glycols, and derivatives of ethylene
glycol. The oil phase may include, but is not limited to, materials such as
Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain
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(C8-C 12) mono, di, and triglycerides, polyoxyethylated glyceryl fatty acid
esters, fatty alcohols, polyglycolized glycerides, saturated polyglycolized
C8-C 10 glycerides, vegetable oils and silicone oil.
[0064] Microemulsions are particularly of interest from the standpoint
of drug solubilization and the enhanced absorption of drugs. Lipid based
microemulsions (both o/w and w/o) have been proposed to enhance the oral
bioavailability of drugs, including peptides (Constantinides et al.,
Plzar~aaceutical Research, 1994, 11, 1385-1390; R.itschel, Meth. Find. Exp.
Clin. Plaa3-macol., 1993, 13, 205). Microemulsions afford advantages of
improved drug solubilization, protection of drug from enzymatic hydrolysis,
possible enhancement of drug absorption due to surfactant-induced
alterations in membrane fluidity and permeability, ease of preparation, ease
of oral administration over solid dosage forms, improved clinical potency,
and decreased toxicity (Constantinides et al., Phas~maceutical Research,
1994, 1 l, 1385; Ho et al., J. Pha~m. Sci., 1996, 85, 138-143). Often
microemulsions may form spontaneously when their components are
brought together at ambient temperature. This may be particularly
advantageous when formulating thermolabile drugs, peptides or
oligonucleotides. Microemulsions have also been effective in the
transdermal delivery of active components in both cosmetic and
pharmaceutical applications. It is expected that the microemulsion
compositions and formulations of the present invention will facilitate the
increased systemic absorption of oligonucleotides and nucleic acids from
the gastrointestinal tract, as well as improve the local cellular uptake of
36
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oligonucleotides and nucleic acids within the gastrointestinal tract, vagina,
buccal cavity and other areas of administration.
[0065] Microemulsions of the present invention may also contain
additional components and additives such as sorbitan monostearate (Grill 3),
Labrasol, and penetration enhancers to improve the properties of the
formulation and to enhance the absorption of the oligonucleotides and
nucleic acids of the present invention. Penetration enhancers used in the
microemulsions of the present invention may be classified as belonging to
one of five broad categories - surfactants, fatty acids, bile salts, chelating
agents, and non-chelating non-surfactants (Lee et al., Critical Reviews irz.
Therapeutic Ds°ug Caf-rie~ Systerras, 1991, p. 92). Each of these
classes has
been discussed above.
Liposomes
[0066] There are many organized surfactant structures besides
microemulsions that have been studied and used for the formulation of
drugs. These include monolayers, micelles, bilayers and vesicles. Vesicles,
such as liposomes, have attracted great interest because of their specificity
and the duration of action they offer fiom the standpoint of drug delivery.
As used in the present invention, the term "liposome" means a vesicle
composed of amphiphilic lipids arranged in a spherical bilayer or bilayers.
[0067] Liposomes are unilamellar or multilamellar vesicles which have
a membrane formed from a lipophilic material and an aqueous interior. The
aqueous portion contains the composition to be delivered. Cationic
liposomes possess the advantage of being able to fuse to the cell wall.
37
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Noncationic liposomes, although not able to fuse as efficiently with the cell
wall, are taken up by macrophages in vivo.
[0068] In order to cross intact mammalian skin, Iipid vesicles must pass
through a series of fine pores, each with a diameter less than 50 nm, under
the influence of a suitable transdermal gradient. Therefore, it is desirable
to
use a liposome, which is highly deformable and able to pass through such
fine pores.
[0069] Further advantages of liposomes include; liposomes obtained
from natural phospholipids are biocompatible and biodegradable; liposomes
can incorporate a wide range of water and lipid soluble drugs; liposomes can
protect encapsulated drugs in their internal compartments from metabolism
and degradation (Rosoff, in Phar-rnaceutical Dosage Foams, Lieberman,
Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y.,
volume 1, P. 245). Important considerations in the preparation of liposome
formulations are the lipid surface charge, vesicle size and the aqueous
volume of the liposomes.
[0070] Liposomes are useful for the transfer and delivery of active
ingredients to the site of action. Because the liposomal membrane is
structurally similar to biological membranes, when liposomes are applied to
a tissue, the liposomes start to merge with the cellular membranes. As the
merging of the liposome and cell progresses, the liposomal contents are
emptied into the cell where the active agent may act.
[0071] Liposomal formulations have been the focus of extensive
investigation as the mode of delivery for many drugs. There is growing
evidence that for topical administration, liposomes present several
38
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advantages over other formulations. Such advantages include reduced side-
effects related to high systemic absorption of the administered drug,
increased accumulation of the administered drug at the desired target, and
the ability to administer a wide variety of drugs, both hydrophilic and
hydrophobic, into the skin.
[0072] Several reports have detailed the ability of liposomes to deliver
agents including high-molecular weight DNA into the skin. Compounds
including analgesics, antibodies, hormones and high-molecular weight
DNAs have been administered to the skin. The majority of applications
resulted in the targeting of the upper epidermis.
[0073] Liposomes fall into two broad classes. Cationic liposomes are
positively charged liposomes, which interact with the negatively charged
DNA molecules to form a stable complex. The positively charged
DNA/liposome complex binds to the negatively charged cell surface and is
internalized in an endosome. Due to the acidic pH within the endosome, the
liposomes are ruptured, releasing their contents into the cell cytoplasm
(Wang et al., BiocIZem. Biophys. Res. Con2mu~z., 1987, 147, 980 - 985)
[0074] Liposomes, which are pH-sensitive or negatively charged, entrap
DNA rather than complex with it. Since both the DNA and the lipid axe
similarly charged, repulsion rather than complex formation occurs.
Nevertheless, some DNA is entrapped within the aqueous interior of these
liposomes. pH-sensitive liposomes have been used to deliver DNA encoding
the thymidine kinase gene to cell monolayers in culture. Expression of the
exogenous gene was detected in the target cells (Zhou et al., Journal of
Contf-olled Release, 1992, 19, 269-274).
39
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[0075] One major type of liposomal composition includes phospholipids
other than naturally derived phosphatidylcholine. Neutral liposome
compositions, for example, can be formed from dimyristoyl
phosphatidylcholine (DMPC) or dipalmitoyl phosphatidylcholine (DPPC).
Anionic liposome compositions generally are formed from dimyristoyl
phosphatidylglycerol, while anionic fusogenic liposomes are formed
primarily from dioleoyl phosphatidylethanolamine (DOPE). Another type of
liposomal composition is formed from phosphatidylcholine (PC) such as, for
example, soybean PC, and egg PC. Another type is formed from mixtures of
phospholipid and/or phosphatidylcholine and/or cholesterol.
[0076] Several studies have assessed the topical delivery of liposomal
drug formulations to the skin. Application of liposomes containing
interferon to guinea pig skin resulted in a reduction of skin herpes sores
while delivery of interferon via other means (e.g. as a solution or as an
emulsion) were ineffective (Weiner et al., Jom°nal of Drug Taf getifZg,
1992,
2, 405-410). Further, an additional study tested the efficacy of interferon
administered as part of a liposomal formulation to the administration of
interferon using an aqueous system, and concluded that the liposomal
formulation was superior to aqueous administration (du Plessis et al.,
Antiviral Research, 1992, 18, 259-265).
[0077] Non-ionic liposomal systems have also been examined to
determine their utility in the delivery of drugs to the skin, in particular
systems comprising non-ionic surfactant and cholesterol. Non-ionic
liposomal formulations comprising Novasome TM I (glyceryl
2S dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and NovasomeTM II
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(glyceryl distearate/ cholesterol/polyoxyethylene-10-stearyl ether) were
used to deliver cyclosporin-A into the dermis of mouse skin. Results
indicated that such non-ionic liposomal systems were effective in
facilitating the deposition of cyclosporin-A into different layers of the skin
(Hu et al. S.T.P.Pharma. Sci., 1994, 4, 6, 466).
[0078] Liposomes also include "sterically stabilized" liposomes, a term,
which, as used herein, refers to liposomes comprising one or more
specialized lipids that, when incorporated into liposomes, result in enhanced
circulation lifetimes relative to liposomes lacking such, specialized lipids.
Examples of sterically stabilized liposomes are those in which part of the
vesicle-forming lipid portion of the liposome (A) comprises one or more
glycolipids, such as monosialoganglioside GMT, or (B) is derivatized with
one or more hydrophilic polyners, such as a polyethylene glycol (PEG)
moiety. While not wishing to be bound by any particular theory, it is
thought in the art that, at least for sterically stabilized liposomes
containing
gangliosides, sphingomyelin, or PEG-derivatized lipids, the enhanced
circulation half life of these sterically stabilized liposomes derives from a
reduced uptake into cells of the reticuloendothelial system (RES) (Allen et
al., FEBS Letters, 1987, 223, 42; Wu et al., Ca~zcey~ Research, 1993, 53,
3765).
[0079] Various liposomes comprising one or more glycolipids are
known in the art. Papahadjopoulos et al. (Alan. N. Y. Acad. Sci., 1987, 507,
64) reported the ability of monosialoganglioside GM,, galactocerebroside
sulfate and phosphatidylinositol to improve blood half lives of liposomes.
These findings were expounded upon by Gabizon et al. (Pnoc. Natl. Acad.
41
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WO 2004/016754 PCT/US2003/025465
Sci. U.S.A., 1988, 85, 6949). U.S. Patent No. 4,837,028 and WO 88/04924,
both to Allen et al., disclose liposomes comprising (1) sphingomyelin and
(2) the ganglioside Gjor a galactocerebroside sulfate ester. U.S. Patent No.
5,543,152 (Webb et al.) discloses liposomes comprising sphingomyelin.
Liposomes comprising 1,2-sn-dimyristoylphosphatidylcholine are disclosed
in WO 97/13499 (Lim et al.).
[0080] Many liposomes comprising lipids derivatized with one or more
hydrophilic polymers, and methods of preparation thereof, are known in the
art. Sunamoto et al. (Bull. Chem. Soc. Jpn., 1980, 53, 2778) described
liposomes comprising a nonionic detergent, 2C,215G that contains a PEG
moiety. Illum et al. (FEBS Lett., 1984, 167, 79) noted that hydrophilic
coating of polystyrene particles with polymeric glycols results in
significantly enhanced blood half lives. Synthetic phospholipids modified
by the attachment of carboxylic groups of polyalkylene glycols (e.g., PEG)
are described by Sears (U.S. Patent Nos. 4,426,330 and 4,534,899).
Klibanov et al. (FEBS Lett., 1990, 268, 235) described experiments
demonstrating that liposomes comprising phosphatidylethanolamine (PE)
derivatized with PEG or PEG stearate have significant increases in blood
circulation half lives. Blume et al. (Bioclaifzaica et Biophysics Acta, 1990,
1029, 91) extended such observations to other PEG derivatized
phospholipids, e.g., DSPE-PEG, formed from the combination of
distearoylphosphatidylethanolamine (DSPE) and PEG. Liposomes having
covalently bound PEG moieties on their external surface are described in
European Patent No. EP 0 445 131 B1 and WO 90/04384 to Fisher.
Liposome compositions containing 1-20 mole percent of PE derivatized
42
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WO 2004/016754 PCT/US2003/025465
with PEG, and methods ofuse thereof, axe described by Woodle et al. (U.S.
Patent Nos. 5,013,SS6 and 5,356,633) and Martin et al. (U.S. Patent No.
5,213,804 and European Patent No. EP 0 496 813 Bl). Liposomes
comprising a number of other lipid-polymer conjugates are disclosed in WO
91/05545 and U.S. Patent No. 5,225,212 (both to Martin et al.) and in WO
94120073 (Zalipsky et al.) Liposomes comprising PEG-modified ceramide
lipids are described in WO 96/10391 (Choi et al.). U.S. Patent Nos.
5,540,935 (Miyazalci et al.) and 5,556,948 (Tagawa et al.) describe PEG-
containing liposomes that can be further derivatized with functional
moieties on their surfaces.
[0081] A limited number of liposomes comprising nucleic acids are
known in the art. WO 96/40062 to Thierry et al. discloses methods for
encapsulating high molecular weight nucleic acids in liposomes. U.S. Patent
No. 5,264,221 to Tagawa et al. discloses protein-bonded liposomes and
asserts that the contents of such liposomes may include an antisense RNA.
U.S. Patent No. 5,665,710 to Rahman et al. describes certain methods of
encapsulating oligodeoxynucleotides in liposomes. WO 97/04787 to Love et
al. discloses liposomes comprising antisense oligonucleotides targeted to the
raf gene.
[0082] Transfersomes are yet another type of liposomes, and are highly
deformable lipid aggregates which are attractive candidates for drug
delivery vehicles. Transfersomes may be described as lipid droplets, which
are so highly deformable that they are easily able to penetrate through pores,
which are smaller than the droplet. Transfersomes are adaptable to the
2S environment in which they are used, e.g. they axe self optimizing (adaptive
43
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WO 2004/016754 PCT/US2003/025465
to the shape of pores in the skin), self repairing, frequently reach their
targets without fragmenting, and often self loading. To make transfersomes
it is possible to add surface edge-activators, usually surfactants, to a
standard liposomal composition. Transfersomes have been used to deliver
serum albumin to the skin. The transfersome-mediated delivery of serum
albumin has been shown to be as effective as subcutaneous injection of a
solution containing serum albumin.
[0083] Surfactants find wide application in formulations such as
emulsions (including microemulsions) and liposomes. The most common
way of classifying and ranking the properties of the many different types of
surfactants, both natural and synthetic, is by the use of the
hydrophile/lipophile balance (HLB). The nature of the hydrophilic group
(also known as the "head") provides the most useful means for categorizing
the different surfactants used in formulations (Rieger, in
Phar°naaceistical
Dosage Fo~nas, Marcel Dekker, Inc., New York, NY, 1988, p. 285)
[0084] If the surfactant molecule is not ionized, it is classified as a
nonionic surfactant. Nonionic surfactants fmd wide application in
pharmaceutical and cosmetic products and are usable over a wide range of
pH values. In general their HLB values range from 2 to about 18 depending
on their structure. Nonionic surfactants include nonionic esters such as
ethylene glycol esters, propylene glycol esters, glyceryl esters, polyglyceryl
esters, sorbitan esters, sucrose esters, and ethoxylated esters. Nonionic
alkanolamides and ethers such as fatty alcohol ethoxylates, propoxylated
alcohols, and ethoxylated/propoxylated block polymers are also included in
44
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this class. The polyoxyethylene surfactants are the most popular members of
the nonionic surfactant class.
[0085] If the surfactant molecule carries a negative charge when it is
dissolved or dispersed in water, the surfactant is classified as anionic.
Anionic surfactants include carboxylates such as soaps, acyl lactylates, acyl
amides of amino acids, esters of sulfuric acid such as alkyl sulfates and
ethoxylated alkyl sulfates, sulfonates such as alkyl benzene sulfonates, acyl
isethionates, aryl taurates and sulfosuccinates, and phosphates. The most
important members of the anionic surfactant class are the alkyl sulfates and
the soaps.
[0086) If the surfactant molecule carries a positive charge when it is
dissolved or dispersed in water, the surfactant is classified as cationic.
Cationic surfactants include quaternary ammonium salts and ethoxylated
amines. The quaternary ammonium salts are the most used members of this
class.
[0087] If the surfactant molecule has the ability to carry either a positive
or negative charge, the surfactant is classified as amphoteric. Amphoteric
surfactants include acrylic acid derivatives, substituted alkylamides, N-
alkylbetaines and phosphatides.
[0088] The use of surfactants in drug products, formulations and in
emulsions has been reviewed (Rieger, in Pharmaceutical Dosage Forms,
Marcel Dekker, Inc., New York, NY, 1988, p. 285). Penetration Enhancers
[0089] In one embodiment, the present invention employs various
penetration enhancers to effect the efficient delivery of nucleic acids
particularly oligonucleotides, to the skin of animals. Most drugs are present
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
in solution in both ionized and nonionized forms. However, usually only
lipid soluble or lipophilic drugs readily cross cell membranes. It has been
discovered that even non-lipophilic drugs may cross cell membranes if the
membrane to be crossed is treated with a penetration enhancer. In addition
to aiding the diffusion of non-lipophilic drugs across cell membranes,
penetration enhancers also enhance the permeability of lipophilic drugs.
[0090] Penetration enhancers may be classified as belonging to one of
five broad categories, i.e., surfactants, fatty acids, bile salts, chelating
agents, and non-chelating nonsurfactants (Lee et al., Critical Reviews iu
Therapeutic Drug Carrier Systems, 1991, p.92). Each of the above
mentioned classes of penetration enhancers are described below in greater
detail.
[0091] Surfactants: In connection with the present invention, surfactants
(or "surface-active agents") are chemical entities which, when dissolved in
an aqueous solution, reduce the surface tension of the solution or the
interfacial tension between the aqueous solution and another liquid, with the
result that absorption of oligonucleotides through the mucosa is enhanced.
In addition to bile salts and fatty acids, these penetration enhancers
include,
for example, sodium lauryl sulfate, polyoxyethylene-9-lauryl ether and
polyoxyethylene-20-cetyl ether) (Lee et al., Critical Reviews in Therapeutic
Drug Carrier Systems, 1991, p.92); and perfluorochemical emulsions, such
as FC-43. Takahashi et al., J. Pharm. Pharmacol., 1988, 40, 252).
[0092] Fatty acids: Various fatty acids and their derivatives which act as
penetration enhancers include, for example, oleic acid, lauric acid, capric
acid (n-decanoic acid), myristic acid, palmitic acid, stearic acid, linoleic
46
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WO 2004/016754 PCT/US2003/025465
acid, linolenic acid, dicaprate, tricaprate, monoolein (1-monooleoyl-.rac-
glycerol), dilaurin, caprylic acid, arachidonic acid, glycerol 1-monocaprate,
1-dodecylazacycloheptan-2-one, acylcarnitines, acylcholines, C,_~o alkyl
esters thereof (e.g., methyl, isopropyl and t-butyl), and mono- and di-
glycerides thereof (i.e., oleate, laurate, caprate, myristate, palmitate,
stearate, linoleate, etc.) (Lee et al., Critical Reviews in
Thef°apeutic D~°ug
Cap°rier Systef~as, 1991, p.92; Muranishi, Critical Reviews in
Therapeutic
Drug Carrier Systems, 1990, 7, 1-33; El Hariri et al., J. Phaf°na.
Pharmacol.,
1992, 44, 651-654).
[0093] Bile salts: The physiological role of bile includes the facilitation
of dispersion and absorption of lipids and fat-soluble vitamins (Brunton,
Chapter 38 in: Goodman & Gilman's The Pharmacological Basis of
They°apeutics, 9th Ed., Hardman et al. Eds. McGraw-Hill, New York,
1996,
pp. 934-935). Various natural bile salts, and their synthetic derivatives, act
as penetration enhancers. Thus the term "bile salts" includes any of the
naturally occurring components of bile as well as any of their synthetic
derivatives. The bile salts of the invention include, for example, cholic acid
(or its pharmaceutically acceptable sodium salt, sodium cholate),
dehydrocholic acid (sodium dehydrocholate), deoxycholic acid (sodium
deoxycholate), glucholic acid (sodium glucholate), glycholic acid (sodium
glycocholate), glycodeoxycholic acid (sodium glycodeoxycholate),
taurocholic acid (sodium taurocholate), taurodeoxycholic acid (sodium
taurodeoxycholate), chenodeoxycholic acid (sodium chenodeoxycholate),
ursodeoxycholic acid (UDCA), sodium tauro-24,25-dihydro-fusidate
(STDHF), sodium glycodihydrofusidate'and polyoxyethylene-9-lauryl ether
47
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(POE) (Lee et al., Critical Reviews in Tlzerapeutic Drug Carrier Systems,
1991, page 92; Swinyard, Chapter 39 In: Renzirzgton's Pharmaceutical
Sciences, 18th Ed., Gennaro, ed., Maclc Publishing Co., Easton, PA, 1990,
pages 782-783; Muranishi, Critical Reviews in Therapeutic Drug Carrier
Systems, 1990, 7, 1-33; Yamamoto et al., J. Pharnz. Exp. Ther., 1992, 263,
25; Yamashita et al., J. Plzarm. Sci., 1990, 79, 579-583).
[0094] Chelating Agents: Chelating agents, as used in connection with
the present invention, can be defined as compounds that remove metallic
ions from solution by forming complexes therewith, with the result that
absorption of oligonucleotides through the mucosa is enhanced. With
regards to their use as penetration enhancers in the present invention,
chelating agents have the added advantage of also serving as DNase
inhibitors, as most characterized DNA nucleases require a divalent metal ion
for catalysis and are thus inhibited by chelating agents (Jarrett, J.
Chr°omatogr°., 1993, 618, 315-339). Chelating agents of the
invention
include but are not limited to disodium. ethylenediaminetetraacetate
(EDTA), citric acid, salicylates (e.g., sodium salicylate, 5-methoxysalicylate
and homovanilate), N-acyl derivatives of collagen, laureth-9 and N-amino
acyl derivatives of beta-diketones (enamines)(Lee et al., Critical Reviews irz
Therapeutic Dr°ug Car°r°ier Systems, 1991, page 92;
Muranishi, CT°itical
Reviews in Therapeutic Drug Carrier Systenzs, 1990, 7, 1-33; Buur et al., .I.
Control Rel., 1990, 14, 43-51).
[0095] Non-chelating non-surfactants: As used herein, nonchelating
non-surfactant penetration enhancing compounds can be defined as
compounds that demonstrate insignificant activity as chelating agents or as
48
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WO 2004/016754 PCT/US2003/025465
surfactants but that nonetheless enhance absorption of oligonucleotides
through the alimentary mucosa (Muranishi, C~°itical Reviews in
Therapeutic
Drug Carrier Systems, 1990, 7, 1-33). This class of penetration enhancers
include, for example, unsaturated cyclic ureas, 1-alkyl- and 1-
alkenylazacyclo-alkanone derivatives (Lee et al., Critical Reviews ih
Therapeutic D~°ug Carrier Systefns, 1991, page 92); and non-
steroidal anti-
inflammatory agents such as diclofenac sodium, indomethacin and
phenylbutazone (Yamashita et al., J. Pharm. Pharmacol., 1987, 39, 621-
626).
[0096] Agents that enhance uptake of oligonucleotides at the cellular
level may also be added to the pharmaceutical and other compositions of the
present invention. For example, cationic lipids, such as lipofectin (Junichi
et
al, U.S. Patent No. 5,705,188), cationic glycerol derivatives, and
polycationic molecules, such as polylysine (Lollo et al., PCT Application
WO 97/30731), are also known to enhance the cellular uptake of
oligonucleotides.
[0097] Other agents may be utilized to enhance the penetration of the
administered nucleic acids, including glycols such as ethylene glycol and
propylene glycol, pyrrols such as 2-pyrrol, azones, and terpenes such as
limonene and menthone.
Carriers
[0098] Certain compositions of the present invention also incorporate
carrier compounds in the formulation. As used herein, "carrier compound"
or "carrier" can refer to a nucleic acid, or analog thereof, which is inert
(i.e.,
does not possess biological activity per se) but is recognized as a nucleic
49
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WO 2004/016754 PCT/US2003/025465
acid by in vivo processes that reduce the bioavailability of a nucleic acid
having biological activity by, for example, degrading the biologically active
nucleic acid or promoting its removal from circulation. The
coadministration of a nucleic acid and a carrier compound, typically with an
excess of the latter substance, can result in a substantial reduction of the
amount of nucleic acid recovered in the liver, kidney or other
extracirculatory reservoirs, presumably due to competition between the
carrier compound and the nucleic acid for a common receptor. For example,
the recovery of a partially phosphorothioate oligonucleotide in hepatic tissue
can be reduced when it is coadministered with polyinosinic acid, dextran
sulfate, polycytidic acid or 4-acetamido-4'isothiocyano-stilbene-2,2'
disulfonic acid (Miyao et al., Azztisense Res. Dev., 1995, 5, 115-121;
Takakura et al., Azztisense & Nucl. Acid Dz°ug Dev., 1996, 6, 177-
183).
Excipients
[0099] In contrast to a carrier compound, a "pharmaceutical carrier" or
"excipient" is a pharmaceutically acceptable solvent, suspending agent or
any other pharmacologically inert vehicle for delivering one or more nucleic
acids to an animal. The excipient may be liquid or solid and is selected, with
the planned manner of administration in mind, so as to provide~for the
desired bulk, consistency, etc., when combined with a nucleic acid and the
other components of a given pharmaceutical composition. Typical
pharmaceutical carriers include, but are not limited to, binding agents (e.g.,
pregelatinized maize starch, polyvinylpyrrolidone or hydroxypropyl
methylcellulose, etc.); fillers (e.g., lactose and other sugars,
microcrystalline
cellulose, pectin, gelatin, calcium sulfate, ethyl cellulose, polyacrylates or
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calcium hydrogen phosphate, etc.); lubricants (e.g., magnesium stearate,
talc, silica, colloidal silicon dioxide, stearic acid, metallic stearates,
hydrogenated vegetable oils, coin starch, polyethylene glycols, sodium
benzoate, sodium acetate, etc.); disintegr ants (e.g., starch, sodium starch
glycolate, etc.); and wetting agents (e.g., sodium lauryl sulphate, etc.).
[00100] Pharmaceutically acceptable organic or inorganic excipient
suitable for non-parenteral administration, which does not deleteriously
react with nucleic acids, can also be used to formulate t1e compositions of
the present invention. Suitable pharmaceutically acceptable carriers include,
but are not limited to, water, salt solutions, alcohols, polyethylene glycols,
gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous
paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.
[00101] Formulations for topical administration of nucleic acids may
include sterile and non-sterile aqueous solutions, non-aqueous solutions in
common solvents such as alcohols, or solutions of the nucleic acids in liquid
or solid oil bases. The solutions may also contain buffers, diluents and other
suitable additives. Pharmaceutically acceptable organic or inorganic
excipients suitable for non-parenteral administration, which do not
deleteriously react with nucleic acids, can be used.
[00102] Suitable pharmaceutically acceptable excipients include, but are
not limited to, water, salt solutions, alcohol, polyethylene glycols, gelatin,
lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin,
hydroxymethylcellulose, polyvinylpyrrolidone and the like.
Other Components
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[00103] The compositions of the present invention may additionally
contain other adjunct components conventionally found in pharmaceutical
compositions, at their art-established usage levels. Thus, for example, the
compositions may contain additional, compatible, pharmaceutically-active
materials such as, for example, antipruritics, astringents, local anesthetics
or
anti-inflammatory agents, or may contain additional materials useful in
physically formulating various dosage forms of the compositions of the
present invention, such as dyes, flavoring agents, preservatives,
antioxidants, opacifiers, thickening agents and stabilizers. However, such
materials, when added, should not unduly interfere with the biological
activities of the components of the compositions of the present invention.'
The formulations can be sterilized and, if desired, mixed with auxiliary
agents, e.g., lubricants, preservatives, stabilizers, wetting agents,
emulsifiers, salts for influencing osmotic pressure, buffers, colorings,
flavorings and/or aromatic substances and the like which do not
deleteriously interact with the nucleic acids) of the formulation.
[00104] Aqueous suspensions may contain substances, which increase the
viscosity of the suspension including, for example, sodium
carboxymethylcellulose, sorbitol, and/or dextran. The suspension may also
contain stabilizers.
[00105] Certain embodiments of the invention provide pharmaceutical
compositions containing (a) one or more antisense compounds and (b) one
or more other chemotherapeutic agents which function by a non-antisense
mechanism. Examples of such chemotherapeutic agents include, but are not
limited to, anticancer drugs such as daunorubicin, dactinomycin,
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doxorubicin, bleomycin, mitomycin, nitrogen mustard, chlorambucil,
melphalan, cyclophosphamide, 6-mercaptopurine, 6-thioguanine, cytarabine
(CA), S-fluorouracil (S-FU), floxuridine (S-FUdR), methotrexate (MTX),
colchicine, vincristine, vinblastine, etoposide, teniposide, cisplatin and
S diethylstilbestrol (DES). See, generally, The Mef~ck Manual of Diagnosis
and Thef°apy, 15th Ed., Berkow et al., eds., 1987, Rahway, N.J., pages
1206-
1228). Anti-inflammatory drugs, including but not limited to nonsteroidal
anti-inflammatory drugs and corticosteroids, and antiviral drugs, including
but not limited to ribivirin, vidarabine, acyclovir and ganciclovir, may also
be combined in compositions of the invention. See, generally, The Merck
Ma3aual of Diagnosis afad Therapy, 1 Sth Ed., Berkow et al., eds., 1987,
Rahway, N.J., pages 2499-2506 and 46-49, respectively). other non-
antisense chemotherapeutic agents are also within the scope of this
invention. Two or more combined compounds may be used together or
1 S sequentially.
[00106] In another related embodiment, compositions of the invention
may contain one or more antisense compounds, particularly
oligonucleotides, targeted to a first nucleic acid and one or more additional
antisense compounds targeted to a second nucleic acid target. Numerous
examples of antisense compounds are known in the art. Two or more
combined compounds may be used together or sequentially.
[00107] The formulation of therapeutic compositions and their
subsequent administration is believed to be within the skill of those in the
art. Dosing is dependent on severity and responsiveness of the disease state
2S to be treated, with the course of treatment lasting from several days to
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several months, or until a cure is effected or a diminution of the disease
state
is achieved. Optimal dosing schedules can be calculated from measurements
of drug accumulation in the body of the patient. Persons of ordinary skill
can easily determine optimum dosages, dosing methodologies and repetition
rates. Optimum dosages may vary depending on the relative potency of
individual oligonucleotides, and can generally be estimated based on ECsos
found to be effective in in vitro and in viva animal models. In general,
dosage is from 0.01 ~.g to 100 g per kg of body weight, and may be given
once or more daily, weekly, monthly or yearly, or even once every 2 to 20
years. Persons of ordinary skill in the art can easily estimate repetition
rates
for dosing based on measured residence times and concentrations of the
drug in bodily fluids or tissues. Following successful treatment, it may be
desirable to have the patient undergo maintenance therapy to prevent the
recurrence of the disease state, wherein the oligonucleotide is administered
in maintenance doses, ranging from 0.01 ~.g to 100 g per kg of body weight,
once or more daily, to once every 20 years.
[00108] While the present invention has been described with specificity
in accordance with certain of its preferred embodiments, the following
examples serve only to illustrate the invention and are not intended to limit
the same.
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EXAMPLES
Example 1
Nucleoside Phosphoramidites for Oligonucleotide Synthesis Deoxy and
2'-alkoxy amidites
(00109] 2'-Deoxy and 2'-methoxy beta-cyanoethyldiisopropyl
phosphoramidites are available from commercial sources (e.g. Chemgenes,
Needham MA or Glen Research, Inc. Sterling VA). Other 2'-O-alkoxy
substituted nucleoside amidites are prepared as described in U.S. Patent
5,506,351, herein incorporated by reference. For oligonucleotides
synthesized using 2'-alkoxy amidites, the standard cycle for unmodified
oligonucleotides is utilized, except the wait step after pulse delivery of
tetrazole and base is increased to 360 seconds.
[00110] Oligonucleotides containing 5-methyl-2'-deoxycytidine (5-Me-
C) nucleotides are synthesized according to published methods [Sanghvi, et.
al., Nucleic Acids Research, 1993, 21, 3197-3203] using commercially
available phosphoramidites (Glen Research, Sterling VA or ChemGenes,
Needham MA).
2'-Fluoro amidites
2'-Fluorodeoxyadenosine amidites
[00111] 2'-fluoro oligonucleotides are synthesized as described
previously [Kawasaki, et. al., J. Med. Claena., 1993, 36, 831-841] and United
States patent 5,670,633, herein incorporated by reference. Briefly, the
protected nucleoside N6-benzoyl-2'-deoxy-2'-fluoroadenosine is
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synthesized utilizing commercially available 9-beta-D-
arabinofuranosyladenine as starting material and by modifying literature
procedures whereby the 2'-alpha-fluoro atom is introduced by a SN2-
displacement of a 2'-beta-trityl group. Thus N6-benzoyl-9-beta-D-
arabinofuranosyladenine is selectively protected in moderate yield as the
3',5'-ditetrahydropyranyl (THP) intermediate. Deprotection of the THP and
N6-benzoyl groups is accomplished using standard methodologies and
standard methods are used to obtain the 5'-dimethoxytrityl-(DMT) and 5'-
DMT-3'-phosphoramidite intermediates.
2'-Fluorodeoxyguanosine
[00112] The synthesis of 2'-deoxy-2'-fluoroguanosine is accomplished
using tetraisopropyldisiloxanyl (TPDS) protected 9-beta-D-
arabinofuranosylguanine as starting material, and conversion to the
intermediate diisobutyrylarabinofuranosylguanosine. Deprotection of the
TPDS group is followed by protection of the hydroxyl group with THP to
give diisobutyryl di-THP protected arabinofuranosylguanine. Selective O-
deacylation and triflation is followed by treatment of the crude product with
fluoride, then deprotection of the THP groups. Standard methodologies are
used to obtain the 5'-DMT- and 5'-DMT-3'-phosphoramidites.
2'-Fluorouridine
[00113] Synthesis of 2'-deoxy-2'-fluorouridine is accomplished by the
modification of a literature procedure in which 2,2'anhydro-1-beta-D-
arabinofuranosyluracil is treated with 70% hydrogen fluoride-pyridine.
Standard procedures are used to obtain the 5'-DMT and 5'-DMT-3'-
phosphoramidites.
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2'-Fluorodeoxycytidine
[00114] 2'-deoxy-2'-fluorocytidine is synthesized via amination of 2'-
deoxy-2'-fluorouridine, followed by selective protection to give N4-
benzoyl-2'-deoxy-2'-fluorocytidine. Standard procedures are used to obtain
the 5'-DMT and 5'-DMT-3'phosphoramidites.
2'-O-(2-Methoxyethyl) modified amidites
[00115] 2'-O-Methoxyethyl-substituted nucleoside amidites are prepared
as follows, or alternatively, as per the methods of Martin, F., Helvetica
Chirnica Acta, 1995, 78, 486-504.
2,2'-Anhydro[1-(beta-D-arabinofuranosyl)-5-methyluridinel
[00116] 5-Methyluridine (ribosylthymine, commercially available
through Yamasa, Choshi, Japan) (72.0 g, 0.279 M), diphenylcarbonate (90.0
g, 0.420 M) and sodium bicarbonate (2.0 g, 0.024 M) are added to DMF
(300 mL). The mixture is heated to reflux, with stirnng, allowing the
evolved carbon dioxide gas to be released in a controlled manner. After 1
hour, the slightly darkened solution is concentrated under reduced pressure.
The resulting syrup is poured into diethylether (2.5 L), with stirring. The
product formed a gum. The ether is decanted and the residue is dissolved in
a minimum amount of methanol (ca. 400 mL). The solution is poured into
fresh ether (2.5 L) to yield a stiff gum. The ether is decanted and the gum is
dried in a vacuum oven (60°C at 1 mm Hg for 24 h) to give a solid that
is
crushed to a light tan powder. The material is used as is for further
reactions
(or it can be purified further by column chromatography using a gradient of
methanol in ethyl acetate (10-25%) to give a white solid.
2'-O-Methoxyethyl-5-methyluridine
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[00117] 2,2'-Anhydro-5-methyluridine (195 g, 0.81 M), tris(2-
methoxyethyl)borate (231 g, 0.98 M) and 2-methoxyethanol (1.2 L) are
added to a 2 L stainless steel pressure vessel and placed in a pre-heated oil
bath at 160°C. After heating for 48 hours at 155-160°C, the
vessel is opened
and the solution evaporated to dryness and triturated with MeOH (200 mL).
The residue is suspended in hot acetone (1 L). The insoluble salts are
filtered, washed with acetone (150 mL) and the filtrate evaporated. The
residue (280 g) is dissolved in CH3CN (600 mL) and evaporated. A silica
gel column (3 lcg) is packed in CH2Cl2 /acetone /MeOH (20:5:3) containing
0.5% Et3NH. The residue is dissolved in CHzCl2 (250 mL) and adsorbed
onto silica (150 g) prior to loading onto the column. The product is eluted
with the packing solvent to give the title product. Additional material can be
obtained by reworking impure fractions.
2'-O-Methoxyethyl-5'-O-dimethoxytrityl-5-methyluridine
[00118] 2'-O-Methoxyethyl-5-methyluridine (160 g, 0.506 M) is co-
evaporated with pyridine (250 mL) and the dried residue dissolved in
pyridine (1.3 L). A first aliquot of dimethoxytrityl chloride (94.3 g, 0.278
M) is added and the mixture stirred at room temperature for one hour. A
second aliquot of dimethoxytrityl chloride (94.3 g, 0.278 M) is added and
the reaction stirred for an additional one hour. Methanol (170 mL) is then
added to stop the reaction. The solvent is evaporated and triturated with
CH3CN (200 mL) The residue is dissolved in CHCl (1.5 L) and extracted
with 2x500 mL of saturated NaHC03 and 2x500 mL of saturated NaCI. The
organic phase is dried over Na2S04, filtered, and evaporated. The residue is
purified on a 3.5 kg silica gel column, packed and eluted with
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EtOAc/hexane/ acetone (5:5:1) containing 0-5% Et3NH. The pure fractions
are evaporated to give the title product.
3'-O-Acetyl-2'-O-methoxyethyl-5'-O-dimethoxytrityl-5-methyluridine
[00119) 2'-O-Methoxyethyl-5'-O-dimethoxytrityl-5-methyluridine (106
g, 0.167 M), DMF/pyridine (750 mL of a 3:1 mixture prepared from 562 mL
ofDMF and 188 mL ofpyridine) and acetic anhydride (24.38 mL, 0.258 M)
are combiiled and stirred at room temperature for 24 hours. The reaction is
monitored by TLG by first quenching the TLC sample with the addition of
MeOH. Upon completion of the reaction, as judged by TLC, MeOH (50
mL) is added and the mixture evaporated at 35°C. The residue is
dissolved
in CHC13 (800 mL) and extracted with 2x200 mL of saturated sodium
bicarbonate and 2x200 mL of saturated NaCl. The water layers are back
extracted with 200 mL of CHC13. The combined organics are dried with
sodium sulfate and evaporated to a residue. The residue is purified on a 3.5
kg silica gel column and eluted using EtOAc/hexane(4:1). Pure product
fractions are evaporated to yield the title compounds.
3'-O-Acetyl-2'-O-methoxyethyl-5'-O-dimethoxytrityl-5-methyl-4-
triazoleuridine
[00120) A first solution is prepared by dissolving 3'-.O-acetyl-2'-O-
methoxyethyl-5'-O-dimethoxytrityl-5-methyluridine (96 g, 0.144 M) in
CH3CN (700 mL) and set aside. Triethylamine (189 mL, 1.44 M) is added to
a solution of triazole (90 g, 1.3 M) in CH3CN (1 L), cooled to -5°C and
stirred for 0.5 h using an overhead stirrer. POC 13 is added dropwise, over a
minute period, to the stirred solution maintained at 0-10°C, and the
25 resulting mixture stirred for an additional 2 hours. The first solution is
added
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dropwise, over a 45 minute period, to the latter solution. The resulting
reaction mixture is stored overnight in a cold room. Salts are filtered from
the reaction mixture and the solution is evaporated. The residue is dissolved
in EtOAc (1 L) and the insoluble solids are removed by filtration. The
filtrate is washed with 1x300 mL of NaHC03 and 2x300 mL of saturated
NaCI, dried over sodium sulfate and evaporated. The residue is triturated
with EtOAc to give the title compound.
2'-O-Methoxyethyl-5'-O-dimethoxytrityl-5-methylcytidine
[00121] A solution of 3'-O-acetyl-2'-O-methoxyethyl-5'-O-
dimethoxytrityl-5-methyl-4-triazoleuridine (103 g, 0.141 M) in dioxane
(500 mL) and NH40H (30 mL) is stirred at room temperature fox 2 hours.
The dioxane solution is evaporated and the residue azeotroped with MeOH
(2x200 mL). The residue is dissolved in MeOH (300 mL) and transferred to
a 2 liter stainless steel pressure vessel. MeOH (400 mL) saturated with NH3
gas is added and the vessel heated to 100°C for 2 hours (TLC showed
complete conversion). The vessel contents are evaporated to dryness and the
residue is dissolved in EtOAc (500 rnL) and washed once with saturated
NaCl (200 mL). The organics are dried over sodium sulfate and the solvent
is evaporated to give the title compound.
N4-Benzoyl-2'-O-methoxyethyl-5'-O-dimethoxytrityl-5-methylcytidine
[00122] 2'-O-Methoxyethyl-5'-O-dimethoxytrityl-5-methylcytidine (85
g, 0.134 M) is dissolved in DMF (800 mL) and benzoic anhydride (37.2 g,
0.165 M) is added with stirring. After stirring for 3 hours, TLC showed the
reaction to be approximately 95% complete. The solvent 'is evaporated and
the residue azeotroped with MeOH (200 mL). The residue is dissolved in
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CHC13 (700 mL) and extracted with saturated NaHCO, (2x300 mL) and
saturated NaCl (2x300 mL) , dried over MgS04 and evaporated to give a
residue. The residue is chromatographed on a I.5 kg silica column using
EtOAc/hexane (1:1) containing 0-5% Et3NH as the eluting solvent. The pure
product fractions are evaporated to give the title compound.
N4-Benzoyl-Z'-O-methoxyethyl-5'-O-dimethoxytrityl-5-methylcytidine-
3'-amidite
[00123] N4-Benzoyl-2'-O-methoxyethyl-5'-O-dimethoxytrityl-5-
methylcytidine (74 g, 0.10 M) is dissolved in CHZC12 (1 L) Tetrazole
diisopropylamine (7.1 g) and 2-cyanoethoxy-tetra(isopropyl)phosphite (40.5
mL, 0.123 M) are added with stirring, under a nitrogen atmosphere. The
resulting mixture is stirred for 20 hours at room temperature (TLC showed
the reaction to be 95% complete). The reaction mixture is extracted with
saturated NaHC03 (1x300 mL) and saturated NaCI (3x300 mL). The
aqueous washes are back-extracted with CH2Clz (300 mL), and the extracts
are combined, dried over MgSO4 and concentrated. The residue obtained is
chromatographed on a 1.5 kg silica column using EtOAc/hexane (3:1 ) as the
eluting solvent. The pure fractions were combined to give the title
compound.
2'-O-(Aminooxyethyl) nucleoside amidites and 2'-O-
(dimethylaminooxyethyl) nucleoside amidites
2'-(Dimethylaminooxyethoxy) nucleoside amidites
[00124] 2'-(Dimethylaminooxyethoxy) nucleoside amidites [also known
in the art as 2'-O-(dimethylaminooxyethyl) nucleoside amidites] are
prepared as described in the following paragraphs. Adenosine, cytidine and
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guanosine nucleoside amidites axe prepared similarly to the thymidine (5-
methyluridine) except the exocyclic amines are protected with a benzoyl
moiety in the case of adenosine and cytidine and with isobutyryl in the case
of guanosine.
5'-O-tert-Butyldiphenylsilyl -02 -2'-anhydro-5-methyluridine
(00125] OZ -2'-anhydro-5-methyluridine (Pro. Bio. Sint., Varese, Italy,
100.Og, 0.4'6 mmol), dimethylaminopyridine (0.66g, 0.013eq, 0.0054mmol)
are dissolved in dry pyridine (500 ml) at ambient temperature under an
argon atmosphere and with mechanical stirring. tert-
Butyldiphenylchlorosilane (125.8g, 119.OmL, l.leq, 0.458mmo1) is added
in one portion. The reaction is stirred for 16 h at ambient temperature. TLC
(Rf 0.22, ethyl acetate) indicated a complete reaction. The solution is
concentrated under reduced pressure to a thick oil. This is partitioned
between dichloromethane (1 L) and saturated sodium bicarbonate (2x1 L)
and brine (1 L). The organic layer is dried over sodium sulfate and
concentrated under reduced pressure to a thick oil. The oil is dissolved in a
1:1 mixture of ethyl acetate and ethyl ether (600mL) and the solution is
cooled to -10°C. The resulting crystalline product is collected by
filtration,
washed with ethyl ether (3x200 mL), and dried (40°C, lmm Hg, 24 h) to a
white solid
5'-O-tert-Butyldiphenylsilyl-2'-O-(2-hydroxyethyl)-5-methyluridine
[00126] In a 2 L stainless steel, unstirred pressure reactor is added borane
in tetrahydrofuran (1.0 M, 2.0 eq, 622 mL). In the fume hood and with
manual stirring, ethylene glycol (350 mL, excess) is added cautiously at first
until the evolution of hydrogen gas subsides. 5'-O-tent-Butyldiphenylsilyl-
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OZ-2'anhydro-5-methyluridine (149 g, 0.3' 1 mol) and sodium bicarbonate
(0.074 g, 0.003 ec~ are added with manual stirring. The reactor is sealed and
heated in an oil bath until an internal temperature of 160°C is reached
and
then maintained for 16 h (pressure < 100 psig). The reaction vessel is cooled
to ambient and opened. TLC (Rf 0.67 for desired product and Rf 0.82 for
ara-T side product, ethyl acetate) indicated about 70% conversion to the
product. In order to avoid additional side product formation, the reaction is
stopped, concentrated under reduced pressure (10 to lmrn, Hg) in a warm
water bath (40-100°C) with the more extreme conditions used to remove
the
ethylene glycol. [Alternatively, once the low boiling solvent is gone, the
remaining solution can be partitioned between ethyl acetate and water. The
product will be in the organic phase.] The residue is purified by column
chromatography (2kg silica gel, ethyl acetate-hexanes gradient 1:1 to 4:1 ).
The appropriate fractions are combined, stripped and dried to product as a
white crisp foam, contaminated starting material, and pure reusable starting
material.
2'-O-([2-phthalimidoxy)ethyl]-5'-t-butyldiphenylsilyl-5-methyluridine
[00127] 5'-O-tert-Butyldiphenylsilyl-2'-O-(2-hydroxyethyl)-5-
methyluridine (20g, 36.98mmol) is mixed with triphenylphosphine (11.63g,
44.36mmo1) and N-hydroxyphthalimide (7.24g, 44.36mmo1). It is then dried
over PZOS under high vacuum for two days at 40°C. The reaction mixture
is
flushed with argon and dry THF (369.8mL, Aldrich, sure seal bottle) is
added to get a clear solution. Diethyl-azodicarboxylate (6.98mL,
44.36mmo1) is added dropwise to the reaction mixture. The rate of addition
is maintained such that resulting deep red coloration is just discharged
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before adding the next drop. After the addition is complete, the reaction is
stirred for 4 hrs. By that time TLC showed the completion of the reaction
(ethylacetate:hexane, 60:40). The solvent is evaporated in vacuum. Residue
obtained is placed on a flash column and eluted with ethyl acetate:hexane
(60:40), to get 2'-O-([2-phthalimidoxy)ethyl]-5'-t-butyldiphenylsilyl-5-
methyluridine as white foam.
5'-O-tart-butyldiphenylsilyl-2'-O-[(2-formadoximinooxy)ethyl]-5-
methyluridine
[00128] 2'-O-([2-phthalimidoxy)ethyl]-S'-t-butyldiphenylsilyl-5-
methyluridine (3.1g, 4.Smmo1) is dissolved in dry CHZC12 (4.SmL) and
methylhydrazine (300mL, 4.64mmo1) is added dropwise at-10°C to
0°C.
After 1 h the mixture is filtered, the filtrate is washed with ice cold CH2C12
and the combined organic phase is washed with water, brine and dried over
anhydrous Na2S04. The solution is concentrated to get 2'-O(aminooxyethyl)
thymidine, which is then dissolved in MeOH (67.SmL). To this
formaldehyde (20% aqueous solution, w/w, 1.1 eq.) is added and the
resulting mixture is stirred for 1 h. Solvent is removed under vacuum;
residue chromatographed to get S'-O-tent-butyldiphenylsilyl-2'-O-[(2-
formadoximinooxy) ethyl]-S-methyluridine as White foam.
5'-O-tart-Sutyldiphenylsilyl-2'-O-[N,N-dimethylaminooxyethyl]-5-
methyluridine
[40129] 5'-O-tart-butyldiphenylsilyl-2'-O-[(2- formadoximinooxy)ethyl]-
S-methyluridine (1.77g, 3.12mmo1) is dissolved in a solution of 1M
pyridinium p-toluenesulfonate (PPTS) in dry MeOH (30.6mL). Sodium
cyanoborohydride (0.39g, 6.13mmol) is added to this solution at 10°C
under
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inert atmosphere. The reaction mixture is stirred for 10 minutes at
10°C.
After that the reaction vessel is removed from the ice bath and stirred at
room temperature for 2 h, the reaction monitored by TLC (5% MeOH in
CHZC12). Aqueous NaHC03 solution (5%, lOmL) is added and extracted
with ethyl acetate (2x20mL). Ethyl acetate phase is dried over anhydrous
Na2S04, evaporated to dryness. Residue is dissolved in a solution of 1M
PPTS in MeOH (30.6mL). Formaldehyde (20% w/w, 30mL, 3.37mmo1) is
added and the reaction mixture is stirred at room temperature for 10
minutes. Reaction mixture cooled to 10°C in an ice bath, sodium
cyanoborohydride (0.39g, 6.13mmo1) is added, and reaction mixture stirred
at 10°C for 10 minutes. After 10 minutes, the reaction mixture is
removed
from the ice bath and stirred at room temperature for 2 hrs. To the reaction
mixture 5% NaHCO3 (25mL) solution is added and extracted with ethyl
acetate (2x25mL). Ethyl acetate layer is dried over anhydrous Na2SO4 and
evaporated to dryness. The residue obtained is purified by flash column
chromatography and eluted with 5% MeOH in CHZCh to get 5'-O-
tertbutyldiphenylsilyl-2'-O-[N,N-dimethylaminooxyethyl]-5- methyluridine
as a white foam.
2'-O-(dimethylaminooxyethyl)-5-methyluridine
(00130] Triethylamine trihydrofluoride (3.91mL, 24.Ommo1) is dissolved
in dry THF and triethylamine (1.67mL, l2mmol, dry, kept over I~OH). This
mixture of triethylamine-2HF is then added to 5'-O-tert-butyldiphenylsilyl-
2'-O-[N,N-dimethylaminooxyethyl]-5-methyluridine (1.408, 2.4mmo1) and
stirred at room temperature for 24 hrs. Reaction is monitored by TLC (5%
MeOH in CHZCl2). Solvent is removed under vacuum and the residue placed
CA 02495398 2005-02-10
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on a flash column and eluted with 10% MeOH in CHZC12 to get 2'-O-
(dimethylaminooxyethyl)-5-methyluridine.
5'-O-DMT-2'-O-(dimethylaminooxyethyl)-5-methyluridine
[00131] 2'-O-(dimethylaminooxyethyl)-5-methyluridine (750mg,
2.17mmol) is dried over P205 under high vacuum overnight at 40°C. It is
then co-evaporated with anhydrous pyridine (20mL). The residue obtained
is dissolved in pyridine (llmL) under argon atmosphere. 4-
dimethylaminopyridine (26.Smg, 2.60mmo1), 4,4'-dimethoxytrityl chloride
(880mg, 2.60mmo1) is added to the mixture and the reaction mixture is
stirred at room temperature until all of the starting material disappeared.
Pyridine is removed under vacuum and the residue chromatographed and
eluted with 10% MeOH in CH2C12 (containing a few drops of pyridine) to
get 5'-O-DMT-2'-0(dimethylamino-oxyethyl)-5-methyluridine.
5'-O-DMT-2'-O-(2-N,N-dimethylaminooxyethyl)-5-methyluridine-3'-
[(2-cyanoethyl)-N,N- diisopropylphosphoramidite]
[00132] 5'-O-DMT-2'-O-(dimethylaminooxyethyl)-5-methyluridine
(1.08g, 1.67mmo1) is co-evaporated with toluene (20mL). To the residue
N,N-diisopropylamine tetrazonide (0.29g, 1.67mmo1) is added and dried
over P20, under high vacuum overnight at 40°C. Then the reaction
mixture
is dissolved in anhydrous acetonitrile (8.4mL) and 2-cyanoethyl-N,N,NI,N~-
tetraisopropylphosphoramidite (2.12mL, 6.08mmo1) is added. The reaction
mixture is stirred at ambient temperature for 4 hrs under inert atmosphere.
The progress of the reaction is monitored by TLC (hexane:ethyl acetate 1:1).
The solvent is evaporated, then the residue is dissolved in ethyl acetate
(70mL) and washed with 5% aqueous NaHC03 (40mL). Ethyl acetate layer
66
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is dried over anlrydrous NazS04 and concentrated. Residue obtained is
chromatographed (ethyl acetate as eluent) to get S'-O-DMT-2'-O-(2-N,N-
dimethylaminooxyethyl)-S-methyluridine-3'-[(2-cyanoethyl)-N,N-
diisopropylphosphoramidite] as a foam.
S 2'-(Aminooxyethoxy) nucleoside amidites
[00133] 2'-(Aminooxyethoxy) nucleoside amidites [also known in the art
as 2'-O-(aminooxyethyl) nucleoside amidites] are prepared as described in
the following paragraphs. Adenosine, cytidine and thymidine nucleoside
amidites are prepared similarly.
N2-isobutyryl-6-O-diphenylcarbamoyl-2'-O-(Z-ethylacetyl)-5'-O-(4,4'-
dimethoxytrityl)guanosine-3'-[(2-cyanoethyl)-N,N-
diisopropylphosphoramidite]
[40134] The 2'-O-aminooxyethyl guanosine analog may be obtained by
selective 2'-O-alkylation of diaminopurine riboside. Multigram quantities of
1 S diaminopurine riboside may be purchased from Schering AG (Berlin) to
provide 2'-O-(2-ethylacetyl) diaminopurine riboside along with a minor
amount of the 3'-O-isomer. 2'-O-(2-ethylacetyl) diaminopurine riboside
may be resolved and converted to 2'-O-(2ethylacetyl)guanosine by
treatment with adenosine deaminase. (McGee, D. P. C., Cook, P. D.,
Guinosso, C. J., WO 94/02501 A1940203.) Standard protection procedures
should afford 2'-O-(2-ethylacetyl)-S'-O-(4,4'-dimethoxytrityl)guanosine
and 2-N-isobutyryl-6-O-diphenylcarbamoyl-2'-O-(2-ethylacetyl)-S'-O-
(4,4'-dimethoxytrityl)guanosine which may be reduced to provide 2-N-
isobutyryl-6-O-diphenylcarbamoyl-2'-O-(2-ethylacetyl)-S'-O-(4,4'-
2S dimethoxytrityl)guanosine. As before the hydroxyl group may be displaced
67
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by N-hydroxyphthalimide via a Mitsunobu reaction, and the protected
nucleoside may phosphitylated as usual to yield 2-N-isobutyryl-6-O-
diphenylcarbamoyl-2'-O-(2-ethylacetyl)-5'-O-(4,4'-
dimethoxytrityl)guanosine-3'-[(2-cyanoethyl)-N,N-
diisopropylphosphoramiditel.
2'-dimethylaminoethoxyethoxy (2'-DMAEOE) nucleoside amidites
[00135] 2'-dimethylaminoethoxyethoxy nucleoside amidites (also known
in the art as 2'-O-dimethylaminoethoxyethyl, i.e., 2'O-CH2-O-CH2-
N(CH2)Z, or 2'-DMAEOE nucleoside amidites) are prepared as follows.
Other nucleoside amidites are prepared similarly.
2'-O-[2(2-N,N-dimethylaminoethoxy)ethyl]-5-methyl uridine
j00136] 2[2-(Dimethylamino)ethoxylethanol (Aldrich, 6.66 g, 50 mmol)
is slowly added to a solution of borane in tetrahydrofuran (1 M, 10 mL, 10
mmol) with stirring in a 100 mL bomb. Hydrogen gas evolves as the solid
dissolves. 02-, 2' - anhydro-5-methyluridine (1.2 g, 5 mmol), and sodium
bicarbonate (2.5 mg) are added and the bomb is sealed, placed in an oil bath,
and heated to 155°C for 26 hours. The bomb is cooled to room
temperature
and opened. The crude solution is concentrated and the residue partitioned
between water (200 mL) and hexanes (200 mL). The excess phenol is
extracted into the hexane layer. The aqueous layer is extracted with ethyl
acetate (3x200 mL) and the combined organic layers are washed once with
water, dried over anhydrous sodium sulfate and concentrated. The residue is
columned on silica gel using methanol/methylene chloride 1:20 (which has
2% triethylamine) as the eluent. As the column fractions are concentrated a
68
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colorless solid forms which is collected to give the title compound as a
white solid.
5'-O-dimethoxytrityl-2'-O-[2(2-N,N-dimethylaminoethoxy) ethyl)]-S-
methyl uridine
[00137] To 0.5 g (1.3 mmol) of 2'-O-[2(2-N,N-
dimethylaminoethoxy)ethyl)1-5-methyl uridine in anhydrous pyridine (8
mL), triethylamine (0.36 mL) and dimethoxytrityl chloride (DMT-Cl, 0.87
g, 2 eq.) are added and stirred for 1 hour. The reaction mixture is poured
into water (200 mL) and extracted with CH2C12 (2x200 mL). The combined
CHZC12 layers are washed with saturated NaHC03 solution, followed by
saturated NaCI solution and dried over anhydrous sodium sulfate.
Evaporation of the solvent followed by silica gel chromatography using
MeOH: CH2C12:Et3N (20:1, v/v, with 1% triethylamine) gives the title
compound.
5'-O-Dimethoxytrityl-2'-O-[2(2-N,N-dimethylaminoethoxy)ethyl)]-5-
methyl uridine-3'-O-(cyanoethyl-N,N-diisopropyl)phosphoramidite
[00138] Diisopropylaminotetrazolide (0.6 g) and 2-cyanoethoxyN,N-
diisopropyl phosphoramidite (1.1 mL, 2 eq.) are added to a solution of 5'-O-
dimethoxytrityl-2'-O-[2(2-N,N-dimethylaminoethoxy)ethyl)]-5-
methyluridine (2.17 g, 3 mmol) dissolved in CHZC12 (20 mL) under an
atmosphere of argon. The reaction mixture is stirred overnight and the
solvent evaporated. The resulting residue is purified by silica gel flash
column chromatography with ethyl acetate as the eluent to give the title
compound.
69
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CA 02495398 2005-02-10
Example 2
Oligonucleotide synthesis
[00139] Unsubstituted and substituted phosphodiester (P=O)
oligonucleotides are synthesized on an automated DNA synthesizer
(Applied Biosystems model 380B) using standard phosphoramidite
chemistry with oxidation by iodine.
[00140] Phosphorothioates (P=S) are synthesized as for the
phosphodiester oligonucleotides except the standard oxidation bottle is
replaced by 0.2 M solution of 3H-1,2-benzodithiole-3-one 1,1-dioxide in
acetonitrile for the stepwise thiation of the phosphite linkages. The thiation
wait step is increased to 68 sec and is followed by the capping step. After
cleavage from the CPG column and deblocking in concentrated ammonium
hydroxide at 55'C (18 h), the oligonucleotides are purified by precipitating
twice with 2.5 volumes of ethanol from a 0.5 M NaCI solution. Phosphinate
oligonucleotides are prepared as described in U.S. Patent 5,508,70 .
[00141) Alkyl phosphonate oligonucleotides are prepared as described in
U.S. Patent 4,469,863, herein incorporated by reference.
[00142] 3'-Deoxy-3'-methylene phosphonate oligonucleotides are
prepared as described in U.S. Patents 5,610,289 or 5,625,050 .
[00143] Phosphoranudite oligonucleotides are prepared as described in
U.S. Patent, 5,256,775 or U.S. Patent 5,366,878 .
~o
51067-55
CA 02495398 2005-02-10
[00144] Alkylphosphonothioate oligonucleotides are prepared as
described in WO 94/17093 and WO 94/02499 .
[00145] 3'-Deoxy-3'-amino phosphoramidate oligonucleotides are
prepared as descn'bed in U.S. Patent 5,476,925 . ,
[00146] Phosphotriester oligonucleotides are prepared as described in
U.S. Patent 5,023,243.
[00147] Borano phosphate oligonucleotides are prepared as described in
U.S. Patents 5,130,302 and 5,177,198 .
Example 3
Oligonucleoside Synthesis
[00148] llethylenemeQ~ylimino linked oligonucleosides, also ideutifie~l
as MMI linked oligonucleosides, methylenedimethylhydrazo linked
oligonucleosides, also identified as MDH linked oligonucleosides, and
methylenecarbonylamino linked oliganucleosides, also identified as amide-3
linked oligonucleosides, and methyleneaminocarbonyl linked
oligonucleosides, also identified as amide-4 linked oligonucleosides, as well
as mixed backbone compounds having, for instance, alternating MIvB and
P~ or P=S linkages are prepared as described in U.S. Patents 5,378,825;
5,386,023; 5,489,677; 5,602,240; and 5,610,289.
71
' CA 02495398 2005-02-10
5106'7-55
[00149] Formacetal and thioformacetal linked oligonucleosides are
prepared as described in U.S. Patents 5,264,562 and 5,264,564 .
[00150] Ethylene oxide linked oligonucleosides are prepared as described
in U.S. Patent 5,223,618
Example 4
PNA Synthesis
(00151] Peptide nucleic acids (PNAs) are prepared in accordance with
any of the various procedures referred to in Peptide Nucleic Acids (PNA):
Synthesis, Properties and Potential Applications, Bioorganic & Medicinal
Chemistry, 1996, 4, 523. They may also be prepared in accordance with
U.S. Patents 5,539,082; 5,700,922; and 5,719,262 .
Example 5
Synthesis of Chimeric Oligonucleotides
[00152] Chimeric oligonucleotides, oligonucleosides or mixed
oligonucleotides/oligonucleosides of the invention caa be of several
different types. These include a first type wherein the "gap" segment of
linked nucleosides is positioned between 5' and 3' "wing" segments of
linked nucleosides and a second "open end" type wherein the "gap" segment
is located at either the 3' or the 5' terminus of the oligomeric compound.
Oligonucleotides of the first type are also known in the art as "gapmers" or
72
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gapped oligonucleotides. Oligonucleotides of the second type are also
known in the art as "hemimers" or "wingmers".
[2'-O-Me]--[2'-deoxy]--[2'-O-Me] Chimeric Phosphorothioate
Oligonucleotides
[00153] Chimeric oligonucleotides having 2'-O-alkyl phosphorothioate
and 2'-deoxy phosphorothioate oligonucleotide segments are synthesized
using an Applied Biosystems automated DNA synthesizer Model 380B, as
above. Oligonucleotides are synthesized using the automated synthesizer
and 2'-deoxy-5'-dimethoxytrityl-3'-O-phosphoramidite for the DNA
portion and 5'-dimethoxytrityl-2'-O-methyl-3'-O-phosphoramidite for 5'
and 3' wings. The standard synthesis cycle is modified by increasing the
wait step after the delivery of tetrazole and base to 600 s repeated four
times
for RNA and twice for 2'-O-methyl. The fully protected oligonucleotide is
cleaved from the support and the phosphate group is deprotected in 3:1
ammonia/ethanol at room temperature overnight then lyophilized to dryness.
Treatment in methanolic ammonia for 24 hrs at room temperature is then
done to deprotect all bases and sample is again lyophilized to dryness. The
pellet is resuspended in 1 M TBAF in THF for 24 hrs at room temperature to
deprotect the 2' positions. The reaction is then quenched with 1M TEAA
and the sample is then reduced to 1/2 volume by rotovac before being
desalted on a G25 size exclusion column. The oligo recovered is then
analyzed spectrophotometrically for yield and for purity by capillary
electrophoresis and by mass spectrometry.
[2'-O-(2-Methoxyethyl)]--[2'-deoxy]--[2'-O-(Methoxyethyl)] Chimeric
Phosphorothioate Oligonucleotides
73
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CA 02495398 2005-02-10
[00154] [2'-O-(2: raethoxyethyl)]--[2'-deoxy]-[-2'-O-(methoxyethyl)]
chimeric phosphorothioate oligonucleotides are prepared as per the
procedure above for the 2'-O-methyl chimeric oligonucleotide, with the
substitution of phorothioate oligonucleotides are prepared as per the
procedure above 2'-O-(methoxyethyl) amidites far the 2'-O methyl
amidites.
[2'-O-(2-Methoxyethyl)Phosphodiester]-[2'-deoxy PhosphorothioateJ-
[2'-O-(~-Methoxyethyl)] Phosphodiester] Chimeric Oligonncleotldes
[00155] [2'-O-(2-methoxyethyl phosphodiester]--[2'-deoxy
phosphorothioate]-[2'-O-(methcixyethyl) phosphodiester] chimeric
oligonucleotides are prepared as per the above procedure for the 2'-O-
methyl chimeric oligonucleotide with the substitution of 2'-O-
(methoxyethyl) amidites for the 2'-O-methyl amidites, oxidization with
iodine to generate the phosphodiester internucleotide linkages within the
wing pvrlions of the chimeric structures and sulfurization utilizing 3,H-1,2
benzodithiole-3-one 1,1 dioxide (Beaucage Reagent) to generate the
phosphorothioate internucleotide linkages for the center gap.
[00156] Other chimeric oligonucleotides, chimeric oligonucleosides aad
mixed chimeric oligonucleotidesloligonucleosides are synthesized according
to United States patent 5,623,065 .
lFacample 6
Oligonucleotide Isolation
[00157] After cleavage from the controlled pore glass column (Applied
Biosystems) and deblocking in concentrated ammonium hydroxide at 55'C
~4
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for 18 hours, the oligonucleotides or oligonucleosides are purified by
precipitation twice out of 0.5 M NaCI with 2.5 volumes ethanol.
Synthesized oligonucleotides are analyzed by polyacrylamide gel
electrophoresis on denaturing gels and judged to be at least 85% full-length
material. The relative amounts of phosphorothioate and phosphodiester
linkages obtained in synthesis are periodically checked by "P nuclear
magnetic resonance spectroscopy, and for some studies oligonucleotides are
purified by HPLC, as described by Chiang et al., J. Biol. Chem. 1991, 266,
18162-18171.
Example 7
Oligonucleotide Synthesis - 96 Well Plate Format
[00158] Oligonucleotides are synthesized via solid phase P(III)
phosphoramidite chemistry on an automated synthesizer capable of
assembling 96 sequences simultaneously in a standard 96 well format.
Phosphodiester internucleotide linkages are afforded by oxidation with
aqueous iodine. Phosphorothioate internucleotide linkages are generated by
sulfurization utilizing 3,H-1,2 benzodithiole-3-one 1,1 dioxide (Beaucage
Reagent) in anhydrous acetonitrile. Standard base-protected beta-
cyanoethyldiisopropyl phosphoramidites can be purchased from commercial
vendors (e.g. PE-Applied Biosystems, Foster City, CA, or Pharmacia,
Piscataway, NJ). Non-standard nucleosides are synthesized as per known
literature or patented methods. They are utilized as base protected
betacyanoethyldiisopropyl phosphoramidites.
7s
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
[00159] 0ligonucleotides are cleaved from support and deprotected with
concentrated NH40H at elevated temperature (55-60°C) for 12-16 hours
and
the released product then dried in vacuo. The dried product is then re-
suspended in sterile water to afford a master plate from which all analytical
and test plate samples are then diluted utilizing robotic pipettors.
Example 8
Oligonucleotide Analysis - 96 Well Plate Format
[00160] The concentration of oligonucleotide in each well is assessed by
dilution of samples and UV absorption spectroscopy. The full-length
integrity of the individual products is evaluated by capillary electrophoresis
(CE) in either the 96 well format (Beckman P/ACETM MDQ) or, for
individually prepared samples, on a commercial CE apparatus (e.g.,
Beckman P/ACETM 5000, ABI 270). Base and backbone composition is
confirmed by mass analysis of the compounds utilizing electrospray-mass
spectroscopy. All assay test plates are diluted from the master plate using
single and mufti-channel robotic pipettors. Plates are judged to be
acceptable if at least 85% of the compounds on the plate are at least 85%
full length.
Example 9
Cell culture and oligonucleotide treatment
[00161] The effect of antisense compounds on target nucleic acid
expression can be tested in any of a variety of cell types provided that the
target nucleic acid is present at measurable levels. This can be routinely
76
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determined using, for example, PCR or Northern blot analysis. The
following 6 cell types are provided for illustrative purposes, but other cell
types can be routinely used, provided that the target is expressed in the cell
type chosen. This can be readily determined by methods routine in the art,
S for example Northern blot analysis, Ribonuclease protection assays, or RT-
PCR.
T-24 cells:
[00162] The human transitional cell bladder carcinoma cell line T-24 is
obtained from the American Type Culture Collection (ATCC) (Manassas,
VA). T-24 cells are routinely cultured in complete McCoy's SA basal media
(Gibco/Life Technologies, Gaithersburg, MD) supplemented with 10% fetal
calf serum (Gibco/Life Technologies, Gaithersburg, MD), penicillin 100
units per mL, and streptomycin 100 micrograms per mL (Gibco/Life
Technologies, Gaithersburg, MD). Cells are routinely passaged by
1 S trypsinization and dilution when they reached 90% confluence. Cells are
seeded into 96-well plates (Falcon-Primaria #3872) at a density of 7000
cells/well for use in RT-PCR analysis.
[00163] For Northern blotting or other analysis, cells may be seeded onto
100 mm or other standard tissue culture plates and treated similarly, using
appropriate volumes of medium and oligonucleotide.
AS49 cells:
[00164] The human lung carcinoma cell line AS49 can be obtained from
the American Type Culture Collection (ATCC) (Manassas, VA). AS49 cells
axe routinely cultured in DMEM basal media (GibcolLife Technologies,
2S Gaithersburg, MD) supplemented with 10% fetal calf serum (Gibco/Life
77
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Technologies, Gaithersburg, MD), penicillin 100 units per mL, and
streptomycin 100 micrograms per mL (Gibco/Life Technologies,
Gaithersburg, MD). Cells are routinely passaged by trypsinization and
dilution when they reached 90% confluence.
NHDF cells:
[00165] Human neonatal dermal fibroblast (NHDF) can be obtained from
the Clonetics Corporation (Walkersville MD). NHDFs are routinely
maintained in Fibroblast Growth Medium (Clonetics Corporation,
Walkersville MD) supplemented as reconnmended by the supplier. Cells are
maintained for up to 10 passages as recommended by the supplier.
HEK cells:
[00166] Human embryonic keratinocytes (HEK) can be obtained from the
Clonetics Corporation (Walkersville MD). HEKs are routinely maintained
in I~eratinocyte Growth Medium (Clonetics Corporation, Walkersville MD)
formulated as recommended by the supplier. Cells are routinely maintained
for up to 10 passages as recommended by the supplier.
MCF-7 cells:
[00167] The human breast carcinoma cell line MCF-7 is obtained from
the American Type Culture Collection (Manassas, VA). MCF-7 cells are
routinely cultured in DMEM low glucose (Gibco/Life Technologies,
Gaithersburg, MD) supplemented with 10% fetal calf serum (GibcolLife
Technologies, Gaithersburg, MD). Cells are routinely passaged by
trypsinization and dilution when they reached 90% confluence. Cells are
seeded into 96-well plates (Falcon-Primaria #3872) at a density of 7000
cells/well for use in RT-PCR analysis.
CA 02495398 2005-02-10
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[00168] For Northern blotting or other analyses, cells may be seeded onto
100 mm or other standard tissue culture plates and treated similarly, using
appropriate volumes of medium and oligonucleotide.
LA4 cells:
[00169] The mouse lung epithelial cell line LA4 is obtained from the
American Type Culture Collection (Manassas, VA). LA4 cells are routinely
cultured in F 12K medium (Gibco/Life Technologies, Gaithersburg, MD)
supplemented with 15% fetal calf serum (Gibco/Life Technologies,
Gaithersburg, MD). Cells are routinely passaged by trypsinization and
dilution when they reached 90% confluence. Cells are seeded into 96-well
plates (Falcon-Primaria #3872) at a density of 3000-6000 cells/ well for use
in RT-PCR analysis.
[00170] For Northern blotting or other analyses, cells may be seeded onto
100 mm or other standard tissue culture plates and treated similarly, using
appropriate volumes of medium and oligonucleotide.
Treatment with antisense compounds:
[00171] When cells reached 80% confluence, they are treated with
oligonucleotide. For cells grown in 96-well plates, wells are washed once
with 200 ~.L OPTI-MEMtm-1 reduced-serum medium (Gibco BRL) and then
treated with 130 gL of OPTI-MEMTMTM-1 containing 3.75 ~g/mL
LIPOFECTINTM (Gibco BRL) and the desired concentration of
oligonucleotide. After 4-7 hours of treatment, the medium is replaced with
fresh medium. Cells are harvested 16-24 hours after oligonucleotide
treatment.
79
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[00172] The concentration of oligonucleotide used varies from cell line to
cell line. To determine the optimal oligonucleotide concentration for a
particular cell line, the cells are treated with a positive control
oligonucleotide at a range of concentrations.
Example 10
Analysis of oligonucleotide inhibition of Navl.3 expression
[00173] Antisense modulation of Navl.3 expression can be assayed in a
variety of ways known in the art. For example, Navl .3 mRNA levels can be
quantitated by, e.g., Northern blot analysis, competitive polymerase chain
reaction (PCR), or real-time PCR (RT-PCR). Real-time quantitative PCR is
presently preferred. RNA analysis can be performed on total cellular RNA
or poly(A)+ mRNA. Methods of RNA isolation are taught in, for example,
Ausubel, F~M. et al., Cu~f°ent Protocols ih Molecular Biology,
Volume l,
pp. 4.1.1-4.2.9 and 4.5.1-4.5.3, John Wiley & Sons, Inc., 1993. Northern
blot analysis is routine in the art and is taught in, for example, Ausubel,
F.M. et al., Current Protocols in Molecular Biology, Volume 1, pp. 4.2.1-
4.2.9, John Wiley ~ Sons, Inc., 1996. Real-time quantitative (PCR) can be
conveniently accomplished using the commercially available ABI PRISMTM
7700 Sequence Detection System, available from PE-Applied Biosystems,
Foster City, CA and used according to manufacturer's instructions. Prior to
quantitative PCR analysis, primer-probe sets specific to the target gene
being measured are evaluated for their ability to be "multiplexed" with a
GAPDH amplification reaction. In multiplexing, both the target gene and
the internal standard gene GAPDH are amplified concurrently in a single
so
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
sample. In this analysis, mRNA isolated from untreated cells is serially
diluted. Each dilution is amplified in the presence of primer-probe sets
specific for GAPDH only, target gene only ("single-plexing"), or both
(multiplexing). Following PCR amplification, standard curves of GAPDH
and target mRNA signal as a function of dilution are generated from both
the single-plexed and multiplexed samples. If both the slope and correlation
coefficient of the GAPDH and target signals generated from the multiplexed
samples fall within 10% of their corresponding values generated from the
single-plexed samples, the primer-probe set specific for that target is
deemed as multiplexable. Other methods of PCR are also known in the art.
[00174] Protein levels of Navl .3 can be quantitated in a variety of ways
well known in the art, such as immunoprecipitation, Western blot analysis
(immunoblotting), ELISA or fluorescence-activated cell sorting (FACS).
Antibodies directed to Navl .3 can be identified and obtained from a variety
of sources, such as the MSRS catalog of antibodies (Aerie Corporation,
Birmingham, MI), or can be prepared via conventional antibody generation
methods. Methods for preparation of polyclonal antisera are taught in, for
example, Ausubel, F.M. et al., Curs°ent Protocols in Molecular Biology,
Volume 2, pp. 11.12.1-11.12.9, John Wiley & Sons, Inc., 1997. Preparation
of monoclonal antibodies is taught in, for example, Ausubel, F.M. et al.,
Curf~ent Protocols in Molecular Biology, Volume 2, pp. 11.4.1-11.11.5,
John Wiley Sons, Inc., 1997.
[00175] Immunoprecipitation methods are standard in the art and can be
found at, for example, Ausubel, F.M. et al., Current Pf°otocols isa
Molecular
Biology, Volume 2, pp. 10.16.110.16.11, John Wiley & Sons, Inc., 1998.
81
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Western blot (immunoblot) analysis is standard in the art and can be found
at, for example, Ausubel, F.M. et al., Current Protocols in Molecular
Biology, Volume 2, pp. 10.8.1-10.8.21, John Wiley Sons, Inc., 1997.
Enzyme-linked immunosorbent assays (ELISA) are standard in the art and
can be found at, for example, Ausubel, F.M. et al., Curs°ent Protocols
ira
Molecular Biology, Volume 2, pp. 11.2.1-11.2.22, John Wiley & Sons, Inc.,
1991.
Example 11
Poly(A)+ mRNA isolation
[00176] Poly(A)+ mRNA is isolated according to Miura et al., Clin.
Che~i., 1996, 42, 1758-1764. Other methods for poly(A)+ mRNA isolation
are taught in, for example, Ausubel, F.M. et al., Curre~at Protocols ire
Molecular Biology, Volume 1, pp. 4.5.1-4.5.3, John Wiley & Sons, Inc.,
1993. Briefly, for cells grown on 96-well plates, growth medium is removed
from the cells and each well is washed with 200 ~,L cold PBS. 60~L lysis
buffer (10 mM Tris-HCI, pH 7.6, 1 mM EDTA, 0.5 M NaCI, 0.5% NP-40,
mM vanadyl-ribonucleoside complex) is added to each well, the plate is
gently agitated and then incubated at room temperature for five minutes. 55
20 ~L of lysate is transferred to Oligo d(T) coated 96-well plates (AGCT Inc.,
Irvine CA). Plates are incubated for 60 minutes at room temperature,
washed 3 times with 200 ~,L of wash buffer (10 mM Tris-HC1 pH 7.6, 1
mM EDTA, 0.3 M NaCI). After the final wash, the plate is blotted on paper
towels to remove excess wash buffer and then air-dried for 5 minutes. 60 pL
of elution buffer (5 mM Tris-HCl pH 7.6), preheated to 70°C is added to
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each well, the plate is incubated on a 90°C hot plate for 5 minutes,
and the
eluate is then transferred to a fresh 96-well plate.
[00177] Cells grown on 100 mm or other standard plates may be treated
similarly, using appropriate volumes of all solutions.
Example 12
Total RNA Isolation
[00178] Total mRNA is isolated using an RNEASY 96TM kit and buffers
purchased from Qiagen Inc. (Valencia CA) following the manufacturer's
recommended procedures. Briefly, for cells grown on 96-well plates, growth
medium is removed from the cells and each well is washed with 200 ~,L
cold PBS. 100 ~L Buffer RLT is added to each well and the plate vigorously
agitated for 20 seconds. 100 ~,L of 70% ethanol is then added to each well
and the contents mixed by pipetting three times up and down. The samples
are then transferred to the RNEASY 96TM well plate attached to a QIAVACTM
manifold fitted with a waste collection tray and attached to a vacuum
source. Vacuum is applied for 15 seconds. 1 mL of Buffer RWl is added to
each well of the RNEASY 96TM plate and the vacuum again applied for 15
seconds. 1 mL of Buffer RPE is then added to each well of the RNEASY
96TM plate and the vacuum applied for a period of 15 seconds. The Buffer
RPE wash is then repeated and the vacuum is applied for an additional 10
minutes. The plate is then removed from the QIAVACTM manifold and
blotted dry on paper towels. The plate is then re-attached to the QIAVACT~~
manifold fitted with a collection tube rack containing 1.2 mL collection
tubes. RNA is then diluted by pipetting 60~.L water into each well,
83
CA 02495398 2005-02-10
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incubating one minute, and then applying the vacuum for 30 seconds. The
elution step is repeated with an additional 60~L water.
[00179] The repetitive pipetting and elution steps may be automated
using a QIAGEN Bio-Robot 9604 (Qiagen, Inc., Valencia CA). Essentially,
after lysing of the cells on the culture plate, the plate is transferred to
the
robot deck where the pipetting, DNase treatment and elution steps are
carried out.
Example 13
Real-time Quantitative PCR Analysis of Navl.3 mRNA Levels
[00180] Quantitation of Navl .3 mRNA levels is determined by real-time
quantitative PCR using the ABI PRISMTM 7700 Sequence Detection System
(PE-Applied Biosystems, Foster City, CA) according to manufacturer's
instructions. This is a closed-tube, non-gel-based, fluorescence detection
system which allows high-throughput quantitation of polymerase chain
reaction (PCR) products in real-time. As opposed to standard PCR, in which
amplification products are quantitated after the PCR is completed, products
in real-time quantitative PCR are quantitated as they accumulate. This is
accomplished by including in the PCR reaction an oligonucleotide probe
that anneals specifically between the forward and reverse PCR primers, and
contains two fluorescent dyes. A reporter dye (e.g., JOE, FAMTM, or VIC,
obtained from either Operon Technologies Inc., Alameda, CA or PE-
Applied Biosystems, Foster City, CA) is attached to the 5' end of the probe
and a quencher dye (e.g., TAMRA, obtained from either Operon
Technologies Inc., Alameda, CA or PE-Applied Biosystems, Foster City,
84
CA 02495398 2005-02-10
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CA) is attached to the 3' end of the probe. When the probe and dyes are
intact, reporter dye emission is quenched by the proximity of the 3'
quencher dye. During amplification, annealing of the probe to the target
sequence creates a substrate that can be cleaved by the 5'-exonuclease
activity of Taq polymerase. During the extension phase of the PCR
amplification cycle, cleavage of the probe by Taq polymerase releases the
reporter dye from the remainder of the probe (and hence from the quencher
moiety) and a sequence-specific fluorescent signal is generated. With each
cycle, additional reporter dye molecules are cleaved from their respective
probes, and the fluorescence intensity is monitored at regular intervals by
laser optics built into the ABI PRISMTM 7700 Sequence Detection System.
In each assay, a series of parallel reactions containing serial dilutions of
mRNA from untreated control samples generates a standard curve that is
used to quantitate the percent inhibition after antisense oligonucleotide
treatment of test samples.
[00181] PCR reagents can be obtained from PE-Applied Biosystems,
Foster City, CA. RT-PCR reactions are carried out by adding 25 ~.L PCR
cocktail (lx TAQMANTM buffer A, 5.5 MM MgCl2, 300 ~.M each of dATP,
dCTP and dGTP, 600 pM of dUTP, 100 nM each of forward primer, reverse
primer, and probe, 20 Units RNAse inhibitor, 1.25 Units AMPLITAQ
GOLDTM, and 12.5 Units MuLV reverse transcriptase) to 96 well plates
containing 25 ~,L poly(A) mRNA solution. The RT reaction is carried out by
incubation for 30 minutes at 48°C. Following a 10 minute incubation at
95°C to activate the AMPLITAQ GOLDTM, 40 cycles of a two-step PCR
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
protocol are carried out: 95°C for 15 seconds (denaturation) followed
by
60°C for 1.5 minutes (annealing/extension).
[00182] Probes and primers to human Navl.3 were designed to hybridize
to a human Navl .3 sequence, using published sequence, information
(GenBank accession number NM 006922, incorporated herein as Figure 1.
For human Navl .3 the PCR primers were:
forward primer: TTGACTTTGTGGTGGTGATTCTCT SEQ ID N0:9097
reverse primer: CGTAGGATTCGGCCAATCCT SEQ TD N0:9098 and the
PCR probe is: FAM- ACCTTGTTCCGAGTGATCCGTCTTGC SEQ ID
NO : 9 0 9 9 -TAMRA where FAMTM (PE-Applied Biosystems, Foster City,
CA) is the fluorescent reporter dye) and TAMRA (PE-Applied Biosystems,
Foster City, CA) is the quencher dye. For human cyclophilin the PCR
primers were:
forward primer: CCCACCGTGTTCTTCGACAT SEQ ID NO : 910 0
reverse primer: TTTCTGCTGTCTTTGGGACCTT SEQ ID NO : 9101 and
the PCR probe is: 5' JOE- CGCGTCTCCTTTGAGCTGTTTGCA SEQ ID
NO : 9102 - TAMRA 3' where JOE (PE-Applied Biosysterns, Foster City,
CA) is the fluorescent reporter dye) and TAMRA (PE-Applied Biosystems,
Foster City, CA) is the quencher dye.
Example 14
Antisense inhibition of human Navl.3 expression by chimeric
phosphorothioate oligonucleotides having 2'-MOE wings and a deoxy
gap
86
CA 02495398 2005-02-10
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[00183] In accordance with the present invention, a series of
oligonucleotides are designed to target different regions of the human
Navl.3 RNA, using published sequences (NM 006922, incorporated herein
as Figure 1. The oligonucleotides are shown in Table 1. "Position"
indicates the first (5'-most) nucleotide number on the particular target
sequence to which the oligonucleotide binds. The indicated parameters for
each oligo were predicted using RNAstructure 3.7 by David H. Mathews,
Michael Zuker, and Douglas H. Turner. All compounds in Table 1 are
chimeric oligonucleotides ("gapmers") 20 nucleotides in length, composed
of a central "gap" region consisting of ten 2'deoxynucleotides, which is
I flanked on both sides (5' and 3' directions) by four-nucleotide "wings". The
wings are composed of 2'-methoxyethyl (2'-MOE) nucleotides. The
internucleoside (backbone) linkages are phosphorothioate (P=S) throughout
the oligonucleotide. Cytidine residues in the 2'-MOE wings are 5-
methylcytidines. All cytidine residues are 5-methylcytidines.
s7
CA 02495398 2005-02-10
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TABLE 1
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CTTTTCTTCCTCCGGTTCCT
1969 SEQ ID NO:l -28.5 -28.9 80.8 0 0 -6.6
TTTTCTTCCTCCGGTTCCTC
1968 SEQ ID N0:2 -28 -28.4 80.7 0 0 -6.6
TCTTTTCTTCCTCCGGTTCC
1970 SEQ ID N0:3 -28 -28.4 80.7 0 0 -6.6
CCTCCGGTTCCTCCATTCTT
1961 SEQ ID N0:4 -27.8 -30.5 82.5 -2.1 -0.3 -6.6
TTCTTCCTCCGGTTCCTCCA
1966 SEQ ID N0:5 -27.8 -30.9 84.4 -2.l -0.8 -6.6
TCCTCCGGTTCCTCCATTCT
1962 SEQ ID N0:6 -27.7 -30.8 83.9 -2.1 -0.8 -6.6
TCTTCCTCCGGTTCCTCCAT
1965 SEQ ID N0:7 -27.7 -30.8 83.9 -2.1 -0.8 -6.6
CTTCCTCCGGTTCCTCCATT
1964 SEQ ID N0:8 -27.4 -30.5 82.5 -2.1 -0.8 -6.6
TTTCTTCCTCCGGTTCCTCC
1967 SEQ ID N0:9 -27 -30.3 83.8 -3.3 0 -6.6
TTCCTCCGGTTCCTCCATTC
1963 SEQ ID N0:10 -26.9 -30 82.4 -2.1 -0.8 -6
TCTTCTTTTCTTCCTCCGGT
1973 SEQ ID N0:11 -26.9 -27.3 79.1 0 0 -6.6
CTTCTTTTCTTCCTCCGGTT
1972 SEQ ID N0:12 -26.6 -27 77.6 0 0 -6.6
TTCTTTTCTTCCTCCGGTTC
1971 SEQ TD N0:13 -26.1 -26.5 77.4 0 0 -6.6
CTCCGGTTCCTCCATTCTTT
1960 SEQ ID N0:14 -25.5 -28.6 79.5 -2.1 -0.8 -6.6
ACATCCTTTGCCCGACCTCT
2212 SEQ ID N0:15 -24.3 -30 79.2 -5.7 0 -3
CTGTCTTCTTTTCTTCCTCC
1976 SEQ ID N0:16 -24.1 -26.2 78.6 -2.1 0 0
GGGTCCCCACGGTCTCCCTT
5683 SEQ ID N0:17 -24.1 -34.8 90.5 -9.4 -1.2 -7
GTCTTCTTTTCTTCCTCCGG
1974 SEQ ID N0:18 -24 -27.3 79.1 -3.3 0 -6
TGTCTTCTTTTCTTCCTCCG ,
1975 SEQ ID N0:19 -24 -26.1 76.1 -2.1 0 -2.2
TGCCTTTGTTCTGTAGTACT
8639 SEQ ID N0:20 -24 -24.4 73.7 0.3 0 -5.7
TATCTTGTTCCTTTTTGGGC
57g SEQ ID N0:21 -23.8 -24.3 72.7 0.3 -0.2 -3.1
GTTCTGTAGTACTGCTTGGT
8632 SEQ ID N0:22 -23.8 -24.7 76 -0.7 0 -7.1
GATTCCACCAGATCTTCCCT
4035 SEQ ID N0:23 -23.5 -28 77.4 -4.5 0 -5.8
TGGGTCCCCACGGTCTCCCT
5684 SEQ ID N0:24 -23.4 -34.7 89.8 -9.4 -1.9 -9.4
ATTTGCCTTTGTTCTGTAGT
8642 SEQ ID N0:25 -23.4 -23.8 72.3 0.3 0 -3
ATCTTGTTCCTTTTTGGGCT
578 SEQ ID N0:26 -23.3 -25.5 75.4 -1.6 -0.2 -3.8
TCCGGTTCCTCCATTCTTTA
1959 SEQ ID N0:27 -23.3 -27.4 76.9 -3.1 -0.8 -6.6
88
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kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GGTCCCCACGGTCTCCCTTA
5682 SEQ ID N0:28 -23.3 -33.3 87.4 -9.4 -0.3 -3.5
AGGAAGTGGTGTTGGTTTCA
1332 SEQ ID N0:29 -23.2 -23.7 71.8 1.7 -0.2 -4.1
ATGGGTCCCCACGGTCTCCC
5685 SEQ ID N0:30 -23.2 -33.8 87.9 -9.4 -l.1 -9.1
TTGCCTTTGTTCTGTAGTAC
8640 SEQ ID N0:31 -23.2 -23.6 71.9 0.3 0 -4.7
GTAGGAAGTGGTGTTGGTTT
1334 SEQ ID N0:32 -23.1 -23.5 71.8 1.7 0 -1.3
TTCCACCAGATCTTCCCTTT
4033 SEQ ID N0:33 -23.1 -27.6 76.9 -4.5 0 -5.8
TTTGCCTTTGTTCTGTAGTA
8641 SEQ ID N0:34 -23.1 -23.5 71.7 0.3 0 -3
AGTAGGAAGTGGTGTTGGTT
1335 SEQ ID NO:35 -23 -23.4 71.7 1.7 0 -l.3
CTCTGTCTTCTTTTCTTCCT
1978 SEQ ID N0:36 -23 -25.1 76.8 -2.1 0 0
ATTCCACCAGATCTTCCCTT
4034 SEQ TD N0:37 -23 -27.5 76.5 -4.5 0 -5.8
GGGGTAGTGCTCCATGGCCA
2801 SEQ ID N0:38 -22.9 -31.2 86.2 -7.4 -0.5 -9.3
AACATCCTTTGCCCGACCTC
2213 SEQ ID N0:39 -22.7 -28.4 75.1 -5.7 0 -3
TCTGTCTTCTTTTCTTCCTC
1977 SEQ ID N0:40 -22.5 -24.6 76.6 -2.1 0 0
TCTCTGTCTTCTTTTCTTCC
1979 SEQ ID NO:41 -22.5 -24.6 76.6 -2.1 0 0
TCTTGTTCCTTTTTGGGCTT
577 SEQ ID N0:42 -22.4 -25.6 75.8 -2.7 -0.2 -3.8
CATCCTTTGCCCGACCTCTG
2211 SEQ ID N0:43 -22.4 -29.8 78.5 -7.4 0 -3
GATTTTCTCTGACCTCTTTT
6447 SEQ ID N0:44 -22.4 -22.8 69.1 0.6 0 -2.4
GGAAGTGGTGTTGGTTTCAA
1331 SEQ ID N0:45 -22.3 -23 69 1.7 -0.4 -4.1
TAGGAAGTGGTGTTGGTTTC
1333 SEQ ID N0:46 -22.3 -22.7 69.9 1.7 0 -2.6
TGATTTTCTCTGACCTCTTT
6448 SEQ ID N0:47 -22.3 -22.7 68.6 0.6 0 -2.4
GGTTTTGTCAGTAGGCAGTA
7780 SEQ ID N0:48 -22.3 -24.5 75.6 -2.2 0.2 -4
AAGTAGGAAGTGGTGTTGGT
1336 SEQ ID N0:49 -22.2 -22.6 68.7 1.7 0 -1.2
TTATCTTGTTCCTTTTTGGG
580 SEQ ID N0:50 -22.1 -22.6 68.5 0.3 -0.2 -3.l
AGATTCCACCAGATCTTCCC
4036 SEQ ID N0:51 -22.1 -27.1 75.8 -4.5 -0.2 -5.8
AGGTTTTGTCAGTAGGCAGT
7781 SEQ ID N0:52 -22.1 -24.8 76.6 -2.2 -0.1 -4
TGTTCTGTAGTACTGCTTGG
8633 SEQ ID N0:53 -22.1 -23.5 71.9 -0.7 0 -7.8
GCCTTTGTTCTGTAGTACTG
8638 SEQ ID N0:54 -22.1 -24.4 73.7 -2.3 0 -6
TTGATTTTCTCTGACCTCTT
6449 SEQ ID N0:55 -22 -22.7 68.6 -0.4 0 -2.4
GCTTTTAATTTGCCTTTGTT
8649 SEQ ID N0:56 -22 -22.4 66.7 0.3 0 -3.1
89
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kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTTTTGTCAGTAGGCAGTAT
7779 SEQ ID N0:57 -21.9 -23.3 72.6 -0.7 -0.1 -4
TGCTTTTAATTTGCCTTTGT
8650 SEQ ID N0:58 -21.9 -22.3 66.3 0.3 0 -3.6
TGGGGTAGTGCTCCATGGCC
2802 SEQ ID N0:59 -21.8 -30.5 85 -7.4 -1.2 -8.1
TTAATTTGCCTTTGTTCTGT
8645 SEQ ID N0:60 -21.6 -22 66.4 0.3 0 -3
GGGTAGTGCTCCATGGCCAT
2800 SEQ ID N0:61 -21.5 -30 83.5 -7.4 -0.4 -10
AATTTGCCTTTGTTCTGTAG
8643 SEQ ID NO:62 -21.5 -21.9 66.3 0.3 0 -2.3
CTCTCTGTCTTCTTTTCTTC
1980 SEQ ID N0:63 -21.4 -23.5 74.7 -2.1 0 0
GTCCCCACGGTCTCCCTTAA
5681 SEQ ID N0:64 -21.4 -31.4 82.4 -9.4 -0.3 -3.5
CAACATCCTTTGCCCGACCT
2214 SEQ ID N0:65 -21.3 -28.7 74.6 -7.4 0 -3
CCATCTGTATTCGAAGGGCA
6075 5EQ ID N0:66 -21.2 -25 70.4 -3.8 0 -7.1
CCATCTGTTTTTTCTGGAGT
6331 SEQ ID N0:67 -21.2 -24 72 -2.8 0 -3.1
TTTGATTTTCTCTGACCTCT
6450 SEQ ID N0:68 -21.2 -22.7 68.6 -1.4 0 -2.4
TAATTTGCCTTTGTTCTGTA
8644 SEQ ID N0:69 -21.2 -21.6 65.5 0.3 0 -3
GCCAGTTCCATGGATCACGA
1029 SEQ ID N0:70 -21.1 -27.4 75.4 -4.9 -0.8 -10.5
ATAGGTTTTGTCAGTAGGCA
7783 SEQ ID N0:71 -21.1 -23.3 71.7 -2.2 0 -4
TTTGTTCTGTAGTACTGCTT
8635 SEQ ID N0:72 -21.1 -22.5 70 -0.7 0 -7.8
ATTATCTTGTTCCTTTTTGG
581 SEQ ID N0:73 -21 -21.4 65.8 0.3 0 -2.9
TTGTTCTGTAGTACTGCTTG
8634 SEQ ID N0:74 -21 -22.4 69.5 -0.7 0 -7.8
TCCTTTGCCCGACCTCTGAA
2209 SEQ ID N0:75 -20.9 -29 76.4 -8.1 0 -3
CCCCACGGTCTCCCTTAACT
5679 SEQ ID N0:76 -20.9 -30.9 79.8 -9.4 -0.3 -3.3
TCCATCTGTATTCGAAGGGC
6076 SEQ ID N0:77 -20.9 -24.7 70.9 -3.8 , 0 -7.1
GCTGTTCGAG'CATCTGCTGA
1806 SEQ ID N0:78 -20.8 -26.9 77.1 -4.5 -1.5 -7.9
TTTGACGCTGTCTTCAGATT
2051 SEQ ID NO:79 -20.6 -22.9 68.1 -0.6 -1.4 -7.6
TTTTGACGCTGTCTTCAGAT
2052 SEQ ID N0:80 -20.6 -22.9 68.1 -0.6 -1.4 -7.6
GATGGGTCCCCACGGTCTCC
5686 SEQ ID N0:81 -20.6 -32.4 86 -10.9 -0.6 -8.8
TCATGTCTTGTTTTATAGGT
6285 SEQ ID N0:82 -20.6 -21 66.3 1.3 0 -4.7
TAGGTTTTGTCAGTAGGCAG
7782 SEQ ID N0:83 -20.6 -23.3 72.1 -2.2 -0.1 -4
TTTTAATTTGCCTTTGTTCT
8647 SEQ ID NO:84 -20.6 -21 64 0.3 0 -3
CTTTTAATTTGCCTTTGTTC
8648 SEQ ID N0:85 -20.6 -21 64 0.3 0 -3
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kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTTTCTCTGACCTCTTTTCC
6445 SEQ ID N0:86 -20.5 -24.6 73.4 -4.1 0 -2.2
TTTAATTTGCCTTTGTTCTG
8646 SEQ ID N0:87 -20.5 -20.9 63.5 0.3 0 -3
TCTCTCTGTCTTCTTTTCTT
1981 SEQ ID N0:88 -20.4 -23.5 74.7 -3.1 0 0
CCCTCTGGGGGAAGTTGTCC
2473 SEQ ID NO:89 -20.4 -29.8 82.2 -7.8 -1.5 -7.6
TCTATAACTTTTGGCTTTCT
3565 SEQ ID N0:90 -20.4 -20.8 64.1 0 0 -3.7
TCCCCACGGTCTCCCTTAAC
5680 SEQ ID N0:91 -20.4 -30.4 79.6 -9.4 -0.3 -3.5
CCATCTTTTCATCCTGCACA
456 SEQ ID N0:92 -20.3 -26.1 74 -5.8 0 -4.8
GAAGTGGTGTTGGTTTCAAA
1330 SEQ ID N0:93 -20.3 -21.1 64 1.7 -0.6 -3.5
AAAGTAGGAAGTGGTGTTGG
1337 SEQ ID N0:94 -20.3 -20.7 63.1 1.7 0 -l.3
AGATAGCCAGCGCCAACATT
4675 SEQ ID N0:95 -20.3 -26.2 71.3 -5.9 0.3 -7.6
TTTCTCTGACCTCTTTTCCT
6444 SEQ ID N0:96 -20.3 -25.4 75 -5.1 0 -2.4
CCGGTTCCTCCATTCTTTAG
1958 SEQ ID N0:97 -20.2 -27 75.5 -5.9 -0.8 -5.4
CAAGATAGCCAGCGCCAACA
4677 SEQ TD N0:98 -20.2 -26.1 69.9 -5.2 -0.5 -7.6
AAGCTGCTTTTAATTTGCCT
8654 SEQ ID N0:99 -20.2 -22.9 66.6 -2.1 0 -8.6
TCCAACATCCTTTGCCCGAC
2216 SEQ ID N0:100 -20.1 -28.2 74.4 -8.1 0 -3
CCTACTCCACTGAAATCTCT
1879 SEQ ID NO:101 -20 -23.7 67.9 -3.7 0 -2.5
GGATTTCTATAACTTTTGGC
3570 SEQ ID N0:102 -20 -20.4 62.5 0 0 -2.8
ATCCAACATCCTTTGCCCGA
2217 SEQ ID N0:103 -19.9 -28 73.8 -8.l 0 -3
ATCACAGCAGTCCCAGATCA
2684 SEQ ID N0:104 -19.9 -26.5 76 -6.6 0 -5.4
CATGTCTTGTTTTATAGGTA
6284 SEQ ID N0:105 -19.9 -20.3 64 1.3 0 -3.5
TGGCCTGCATCTGAGCCATT
1486 SEQ ID N0:106 -19.8 -28.9 79.6 -6.9 -2.2 -7.5
CCTTTGCCCGACCTCTGAAA
2208 SEQ ID N0:107 -19.8 -27.9 72.7 -8.1 0 -2.8
CCAACATCCTTTGCCCGACC
2215 SEQ ID N0:108 -19.8 -29.8 76 -10 0 -3
GGTAGTGCTCCATGGCCATA
2799 SEQ ID N0:109 -19.8 -28.5 80.3 -7.4 -0.4 -10.4
CATGACCAGGAAGAGCAGGA
5450 SEQ ID N0:110 -19.8 -24.2 68.7 -4.4 0 -4.1
AGCCAGTTCCATGGATCACG
1030 SEQ ID N0:111 -19.7 -26.8 74.4 -6 -0.8 -9.7
ATCCTTTGCCCGACCTCTGA
2210 SEQ ID N0:112 -19.7 -29.7 78.8 -10 0 -3
CTATAACTTTTGGCTTTCTA
3564 SEQ~ID N0:113 -19.7 -20.1 62 0 0 -3.7
GATTTCTATAACTTTTGGCT
3569 SEQ ID N0:114 -19.7 -20.1 61.9 0 0 -3.7
91
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kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTCTTGTTTTATAGGTAAGT
6281 SEQ ID N0:115 -19.7 -20.1 64.2 1.3 0 -2.7
AATAGGTTTTGTCAGTAGGC
7784 SEQ TD NO:116 -19.7 -21.9 67.8 -2.2 0 -2.8
CCATTTGAATCCATTGTGCC
1360 SEQ ID N0:117 -19.6 -25 69.7 -5.4 0 -3
CTTGTTTTGCTATTGCGTCT
2179 SEQ TD N0:118 -19.6 -24.1 71.2 -2.9 -1.5 -4
TTCTATAACTTTTGGCTTTC
3566 SEQ ID N0:119 -19.6 -20 62.4 0 0 -3.7
GTGCCATCTTTTCATCCTGC
459 SEQ ID N0:120 -19.5 -27.5 79 -8 0 -3
CTTGTTCCTTTTTGGGCTTC
576 SEQ ID N0:121 -19.5 -25.6 75.8 -5.6 -0.2 -3.8
ATGTTTTCCCAGCAGCACGT
1650 SEQ ID N0:122 -19.5 -27.8 77.3 -8.3 0 -5.4
AGCTGTTCGAGCATCTGCTG
1807 SEQ ID N0:123 -19.5 -26.3 76 -4.5 -2.3 -9.1
CCCACGGTCTCCCTTAACTG
5678 SEQ ID N0:124 -19.5 -28.9 76.4 -9.4 0.2 -3.5
ATCTTTTCATCCTGCACATT
454 SEQ ID N0:125 -19.4 -23.5 69.5 -4.1 0 -4.8
ACATGACCAGGAAGAGCAGG
5451 SEQ ID N0:126 -19.4 -23.8 68 -4.4 0 -5.2
ATCATGTCTTGTTTTATAGG
6286 SEQ ID N0:127 -19.4 -19.8 62.8 l.3 0 -4.7
TTCTCTGACCTCTTTTCCTT
6443 SEQ ID N0:128 -19.4 -25.4 75 -6 0 -2.4
GAGCAGCATAGGCAATATTA
7564 SEQ ID N0:129 -19.4 -21.8 64.8 -1.4 -0.8 -6.2
GCATCTGAGCCATTTCCACA
1480 SEQ ID N0:130 -19.3 -27.1 76 -7.8 0 -3.8
ACCTACTCCACTGAAATCTC
1880 SEQ 2D N0:131 -19.3 -23 66.6 -3.7 0 -2.5
TTTCTATAACTTTTGGCTTT
3567 SEQ ID N0:132 -19.3 -19.7 61.3 0 0 -3.7
GTTTACGTTTCAAAGTGGTT
6147 SEQ ID N0:133. -19.3 -20.9 63.5 -1.6 0 -4.8
TGTTTTCCCAGCAGCACGTA
1649 SEQ ID N0:134 -19.2 -27.5 76.7 -8.3 0 -5.4
TTGACGCTGTCTTCAGATTC
2050 SEQ ID N0:135 -19.2 -23.2 69.4 -2.5 , -1.4 -7.6
TGTTTTGCTATTGCGTCTTG
2177 SEQ ID N0:136 -19.2 -23.2 69 -2.4 -1.5 -4
TCACAGCAGTCCCAGATCAA
2683 SEQ ID N0:137 -19.2 -25.8 73.5 -6.6 0 -5.4
CAGTAGCAGCAAGGTTGTCT
3438 SEQ ID N0:138 -19.2 -24.9 74.5 -5.7 0 -4.6
ATTTCTATAACTTTTGGCTT
3568 SEQ ID N0:139 -19.2 -19.6 60.9 0 0 -3.7
CATCTGTATTCGAAGGGCAT
6074 SEQ ID N0:140 -19.2 -23 66.8 -3.8 0 -7.1
TTCCATCTGTATTCGAAGGG
6077 SEQ ID N0:141 -19.2 -23 67 -3.8 0 -7.1
TGTTTACGTTTCAAAGTGGT
6148 SEQ ID N0:142 -19.2 -20.8 63 -1.6 0 -4.5
CTTGTTTTATAGGTAAGTCA
6279 SEQ ID N0:143 -19.2 -19.6 62.1 1.3 0 -2.3
92
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
_ kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTCAATAATCATGTCTTGTT
6293 SEQ ID N0:144 -19.2 -19.6 61.4 1.3 0 -4.7
GTTTGTCAATAATCATGTCT
6297 SEQ ID N0:145 -19.2 -19.6 61.4 1.3 0 -4.7
CATCTGTTTTTTCTGGAGTG
6330 SEQ ID N0:146 -19.2 -22 67.9 -2.8 0 -2.7
ATTTTCTCTGACCTCTTTTC
6446 SEQ ID N0:147 -19.2 -22.6 69.4 -3.4 0 -2.4
GATCTAGGTTTGAGTGTTTG
8096 SEQ ID N0:148 -19.2 -21.4 67.1 -2.2 0 -4.1
TGATCTAGGTTTGAGTGTTT
8097 SEQ ID N0:149 -19.2 -21.4 67.1 -2.2 0 -4.9
CATGGTTTGGCCAGCGACCT
3329 SEQ ID N0:150 -19.1 -29.3 78.5 -8.4 -1.4 -11.4
TGTCAATAATCATGTCTTGT
6294 SEQ ID N0:151 -19.1 -19.5 60.9 1.3 0 -4.7
ATGATCTAGGTTTGAGTGTT
8098 SEQ ID N0:152 -19.1 -21.3 66.7 -2.2 0 -4.9
TGCCATCTTTTCATCCTGCA
458 SEQ ID N0:153 -19 -27 76.5 -8 0 -4.7
TTGTTCCTTTTTGGGCTTCT
575 SEQ ID N0:154 -19 -25.6 75.8 -6.6 0.4 -3.8
AAGTGGTGTTGGTTTCAAAA
1329 SEQ ID NO:155 -19 -19.8 60.5 1.7 -0.6 -3.1
TGTCTTCCATCTGTATTCGA
6081 SEQ ID N0:156 -19 -23.8 70.6 -4.8 0 -4.4
TTTTGATTTTCTCTGACCTC
6451 SEQ ID N0:157 -19 -21.9 66.9 -2.9 0 -2.4
GAAGTTGTTTATCAGGCTAT
7435 SEQ ID N0:158 -19 -21 64.8 -2 0 -5.2
AGAAGTTGTTTATCAGGCTA
7436 SEQ ID N0:159 -19 -21 65.1 -2 0 -5.2
TAGAAGTTGTTTATCAGGCT
7437 SEQ ID N0:160 -19 -21 65.1 -2 0 -5.2
AGAGCAGCATAGGCAATATT
7565 SEQ ID N0:161 -19 -22.1 65.7 -1.4 -1.6 -6.7
CATCTTTTCATCCTGCACAT
455 SEQ ID N0:162 -18.9 -24.1 70.3 -5.2 0 -4.8
GCCATCTTTTCATCCTGCAC
457 SEQ ID N0:163 -18.9 -27.2 77.3 -8.3 0 -4.8
CATTATCTTGTTCCTTTTTG
582 SEQ ID N0:164 -18.9 -20.9 64.3 -2 0 -1.3
CCCAGCAGCACGTAATGTCA
1643 SEQ ID N0:165 -18.9 -27.2 74.2 -8.3 0 -5.4
TCTTGTTTTATAGGTAAGTC
6280 SEQ ID N0:166 -18.9 -19.3 62.3 1.3 0 -2.7
CTTTGCCACTTTGTTCATGG
8276 SEQ ID N0:167 -18.9 -24.5 71.3 -5.6 0.4 -4.7
TCTTTTCATCCTGCACATTT
453 SEQ ID N0:168 -18.8 -23.6 69.9 -4.8 0 -4.8
TAAAGTAGGAAGTGGTGTTG
1338 SEQ ID N0:169 -18.8 -19.2 59.8 1.7 0 -1.3
AAGCTGTTCGAGCATCTGCT
1808 SEQ TD N0:170 -18.8 -25.6 73.7 -4.5 -2.3 -9.6
TTGTTTTGCTATTGCGTCTT
2178 SEQ ID N0:171 -18.8 -23.3 69.5 -2.9 -1.5 -4
TCACGGCTCTTTGCCTTCCA
2571 SEQ ID N0:172 -18.8 -29.4 80.5 -7.9 -2.7 -6.2
93
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Tnter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CACAGCAGTCCCAGATCAAG
2682 SEQ ID N0:173 -18.8 -25.4 72.1 -6.6 0 -5.4
GCATGGTTTTGATAGTCTTT
4170 SEQ ID N0:174 -18.8 -22.2 68.2 -3.4 0 -5
AAGATAGCCAGCGCCAACAT
4676 SEQ ID N0:175 -18.8 -25.4 68.9 -5.9 -0.5 -7.6
AGTTGTTTATCAGGCTATAT
7433 SEQ ID N0:176 -18.8 -20.8 65.1 -2 0 -5.2
CCAGTTCCATGGATCACGAA
1028 SEQ ID N0:177 -18.7 -24.9 69 -4.9 -0.1 -10.5
GGCCTGCATCTGAGCCATTT
1485 SEQ ID N0:178 -18.7 -29 80.2 -8.7 -l.5 -7.4
GCTTGTTTTGCTATTGCGTC
2180 SEQ ID N0:179 -18.7 -25 73.6 -4.7 -1.5 -5.3
ACAGCAGTCCCAGATCAAGA
2681 SEQ ID N0:180 -18.7 -25.3 72.3 -6.6 0 -5.4
GGCACATGGTTTGGCCAGCG
3333 SEQ ID N0:181 -18.7 -29.5 79.6 -8.4 -2.4 -9.4
AAGATTCCACCAGATCTTCC
4037 SEQ ID N0:182 -18.7 -24.4 69.9 -4.5 -1.1 -5.8
AGCATGGTTTTGATAGTCTT
4171 SEQ ID N0:183 -18.7 -22.1 68.1 -3.4 0 -5
AGTGGTTGTAATAGGCTCAT
6134 SEQ TD N0:184 -18.7 -22.6 68.7 -3.9 0 -3.7
TCCCAGCAGCACGTAATGTC
1644 5EQ ID N0:185 -18.6 -26.9 74.8 -8.3 0 -4.9
CCTTCTCTTTCTGACTTCCG
2507 SEQ ID N0:186 -18.6 -26.1 74.5 -7.5 0 -2.6
GCCTTCCAGAGGAATCCTCC
2559 SEQ TD N0:187 -18.6 -29.3 80.1 -8.5 -2.2 -11.2
GCTCTTTGCCTTCCAGAGGA
2566 SEQ ID N0:188 -18.6 -28.5 80.9 -8.5 -l.3 -5.6
ACATGGTTTGGCCAGCGACC
3330 SEQ ID N0:189 -18.6 -28.6 77.2 -8.4 -1.4 -10.4
CTTCTTTTTCTGCTGGTTGA
4883 SEQ ID N0:190 -18.6 -23.8 72.1 -5.2 0 -3.7
TAGAGCAGCATAGGCAATAT
7566 SEQ ID N0:191 -18.6 -21.7 64.7 -1.4 -l.6 -6.7
ATAGAGCAGCATAGGCAATA
7567 SEQ ID N0:192 -18.6 -21.7 64.7 -1.4 -1.6 -6.7
GCTTATGCCTCCGCTTCGCT
1 SEQ ID N0:193 -18.5 -31.1 82.6 -11.7 , -0.8 -4.9
GTTTTCCCAGCAGCACGTAA
1648 SEQ ID N0:194 -18.5 -26.8 74.4 -8.3 0 -5.4
CTTTTGACGCTGTCTTCAGA
2053 SEQ ID N0:195 -18.5 -23.8 70.2 -3.8 -1.4 -6.9
ACACCAAGGTGAGGTTTCCT
3117 SEQ ID N0:196 -18.5 -26 74 -6.4 -0.8 -9.6
TCGAAGATTCCACCAGATCT
4040 SEQ ID N0:197 -18.5 -23.7 67.3 -4.5 -0.4 -6
GTTTCTGAGGTTTCTTGGAT
4971 SEQ ID N0:198 -18.5 -23.1 71.1 -4.6 0 -28
ACCTGTCTTCCATCTGTATT
6084 SEQ ID N0:199 -18.5 -25.1 74 -6.6 0 -17
TTACGTTTCAAAGTGGTTGT
6145 SEQ TD N0:200 -18.5 -20.8 63 -1.6 -0.4 -5.6
TGTCTTGTTTTATAGGTAAG
6282 SEQ ID N0:201 -18.5 -18.9 60.7 1.3 0 -24
94
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATGTCTTGTTTTATAGGTAA
6283 SEQ ID N0:202 -18.5 -18.9 60.4 1.3 0 -2.1
GTTGTTTATCAGGCTATATA
7432 SEQ ID N0:203 -18.5 -20.5 64.2 -2 0 -5.2
GAATAGGTTTTGTCAGTAGG
7785 SEQ ID N0:204 -18.5 -20.7 64.7 -2.2 0 -2.6
TTCTGTAGTACTGCTTGGTG
8631 SEQ ID NO:205 -18.5 -23.5 71.9 -4.5 0 -7.8
TTTTCCCAATAGTCTTGAGT
1612 SEQ ID N0:206 -18.4 -22.8 68.1 -3.9 -0.2 -2.9
CTCTCTCTGTCTTCTTTTCT
1982 5EQ ID N0:207 -18.4 -24.3 76.5 -5.9 0 0
GGCTCTTTGCCTTCCAGAGG
2567 SEQ ID NO:208 -18.4 -29.1 82.2 -8.5 -2.2 -7.7
TCCACCAGATCTTCCCTTTG
4032 SEQ ID N0:209 -18.4 -27.5 76.3 -9.1 0 -5.8
CATGTTACCCGTTGTCATGT
4568 SEQ ID NO:210 -18.4 -25.5 72.4 -6.3 -0.6 -4.7
AACTTCTTTTTCTGCTGGTT
4885 SEQ TD N0:211 -18.4 -22.7 68.9 -4.3 0 -3.7
GTGGTTGTAATAGGCTCATA
6133 SEQ ID N0:212 -18.4 -22.3 67.8 -3.9 0 -3.7
TCACTGTCTTGTATAGGCAC
6600 SEQ ID N0:213 -18.4 -23.3 70.9 -4.2 -0.5 -4
TTCACTGTCTTGTATAGGCA
6601 SEQ ID N0:214 -18.4 -23.2 70.7 -4.1 -0.4 -4
ATCTAGGTTTGAGTGTTTGA
8095 SEQ ID N0:215 -18.4 -21.4 67.1 -3 0 -4
ATTAAAGTAGGAAGTGGTGT
1340 SEQ ID N0:216 -18.3 -19.2 59.9 -0.8 0 -3
CATTAAAGTAGGAAGTGGTG
1341 SEQ ID N0:217 -18.3 -18.7 58.1 0.9 0 -3
TTCCCAGCAGCACGTAATGT
1645 SEQ ID N0:218 -18.3 -26.6 73.5 -8.3 0 -5.4
CTGTTCGAGCATCTGCTGAA
1805 SEQ ID NO:219 -18.3 -24.4 70.3 -4.5 -1.5 -9.5
GTTTTGCTATTGCGTCTTGG
2176 SEQ TD N0:220 -18.3 -24.4 71.8 -5.2 -0.8 -4.2
GTACAGACAATCCCTCCACA
3000 SEQ ID N0:221 -18.3 -25.9 72 -7.6 0 -4.6
TAGCATGGTTTTGATAGTCT
4172 SEQ ID N0:222 -18.3 -21.7 67.1 -3.4 0 -5
CTCAGGGGCTCTGCACTTTC
5809 SEQ ID N0:223 -18.3 -27.8 81.1 -8.5 -0.9 -4.8
GTCTTCCATCTGTATTCGAA
6080 SEQ ID N0:224 -18.3 -23.1 68.4 -4.8 0 -6.8
AGTTTGTCAATAATCATGTC
6298 SEQ ID N0:225 -18.3 -18.7 59.5 1.3 0 -4.7
AATGATCTAGGTTTGAGTGT
8099 SEQ ID N0:226 -18.3 -20.5 63.9 -2.2 0 -4.9
CCATTAAAGTAGGAAGTGGT
1342 SEQ ID N0:227 -18.2 -20.7 62 -2.5 0 -3.3
CACCAAGGTGAGGTTTCCTA
3116 SEQ ID N0:228 -18.2 -25.5 72.8 -6.4 -0.5 -9
TGGATTTCTATAACTTTTGG
3571 SEQ ID N0:229 -18.2 -18.6 58.3 0 0 -2.3
TGCTGTTGCCAAAGGTCTCA
5547 SEQ ID N0:230 -18.2 -25.9 74.1 -6.8 -0.8 -4.4
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Tntra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CGTTTCAAAGTGGTTGTAAT
6142 SEQ ID N0:231 -18.2 -19.8 60 -1.6 0.2 -3.2
AATAGAGCAGCATAGGCAAT
7568 SEQ ID N0:232 -18.2 -21.3 63.1 -1.4 -1.6 -6.7
TCATTATCTTGTTCCTTTTT
583 SEQ ID N0:233 -18.1 -21.3 66 -3.2 0 -1.9
AGTTCCATGGATCACGAAGA
1026 SEQ ID N0:234 -18.1 -22.8 65.9 -3.4 0 -10.5
CAGCCAGTTCCATGGATCAC
1031 SEQ ID N0:235 -18.1 -26.7 75.6 -7.4 -0.8 -10
CGCTGAGACATTGCCCAGGT
1094 SEQ ID N0:236 -18.1 -28.6 77.2 -10 -0.2 -4.1
TGCATCTGAGCCATTTCCAC
1481 SEQ ID N0:237 -18.1 -26.4 74.7 -7.8 -0.1 -4.8
CAACTGCCTGAGCTTCTTCC
1839 SEQ ID N0:238 -18.1 -27 76 -8.2 -0.4 -5.2
CTACTCCACTGAAATCTCTT
1878 SEQ ID N0:239 -18.1 -21.8 64.6 -3.7 0 -2.5
TATAACTTTTGGCTTTCTAA
3563 SEQ ID N0:240 -18.1 -18.5 58 0 0 -3.7
GATAGCCAGCGCCAACATTA
4674 SEQ ID N0:241 -18.1 -25.9 70.5 -7.1 -0.5 -7.6
GCAGCGTGCGGATCCCCTTT
5385 SEQ ID N0:242 -18.1 -32.2 83.3 -12.4 -1.4 -11.1
AGCAGCGTGCGGATCCCCTT
5386 SEQ ID N0:243 -18.1 -32.1 83.3 -11.8 -2.2 -11.1
TTGTTTACGTTTCAAAGTGG
6149 SEQ ID N0:244 -18.1 -19.7 60.3 -1.6 0 -4.8
TCAATAATCATGTCTTGTTT
6292 SEQ ID N0:245 -18.1 -18.5 58.5 1.3 0 -4.7
TTTGTCAATAATCATGTCTT
6296 SEQ ID N0:246 -18.1 -18.5 58.5 1.3 0 -4.7
AAGTTGTTTATCAGGCTATA
7434 SEQ ID N0:247 -18.1 -20.1 62.8 -2 0 -5.2
ATAGAAGTTGTTTATCAGGC
7438 SEQ ID N0:248 -18.1 -20.1 63 -2 0 -5
CCTTTTTGGGCTTCTTGGCT
570 SEQ ID N0:249 -18 -27.8 79.3 -8.8 -0.9 -4.3
TCCTTTTTGGGCTTCTTGGC
571 SEQ ID N0:250 -18 -27.3 79.1 -8.8 -0.2 -4
TATGTTTTCCCAGCAGCACG
1651 SEQ ID N0:251 -18 -26.3 73.3 -8.3 , 0 -5.4
TACTGTTGCGTCGCTCTCCA
2322 SEQ ID N0:252 -18 -28.2 78.4 -9.6 -0.3 -6.9
ACCTTCTCTTTCTGACTTCC
2508 SEQ ID N0:253 -18 -25.5 75.3 -7.5 0 -2.6
GCAGTCCCAGATCAAGAACA
2678 SEQ ID N0:254 -18 -24.6 69.7 -6.6 0 -5.4
GTAGTGCTCCATGGCCATAA
2798 SEQ ID N0:255 -18 -26.6 75 -7.4 0.3 -10.4
TGGCCAACACCAAGGTGAGG
3123 SEQ ID N0:256 -18 -26.3 71.8 -6.7 -1 -11.2
CAGGAAGGAGTGGAAGAAGT
3254 SEQ ID N0:257 -18 -21 62.8 -3 0 -1.6
GCAAGATAGCCAGCGCCAAC
4678 SEQ ID N0:258 -18 -27.2 72.8 -8.5 -0.5 -7.6
GGTTTCTGAGGTTTCTTGGA
4972 SEQ ID N0:259 -18 -24.3 74 -6.3 0 -2.8
96
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAGTGGTTGTAATAGGCTCA
6135 SEQ ID N0:260 -18 -21.9 66.4 -3.9 0 -3.7
TTGTCAATAATCATGTCTTG
6295 SEQ ID N0:261 -18 -18.4 58.1 1.3 p -4.7
TTTTTCTGGTTTGTCTTTCT
6416 SEQ ID N0:262 -18 -22.3 70.2 -4.3 0 -1.5
GTCATGGGGTAGTGCTCCAT
2806 SEQ ID N0:263 -17.9 -27.8 80.9 -7.9 -2 -8.9
AGTCATGGGGTAGTGCTCCA
2807 SEQ ID N0:264 -17.9 -27.8 81.4 -8.9 -0.9 -7.2
GCTGTTGCCAAAGGTCTCAA
5546 SEQ ID N0:265 -17.9 -25.2 71.8 -6.8 -0.1 -3.7
TCTCTGACCTCTTTTCCTTT
6442 SEQ ID N0:266 -17.9 -25.4 75 -7.5 0 -2.4
TTTGGTGTAGTTACAATGTT
6756 SEQ ID N0:267 -17.9 -20 62.6 -2.1 0.3 -4.4
GATTTTCCCAATAGTCTTGA
1614 SEQ ID N0:268 -17.8 -22.2 65.9 -3.9 -0.2 -2.7
AACTGCCTGAGCTTCTTCCT
1838 SEQ ID N0:269 -17.8 -27.2 76.8 -8.2 -1.1 -5.2
CACCTACTCCACTGAAATCT
1881 SEQ ID N0:270 -17.8 -23.3 66.2 -5.5 0 -2.5
TCTTTTGACGCTGTCTTCAG
2054 SEQ ID N0:271 -17.8 -23.6 70.5 -4.7 -1 -7.6
CTTCTCTTTCTGACTTCCGT
2506 SEQ ID N0:272 -17.8 -25.3 74.3 -7.5 0 -2.6
CAGCAGTCCCAGATCAAGAA
2680 SEQ ID N0:273 -17.8 -24.4 69.4 -6.6 0 -5.4
CCACAAGGTTTCCAATGACC
3375 SEQ ID N0:274 -17.8 -24.7 68.4 -6.2 -0.4 -4.7
CTAGCATGGTTTTGATAGTC
4173 SEQ ID NO:275 -17.8 -21.7 67.1 -3.4 -0.1 -5
ACATGTTACCCGTTGTCATG
4569 SEQ ID N0:276 -17.8 -24.5 69.7 -5.4 -1.2 -7.l
CAATAATCATGTCTTGTTTT
6291 SEQ ID NO:277 -17.8 -18.2 57.5 1.3 0 -4.7
CCCATCTGTTTTTTCTGGAG
6332 SEQ ID N0:278 -17.8 -24.8 72.3 -7 0 -3.5
GTTCCATGGATCACGAAGAA
1025 SEQ ID N0:279 -17.7 -22.1 63.6 -3.4 0 -10
AGATTTTCCCAATAGTCTTG
1615 SEQ ID N0:280 -17.7 -21.6 64.8 -3.9 0 -2.8
ACCAAGGTGAGGTTTCCTAG
3115 SEQ ID NO:281 -17.7 -24.8 72 -6.4 -0.5 -6.8
ATAACTTTTGGCTTTCTAAA
3562 SEQ ID N0:282 -17.7 -18.1 56.6 0 0 -3.8
TTCGAAGATTCCACCAGATC
4041 SEQ ID N0:283 -17.7 -22.9 65.8 -4.5 -0.4 -6.2
ATGTTACCCGTTGTCATGTT
4567 SEQ ID N0:284 -17.7 -24.9 71.7 -7.2 0 -4.7
CTTTTTCTGCTGGTTGAAGT
4880 SEQ ID N0:285 -17.7 -22.9 69.2 -5.2 0 -3.7
ACTCAGGGGCTCTGCACTTT
5810 SEQ ID N0:286 -17.7 -27.6 79.9 -8.9 -0.9 -4.8
AACCTGTCTTCCATCTGTAT
6085 SEQ ID N0:287 -17.7 -24.3 71.1 -6.6 0 -2.1
ACGTTTCAAAGTGGTTGTAA
6143 SEQ ID N0:288 -17.7 -20 60.6 -1.6 -0.4 -5.2
97
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTAAAGTAGGAAGTGGTGTT
1339 SEQ ID N0:289 -17.6 -19.3 60.3 -1.7 0 -2
CATTTGAATCCATTGTGCCA
1359 SEQ ID N0:290 -17.6 -23.7 67.3 -6.1 0 -3
TAAGCTGTTCGAGCATCTGC
1809 SEQ ID NO:291 -17.6 -24.4 71.1 -4.5 -2.3 -7.6
TTTTGCTATTGCGTCTTGGG
2175 SEQ ID N0:292 -17.6 -24.4 71 -5.2 -l.5 -5
ACTGTTGCGTCGCTCTCCAT
2321 SEQ ID N0:293 -17.6 -28.5 79 -10.3 -0.3 -6.9
AAACTTCTTTTTCTGCTGGT
4886 SEQ ID N0:294 -17.6 -21.9 66.2 -4.3 0 -3.7
CATCCTCACTCAGGGGCTCT
5817 SEQ ID N0:295 -17.6 -28.9 82.5 -10.4 -0.8 -7.6
CTGTATTCGAAGGGCATCCA
6071 SEQ ID N0:296 -17.6 -25 70.4 -6.2 -1.1 -8
TTTACGTTTCAAAGTGGTTG
6146 SEQ ID N0:297 -17.6 -19.7 60.3 -1.6 -0.1 -5
TTGTTTTATAGGTAAGTCAA
6278 SEQ ID N0:298 -17.6 -18 57.8 1.3 0 -2.4
TAGTTTGTCAATAATCATGT
6299 SEQ ID N0:299 -17.6 -18 57.5 1.3 0 -4.7
GTGTTTGGTGTAGTTACAAT
6759 SEQ 2D NO:300 -17.6 -21.1 65.6 -3 -0.2 -4.6
CATCTGAGCCATTTCCACAG
1479 SEQ ID N0:301 -17.5 -25.3 72 -7.8 0 -3.7
CTGGCCTGCATCTGAGCCAT
1487 SEQ TD N0:302 -17.5 -29.7 81.1 -9.9 -2.3 -7.5
TTTGCTATTGCGTCTTGGGG
2174 SEQ ID N0:303 -17.5 -25.5 73.3 -6.4 -1.5 -5
CTCACGGCTCTTTGCCTTCC
2572 SEQ ID N0:304 -17.5 -29.6 81.4 -9.9 -2.2 -5.7
ACAGACAATCCCTCCACATT
2998 SEQ ID NO:305 -17.5 -25.1 69.8 -7.6 0 -2.1
ATGATGGCCAACACCAAGGT
3127 SEQ ID N0:306 -17.5 -25.1 69 -6.7 -0.8 -6.3
ACGATGATGGCCAACACCAA
3130 SEQ ID N0:307 -17.5 -24.3 65.5 -5.9 -0.8 -6.3
TCAGTAGCAGCAAGGTTGTC
3439 SEQ ID N0:308 -17.5 -24.4 74.2 -6.9 0 -5.4
TTCCCATCTCTAAGATAATT
3655 SEQ ID N0:309 -17.5 -20.5 61.5 -2.4 -0.3 -4.3
GTTCACCTTCTCGGGGTAGA
3912 SEQ ID N0:310 -17.5 -27.2 78.3 -8.7 -0.9 -4.9
TTTTCGAAGATTCCACCAGA
4043 SEQ TD NO:3ll -17.5 -22.7 65.1 -4.5 -0.4 -6.8
TAGCCAGCGCCAACATTATC
4672 SEQ ID N0:312 -17.5 -25.7 70.8 -7.5 -0.5 -7.6
TCTGCTGGTTGAAGTTATCT
4875 SEQ ID N0:313 -17.5 -22.7 69.1 -5.2 0 -3.7
AACATGACCAGGAAGAGCAG
5452 SEQ TD N0:314 -17.5 -219 63.4 -4.4 0 -5.2
ATGCTGTTGCCAAAGGTCTC
5548 SEQ ID N0:315 -17.5 -25.2 72.9 -6.8 -0.8 -4.4
CCACGGTCTCCCTTAACTGA
5677 SEQ ID N0:316 -17.5 -27.5 74.3 -9.4 -0.3 -3.5
AATCATGTCTTGTTTTATAG
6287 SEQ ID N0:317 -17.5 -17.9 57.8 1.3 0 -47
98
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Position oligo bindingformationDuplexstructureoligo oligo
ATAATCATGTCTTGTTTTAT
6289 SEQ ID N0:318 -17.5 -17.9 57.6 1.3 0 -4.1
AAATAGAGCAGCATAGGCAA
7569 SEQ ID N0:319 -17.5 -20.6 61.1 -1.4 -1.6 -6.7
AAAATAGAGCAGCATAGGCA
7570 SEQ ID N0:320 -17.5 -20.6 61.1 -1.4 -1.6 -6.7
GTAAAATAGAGCAGCATAGG
7572 SEQ ID N0:321 -17.5 -l9 58.3 -1.4 0 -5.4
ATTGCCTTTCCTTTATTCAT
748 SEQ ID N0:322 -17.4 -23.4 68.9 -6 0 -3
GCAACTGCCTGAGCTTCTTC
1840 SEQ ID N0:323 -17.4 -26.8 76.8 -8.2 -1.1 -5.2
GATCCAACATCCTTTGCCCG
2218 SEQ ID N0:324 -17.4 -28 73.8 -10.6 0 -3.3
TTACTGTTGCGTCGCTCTCC
2323 SEQ ID N0:325 -17.4 -27.6 77.8 -9.6 -0.3 -6.9
CAGACAATCCCTCCACATTT
2997 SEQ ID N0:326 -17.4 -25 69.6 -7.6 0 -2.1
CAGTACAGACAATCCCTCCA
3002 SEQ ID N0:327 -17.4 -25.7 71.8 -7.6 -0.4 -5.3
TTTCGAAGATTCCACCAGAT
4042 SEQ ID N0:328 -17.4 -22.6 64.7 -4.5 -0.4 -6.8
TCTAGCATGGTTTTGATAGT
4174 SEQ ID N0:329 -17.4 -21.7 67.1 -3.4 -0.7 -4.3
GCTGAAGTTTAACATCTCGT
4758 SEQ ID N0:330 -17.4 -21.6 64.4 -4.2 0 -3.6
GGCTGAAGTTTAACATCTCG
4759 SEQ ID N0:331 -17.4 -21.6 63.8 -4.2 0 -4.6
CACTCAGGGGCTCTGCACTT
5811 SEQ ID N0:332 -17.4 -28.2 80.5 -9.8 -0.9 -4.8
CCCTGCTTCACAGAGTTGCA
6637 SEQ ID N0:333 -17.4 -28.1 78.8 -9.4 -1.2 -7
TGGTGTAGTTACAATGTTCA
6754 SEQ ID N0:334 -17.4 -20.9 64.7 -3 -0.2 -4.6
AGCAGCATAGGCAATATTAA
7563 SEQ ID N0:335 -17.4 -20.5 61.4 -1.4 -1.6 -6.7
TAAAATAGAGCAGCATAGGC
7571 SEQ ID N0:336 -17.4 -19.6 59.4 -l.4 -0.5 -5.4
GGTTATATTGAGGCAACCAT
8130 SEQ ID N0:337 -17.4 -22.5 65.7 -3.7 -1.3 -5.6
AGGTATCTCATCCCTGTCAA
267 SEQ ID N0:338 -17.3 -25.4 74.1 -8.1 0 -3.1
GCTGAGACATTGCCCAGGTC
1093 SEQ ID N0:339 -17.3 -28.2 79.3 -10.4 -0.2 -4.4
GCCATTAAAGTAGGAAGTGG
1343 SEQ ID N0:340 -17.3 -21.3 63 -4 0 -3.7
TTTTCCCAGCAGCACGTAAT
1647 SEQ 2D N0:341 -17.3 -25.6 71.2 -8.3 0 -5.4
AGCAGTCCCAGATCAAGAAC
2679 SEQ ID N0:342 -17.3 -23.9 68.9 -6.6 0 -5.4
ACCAAGCTCCATTAAACTGA
2972 SEQ ID N0:343 -17.3 -22.1 63.1 -4.8 0 -5
CAATCAGGAAGGAGTGGAAG
3258 SEQ ID N0:344 -17.3 -20.3 60.9 -3 0 -3.9
CGAAGATTCCACCAGATCTT
4039 SEQ ID N0:345 -17.3 -23.4 66.2 -4.5 -1.5 -5.8
AGCCAGCGCCAACATTATCA
4671 SEQ ID N0:346 -17.3 -26.7 72.4 -8.7 -0.5 -6.8
99
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/mo1kcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTGTTTATCAGGCTATATAT
7431 SEQ ID N0:347 -17.3 -19.3 60.9 -2 0 -5.2
CAGGATACATCCCTGTTGGA
7500 SEQ ID N0:348 -17.3 -25.5 72.3 -6.7 -1.4 -6.9
TTGAGTAAAATAGAGCAGCA
7576 SEQ ID N0:349 -17.3 -18.8 57.9 -1.4 0 -5.4
AGAATAGGTTTTGTCAGTAG
7786 SEQ ID N0:350 -17.3 -19.5 62.1 -2.2 0 -2.7
TTGCCACTTTGTTCATGGCT
8274 5EQ ID N0:351 -17.3 -26.2 75.3 -5.6 -3.3 -9.1
TTTGCCACTTTGTTCATGGC
8275 SEQ TD N0:352 -17.3 -25.4 73.7 -5.6 -2.5 -8.1
ATTTTCCCAATAGTCTTGAG
1613 SEQ ID N0:353 -17.2 -21.6 64.8 -3.9 -0.2 -2.7
TTTCCCAGCAGCACGTAATG
1646 SEQ ID N0:354 -17.2 -25.5 70.7 -8.3 0 -5.4
AACCCACCTACTCCACTGAA
1885 SEQ ID N0:355 -17.2 -26.2 70.3 -9 0 -1.7
ATGTGCTGTGTTCATCATCA
2253 SEQ ID N0:356 -17.2 -23.7 71.9 -6.5 0 -3.6
GATGGCCAACACCAAGGTGA
3125 SEQ ID N0:357 -17.2 -25.7 70.3 -6.7 -0.8 -11.7
TGATGGCCAACACCAAGGTG
3126 SEQ ID N0:358 -17.2 -25.1 68.9 -6.7 -0.8 -9.8
GATGATGGCCAACACCAAGG
3128 SEQ TD N0:359 -17.2 -24.5 67.3 -6.7 -0.3 -6.3
TCAGGAAGGAGTGGAAGAAG
3255 SEQ ID N0:360 -17.2 -20.2 61.2 -3 0 -2.4
ATCAGGAAGGAGTGGAAGAA
3256 SEQ ID N0:361 -17.2 -20.2 60.9 -3 0 -2.9
AATCAGGAAGGAGTGGAAGA
3257 SEQ ID N0:362 -17.2 -20.2 60.9 -3 0 -2.9
AGGTTGTCTGAGCTAAATGA
3427 SEQ ID N0:363 -17.2 -21.2 64.4 -4 0 -5.1
ATTCCCATCTCTAAGATAAT
3656 SEQ ID N0:364 -17.2 -20.4 61.2 -2.5 -0.5 -3.9
CATGGTTTTGATAGTCTTTC
4169 SEQ ID N0:365 -17.2 -20.8 65.3 -3.6 0 -3.7
ATTCTAGCATGGTTTTGATA
4176 SEQ ID N0:366 -17.2 -20.6 63.7 -3.4 0 -5
TATTCTAGCATGGTTTTGAT
4177 SEQ ID N0:367 -17.2 -20.6 63.7 -3.4 0 -5
GAGCAGCGTGCGGATCCCCT
5387 SEQ ID N0:368 -17.2 -32.6 84.2 -13.2 -2.2 -11.1
TCAGGGGCTCTGCACTTTCT
5808 SEQ ID N0:369 -17.2 -27.8 81.1 -9.6 -0.9 -4.8
TAATCATGTCTTGTTTTATA
6288 SEQ ID N0:370 -17.2 -17.6 57 1.3 0 -4.7
TGAGTAAAATAGAGCAGCAT
7575 SEQ ID N0:371 -17.2 -18.7 57.6 -1.4 0 -5.4
TTGAGGCAACCATAGTTGGT
8123 SEQ TD N0:372 -17.2 -24 69.7 -4.4 -2.4 -7.5
TGTTCCTTTTTGGGCTTCTT
574 SEQ ID N0:373 -17.1 -25.6 75.8 -8 -0.2 -3.8
AGTGGTGTTGGTTTCAAAAG
1328 SEQ ID N0:374 -17.1 -20.5 62.9 -2.6 -0.6 -3.1
TACAGACAATCCCTCCACAT
2999 SEQ ID N0:375 -17.1 -24.7 68.9 -7.6 0 -2.1
100
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGGCACATGGTTTGGCCAGC
3334 SEQ ID N0:376 -17.1 -28.7 80.4 -8.4 -3.2 -9.6
ATAGCCAGCGCCAACATTAT
4673 SEQ ID N0:377 -17.1 -25.3 69.3 -7.5 -0.5 -7.6
CAAACTTCTTTTTCTGCTGG
4887 SEQ ID N0:378 -17,1 -21.4 64.2 -4.3 0 -3.7
GTTGCCAAAGGTCTCAAAGT
5543 SEQ ID N0:379 -17.1 -23 67 -5.9 0 -4
AGAGGAGGATCCAGGGCAGC
5923 SEQ ID N0:380 -17.1 -28 79.9 -8.3 -2.6 -9
TGGACAGAGCAGGTTGAATT
7648 SEQ ID N0:381 -17.1 -22.3 66.1 -5.2 0 -4.1
TTTGAATCCATTGTGCCATT
1357 SEQ ID N0:382 -17 -23.1 66.6 -6.1 0 -3.1
AAGATTTTCCCAATAGTCTT
1616 SEQ ID N0:383 -17 -20.9 62.8 -3.9 0 -3.5
CCTGTTGCTTTTTAAGCTGT
1821 SEQ ID N0:384 -17 -24.2 71.1 -4.6 -2.6 -7.1
TTCCTGTTGCTTTTTAAGCT
1823 SEQ ID N0:385 -17 -23.5 69.9 -3.9 -2.6 -7.1
CTCTTTCTGACTTCCGTTTC
2503 SEQ ID N0:386 -17 -24.5 72.6 -7.5 0 -2.7
TCTCTTTCTGACTTCCGTTT
2504 SEQ ID N0:387 -17 -24.5 72.6 -7.5 0 -2.6
TTCTCTTTCTGACTTCCGTT
2505 SEQ ID N0:388 -17 -24.5 72.6 -7.5 0 -2.6
TTGCCTTCCAGAGGAATCCT
2561 SEQ ID N0:389 -17 -27 75.1 -8.5 -1.3 -9.8
CAGTCATGGGGTAGTGCTCC
2808 SEQ ID N0:390 -17 -27.8 81.4 -10.3 -0.1 -6.7
AGGAAGGAGTGGAAGAAGTC
3253 SEQ ID N0:391 -17 -20.7 63.1 -3.7 0 -1.8
ATGGATTTCTATAACTTTTG
3572 SEQ ID N0:392 -17 -17.4 55.7 0 0 -2.3
TGTTCACCTTCTCGGGGTAG
3913 SEQ ID N0:393 -17 -26.6 76.8 -8.7 -0.7 -4.2
ATATTCTAGCATGGTTTTGA
4178 SEQ ID N0:394 -17 -20.6 63.7 -3.6 0 -5
AACATGTTACCCGTTGTCAT
4570 SEQ ID N0:395 -17 -23.8 67.6, -6.3 0 -8.1
TTCTTTTTCTGCTGGTTGAA
4882 SEQ ID N0:396 -17 -22.2 67.5 -5.2 0 -3.7
TCTGAGGTTTCTTGGATCCA
4968 SEQ ID N0:397 -17 -24.8 73.6 -6.9 O.l -9.7
TCAGACGTAGGATTCGGCCA
5355 SEQ ID N0:398 -17 -26.4 73.1 -8.8 -0.3 -7.2
AGATGGGTCCCCACGGTCTC
5687 SEQ ID N0:399 -17 -30.4 83 -12.5 -0.6 -8.8
CTGTCTTCCATCTGTATTCG
6082 SEQ ID N0:400 -17 -24.1 71.3 -7.1 0 -2.4
AAACCTGTCTTCCATCTGTA
6086 SEQ ID N0:401 -17 -23.6 68.8 -6.6 0 -2.1
TAAACCTGTCTTCCATCTGT
6087 SEQ ID N0:402 -17 -23.6 68.8 -6.6 0 -2
CAGGGTTCTTGTATACTGTT
6931 SEQ ID N0:403 -17 -22.8 69.9 -5.8 0 -6.5
ATGGACAGAGCAGGTTGAAT
7649 SEQ ID N0:404 -17 -22.2 65.8 -5.2 0 -4.1
101
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATATTGAGGCAACCATAGTT
8126 SEQ ID N0:405 -17 -21.3 63.4 -3.7 -0.3 -3.7
CCACTTTGTTCATGGCTAAA
8271 SEQ ID N0:406 -17 -22.6 65.6 -5.6 0 -4.7
CATGCACTAGTTTGTTGTAA
8608 SEQ ID N0:407 -17 -20.9 63.9 -3.9 0 -5.5
ATTTGAATCCATTGTGCCAT
1358 5EQ ID N0:408 -16.9 -23 66.2 -6.1 0 -3.1
GTCCCATTTGAATCCATTGT
1363 SEQ ID N0:409 -16.9 -24.8 70.5 -7.9 0 -2.2
TCGACCAGCCTTCACACAGA
1523 SEQ ID N0:410 -16.9 -27 74.2 -10.1 0 -4.2
TCCTGTTGCTTTTTAAGCTG
1822 SEQ ID N0:411 -16.9 -23.4 69.4 -3.9 -2.6 -7.1
TGCCTTCCAGAGGAATCCTC
2560 SEQ ID N0:412 -16.9 -27.3 76.4 -8.5 -1.8 -10.8
GTGCTCCATGGCCATAAAGA
2795 SEQ ID N0:413 -16.9 -25.6 71.2 -7.4 -0.4 -10.4
AGTACAGACAATCCCTCCAC
3001 SEQ ID N0:414 -16.9 -25.2 71.2 -7.6 -0.4 -5.3
GCACATGGTTTGGCCAGCGA
3332 SEQ ID N0:415 -16.9 -28.9 78.4 -10.4 -l.5 -8.8
TTTAATACACCCTTCAGTAA
3977 SEQ ID N0:416 -16.9 -20.3 60.7 -3.4 0 -3.6
TTTTTCTGCTGGTTGAAGTT
4879 SEQ ID N0:417 -16.9 -22.1 67.5 -5.2 0 -3.7
TCTTTTTCTGCTGGTTGAAG
4881 SEQ ID N0:418 -16.9 -22.1 67.4 -5.2 0 -4
TGTTGCCAAAGGTCTCAAAG
5544 SEQ ID N0:419 -16.9 -21.8 63.8 -4.9 0 -4
CGTTGATACCCTGCTTCACA
6645 SEQ ID N0:420 -16.9 -26.3 72.6 -9.4 0 -3.6
GGTGTTTGGTGTAGTTACAA
6760 SEQ ID N0:421 -16.9 -22.3 68.5 -4.9 -0.2 -4.6
GTTTATCAGGCTATATATAT
7429 SEQ ID N0:422 -16.9 -18.9 60 -2 0 -5
TGTTTATCAGGCTATATATA
7430 SEQ ID N0:423 -16.9 -18.9 59.9 -2 0 -4.5
GAGTAAAATAGAGCAGCATA
7574 SEQ ID N0:424 -16.9 -18.4 57.1 -1.4 0 -5.4
TTTTGTCAGTAGGCAGTATC
7778 SEQ ID N0:425 -16.9 -22.5 70.6 -5.l -0.1 -4
GCCACTTTGTTCATGGCTAA
8272 SEQ TD N0:426 -16.9 -25.1 72 -5.6 -2.6 -8.3
TGCCACTTTGTTCATGGCTA
8273 SEQ ID N0:427 -16.9 -25.8 74.3 -5.6 -3.3 -9.1
ATCTCATTTATTCTTACAAT
347 SEQ TD N0:428 -16.8 -17.7 56.8 -0.7 0 -1.6
ACTGCCTGAGCTTCTTCCTG
1837 SEQ TD N0:429 -16.8 -27.9 79.2 -9.9 -1.1 -5.2
CCAAACTTCTTTTTCTGCTG
4888 SEQ ID N0:430 -16.8 -22.2 65.3 -5.4 0 -3.6
CAGGAAGAGCAGGAGGCCGA
5444 SEQ ID N0:431 -16.8 -27.1 74.1 -9.4 -0.8 -7.7
AAACATGACCAGGAAGAGCA
5453 SEQ ID N0:432 -16.8 -21.2 61.3 -4.4 0 -5.2
AATAATCATGTCTTGTTTTA
6290 SEQ TD N0:433 -16.8 -17.2 55.6 1.3 0 -4.7
102
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CACTGTCTTGTATAGGCACT
6599 SEQ ID N0:434 -16.8 -23.8 71.3 -6.3 -0.5 -4
CTTTTCATCCTGCACATTTA
452 SEQ ID N0:435 -16.7 -22.9 67.7 -6.2 0 -4.8
AATTGCCTTTCCTTTATTCA
749 SEQ ID N0:436 -16.7 -22.7 66.6 -6 0 -3
CCATGGATCACGAAGAAACG
1022 SEQ ID N0:437 -16.7 -20.7 58.4 -3.4 0 -8.5
CCAGCCAGTTCCATGGATCA
1032 SEQ ID N0:438 -16.7 -28.5 78.6 -10.6 -0.8 -10
GGTGTTGGTTTCAAAAGCAG
1325 SEQ ID N0:439 -16.7 -21.8 65.2 -4.3 -0.6 -0.8
ACTGGCCTGCATCTGAGCCA
1488 SEQ ID N0:440 -16.7 -29.9 81.8 -ll -2.2 -7.5
TTTAAGCTGTTCGAGCATCT
1811 SEQ ID N0:441 -16.7 -22.8 67.6 -4.5 -1.5 -7.4
CGGTTCCTCCATTCTTTAGC
1957 SEQ ID N0:442 -16.7 -26.8 76.3 -9.2 -0.8 -3.6
CACGGCTCTTTGCCTTCCAG
2570 SEQ ID NO:443 -16.7 -29 79.1 -9.6 -2.7 -6.2
TCCATGGCCATAAAGAGGGT
2791 SEQ ID N0:444 -16.7 -25.3 70.7 -7.4 0 -10.4
ATCAGTAGCAGCAAGGTTGT
3440 SEQ ID N0:445 -16.7 -24 72.3 -7.3 0 -5.4
TTCCATTCCCATCTCTAAGA
3660 SEQ ID N0:446 -16.7 -24.6 70.6 -7.9 0 -2.8
GCTTGTTCACCTTCTCGGGG
3916 SEQ ID N0:447 -16.7 -28.5 80.3 -11.3 -0.2 -3.4
TTCTGCTGGTTGAAGTTATC
4876 SEQ ID N0:448 -16.7 -21.9 67.4 -5.2 0 -3.7
TTTCTGAGGTTTCTTGGATC
4970 SEQ ID N0:449 -16.7 -22.3 69.2 -5.6 0 -4.7
TGTATTCGAAGGGCATCCAT
6070 SEQ ID N0:450 -16.7 -24.1 68.5 -6.2 -1.1 -8.2
ATTGAGGCAACCATAGTTGG
8124 SEQ TD N0:451 -16.7 -22.8 66.4 -3.7 -2.4 -6.8
GTTATATTGAGGCAACCATA
8129 SEQ ID N0:452 -16.7 -21 62.6 -3.7 -0.3 -4
AGGTTATATTGAGGCAACCA '
8131 SEQ ID N0:453 -16.7 -22.5 65.9 -3.7 -2.1 -6.3
TCATGCACTAGTTTGTTGTA
8609 SEQ ID N0:454 -16.7 -22 67.9 -5.3 0 -5.7
GGTATCTCATCCCTGTCAAA
266 SEQ ID N0:455 -16.6 -24.7 71.4 -8.1 0 -2.4
TTGAATCCATTGTGCCATTA
1356 SEQ ID N0:456 -16.6 -22.7 65.7 -6.1 0 -3.1
GTTCGAGCATCTGCTGAAAT
1803 SEQ ID N0:457 -16.6 -22.8 66.2 -4.5 -1.7 -9.7
TGTTCGAGCATCTGCTGAAA
1804 SEQ ID N0:458 -16.6 -22.8 66.1 -4.5 -1.7 -9.7
CCAAGGTGAGGTTTCCTAGA
3114 SEQ ID N0:459 -16.6 -25.2 72.7 -7.9 -0.5 -4.4
ATGGCCAACACCAAGGTGAG
3124 SEQ ID NO:460 -16.6 -25.1 69.3 -6.7 -0.8 -11.7
CAAGGTTGTCTGAGCTAAAT
3429 SEQ ID N0:461 -16.6 -20.6 62.2 -4 0 -5.5
GTCTTGACCTCCAAACTTCT
4898 SEQ ID N0:462 -16.6 -24.5 70.5 -7.4 -0.1 -3.9
103
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAAGTGGTTGTAATAGGCTC
6136 SEQ ID N0:463 -16.6 -20.5 62.9 -3.9 0 -3.7
TTTAGTTTGTCAATAATCAT
6301 SEQ ID N0:464 -16.6 -l7 55.2 1.3 0 -2.9
ATTTAGTTTGTCAATAATCA
6302 SEQ ID N0:465 -16.6 -17 55.2 l.3 0 -2.9
CTTTTGATTTTCTCTGACCT
6452 SEQ ID N0:466 -16.6 -22.4 67.4 -5.8 0 -2.4
GGCAGATATGGAAGTTAAAA
6808 SEQ ID N0:467 -16.6 -18 55.5 0 -1.3 -5.5
ATTGAGTAAAATAGAGCAGC
7577 SEQ ID N0:468 -16.6 -18.1 56.7 -1.4 0 -4.1
TTTGTCAGTAGGCAGTATCC
7777 SEQ ID N0:469 -16.6 -24.4 74.3 -7.3 -0.1 -4
AAGAATAGGTTTTGTCAGTA
7787 SEQ TD N0:470 -16.6 -18.8 59.7 -2.2 0 -2.7
TATATTGAGGCAACCATAGT
8127 SEQ ID N0:471 -16.6 -20.9 62.5 -3.7 -0.3 -4
TATCTCATTTATTCTTACAA
348 SEQ ID N0:472 -16.5 -17.4 56.2 -0.7 0 -0.9
ATCATTATCTTGTTCCTTTT
584 SEQ ID N0:473 -16.5 -21.2 65.6 -4.7 0 -1.9
CGACCAGCCTTCACACAGAT
1522 SEQ ID N0:474 -16.5 -26.6 72.6 -10.1 0 -3.2
GCTCCATGGCCATAAAGAGG
2793 SEQ ID N0:475 -16.5 -25.6 70.9 -7.4 0 -11.5
CGATGATGGCCAACACCAAG
3129 SEQ ID N0:476 -16.5 -24.1 65.2 -6.7 -0.8 -6.3
GGTTGTCTGAGCTAAATGAA
3426 SEQ ID N0:477 -16.5 -20.5 62 -4 0 -5.l
CATGGATTTCTATAACTTTT
3573 SEQ ID NO:478 -16.5 -18.1 57 -l.6 0 -3.7
TTCTAGCATGGTTTTGATAG
4175 SEQ ID NO:479 -16.5 -20.6 64 -3.4 -0.4 -5
TTTTCTGCTGGTTGAAGTTA
4878 SEQ ID N0:480 -16.5 -21.7 66.5 -5.2 0 -3.7
TTCCTTGGAATTTGTTTGCT
5004 SEQ ID N0:481 -16.5 -22.9 67.7 -5.6 -0.6 -6.3
ATCCTCACTCAGGGGCTCTG
5816 SEQ ID N0:482 -16.5 -28.2 81.2 -10.8 -0.8 -7.6
GGTTGTAATAGGCTCATAAG
6131 SEQ ID N0:483 -16.5 -20.4 62.6 -3.9 0 -3.7
TGGTTGTAATAGGCTCATAA
6132 SEQ ID N0:484 -16.5 -20.4 62.2 -3.9 0 -3.7
TTAGTTTGTCAATAATCATG
6300 SEQ ID N0:485 -16.5 -16.9 54.8 l.3 0 -4.1
CATTTAGTTTGTCAATAATC
6303 SEQ ID N0:486 -16.5 -17 55.2 -0.2 0 -2.9
TCCCATCTGTTTTTTCTGGA
6333 SEQ ID N0:487 -16.5 -25.2 73.7 -8.7 0 -3.5
TCTGTAGTACTGCTTGGTGA
8630 SEQ ID N0:488 -16.5 -24 73 -7 0 -7.8
TGCTTATGCCTCCGCTTCGC
2 SEQ TD N0:489 -16.4 -30.2 80.5 -12.9 -0.8 -5
TTGCCTTTCCTTTATTCATT
747 SEQ ID NO:490 -16.4 -23.5 69.3 -7.1 0 -3
ATCCATTGTGCCATTAAAGT
1352 SEQ ID N0:491 -16.4 -22.5 65.3 -6.l 0 -3.1
104
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGACGCTGTCTTCAGATTCG
2049 SEQ ID N0:492 -16.4 -23.9 69.1 -5.8 -1.7 -7.6
GTCCCAGATCAAGAACACAT
2675 SEQ TD N0:493 -16.4 -23 65.9 -6.6 0 -5.4
AGTCCCAGATCAAGAACACA
2676 SEQ ID N0:494 -16.4 -23 66.2 -6.6 0 -5.4
CAGTCCCAGATCAAGAACAC
2677 SEQ ID N0:495 -16.4 -23 66.2 -6.6 0 -5.4
CATCACAGCAGTCCCAGATC
2685 SEQ ID N0:496 -16.4 -26.5 76 -10.1 0 -4.1
CTCCATGGCCATAAAGAGGG
2792 SEQ ID N0:497 -16.4 -25 69.4 -7.4 0 -10.4
CCACCAGATCTTCCCTTTGC
4031 SEQ ID N0:498 -16.4 -28.9 78.9 -12.5 0 -5.6
TTTCTGCTGGTTGAAGTTAT
4877 SEQ ID N0:499 -16.4 -21.6 66.1 -5.2 0 -3.4
CAGGGGCTCTGCACTTTCTT
5807 SEQ ID N0:500 -16.4 -27.5 79.6 -10.5 -0.3 -4.8
CCTGTCTTCCATCTGTATTC
6083 SEQ ID N0:501 -16.4 -25.3 75.2 -8.9 0 -1.6
ACCCTGCTTCACAGAGTTGC
6638 SEQ ID N0:502 -16.4 -27.6 78.4 -9.9 -1.2 -4.8
ACGTTGATACCCTGCTTCAC
6646 SEQ ID N0:503 -16.4 -25.8 72.1 -9.4 0 -4.4
GTTTGGTGTAGTTACAATGT
6757 SEQ ID N0:504 -16.4 -21.1 65.6 -4.2 -0.2 -4.6
TGTTTGGTGTAGTTACAATG
6758 SEQ ID N0:505 -16.4 -19.9 62.1 -3 -0.2 -4.6
TGGCAGATATGGAAGTTAAA
6809 SEQ ID N0:506 -16.4 -18.7 57.3 -0.8 -1.3 -5.5
AAATGATCTAGGTTTGAGTG
8100 SEQ ID N0:507 -16.4 -7.8.6 58.5 -2.2 0 -4.9
CCCAATAAGTGAAATGCAAT
8479 SEQ ID N0:508 -16.4 -19.2 56.2 -2.8 0 -5.6
GAATCATGCACTAGTTTGTT
8612 SEQ ID N0:509 -16.4 -21 64.2 -4.6 0 -5.7
GGTGGTTACTACTATTATTA
8731 SEQ ID N0:510 -16.4 -19.8 62.1 -2.9 -0.1 -3.9
TTCCTTTTTGGGCTTCTTGG
572 SEQ ID N0:511 -16.3 -25.6 74.9 -8.8 -0.2 -3.8
TTTCCCAATAGTCTTGAGTC
1611 SEQ ID N0:512 -16.3 -23.1 69.4 -6.8 0.3 -3.3
CTTCCTGTTGCTTTTTAAGC
1824 SEQ ID N0:513 -16.3 -23.5 69.9 -5.4 -1.8 -6.1
CCTGCTTTCGCCGTCTTCAA
2273 SEQ ID N0:514 -16.3 -28.6 76.9 -11.6 -0.5 -3.6
TGACTAACGTTACTGTTGCG
2332 SEQ ID N0:515 -16.3 -21.7 62.9 -5.4 0.1 -7.8
TTTGCCTTCCAGAGGAATCC
2562 SEQ ID N0:516 -16.3 -26.2 73.6 -8.5 -1.3 -6
AGTGCTCCATGGCCATAAAG
2796 SEQ ID N0:517 -16.3 -25 70.2 -7.4 -0.4 -10.4
GAAGATTCCACCAGATCTTC
4038 SEQ ID N0:518 -16.3 -23 67.5 -4.5 -2.2 -6.8
TCCAGAATGAATATATAGGT
4213 SEQ ID N0:519 -16.3 -18.4 57 -2.1 0 -4.2
ATTCCTTGGAATTTGTTTGC
5005 SEQ ID N0:520 -16.3 -22 65.7 -4.1 -1.5 -8.1
105
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGGAAGAGCAGGAGGCCGAT
5443 SEQ ID N0:521 -16.3 -26.4 73 -9.2 -0.8 -7.7
CCAGGAAGAGCAGGAGGCCG
5445 SEQ ID N0:522 -16.3 -28.5 76.2 -11.3 -0.8 -7.7
ACAGGGTTCTTGTATACTGT
6932 SEQ ID N0:523 -16.3 -22.9 70.1 -5.8 -0.6 -6.5
AGGATACATCCCTGTTGGAA
7499 SEQ ID N0:524 -16.3 -24.1 68.9 -6.7 -1 -6.9
GCAGCATAGGCAATATTAAC
7562 SEQ ID N0:525 -16.3 -20.7 61.8 -2.7 -l.6 -6.7
AGTAAAATAGAGCAGCATAG
7573 SEQ TD N0:526 -16.3 -17.8 56 -1.4 0 -5.4
AATGGACAGAGCAGGTTGAA
7650 SEQ ID N0:527 -16.3 -21.5 63.6 -5.2 0 -4.1
'
AAGGTTATATTGAGGCAACC
8132 SEQ ID N0:528 -16.3 -21.1 62.6 -3.7 -1 -5
TGAATCATGCACTAGTTTGT
8613 SEQ ID N0:529 -16.3 -20.9 63.7 -4.6 0 -5.7
GGTGAATCATGCACTAGTTT
8615 SEQ ID N0:530 -16.3 -22.1 66.5 -4.6 -1.1 -6.2
TTTTTTTTTTTTTCCACCTT
9088 SEQ ID N0:531 -16.3 -21.5 65 -5.2 0 0
TTTTTTTTTTTTTTCCACCT
9089 SEQ ID N0:532 -16.3 -21.5 65 -5.2 0 0
CCTGTGCCATCTTTTCATCC
462 SEQ ID N0:533 -16.2 -27.7 78.1 -11.5 0 -2.7
ACGCTGAGACATTGCCCAGG
1095 SEQ ID N0:534 -16.2 -27.6 74.5 -10.9 -0.2 -4.1
ATCTGAGCCATTTCCACAGA
1478 5EQ ID N0:535 -16.2 -25.2 72.2 -7.8 -1.1 -4.9
CACTGGCCTGCATCTGAGCC
1489 SEQ ID N0:536 -16.2 -29.9 81.8 -12.5 -1.1 -7.5
AAAGATTTTCCCAATAGTCT
1617 SEQ ID N0:537 -16.2 -20.1 60.4 -3.9 0 -3
CCAGCAGCACGTAATGTCAA
1642 SEQ ID N0:538 -16.2 -24.5 68.5 -8.3 0 -5.4
AGGCCATGGCCACCACAGCC
1731 SEQ ID N0:539 -16.2 -33 85.5 -12.2 -2.8 -17.4
TGTGCTGTGTTCATCATCAG
2252 SEQ ID N0:540 -16.2 -23.7 72.3 -6.5 -0.9 -4.4
GTCTTCAAATGTGCTGTGTT
2261 SEQ ID N0:541 -16.2 -22.7 68.8 -6.5 , 0 -3.6
CGTTACTGTTGCGTCGCTCT
2325 SEQ ID N0:542 -16.2 -27.2 75.7 -10.4 -0.3 -6.9
ATCGCAGTACAGACAATCCC
3006 SEQ ID N0:543 -16.2 -24.7 69.4 -7.8 -0.4 -5.3
GGAAACACTCCCGCATCTTA
3531 SEQ ID N0:544 -16.2 -25.2 69 -8.4 -0.3 -5.4
TCTGAGGGAAACGAGCTTCA
5195 SEQ ID N0:545 -16.2 -23 66.2 -6.2 -0.3 -5.2
GACGTAGGATTCGGCCAATC
5352 SEQ ID N0:546 -16.2 -25 69.5 -7.6 -0.7 -10
GATCAGACGTAGGATTCGGC
5357 SEQ ID N0:547 -16.2 -24.3 69.7 -7.6 -0.2 -6.6
GGTCGCATCGGGATCAAACT
5867 SEQ ID N0:548 -16.2 -25.1 69.4 -8.9 0 -6.9
GATACCCTGCTTCACAGAGT
6641 SEQ ID N0:549 -16.2 -26 74.4 -8.5 -1.2 -5.1
106
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Tnter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGGTGTTTGGTGTAGTTACA
6761 SEQ ID N0:550 -16.2 -23 71.3 -6.8 0 -4.4
TTGTCAGTAGGCAGTATCCA
7776 SEQ ID N0:551 -16.2 -25 75.1 -8.3 -0.2 -4
GAAGAATAGGTTTTGTCAGT
7788 SEQ ID N0:552 -16.2 -19.7 61.7 -3.5 0 -2.7
TTATCTCATTTATTCTTACA
349 SEQ ID N0:553 -16.1 -18.2 58.6 -2.1 0 -0.9
ATTATCTCATTTATTCTTAC
350 SEQ ID N0:554 -16.1 -17.5 57.3 -1.3 0 -0.9
CTTTTTGGGCTTCTTGGCTT
569 SEQ ID N0:555 -16.1 -25.9 76 -8.8 -0.9 -3.7
CTAAGCAAAACCCTCTTGCC
993 SEQ ID N0:556 -16.1 -24.6 67.3 -6.5 -2 -6.2
GTGTTGGTTTCAAAAGCAGA
1324 SEQ ID N0:557 -16.1 -21.2 64 -4.3 -0.6 -1.1
GTGGTGTTGGTTTCAAAAGC
1327 SEQ ID N0:558 -16.1 -22.3 66.9 -5.4 -0.6 -3.8
TGCCATTAAAGTAGGAAGTG
1344 SEQ ID N0:559 -16.1 -20.1 60.4 -4 0 -3.5
TCCATTGTGCCATTAAAGTA
1351 SEQ ID N0:560 -16.1 -22.2 64.8 -6.1 0 -3.1
CCTTCTGGACACTGGCCTGC
1498 SEQ ID N0:561 -16.1 -29.8 81.6 -13.7 0 -7.2
CGCAACTGCCTGAGCTTCTT
1841 SEQ ID N0:562 -16.1 -27.2 74.8 -9.9 -1.1 -5.7
AGGGAGCCACGGATACTCAA
2149 SEQ ID N0:563 -16.1 -25.5 70.7 -8.1 -1.2 -4.5
TGCTTGTTTTGCTATTGCGT
2181 SEQ ID N0:564 -16.1 -24.6 71.7 -6.9 -1.5 -5.8
CTCTTTGCCTTCCAGAGGAA
2565 SEQ ID N0:565 -16.1 -26 73.9 -8.5 -1.3 -5.7
GCAGTCTGAATGATCGCAGT
3018 SEQ ID N0:566 -16.1 -24.4 70.8 -7.6 -0.4 -6.3
GTTCCATTCCCATCTCTAAG
3661 SEQ ID N0:567 -16.1 -25.2 72.6 -9.1 0 -l.6
TTAATACACCCTTCAGTAAA
3976 SEQ ID N0:568 -16.1 -19.5 58.5 -3.4 0 -3.6
GTCATGTATTTGCCCTGGTC
5116 SEQ ID N0:569 -16.1 -26.9 78.3 -10.8 0 -4.7
ATACCCTGCTTCACAGAGTT
6640 SEQ ID N0:570 -16.1 -25.5 73.5 -8.5 -0.7 -5.1
TTTATTCTTACAATATCCCT
341 SEQ ID N0:571 -16 -20.3 61.4 -4.3 0 -2.6
TCCATGGATCACGAAGAAAC
1023 SEQ ID N0:572 -16 -20.3 59 -3.4 0 -9.5
GGCCATGGCCACCACAGCCA
1730 SEQ ID N0:573 -16 -33.7 86 -13.4 -3.l -16.7
GCTCTCTCTGTCTTCTTTTC
1983 SEQ ID N0:574 -16 -25.2 79.4 -9.2 0 -2.8
CCATGGCCATAAAGAGGGTA
2790 SEQ ID N0:575 -16 -24.6 68.6 -7.4 0 -10.4
TAGTGCTCCATGGCCATAAA
2797 SEQ ID N0:576 -l6 -24.7 69.4 -7.4 -0.4 -10.4
ACAATCAGGAAGGAGTGGAA
3259 SEQ ID N0:577 -16 -20.5 61.2 -3.7 -0.6 -4.5
TCCCATCTCTAAGATAATTA
3654 SEQ ID N0:578 -16 -20.1 60.7 -3.4 -0.5 -4.7
107
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TCCATTCCCATCTCTAAGAT
3659 SEQ ID N0:579 -l6 -24.5 70.2 -7.9 -0.3 -3.5
TGTTACCCGTTGTCATGTTA
4566 SEQ ID N0:580 -16 -24.6 71.1 -8.6 0 -4.7
ACTTCTTTTTCTGCTGGTTG
4884 SEQ ID N0:581 -16 -23.4 71.3 -7.4 0 -3.7
ATAAACCTGTCTTCCATCTG
6088 SEQ ID N0:582 -16 -22.4 65.6 -6.4 0 -2
TGGCATGGACCTCCTCTTGA
6549 SEQ ID N0:583 -16 -27.9 77.8 -11.4 -0.1 -5.l
GTCTAGGTAGCCATTGGGTT
6713 SEQ ID N0:584 -16 -26.6 78.7 -10 -0.3 -6.3
ATGGCAGATATGGAAGTTAA
6810 SEQ ID N0:585 -16 -19.4 59.2 -2 -1.3 -5.5
ATCATGCACTAGTTTGTTGT
8610 SEQ ID N0:586 -16 -22.3 68.5 -6.3 0 -5.7
~
TTAAGCTGTTCGAGCATCTG
1810 SEQ ID N0:587 -15.9 -22.7 67.1 -4.5 -2.3 -7.3
GTGCTGTGTTCATCATCAGC
2251 SEQ ID N0:588 -15.9 -25.5 77.3 -6.5 -3.1 -7.7
AAGGTTGTCTGAGCTAAATG
3428 SEQ ID N0:589 -15.9 -19.9 60.9 -4 0 -5.5
.
TATTTCAATTCCAGTATTAT
3623 SEQ ID N0:590 -15.9 -18.2 57.6 -2.3 0 -2.5
TTGCTTATTTCAATTCCAGT
3628 SEQ ID N0:591 -15.9 -21.6 65.2 -5.7 0 -3.6
CTTGTTCACCTTCTCGGGGT
3915 SEQ ID N0:592 -15.9 -27.9 79.4 -11.1 -0.7 -4
CAGACGTAGGATTCGGCCAA
5354 SEQ ID N0:593 -15.9 -25.3 69.4 -8.8 -0.3 -7.2
TCATCCTCACTCAGGGGCTC
5818 SEQ ID N0:594 -15.9 -28.4 82.4 -11.6 -0.8 -7.6
GTTGTAATAGGCTCATAAGA
6130 SEQ ID N0:595 -15.9 -19.8 61.3 -3.9 0 -3.8
AGTCTAGGTAGCCATTGGGT
6714 SEQ ID N0:596 -15.9 -26.5 78.7 -10 -0.3 -6.7
GGGTTCTTGTATACTGTTTC
6929 SEQ TD N0:597 -15.9 -22.6 70.5 -6.7 0 -6.3
TAGGTTTGAGTGTTTGACCA
8092 SEQ TD N0:598 -15.9 -23 69.2 -5.8 -1.2 -5.9
TTTTTTTTTTTTCCACCTTA
9087 SEQ ID N0:599 -15.9 -21.1 64 -5.2 0 -0.2
GCAGCACGTTTTTCGATAGC
541 SEQ ID N0:600 -15.8 -24.9 71.1 -8.1 -0.9 -5.8
TGAATCCATTGTGCCATTAA
1355 SEQ ID N0:601 -15.8 -21.9 63.3 -6.1 0 -3.1
AATGTGCTGTGTTCATCATC
2254 SEQ ID N0:602 -15.8 -22.3 68.1 -6.5 0 -3.l
CTGTTGCGTCGCTCTCCATG
2320 SEQ ID N0:603 -15.8 -28.3 78.2 -12.5 0.4 -6.2
CATGGGGTAGTGCTCCATGG
2804 SEQ ID N0:604 -15.8 -27.4 77.8 -7.9 -3.7 -12.3
AATACACCCTTCAGTAAAAC
3974 SEQ ID N0:605 -15.8 -19.2 57.4 -3.4 0 -3.6
CCAATGCACCACTACTGAGA
4122 SEQ ID N0:606 -15.8 -24.5 68.2 -8.7 0 -5.9
AGTTTACTTTCACGTTTTTC
4650 SEQ ID N0:607 -15.8 -20.5 64 -4.7 0 -4.7
108
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal)
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GCCAGCGCCAACATTATCAA
4670 SEQ ID N0:608 -15.8 -26 70 -9.7 0 -7.6
TTCTGAGGTTTCTTGGATCC
4969 SEQ ID N0:609 -15.8 -24.2 72.8 -7.5 0 -9.6
TAAACATGACCAGGAAGAGC
5454 SEQ ID N0:610 -15.8 -20.2 59.6 -4.4 0 -5.2
CGGTCTCCCTTAACTGAGCT
5674 SEQ ID N0:611 -15.8 -27.3 75.6 -10.9 -0.3 -6.2
GGATCCAGGGCAGCTGCAAA
5917 SEQ ID N0:612 -15.8 -27.6 75.7 -8.9 -0.7 -14
CTTCCATCTGTATTCGAAGG
6078 SEQ ID N0:613 -15.8 -22.7 66.4 -6.9 0 -7.1
ACCTCCTCTTGAAGTCCAGT
6541 SEQ ID N0:614 -15.8 -27.2 77.7 -11.4 0 -3
GGCATGGACCTCCTCTTGAA
6548 SEQ ID N0:615 -15.8 -27.2 75.5 -11.4 0 -5
GACAGGGTTCTTGTATACTG
6933 SEQ ID N0:616 -15.8 -22.3 68 -5.8 -0.4 -6.5
TATTTTTCTAGAATGGATTT
7255 SEQ ID N0:617 -15.8 -17 55.1 -1.1 0 -7.4
TTAATAGAAGTTGTTTATCA
7441 SEQ ID N0:618 -15.8 -16.2 53.4 0.4 0 -2.9
ATCCCTGTTGGAAGCTTGCA
7492 SEQ ID N0:619 -15.8 -27 75.6 -10.1 -1 -7.6
CATCCCTGTTGGAAGCTTGC
7493 SEQ ID N0:620 -15.8 -27 75.6 -10.1 -1 -7.2
ACATGCATTAGTGATAGCCT
7544 SEQ ID N0:621 -15.8 -23.4 68.7 -7.6 0 -6.8
GGTAGAAAATGATCTAGGTT
8106 SEQ ID N0:622 -15.8 -18.7 58.3 -2.2 -0.4 -4.9
ACTTTGCCACTTTGTTCATG
8277 SEQ ID N0:623 -15.8 -23.5 69.2 -7.7 0 -4.1
TTTTTTTTTTTCCACCTTAT
9086 SEQ ID N0:624 -15.8 -21 63.7 -5.2 0 -0.5
CATGGATCACGAAGAAACGT
1021 SEQ ID N0:625 -15.7 -19.9 57.7 -3.4 -0.6 -6
CCATTGTGCCATTAAAGTAG
1350 SEQ ID N0:626 -15.7 -21.8 63.6 -6.l 0 -3.1
TGTCCCATTTGAATCCATTG
1364 SEQ ID N0:627 -15.7 -23.6 67.2 -7.9 0 -2.3
AGCAGCACGTAATGTCAACT
1640 SEQ ID N0:628 -15.7 -22.9 66.3 -7.2 0 -5.4
CTTCAAATGTGCTGTGTTCA
2259 SEQ ID N0:629 -15.7 -22.2 66.6 -6.5 0 -3.6
CCTCTGGGGGAAGTTGTCCA
2472 SEQ ID NO:630 -15.7 -28.5 79.7 -10.8 -2 -6.3
GCCCTCTGGGGGAAGTTGTC
2474 SEQ ID N0:631 -15.7 -29.6 83.2 -11.7 -2.2 -8.7
AGTAGCAGCAAGGTTGTCTG
3437 SEQ ID N0:632 -15.7 -24.2 73.1 -8 -0.2 -7
CTTTGCTTATTTCAATTCCA
3630 SEQ ID N0:633 -15.7 -21.4 64.1 -5.7 0 -3.6
TCACCTTCTCGGGGTAGAAC
3910 SEQ ID N0:634 -15.7 -25.4 72.5 -8.7 -0.9 -4.9
GCACCACTACTGAGAAGGAT
4117 SEQ ID N0:635 -15.7 -23.6 67.7 -7 -0.8 -4.7
TGCACCACTACTGAGAAGGA
4118 SEQ ID N0:636 -15.7 -23.6 67.6 -7 -0.8 -6
109
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CTGAGGGAAACGAGCTTCAG
5194 SEQ ID N0:637 -15.7 -22.6 65 -6.2 -0.5 -5.2
ATCAGACGTAGGATTCGGCC
5356 SEQ ID N0:638 -15.7 -25.7 72 -9.5 -0.2 -5.8
ACCAGGAAGAGCAGGAGGCC
5446 SEQ ID N0:639 -15.7 -27.9 77.1 -11.3 -0.8 -6.4
ACTGGGTCGCATCGGGATCA
5871 SEQ ID N0:640 -15.7 -27.7 76.3 -12 0 -6.9
CCTCCTCTTGAAGTCCAGTT
6540 SEQ ID N0:641 -15.7 -27.1 77.4 -11.4 0 -3
CTTCACTGTCTTGTATAGGC
6602 SEQ ID N0:642 -15.7 -23.4 71.6 -7.7 0 -2.8
TACCCTGCTTCACAGAGTTG
6639 SEQ ID N0:643 -15.7 -25.5 73.3 -8.5 -1.2 -5.1
CCCTATAGTCTAGGTAGCCA
6720 SEQ ID N0:644 -15.7 -27.1 77.6 -10 -1.3 -5.6
GGTGTAGTTACAATGTTCAC
6753 SEQ ID N0:645 -15.7 -21.1 65.4 -4.9 -0.2 -4.6
AAAGGTGTTTGGTGTAGTTA
6763 SEQ ID N0:646 -15.7 -20.7 64.4 -5 ~ 0 -1.9
TAAAGGTGTTTGGTGTAGTT
6764 SEQ ID N0:647 -15.7 -20.7 64.4 -5 0 -2.2
TATGGCAGATATGGAAGTTA
6811 SEQ ID N0:648 -15.7 -19.8 60.7 -3.3 -0.6 -5.5
GGGTATTTAATTGACATAGA
7360 SEQ ID N0:649 -15.7 -18.4 57.7 -2.7 0 -2.9
TCAGGCTATATATATATTTG
7424 SEQ ID N0:650 -15.7 -17.7 56.7 -2 0 -6.7
ATCAGGCTATATATATATTT
7425 SEQ ID N0:651 -15.7 -17.7 56.8 -2 0 -6.7
ACAGGATACATCCCTGTTGG
7501 SEQ ID N0:652 -15.7 -25.1 71.5 -6.7 -2.7 -8
CATGCATTAGTGATAGCCTT
7543 SEQ ID N0:653 -15.7 -23.3 68.5 -7.6 0 -6.8
AAAATGATCTAGGTTTGAGT
8101 SEQ ID N0:654 -15.7 -17.9 56.6 -2.2 0 -4.2
TGGTAGAAAATGATCTAGGT
8107 SEQ ID N0:655 -15.7 -18.6 57.9 -2.2 -0.4 -4.9
AGGCAACCATAGTTGGTAGA
8120 SEQ ID N0:656 -15.7 -23.6 69.1 -5.5 -2.4 -8.7
GTGAATCATGCACTAGTTTG
8614 SEQ ID N0:657 -15.7 -20.9 63.7 -4.6 , -0.3 -5.7
GTGGTTACTACTATTATTAT
8730 SEQ ID N0:658 -15.7 -18.6 59.4 -2.9 0 -3
CTCATTTATTCTTACAATAT
345 SEQ ID N0:659 -15.6 -17 54.9 -1.3 0 -2.4
GTGCCATTAAAGTAGGAAGT
1345 SEQ ID N0:660 -15.6 -21.3 63.5 -5.7 0 -3.5
GTATGTTTTCCCAGCAGCAC
1652 SEQ ID N0:661 -15.6 -26.7 77 -11.1 0 -5.4
TGCTCCATGGCCATAAAGAG
2794 SEQ ID N0:662 -15.6 -24.4 68.4 -7.4 -0.4 -10.8
TCGCAGTACAGACAATCCCT
3005 SEQ ID N0:663 -15.6 -25.6 71.3 -10 0.4 -4.5
GACGATGATGGCCAACACCA
3131 SEQ ID N0:664 -15.6 -25.6 68.6 -9.2 -0.6 -5.8
ACCACAAGGTTTCCAATGAC
3376 SEQ ID N0:665 -15.6 -22.9 65.5 -6.2 -1 -4.6
110
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TCATGGATTTCTATAACTTT
3574 SEQ ID N0:666 -15.6 -18.4 58.1 -2.8 0 -5
TTTTAATACACCCTTCAGTA
3978 SEQ ID N0:667 -15.6 -21.1 63.1 -5.5 0 -3.4
CTGCTGGTTGAAGTTATCTA
4874 SEQ ID N0:668 -15.6 -22 66.8 -6.4 0 -3.6
AAGCAAAGAGCAGCGTGCGG
5394 SEQ ID N0:669 -15.6 -25.1 68.5 -7.3 -2.2 -8.5
ATCTGTATTCGAAGGGCATC
6073 SEQ ID N0:670 -15.6 -22.7 67.2 -7.1 0 -7.l
TTGGTGTAGTTACAATGTTC
6755 SEQ ID N0:671 -15.6 -20.3 63.8 -4.2 -0.2 -4.6
GGTTCTTGTATACTGTTTCT
6928 SEQ ID N0:672 -15.6 -22.3 69.8 -6.7 0 -6.3
AGGGTATTTAATTGACATAG
7361 SEQ ID N0:673 -15.6 -17.8 56.5 -2.2 0 -2.9
TCTAGGTTTGAGTGTTTGAC
8094 SEQ ID N0:674 -15.6 -21.6 67.7 -6 0 -4
TATTGAGGCAACCATAGTTG
8125 SEQ ID N0:675 -15.6 -21.3 63.3 -3.7 -2 -5.6
CCAATAAGTGAAATGCAATA
8478 SEQ ID N0:676 -15.6 -16.9 52.3 -1.2 0 -5.6
ATGCACTAGTTTGTTGTAAA
8607 SEQ ID N0:677 -15.6 -19.5 60.5 -3.9 0 -5.7
CTGCCTGAGCTTCTTCCTGT
1836 SEQ ID N0:678 -15.5 -28.9 82.3 -12.2 -1.1 -5.2
TACTCCACTGAAATCTCTTG
1877 SEQ ID N0:679 -15.5 -20.9 62.6 -5.4 0 -2.5
GACGCTGTCTTCAGATTCGG
2048 SEQ ID N0:680 -15.5 -25.1 71.8 -8.1 -1.4 -6.8
TTGCTATTGCGTCTTGGGGA
2173 SEQ TD N0:681 -15.5 -26 74.3 -8.9 -1.5 -6.6
CTTTGCCCGACCTCTGAAAC
2207 SEQ ID N0:682 -15.5 -26.1 70.1 -10.6 0 -3
CTTTCGCCGTCTTCAAATGT
2269 SEQ ID N0:683 -15.5 -24.4 68.5 -8.9 0 -2.8
CACAATCAGGAAGGAGTGGA
3260 SEQ ID N0:684 -15.5 -21.9 64.5 -5.6 -0.6 -4.5
ATGGTTTGGCCAGCGACCTC
3328 SEQ ID N0:685 -15.5 -29 79.2 -11.7 -1.4 -11.4
TGTCTGAGCTAAATGAACTC
3423 SEQ ID N0:686 -15.5 -19.5 59.9 -4 0 -5.1
GTTGTCTGAGCTAAATGAAC
3425 SEQ TD N0:687 -15.5 -19.5 60 -4 0 -5.1
GCTTATTTCAATTCCAGTAT
3626 SEQ ID N0:688 -15.5 -21.2 64.4 -5.7 0 -2.8
TGCTTATTTCAATTCCAGTA
3627 SEQ ID N0:689 -15.5 -21.2 64.3 -5.7 0 -3.6
TTGTTCACCTTCTCGGGGTA
3914 SEQ ID N0:690 -15.5 -26.7 76.8 -10.2 -0.9 -4.2
AGCTTGTTCACCTTCTCGGG
3917 SEQ ID NO:691 -15.5 -27.3 78 -11.3 -0.2 -4.5
CAGCTTGTTCACCTTCTCGG
3918 SEQ ID N0:692 -15.5 -26.8 76.4 -11.3 0 -4.5
TCTTGACCTCCAAACTTCTT
4897 SEQ ID N0:693 -15.5 -23.4 67.6 -7.4 -O.l -2.7
CAGCGTGCGGATCCCCTTTG
5384 SEQ ID N0:694 -15.5 -30.4 79.1 -14.2 -0.4 -7.5
II1
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/mo1kcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATCTGTTTTTTCTGGAGTGG
6329 SEQ ID N0:695 -15.5 -22.5 69.5 -7 0 -2.7
CTTTTTCTGGTTTGTCTTTC
6417 SEQ TD N0:696 -15.5 -22.3 70.2 -6.8 0 -l.5
TTCTTTTTCTGGTTTGTCTT
6419 SEQ ID N0:697 -15.5 -22.3 70.2 -6.8 0 -1.5
TTGGCATGGACCTCCTCTTG
6550 SEQ ID N0:698 -15.5 -27.4 76.8 -11.4 -0.1 -5.1
AGGGTTCTTGTATACTGTTT
6930 SEQ ID N0:699 -15.5 -22.2 69 -6.7 0 -6.3
TCCCTGTTGGAAGCTTGCAA
7491 SEQ ID N0:700 -15.5 -26.3 73.2 -10.1 -0.5 -7.6
GGACAGAGCAGGTTGAATTC
7647 SEQ ID N0:701 -15.5 -22.7 67.8 -7.2 0 -6.4
TTATATTGAGGCAACCATAG
8128 SEQ TD N0:702 -15.5 -19.8 59.8 -3.7 -0.3 -4
TTTTTTTTTTTTTTTCCACC
9090 SEQ ID N0;703 -15.5 -20.7 63.3 -5.2 0 0
TTTTTTTTTTTTTGACCACA
103 SEQ ID N0;704 -15,4 -19.6 60.4 -4.2 0 -2.1
ATGTCCCATTTGAATCCATT
1365 SEQ ID N0:705 -15,4 -23.6 67,3 -8.2 0 -2.4
CAAATGTGCTGTGTTCATCA
2256 SEQ ID N0:706 -15.4 -21.9 65.5 -6.5 0 -3.6
TCTTCAAATGTGCTGTGTTC
2260 SEQ ID N0:707 -15,4 -21.9 67 -6.5 0 -3.6
ACGTTACTGTTGCGTCGCTC
2326 SEQ ID N0:708 -15.4 -26.5 74,3 -10.4 -0.4 -7.1
CTTTGCCTTCCAGAGGAATC
2563 SEQ ID N0:709 -15.4 -25.1 71.9 -8.5 -1.1 -6
GACCAAGCTCCATTAAACTG
2973 SEQ ID N0:710 -15.4 -22.1 63.1 -6.7 0 -4.5
GGAAGGAGTGGAAGAAGTCG
3252 SEQ TD N0:711 -15.4 -21.5 63.2 -5.6 -0.2 -2.7
CACATGGTTTGGCCAGCGAC
3331 SEQ TD N0:712 -15.4 -27.3 74.8 -10.4 -1.4 -8.8
TATTGCCTTCATGGATTTCT
3582 SEQ ID N0:713 -15.4 -23 68.2 -7.6 0.4 -4.7
TCTTTGCTTATTTCAATTCC
3631 SEQ ID N0:714 -15.4 -21.1 64.4 -5.7 0 -2.9
CCTTTGCCTTCTTCTGTACT
4018 SEQ ID N0:715 -15.4 -26.6 77 -11.2 0 -4.8
GCCAACATTATCAAAGTTTA '
4664 SEQ ID N0:716 -15.4 -19.3 58.4 -3.9 0 -4.1
GATGTCTTGACCTCCAAACT
4901 SEQ ID N0:717 -15.4 -23.7 67.8 -7.4 -0.7 -4.9
TGACCAGGAAGAGCAGGAGG
5448 SEQ ID N0:718 -15.4 -24.7 70.4 -9.3 0 -4.1
GGCATAGATAAACATGACCA
5462 SEQ ID N0:719 -15.4 -20.7 60.5 -4.4 -0.8 -5.2
CCCAGCCAGCAGAGGTTGTA
5586 SEQ ID N0:720 -15.4 -29.7 82.1 -13.4 -0.8 -5.2
GAGGAGGATCCAGGGCAGCT
5922 SEQ ID N0:721 -15.4 -28.9 81.6 -10.9 -2.6 -9.3
TTTTCTGGTTTGTCTTTCTC
6415 SEQ ID N0:722 -15.4 -22.6 71.6 -7.2 0 -1.5
TCCCTATAGTCTAGGTAGCC
6721 SEQ ID N0:723 -15.4 -26.8 78.3 -10 -1.3 -5.6
112
WO 2004/016754 PCT/US2003/025465
kcal/
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTTATCAGGCTATATATATA
7428 SEQ ID N0:724 -15.4 -17.4 56.2 -2 0 -6
AGGTTTGAGTGTTTGACCAA
8091 SEQ ID N0:725 -15.4 -22.6 67.4 -5.9 -1.2 -5.9
TGAGGCAACCATAGTTGGTA
8122 SEQ ID N0:726 -15.4 -23.6 68.7 -5.8 -2.4 -8.7
CTTTGTTCTGTAGTACTGCT
8636 SEQ ID N0:727 -15.4 -23.3 71.8 -7.4 0 -7.8
TTTTTTTTTTCCACCTTATA
9085 SEQ ID N0:728 -15.4 -20.6 62.7 -5.2 0 -1.7
TCTCATTTATTCTTACAATA
346 SEQ ID N0:729 -15.3 -17.4 56.2 -2.1 0 -2.2
AAATTGCCTTTCCTTTATTC
750 SEQ ID N0:730 -15.3 -21.3 63.3 -6 0 -3.2
TTCCCAATAGTCTTGAGTCA
1610 SEQ ID N0:731 -15.3 -23.7 70.2 -7.9 -0.2 -5.5
GGTTCCTCCATTCTTTAGCA
1956 SEQ ID N0:732 -15.3 -26.7 77.7 -10.8 -0.3 -4.7
GCTGTCTTCAGATTCGGATT
2045 SEQ ID N0:733 -15.3 -24.2 71.6 -7.4 -1.4 -5.7
CTGCTTTCGCCGTCTTCAAA
2272 SEQ ID N0:734 -15.3 -25.9 71.3 -9.9 -0.5 -3.6
AACCTTCTCTTTCTGACTTC
2509 SEQ ID N0:735 -15.3 -22.8 68.9 -7.5 0 -2.6
ACATTGGCAAATCTATACCA
2659 SEQ ID N0:736 -15.3 -20.9 61.3 -5.1 -0.2 -4.4
'
TCCCAGATCAAGAACACATT
2674 SEQ ID N0:737 -15.3 -21.9 63.3 -6.6 0 -4.6
ATGGGGTAGTGCTCCATGGC
2803 SEQ ID N0:738 -15.3 -28.5 81.3 -11.2 -2 -8.9
CTCAGTCATGGGGTAGTGCT
2810 SEQ ID N0:739 -15.3 -26.7 79.7 -11.4 0 -4.7
GCGGAACACAATCAGGAAGG
3266 SEQ ID N0:740 -15.3 -22.2 62.9 -6.9 0 -3.4
TAATACACCCTTCAGTAAAA
3975 SEQ ID N0:741 -15.3 -18.7 56.4 -3.4 0 -3.6
TTTTTAATACACCCTTCAGT
3979 SEQ ID N0:742 -15.3 -21.5 64 -6.2 0 -2.6
TCCAAACTTCTTTTTCTGCT
4889 SEQ ID N0:743 -15.3 -22.6 66.9 -7.3 0 -3.6
TGTCTTGACCTCCAAACTTC
4899 SEQ ID N0:744 -15.3 -23.6 68.4 -7.4 , -0.7 -4.9
GGGTTTCTGAGGTTTCTTGG
4973 SEQ ID N0:745 -15.3 -24.9 75.4 -9.6 0 -2.5
GGAAGAGCAGGAGGCCGATG
5442 SEQ ID N0:746 -15.3 -26.4 72.6 -10.2 -0.8 -7.7
ATTTTTCTAGAATGGATTTA
7254 SEQ ID N0:747 -15.3 -17 55.1 -1.1 0 -7.7
TAGGGTATTTAATTGACATA
7362 SEQ ID N0:748 -15.3 -17.5 55.8 -2.2 0 -2.9
TATCAGGCTATATATATATT
7426 SEQ ID N0:749 -15.3 -17.3 55.9 -2 0 -6.7
TTATCAGGCTATATATATAT
7427 SEQ ID N0:750 -15.3 -17.3 55.9 -2 0 -6.5
GTTGGTAGAAAATGATCTAG
8109 SEQ ID N0:751 -15.3 -17.5 55.7 -2.2 0.1 -4.9
TAGTTGGTAGAAAATGATCT
8111 SEQ ID N0:752 -15.3 -17.5 55.7 -2.2 0 -4.9
113
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGCCCAATAAGTGAAATGCA
8481 SEQ ID N0:753 -15.3 -21.7 61.7 -6.4 0 -5.2
GTAGTACTGCTTGGTGAATC
8627 5EQ ID N0:754 -15.3 -22.4 68.4 -7.1 0 -7
TTTTTTTTTCCACCTTATAT
9084 SEQ ID N0:755 -15.3 -20.5 62.4 -5.2 0 -2
TCCAGCCAGTTCCATGGATC
1033 SEQ ID N0:756 -15.2 -28.2 79.3 -11.7 -l -10
CCTGCATCTGAGCCATTTCC
1483 SEQ ID N0:757 -15.2 -28.4 78.5 -12.7 -0.1 -4.9
CCAATAGTCTTGAGTCATGA
1607 SEQ ID N0:758 -15.2 -21.8 65.6 -6.1 -0.2 -7.3
GGAGCCACGGATACTCAAGA
2147 SEQ ID N0:759 -15.2 -24.9 69.5 -8.4 -1.2 -4.5
TCTTTGCCTTCCAGAGGAAT
2564 SEQ ID N0:760 -15.2 -25.1 71.9 -8.5 -1.3 -6
ACGGCTCTTTGCCTTCCAGA
2569 SEQ ID N0:761 -15.2 -28.9 79.4 -11 -2.7 -6.4
CCAACACCAAGGTGAGGTTT
3120 SEQ ID N0:762 -15.2 -24.7 69.3 -8.4 -0.8 -9.7
TTGTCTGAGCTAAATGAACT
3424 SEQ ID N0:763 -15.2 -19.2 58.9 -4 0 -5.1
TGGTTCCATTCCCATCTCTA
3663 SEQ ID N0:764 -15.2 -27.1 77.3 -11.9 0 -4.8
TTCCAGAATGAATATATAGG
4214 SEQ ID N0:765 -15.2 -17.3 54.4 -2.l 0 -4.2
AAACATGTTACCCGTTGTCA
4571 SEQ ID N0:766 -15.2 -23.1 65.6 -7.2 0 -9
GTGCAAGATAGCCAGCGCCA
4680 SEQ ID N0:767 -15.2 -28.9 77.5 -12.9 -0.6 -7.7
AGGCTGAAGTTTAACATCTC
4760 SEQ ID N0:768 -15.2 -20.8 63.7 -5.6 0 -4.6
CTTGACCTCCAAACTTCTTT
4896 SEQ ID N0:769 -15.2 -23.1 66.5 -7.4 -0.1 -2.7
TGAGGGAAACGAGCTTCAGC
5193 SEQ ID N0:770 -15.2 -23.5 67.2 -8.3 0.4 -5.3
GTCTGAGGGAAACGAGCTTC
5196 SEQ ID N0:771 -15.2 -23.5 68.3 -8.3 0 -5.2
GTGCGGATCCCCTTTGCTCC
5380 SEQ ID N0:772 -15.2 -32.2 85.1 -16.3 -0.4 -7.5
AGCAAAGAGCAGCGTGCGGA
5393 SEQ ID N0:773 -15.2 -26.4 71.8 -9 , -2.2 -8.5
GACCAGGAAGAGCAGGAGGC
5447 SEQ ID N0:774 -15.2 -26.5 74.9 -10.6 -0.4 -4.8
TTCAAAGTGGTTGTAATAGG
6139 SEQ ID N0:775 -15.2 -18.6 58.3 -2.7 -0.4 -3.8
GACCTCCTCTTGAAGTCCAG
6542 SEQ ID N0:776 -15.2 -26.6 75.5 -11.4 0 -3.3
CTATAGTCTAGGTAGCCATT
6718 SEQ ID N0:777 -15.2 -23.2 70.3 -7.4 -0.3 -4.6
ATATTTTTCTAGAATGGATT
7256 SEQ ID N0:778 -15.2 -16.9 54.7 -1.1 0 -7.7
TCAGCTTTGCTGAGAGCAGA
7337 SEQ ID N0:779 -15.2 -25 74 -6.7 -3.1 -11.4
TTTAATAGAAGTTGTTTATC
7442 SEQ ID N0:780 -15.2 -15.6 52.4 0.4 0 -2.5
GGTTTGAGTGTTTGACCAAT
8090 SEQ ID N0:781 -15.2 -22.6 67.1 -6.7 -0.4 -5.1
114
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GAGCCCAATAAGTGAAATGC
8482 SEQ ID N0:782 -15.2 -21.6 61.8 -6.4 0 -3.3
CAGGTATCTCATCCCTGTCA
268 SEQ ID N0:783 -15.1 -26.8 77.9 -10.4 -1.2 -4.9
ATTTATTCTTACAATATCCC
342 SEQ ID N0:784 -15.1 -19.4 59.4 -4.3 0 -2.6
GAATCCATTGTGCCATTAAA
1354 SEQ ID N0:785 -15.1 -21.2 61.4 -6.1 0 -3.1
GACCAGCCTTCACACAGATG
1521 SEQ ID N0:786 -15.1 -25.8 72.5 -10.7 0 -2.6
TCAAATGTGCTGTGTTCATC
2257 SEQ ID N0:787 -15.1 -21.6 65.8 -6.5 0 -3.6
CGTCTTCAAATGTGCTGTGT
2262 SEQ ID N0:788 -15.1 -23.4 68.6 -8.3 0 -3.6
CCAAGCTCCATTAAACTGAG
2971 SEQ ID N0:789 -15.1 -21.9 62.8 -6.8 0 -5
TAACTTTTGGCTTTCTAAAA
3561 SEQ ID N0:790 -15.1 -17.4 54.8 -1.6 -0.4 -4.3
ATTTCAATTCCAGTATTATT
3622 SEQ ID N0:791 -15.1 -18.6 58.5 -3.5 0 -2.3
TTATTTCAATTCCAGTATTA
3624 SEQ ID N0:792 -15.1 -18.3 57.9 -3.2 0 -2.5
ATACACCCTTCAGTAAAACA
3973 SEQ ID N0:793 -15.1 -20.6 60.4 -5.5 0 -3.6
ATGCACCACTACTGAGAAGG
4119 SEQ ID N0:794 -15.1 -23 66.3 -7 -0.8 -6.8
ATGGTTTTGATAGTCTTTCG
4168 SEQ ID N0:795 -15.1 -20.9 64.3 -5.8 0 -2.9
CTGAGGTTTCTTGGATCCAA
4967 SEQ ID N0:796 -15.1 -23.7 69.4 -6.9 -0.2 -11.5
GCATAGATAAACATGACCAG
5461 SEQ ID N0:797 -15.1 -19.5 58.3 -4.4 0 -5.2
ACGGTCTCCCTTAACTGAGC
5675 SEQ ID N0:798 -15.1 -26.6 74.3 -10.9 -0.3 -3.7
GTCGCATCGGGATCAAACTT
5866 SEQ ID N0:799 -15.1 -24 67.3 -8.9 0 -6.9
AATCCTCCCTTTAATTGCCT
6260 SEQ ID N0:800 -15.1 -25.9 71.2 -10.8 0 -3
CCATTTAGTTTGTCAATAAT
6304 SEQ ID N0:801 -15.1 -18.6 57.8 -3.5 0 -2.9
TTTCTGGTTTGTCTTTCTCA
6414 SEQ ID N0:802 -15.1 -23.2 72.5 -8.1 0 -1.7
TTGATACCCTGCTTCACAGA
6643 SEQ ID N0:803 -15.1 -24.9 71 -8.5 -1.2 -3.8
CAGCTTTGCTGAGAGCAGAA
7336 SEQ ID N0:804 -15.1 -23.9 69.8 -6.7 -2.1 -10.5
GAAAATGATCTAGGTTTGAG
8102 5EQ ID N0:805 -15.1 -17.3 54.9 -2.2 0 -4.9
AGAAAATGATCTAGGTTTGA
8103 SEQ ID N0:806 -15.1 -17.3 54.9 -2.2 0 -4.9
GTACTGCTTGGTGAATCATG
8624 SEQ ID N0:807 -15.1 -22.2 66.4 -7.1 0 -4.6
AGTACTGCTTGGTGAATCAT
8625 SEQ ID N0:808= -15.1 -22.2 66.8 -7.1 0 -5.5
GTTCAGCTTTTTTTTTTTTT
118 SEQ ID N0:809 -15 -20.3 64.5 -5.3 0 -4.5
CGTGTAGCTTCTTGCATACG
428 SEQ ID N0:810 -15 -24.3 69.7 -7.5 -1.8 -6.3
115
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TATAAGTGACTCAAAGGTAT
965 SEQ ID N0:811 -15 -17.4 55.3 -2.4 0 -3.3
GCCTGCATCTGAGCCATTTC
1484 SEQ ID N0:812 -15 -28.2 79.4 -12.7 -0.1 -4.9
TAAAGATTTTCCCAATAGTC
1618 SEQ ID N0:813 -15 -18.9 58 -3.9 0 -3.2
CCACCTACTCCACTGAAATC
1882 SEQ ID N0:814 -15 -24.4 67.9 -9.4 0 -1.7
GTCTGAGCTAAATGAACTCA
3422 SEQ ID N0:815 -15 -20.2 61.2 -4 -1.1 -4.6
GCTCTTTGCTTATTTCAATT
3633 SEQ ID N0:816 -15 -21.4 65.3 -5.7 -0.4 -3.6
TTCGGGTTCAGTTTCAGCTT
3932 SEQ ID N0:817 -15 -25.4 75.6 -10.4 0 -4.5
AAGTTTACTTTCACGTTTTT
4651 SEQ ID N0:818 -15 -19.4 60.3 -3.9 -0.1 -4.9
TGCAAGATAGCCAGCGCCAA
4679 SEQ ID N0:819 -15 -27 72.1 -11.2 -0.6 -7.7
GCGGATCCCCTTTGCTCCTT
5378 SEQ TD N0:820 -15 -32 84.1 -16.3 -0.4 -7.5
GTTTCAAAGTGGTTGTAATA
6141 SEQ ID N0:821 -15 -18.7 58.9 -3 -0.4 -3.8
TTTCTTTTTCTGGTTTGTCT
6420 SEQ ID N0:822 -15 -22.3 70.2 -7.3 0 -1.5
TGATACCCTGCTTCACAGAG
6642 SEQ ID N0:823 -15 -24.8 70.9 -8.5 -1.2 -3.7
AACGTTGATACCCTGCTTCA
6647 SEQ ID N0:824 -15 -24.9 69.3 -9.9 0 -6.4
GGCAACCATAGTTGGTAGAA
8119 SEQ ID N0:825 -15 -22.9 66.6 -5.5 -2.4 -8.7
GCTTGGTGAATCATGCACTA
8619 SEQ ID N0:826 -15 -23.5 68.8 -7.2 -1.2 -5.5
AAAGCTGCTTTTAATTTGCC
8655 SEQ ID N0:827 -15 -21.3 62.7 -5 -0.1 -10.6
ATATTGAAAGAAGATGAGTT
8798 SEQ ID N0:828 -15 -15.4 50.7 0 0 -1.8
TGTTCAGCTTTTTTTTTTTT
119 SEQ ID N0:829 -14.9 -20.2 64 -5.3 0 -4.3
TTATTCTTACAATATCCCTA
340 5EQ ID N0:830 -14.9 -19.9 60.5 -5 0 -2.6
TCTTGCATACGAATTACCTT
419 SEQ ID N0:831 -14.9 -21.5 62.7 -6.6 , 0 -5.1
TTCTTGCATACGAATTACCT
420 SEQ ID N0:832 -14.9 -21.5 62.7 -6.6 0 -5.1
TTATAAGTGACTCAAAGGTA
966 SEQ ID N0:833 -14.9 -17.5 55.7 -2.6 0 -3.5
CATTGTGCCATTAAAGTAGG
1349 SEQ ID N0:834 -14.9 -21 62.4 -6.1 0 -3.4
TGATGCTGCCGCAACTGCCT
1850 SEQ ID N0:835 -14.9 -29.5 77.4 -13 -1.6 -8
ATGCTTCTGAAGAACTTTCC
1917 SEQ ID N0:836 -14.9 -21.6 64.4 -6 -0.4 -8.3
AGCAGTCTGAATGATCGCAG
3019 SEQ ID N0:837 -14.9 -23.2 67.8 -7.6 -0.4 -6.3
TTCATGGATTTCTATAACTT
3575 SEQ ID N0:838 -14.9 -18.4 58.1 -3.5 0 -5
GTGGTTCCATTCCCATCTCT
3664 SEQ ID N0:839 -14.9 -28.6 81.6 -13 -0.4 -5.5
116
CA 02495398 2005-02-10
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kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GGCTGGGGTTGTTTATGAAT
3747 SEQ ID N0:840 -14.9 -23.8 69.9 -8.9 0 -3.7
GTGAGGCTGGGGTTGTTTAT
3751 SEQ ID N0:841 -14.9 -25.7 76.4 -10.8 0 -2.9
CTTCGGGTTCAGTTTCAGCT
3933 SEQ ID N0:842 -14.9 -26.2 77.3 -11.3 0 -4.3
CAATACTGTAGCAGGTTTTT
4059 SEQ ID N0:843 -14.9 -2l 64.1 -6.1 0.2 -4.5
CATATTCTAGCATGGTTTTG
4179 SEQ ID N0:844 -14.9 -20.7 63.6 -5.8 0 -5
GTTTACTTTCACGTTTTTCC
4649 SEQ ID N0:845 -14.9 -22.5 67.7 -7.6 0 -4.7
ATGTCTTGACCTCCAAACTT
4900 SEQ ID N0:846 -14.9 -23.2 66.9 -7.4 -0.7 -4.9
GTGTCTGAGGGAAACGAGCT
5198 SEQ ID N0:847 -14.9 -24.2 69.5 -9.3 0.6 -5.5
TGCGGATCCCCTTTGCTCCT
5379 SEQ ID N0:848 -14.9 -31.9 83.5 -16.3 -0.4 -7.5
TGGCATAGATAAACATGACC
5463 SEQ ID N0:849 -14.9 -20 59.3 -4.4 -0.4 -5.2
GTCATCCTCACTCAGGGGCT
5819 5EQ ID N0:850 -14.9 -29.2 84.3 -13.8 -0.2 -7.6
CATAAACCTGTCTTCCATCT
6089 SEQ ID N0:851 -14.9 -23.1 66.9 -8.2 0 -2
CTAGGTAGCCATTGGGTTTC
6711 SEQ ID N0:852 -14.9 -25.5 75.4 -l0 -0.3 -6.3
TCTAGGTAGCCATTGGGTTT
6712 SEQ ID N0:853 -14.9 -25.5 75.4 -10 -0.3 -6.3
AGACAGGGTTCTTGTATACT
6934 SEQ ID N0:854 -14.9 -22.3 68.4 -6.7 -0.4 -6.5
CCAAGACTTGTGAAGAATGG
7597 SEQ ID N0:855 -14.9 -20 59.3 -4.6 -0.2 -5.4
ATTTATATCATGTTAGGTAA
8304 SEQ ID N0:856 -14.9 -17.1 55.6 -2.2 0 -4.7
AATTTATATCATGTTAGGTA
8305 SEQ ID N0:857 -14.9 -17.1 55.6 -2.2 0 -4.7
TTTTTTTTCCACCTTATATA
9083 SEQ TD N0:858 -14.9 -20.1 61.4 -5.2 0 -3.2
TTCTTTCTCTGTGGATAAGA
51 SEQ ID N0:859 -14.8 -20.8 64.7 -5.2 -0.6 -3.9
TTTTTTTTTTTTTTGACCAC
104 SEQ ID N0:860 -14.8 -19 59.5 -4.2 0 -1.7
TCGGAAAATTGCCTTTCCTT
755 SEQ ID N0:861 -14.8 -23.3 65.2 -6 -2.5 -7.5
GGAGGGTTGCTCAAGGTCAT
904 SEQ ID N0:862 -14.8 -26.1 76.5 -9.3 -2 -4.7
CTTCTGGACACTGGCCTGCA
1497 SEQ ID N0:863 -14.8 -28.5 79.2 -13.7 0 -7.2
CTGTTGCTTTTTAAGCTGTT
1820 SEQ ID N0:864 -14.8 -22.3 67.7 -5.6 -1.9 -6.4
CCCACCTACTCCACTGAAAT
1883 SEQ ID N0:865 -14.8 -26 69.8 -11.2 0 -1.7
TTCAAATGTGCTGTGTTCAT
2258 SEQ ID N0:866 -14.8 -21.3 64.6 -6.5 0 -3.6
GCCTGACTAACGTTACTGTT
2335 SEQ ID N0:867 -14.8 -23.8 68.2 -8.5 0 -7.8
TCCTCCAGCATCTCCATTGA
2545 SEQ TD N0:868 -14.8 -28 78.5 -13.2 p -4.1
117
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TCATGGGGTAGTGCTCCATG
2805 SEQ ID N0:869 -14.8 -26.6 77 -7.9 -3.9 -12.7
GATCGCAGTACAGACAATCC
3007 SEQ ID N0:870 -14.8 -23.3 67.1 -7.8 -0.4 -5.3
CAACACCAAGGTGAGGTTTC
3119 SEQ ID N0:871 -14.8 -23.1 67.2 -7.2 -0.8 -9.6
GCCAACACCAAGGTGAGGTT
3121 SEQ ID N0:872 -14.8 -26.4 73 -10 -l.3 -10.8
GAAACACTCCCGCATCTTAT
3530 SEQ ID N0:873 -14.8 -24 66.6 -9.2 0 -3.6
TTGCCTTCATGGATTTCTAT
3580 SEQ ID N0:874 -14.8 -23 68.2 -7.6 -0.3 -5
ATTGCCTTCATGGATTTCTA
3581 SEQ ID N0:875 -14.8 -23 68.2 -7.6 -0.3 -4.7
TTTGCTTATTTCAATTCCAG
3629 SEQ ID N0:876 -14.8 -20.5 62.4 -5.7 0 -3.6
ATGAAAGTCTCAAACCAGTT
4087 SEQ ID N0:877 -14.8 -19.6 59.2 -4.2 -0.3 -3.5
CAATGCACCACTACTGAGAA
4121 SEQ 2D N0:878 -14.8 -21.8 62.7 -7 0 -5.9
AAAGTTGGACATCCCAAAGA
5483 SEQ ID N0:879 -14.8 -20.9 60.5 -3.9 -2.2 -5.7
CTGGGTCGCATCGGGATCAA
5870 SEQ ID N0:880 -14.8 -26.8 73.3 -12 0 -6.9
AGGATCCAGGGCAGCTGCAA
5918 SEQ ID N0:881 -14.8 -28.3 78.5 -10.6 -l -14
CCTGCTTCACAGAGTTGCAG
6636 SEQ ID N0:882 -14.8 -26.1 75.5 -9.4 -1.9 -7.4
GTAGTTACAATGTTCACTTT
6750 SEQ ID N0:883 -14.8 -19.8 62.2 -5 0 -5.6
TATATTTTTCTAGAATGGAT
7257 SEQ ID N0:884 -14.8 -16.5 53.8 -1.l 0 -7.7
ATATATTTTTCTAGAATGGA
7258 SEQ ID N0:885 -14.8 -16.5 53.8 -1.1 0 -7.7
GATATATTTTTCTAGAATGG
7259 SEQ ID N0:886 -14.8 -16.5 53.8 -1.1 0 -7.7
ATTTAATAGAAGTTGTTTAT
7443 SEQ ID N0:887 -14.8 -15.2 51.1 0.4 0 -2.5
CTAGGTTTGAGTGTTTGACC
8093 SEQ ID N0:888 -14.8 -23.2 70.1 -7.9 -0.1 -3.8
TACTGCTTGGTGAATCATGC
8623 SEQ ID N0:889 -14.8 -22.8 67.4 -7.l , -0.8 -4.6
TAGTACTGCTTGGTGAATCA
8626 SEQ ID N0:890 -14.8 -21.9 66.3 -7.1 0 -6
GCTGCTTTTAATTTGCCTTT
8652 SEQ ID N0:891 -14.8 -23.8 69.3 -9 0 -52
TTTTTTTTTTTTTTTGACCA
105 SEQ ID N0:892 -14.7 -18.9 59.3 -4.2 0 -1.7
TGCCTTTCCTTTATTCATTA
746 SEQ TD N0:893 -14.7 -23.1 68.3 -8.4 0 -3
GAAAATTGCCTTTCCTTTAT
752 SEQ ID N0:894 -14.7 -20.7 60.9 -6 0 -3.2
CTGGACACTGGCCTGCATCT
1494 SEQ ID N0:895 -14.7 -28.4 78.7 -13.7 0 -72
AGTCTTGAGTCATGAGTCGA
1602 SEQ ID N0:896 -14.7 -23.1 70.4 -6.7 0 -11.6
AAATGTGCTGTGTTCATCAT
2255 SEQ ID N0:897 -14.7 -21.2 64.2 -6.5 0 -3.6
118
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGGAGTGGAAGAAGTCGTTC
3249 SEQ ID NO:898 -14.7 -22.1 66.5 -6.9 -0.2 -3.1
GGTTTGGCCAGCGACCTCCA
3326 SEQ ID N0:899 -14.7 -31.7 83.8 -15.7 -0.3 -10.6
TGGTTTGGCCAGCGACCTCC
3327 SEQ ID N0:900 -14.7 -31 82.6 -14.6 -l -11.4
TTGGAAACACTCCCGCATCT
3533 SEQ TD N0:901 -14.7 -25.5 69.4 -9.7 -1 -4.8
TCAGCTTGTTCACCTTCTCG
3919 SEQ ID NO:902 -14.7 -26 75.5 -11.3 0 -4.5
CCAGAATGAATATATAGGTA
4212 SEQ ID N0:903 -14.7 -17.7 55.2 -3 0 -4.2
CTGAGCTGCCAGGGTGAATT
5661 SEQ ID No:904 -14.7 -26.3 74.2 -11.1 0 -7.8
TCTGTATTCGAAGGGCATCC
6072 SEQ ID N0:905 -14.7 -24.7 70.9 -10 0 -7.2
CTTGTTTACGTTTCAAAGTG
6150 SEQ ID N0:906 -14.7 -19.4 59.6 -4.7 0 -4.8
TCTTTTTCTGGTTTGTCTTT
6418 SEQ ID N0:907 -14.7 -22.3 70.2 -7.6 0 -1.5
GTTGATACCCTGCTTCACAG
6644 SEQ ID NO:908 -14.7 -25.5 73 -9.9 -0.8 -3.6
GCAGATATGGAAGTTAAAAA
6807 SEQ ID N0:909 -14.7 -16.1 51.4 0 -1.3 -5.5
TTTAGATATATTTTTCTAGA
7263 SEQ TD N0:910 -14.7 -15.9 53.4 -1.1 0 -5.4
GTTTGAGTGTTTGACCAATG
8089 SEQ ID N0:911 -14.7 -21.4 64.4 -6.2 -0.2 -3.4
GTAGAAAATGATCTAGGTTT
8105 SEQ ID N0:912 -14.7 -17.6 56 -2.2 -0.4 -4.9
AGTTGGTAGAAAATGATCTA
8110 SEQ ID N0:913 -14.7 -17.5 55.7 -2.2 -0.2 -4.9
AAAGGTTATATTGAGGCAAC
8133 SEQ ID N0:914 -14.7 -18.4 56.9 -3.7 0 -4
TGCTTGGTGAATCATGCACT
8620 SEQ ID N0:915 -14.7 -23.8 69.2 -7.2 -1.9 -6.4
GAAGATGAGTTTAGATGCTT
8789 SEQ ID N0:916 -14.7 -19.6 60.9 -4.9 0 -3.6
ACGTGTAGCTTCTTGCATAC
429 SEQ ID N0:917 -14.6 -23.7 70.2 -7.5 -1.5 0
CTGTGCCATCTTTTCATCCT
461 SEQ ID N0:918 -14.6 -26.6 76.5 -l2 0 -3
CTGCAAACATTTATTCCTCA
1289 SEQ ID N0:919 -14.6 -21.3 62.7 -6.7 0 -4.9
TCATGTATGTTTTCCCAGCA
1656 SEQ ID N0:920 -14.6 -25.1 73.1 -10.5 0 -4.7
GAGCTTCTTCCTGTTGCTTT
1830 SEQ ID N0:921 -14.6 -26.3 78 -10.8 -0.7 -5.2
CCGCAACTGCCTGAGCTTCT
1842 SEQ ID N0:922 -14.6 -29.1 77.8 -13.3 -1.1 -5.7
GGAGTGGAAGAAGTCGTTCA
3248 SEQ ID N0:923 -14.6 -22.8 67.5 -6.9 -1.2 -4.1
AAGGCACATGGTTTGGCCAG
3335 SEQ ID N0:924 -14.6 -26.2 73.5 -8.4 -3.2 -9.6
CTTATTTCAATTCCAGTATT
3625 SEQ ID N0:925 -14.6 -19.5 60.5 -4.9 0 -2.5
CTCTTTGCTTTCTTCTAGTT
3845 SEQ TD N0:926 -14.6 -23 71.7 -8.4 0 -4
119
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAGAAATCTAGCCAGCACCA
4285 SEQ ID N0:927 -14.6 -23.4 66 -8.8 0 -4.6
AGATGTCTTGACCTCCAAAC
4902 SEQ ID N0:928 -14.6 -22.8 66.2 -7.4 -0.6 -4.9
GAGGATCATGATGCTGATAT
5057 SEQ ID N0:929 -14.6 -21.1 63.6 -5.6 -0.6 -8.5
TGAGGATCATGATGCTGATA
5058 SEQ ID N0:930 -14.6 -21.1 63.5 -5.6 -0.7 -7.9
GATAAACATGACCAGGAAGA
5456 SEQ ID N0:931 -14.6 -19 56.9 -4.4 0 -5.2
TTGCCAAAGGTCTCAAAGTT
5542 SEQ ID N0:932 -14.6 -21.9 64.3 -7.3 0 -4
TCCTCACTCAGGGGCTCTGC
5815 SEQ ID N0:933 -14.6 -30 86 -13.3 -2.1 -7.7
GCATGGACCTCCTCTTGAAG
6547 SEQ ID N0:934 -14.6 -26 73.2 -11.4 0 -5.1
GAGACAGGGTTCTTGTATAC
6935 SEQ ID N0:935 -14.6 -22 67.8 -6.7 -0.4 -7.4
TACTTTAGATATATTTTTCT
7266 SEQ ID N0:936 -14.6 -16.4 54.4 -1.8 0 -4.3
CCCTGTTGGAAGCTTGCAAA
7490 SEQ ID N0:937 -14.6 -25.2 69.4 -10.1 -0.2 -7.2
TTGGTAGAAAATGATCTAGG
8108 SEQ ID N0:938 -14.6 -17.5 55.3 -2.2 -0.4 -4.9
TAGGTGGTTACTACTATTAT
8733 SEQ ID N0:939 -14.6 -19.7 62 -4.6 -0.1 -3.9
TATTGAAAGAAGATGAGTTT
8797 SEQ ID NO:940 -14.6 -15.5 51 -0.8 0 -2.3
TATATTGAAAGAAGATGAGT
8799 SEQ ID N0:941 -14.6 -l5 49.9 0 0 -2.2
TTCATCCTGCACATTTAATT
449 SEQ ID N0:942 -14.5 -21.2 63.2 -6.7 0 -4.8
CGGAAAATTGCCTTTCCTTT
754 SEQ ID N0:943 -14.5 -23 64.2 -6 -2.5 -7.5
TAAGCAAAACCCTCTTGCCA
992 SEQ ID N0:944 -14.5 -24.4 66.6 -7.9 -2 -6.2
CTGAGACATTGCCCAGGTCC
1092 SEQ ID N0:945 -14.5 -28.4 78.4 -13.2 -0.5 -4.4
AATCCATTGTGCCATTAAAG
1353 SEQ ID N0:946 -14.5 -20.6 60.4 -6.1 0 -3.1
AGCACGTAATGTCAACTGGT
1637 SEQ ID NO:947 -14.5 -22.8 66.3 -8.3 0 -4.8
TGAGCTTCTTCCTGTTGCTT
1831 SEQ ID N0:948 -14.5 -26.2 77.3 -10.8 -0.7 -5.2
CTCAACTTTGATGCTTCTGA
1927 SEQ ID N0:949 -14.5 -21.9 65.6 -7.4 0 -5
AGATCCAACATCCTTTGCCC
2219 SEQ ID N0:950 -14.5 -27.2 74.2 -12.2 -0.1 -4.5
TCCTGCTTTCGCCGTCTTCA
2274 SEQ ID N0:951 -14.5 -29.7 81.1 -14.5 -0.5 -3.6
ACTAACGTTACTGTTGCGTC
2330 SEQ ID N0:952 -14.5 -22.7 66.2 -7.2 -0.9 -7.8
GCATCACAGCAGTCCCAGAT
2686 SEQ ID N0:953 -14.5 -27.9 78.7 -12.9 -0.1 -4.2
TCTTATTGCCTTCATGGATT
3585 SEQ ID N0:954 -14.5 -23 68.2 -7.9 -0.3 -4.7
CATTCCCATCTCTAAGATAA
3657 SEQ ID N0:955 -14.5 -21.1 62.4 -5.9 -0.5 -3.9
120
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CACCTTCTCGGGGTAGAACA
3909 SEQ ID N0:956 -14.5 -25.7 72 -10.2 -0.9 -4.9
AGACGTAGGATTCGGCCAAT
5353 SEQ ID N0:957 -14.5 -24.6 68.3 -9.5 -0.3 -7.5
CATAGATAAACATGACCAGG
5460 5EQ ID N0:958 -14.5 -18.9 56.9 -4.4 0 -5.2
CAGATGGGTCCCCACGGTCT
5688 SEQ ID N0:959 -14.5 -30.7 82.2 -15.3 -0.6 -8.8
ACTTTTGATTTTCTCTGACC
6453 SEQ ID N0:960 -14.5 -21.7 65.9 -7.2 0 -2.4
GACACATATACTTTACCTTC
6520 SEQ ID N0:961 -14.5 -20.4 62.1 -5.9 0 -2.4
GTTGACACATATACTTTACC
6523 SEQ ID N0:962 -14.5 -20.3 61.7 -5.8 0 -2.9
AAATTTATATCATGTTAGGT
8306 SEQ ID N0:963 -14.5 -16.7 54.2 -2.2 0 -4.7
AGATGAGTTTAGATGCTTAT
8787 SEQ ID N0:964 -14.5 -19.4 61.1 -4.9 0 -3.6
TTTTTTTTCTTTCTTTCTCT
61 SEQ ID N0:965 -14.4 -20.3 65.4 -5.9 0 0
AGGGTATAACGTGTCTTCCT
147 SEQ ID N0:966 -14.4 -24.4 71.2 -10 0 -5.3
GTATCTCATCCCTGTCAAAC
265 SEQ ID N0:967 -14.4 -23.7 69.4 -9.3 0 -1.8
TTTTTGGGCTTCTTGGCTTT
568 SEQ ID N0:968 -14.4 -25.1 74.3 -9.7 -0.9 -3.7
TTTATAAGTGACTCAAAGGT
967 SEQ ID N0:969 -14.4 -17.9 56.6 -3.5 0 -4.7
CACTGCAAACATTTATTCCT
1291 SEQ ID N0:970 -14.4 -21.1 61.9 -6.7 0 -4.9
GGACACTGGCCTGCATCTGA
1492 SEQ ID N0:971 -14.4 -28.1 78.1 -13.7 0 -7.2
TAGTCTTGAGTCATGAGTCG
1603 SEQ ID N0:972 -14.4 -22.2 68.3 -6.1 0 -11.5
GGGAGCCACGGATACTCAAG
2148 SEQ ID N0:973 -14.4 -25.5 70.7 -9.8 -1.2 -4.5
GTCTGTGCGGCACAAACAGT
2301 SEQ ID N0:974 -14.4 -25.6 72.2 -8.6 -1.4 -13.2
TAACGTTACTGTTGCGTCGC
2328 SEQ ID N0:975 -14.4 -24.2 68.1 -8.8 -0.9 -7.6
TCAGTCATGGGGTAGTGCTC
2809 SEQ ID N0:976 -14.4 -26.2 79.5 -11.8 0 -4.l
TGCCTTCATGGATTTCTATA
3579 SEQ ID N0:977 -14.4 -22.6 67.3 -7.6 -0.3 -5
ATCTTATTGCCTTCATGGAT
3586 SEQ ID N0:978 -14.4 -22.9 67.8 -7.9 -0.3 -4.7
TCTTTGCTTTCTTCTAGTTC
3844 SEQ ID N0:979 -14.4 -22.5 71.4 -8.1 0 -4
GTTACCCGTTGTCATGTTAA
4565 SEQ ID N0:980 -14.4 -23.9 68.9 -9.5 0 -4.7
TGACCTCCAAACTTCTTTTT
4894 SEQ ID N0:981 -14.4 -22.3 65 -7.9 0 -2.1
GAGGTATGGGTTTCTGAGGT
4980 SEQ ID N0:982 -14.4 -24.8 75.1 -10.4 0 -2.8
TGATCAGACGTAGGATTCGG
5358 SEQ ID N0:983 -14.4 -22.5 65.4 -7.6 -0.2 -6.6
ATAGATAAACATGACCAGGA
5459 SEQ ID N0:984 -14.4 -18.8 56.9 -4.4 0 -5.2
121
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TCTGTTTTTTCTGGAGTGGA
6328 SEQ ID N0:985 -14.4 -23.1 71 -87 0 -2.7
CTCCCATCTGTTTTTTCTGG
6334 SEQ ID N0:986 -14.4 -25.5 74.4 -11.1 0 -3.2
TAGTCTAGGTAGCCATTGGG
6715 SEQ ID N0:987 -14.4 -25 74.3 -10 -0.3 -6.3
ATACATCCCTGTTGGAAGCT
7496 SEQ ID N0:988 -14.4 -25 71.1 -9.9 -0.5 -6.8
GACATAATGGACAGAGCAGG
7655 SEQ ID N0:989 -14.4 -21.5 63.6 -7.1 0 -4.1
ATAGTTGGTAGAAAATGATC
8112 SEQ ID N0:990 -14.4 -16.6 53.7 -2.2 0 -3.9
TATTTGTAATAGCTTTAGTG
8232 SEQ ID N0:991 -14.4 -17.6 57 -3.2 0 -4.6
CTGTAGTACTGCTTGGTGAA
8629 SEQ ID N0:992 -14.4 -22.9 68.7 -8 0 -7.8
CTGCTTATGCCTCCGCTTCG
3 SEQ ID N0:993 -14.3 -29.3 78.2 -14.1 -0.8 -5
TTTTTCTTTCTTTCTCTGTG
58 SEQ ID N0:994 -14.3 -21.2 67.5 -6.9 0 0
TTTTTTTCTTTCTTTCTCTG
60 SEQ ID N0:995 -14.3 -20.2 64.8 -5.9 0 0
GCAAACATTTATTCCTCAGA
1287 SEQ ID N0:996 -14.3 -21 62.4 -6.7 0 -3.4
AAATATCATGTATGTTTTCC
1661 SEQ ID N0:997 -14.3 -18.2 57.2 -3.9 0 -4.9
GGTGGCCTGATTCTGCTCCT
1754 SEQ ID N0:998 -14.3 -30.3 84.8 -15.4 -0.3 -7.2
CAGGGAGCCACGGATACTCA
2150 SEQ ID N0:999 -14.3 -26.9 74 -11.3 -1.2 -4.5
TGCTGTGTTCATCATCAGCA
2250 SEQ ID N0:1000 -14.3 -25 74.7 -6.5 -4.2 -9.6
TAAGGCACATGGTTTGGCCA
3336 SEQ ID N0:1001 -14.3 -25.9 72.7 -8.4 -3.2 -9.1
GGTTTCCAATGACCATGACC
3369 SEQ ID N0:1002 -14.3 -25.3 70.3 -10.1 -0.7 -5
CAATTCCAGTATTATTGGAC
3618 SEQ ID N0:1003 -14.3 -20 60.8 -4.2 -1.4 -7.2
CTCTTTGCTTATTTCAATTC
3632 SEQ ID N0:1004 -14.3 -20 62.5 -5.7 0 -3.6
AGCTCTTTGCTTATTTCAAT
3634 SEQ ID N0:1005 -14.3 -21.3 65.2 -5.7 , -1.2 -4.3
TTTTTCGAAGATTCCACCAG
4044 SEQ ID N0:1006 -14.3 -22.2 64.2 -7.2 -0.4 -6.8
GGTTTTTCGAAGATTCCACC
4046 SEQ TD N0:1007 -14.3 -23.9 68.3 -8.9 -0.4 -6.6
ACCACTACTGAGAAGGATCA
4115 SEQ ID N0:1008 -14.3 -22.2 65.1 -7 -0.8 -6.3
CACCACTACTGAGAAGGATC
4116 SEQ ID N0:1009 -14.3 -22.2 65.1 -7 -0.8 -5.l
GGGAAACGAGCTTCAGCACA
5190 SEQ ID N0:1010 -14.3 -24.5 68.6 -9.3 -0.7 -6.6
AGCGTGCGGATCCCCTTTGC
5383 SEQ ID N0:1011 -14.3 -31.5 82.2 -16.5 -0.4 -7.5
CTGTTGCCAAAGGTCTCAAA
5545 SEQ ID N0:1012 -14.3 -22.7 65.5 -8.4 0 -3.6
CCAGCCAGCAGAGGTTGTAA
5585 SEQ ID N0:1013 -14.3 -27 75.9 -11.8 -0.8 -5.2
122
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GAGCTGCCAGGGTGAATTGT
5659 SEQ ID N0:1014 -14.3 -26.6 75.6 -12.3 0 -5.6
TGAGCTGCCAGGGTGAATTG
5660 SEQ ID N0:1015 -14.3 -25.4 72.1 -11.1 0 -5.6
CCTCACTCAGGGGCTCTGCA
5814 5EQ ID N0:1016 -14.3 -30.3 85 -14.4 -1.6 -5.1
AACTGGGTCGCATCGGGATC
5872 SEQ ID N0:1017 -14.3 -26.3 72.8 -12 0 -6.9
TATAGTCTAGGTAGCCATTG
6717 SEQ ID N0:1018 -14.3 -22.3 68 -7.4 -0.3 -4
AGGCTATATATATATTTGCC
7422 SEQ ID N0:1019 -14.3 -20.4 62.2 -4 -1.3 -12.3
CAGTAGGCAGTATCCAGTGT
7772 SEQ ID N0:1020 -14.3 -25.7 76.9 -11.4 0.6 -4
CACTTTGTTCATGGCTAAAA
8270 SEQ ID N0:1021 -14.3 -19.9 59.9 -5.6 0 -4.7
TGGTGAATCATGCACTAGTT
8616 SEQ ID N0:1022 -14.3 -22 66 -6.5 -1.1 -6.2
GCACGTTTTTCGATAGCAGC
538 SEQ ID NO:1023 -14.2 -24.9 71.1 -9.6 -1 -5.6
AAAATTGCCTTTCCTTTATT
751 SEQ ID N0:1024 -14.2 -20.2 60 -6 0 -3.2
TCTAAGCAAAACCCTCTTGC
994 SEQ ID N0:1025 -14.2 -23 65.3 -7.9 -0.8 -5
CAGTTCCATGGATCACGAAG
1027 SEQ ID N0:1026 -14.2 -22.9 65.7 -7.4 0 -10.5
GTTTCAAAAGCAGAATCGCT
1318 SEQ ID N0:1027 -14.2 -20.7 60.9 -5.7 -0.6 -7
GTTGGTTTCAAAAGCAGAAT
1322 SEQ ID N0:1028 -14.2 -19.3 58.9 -4.3 -0.6 -1.1
TGTTGGTTTCAAAAGCAGAA
1323 SEQ TD N0:1029 -14.2 -19.3 58.8 -4.3 -0.6 -1.1
TGGTGTTGGTTTCAAAAGCA
1326 SEQ ID N0:1030 -14.2 -21.8 64.9 -6.9 -0.4 -4.2
TCTGGACACTGGCCTGCATC
1495 SEQ ID N0:1031 -14.2 -27.9 78.6 -13.7 0 -7.2
ATAGTCTTGAGTCATGAGTC
1604 SEQ ID N0:1032 -14.2 -21.4 68.2 -6.1 0 -10.1
AATAGTCTTGAGTCATGAGT
1605 SEQ ID N0:1033 -14.2 -20.3 64 -6.1 0 -7.3
GCACGTAATGTCAACTGGTA
1636 SEQ ID N0:1034 -14.2 -22.5 65.5 -8.3 0 -4.8
GCCATGGCCACCACAGCCAG
1729 SEQ ID N0:1035 -14.2 -32.5 84 -15.5 -2.8 -11.7
TTTTAAGCTGTTCGAGCATC
1812 SEQ ID N0:1036 -14.2 -22 66 -5.5 -2.3 -7.3
GTTGCTTTTTAAGCTGTTCG
1818 SEQ TD N0:1037 -14.2 -22.6 67.6 -5.8 -2.6 -7.1
TCTTCCTGTTGCTTTTTAAG
1825 SEQ ID N0:1038 -14.2 -22.1 67.1 -7.9 0 -3.6
CTCCTAACCCACCTACTCCA
1890 SEQ ID N0:1039 -14.2 -29.1 77 -14.9 0 -0.3
TGTCTTCAGATTCGGATTTG
2043 SEQ ID N0:1040 -14.2 -21.6 65.4 -7.4 0 -4.4
CTGTCTTCAGATTCGGATTT
2044 SEQ ID N0:1041 -14.2 -22.5 67.6 -7.4 -0.7 -5
ATCCTCCAGCATCTCCATTG
2546 SEQ ID N0:1042 -14.2 -27.4 77.1 -13.2 0 -4.1
123
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CGCAGTACAGACAATCCCTC
3004 SEQ ID N0:1043 -14.2 -25.6 71.3 -10.7 -0.4 -5.3
GTCTGAATGATCGCAGTACA
3015 SEQ ID N0:1044 -14.2 -22.5 66.3 -7.6 -0.4 -6.3
TTTCAATTCCAGTATTATTG
3621 SEQ ID N0:1045 -14.2 -18.6 58.4 -4.4 0 -3.5
CCCTTTGCCTTCTTCTGTAC
4019 SEQ ID N0:1046 -14.2 -27.7 78.7 -13.5 0 -3.8
ATTTCCAGAATGAATATATA
4216 SEQ ID NO:1047 -14.2 -16.2 52.2 -2 0 -5.3
TCAAAGTTTACTTTCACGTT
4654 SEQ ID N0:1048 -14.2 -19.5 59.9 -3.9 -1.3 -8.7
ATAAAGATGTCTTGACCTCC
4906 SEQ ID N0:1049 -14.2 -21.6 63.9 -7.4 0.2 -6.8
CGAAGGGCATCCATCTCTCC
6064 SEQ ID N0:1050 -14.2 -27.7 76.1 -12.3 -1.1 -4.3
GTATTCGAAGGGCATCCATC
6069 SEQ ID N0:1051 -14.2 -24.5 70.2 -9.1 -1.1 -8.2
ATATGGCAGATATGGAAGTT
6812 SEQ ID N0:1052 -14.2 -20.1 61.2 -4.5 -1.3 -4.7
AACATGCATTAGTGATAGCC
7545 SEQ ID N0:1053 -14.2 -21.8 64.5 -7.6 0 -6.8
TTGTGAAGAATGGATTGAGT
7590 SEQ ID NO:1054 -14.2 -18.8 58.3 -4.6 0 -2.9
TAGAAAATGATCTAGGTTTG
8104 SEQ ID N0:1055 -14.2 -16.4 53.1 -2.2 0 -4.9
TAAAAGGTTATATTGAGGCA
8135 SEQ ID N0:1056 -14.2 -17.9 55.9 -3.7 0 -4
GCCCAATAAGTGAAATGCAA
8480 SEQ ID N0:1057 -14.2 -2l 59.7 -6.8 0 -5.6
TTTCTTTCTCTGTGGATAAG
52 SEQ ID N0:1058 -14.1 -20.3 63.6 -6.2 0 -2.9
TTTTTTTTTTTTTTTTGACC
106 SEQ ID N0:1059 -14.1 -18.3 58.3 -4.2 0 -O.l
GTGTAGCTTCTTGCATACGA
427 SEQ ID N0:1060 -14.1 -24.1 71 -8.2 -1.8 -5.2
TCATCCTGCACATTTAATTA
448 SEQ ID N0:1061 -14.1 -20.8 62.3 -6.7 0 -4.8
TTTTCATCCTGCACATTTAA
451 SEQ ID N0:1062 -14.1 -21.3 63.6 -7.2 0 -4.8
ACTGCAAACATTTATTCCTC
1290 SEQ ID N0:1063 -14.1 -20.8 62.1 -6.7 0 -4.9
TTCGAGCATCTGCTGAAATT
1802 SEQ ID N0:1064 -14.1 -21.7 63.5 -6.3 -1.2 -8.9
ACGCTGTCTTCAGATTCGGA
2047 SEQ ID N0:1065 -14.1 -25.1 71.8 -9.5 -l.4 -6.1
CCGTCTTCAAATGTGCTGTG
2263 SEQ ID N0:1066 -14.1 -24.2 69 -10.1 0 -3.6
CCCATTTGCTGGAAGCCCTG
2378 SEQ ID N0:1067 -14.1 -29.4 77.4 -13.1 -2.2 -5.8
CGGAACACAATCAGGAAGGA
3265 SEQ ID N0:1068 -14.1 -21 60.4 -6.9 0 -2.9
TATCTTATTGCCTTCATGGA
3587 SEQ ID N0:1069 -14.1 -22.6 67.3 -7.9 -0.3 -4.7
CCATTCCCATCTCTAAGATA
3658 SEQ ID N0:1070 -14.1 -23.8 68.1 -9 -0.5 -3.9
AGGCTGGGGTTGTTTATGAA
3748 SEQ ID N0:1071 -14.1 -23.8 70.2 -9.7 0 -3.7
124
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTCACCTTCTCGGGGTAGAA
3911 SEQ ID N0:1072 -14.1 -25.3 72.3 -9.7 -1.4 -5.4
GTTTAAAGTCTTCTTCGGGT
3945 SEQ ID N0:1073 -14.1 -22.5 67.9 -8.4 0 -4.7
ACAATACTGTAGCAGGTTTT
4060 SEQ ID N0:1074 -14.1 -21.1 64.3 -6.1 -0.7 -5.3
TTTCCAGAATGAATATATAG
4215 SEQ ID N0:1075 -14.1 -16.2 52.3 -2.1 0 -4.2
ATCAAAGTTTACTTTCACGT
4655 SEQ ID N0:1076 -14.1 -19.4 59.6 -3.9 -1.3 -7.1
TAAAGATGTCTTGACCTCCA
4905 SEQ ID N0:1077 -14.1 -22.3 65.1 -7.4 -0.6 -6.8
AGAGCAGCGTGCGGATCCCC
5388 SEQ ID N0:1078 -14.1 -31.7 82.7 -15.4 -2.2 -11.1
AAGTTGGACATCCCAAAGAT
5482 SEQ ID N0:1079 -14.1 -21.6 62.4 -5.3 -2.2 -5.8
AGGCAAAGTTGGACATCCCA
5487 SEQ ID N0:1080 -14.1 -25.4 70.8 -10.4 -0.8 -5.6
TTTCAAAGTGGTTGTAATAG
6140 SEQ ID N0:1081 -14.1 -17.5 56 -2.7 -0.4 -3.8
CAATCCTCCCTTTAATTGCC
6261 5EQ ID N0:1082 -14.1 -25.7 70.5 -11.6 0 -3.3
TCCCATTTAGTTTGTCAATA
6306 SEQ ID NO:1083 -14.1 -21.7 65.1 -7.6 0 -2.9
CTCTGACCTCTTTTCCTTTG
6441 SEQ ID N0:1084 -14.1 -25 73.1 -10.9 0 -2.4
ACTTCACTGTCTTGTATAGG
6603 SEQ ID N0:1085 -14.1 -21.8 67.6 -7.7 0 -2.4
ATCAGCTTTGCTGAGAGCAG
7338 SEQ ID N0:1086 -14.1 -24.4 72.6 -6.7 -3.6 -11.8
ACATAATGGACAGAGCAGGT
7654 SEQ ID N0:1087 -14.1 -22.1 65.4 -8 0 -4.1
GTAGGCAGTATCCAGTGTGT
7770 SEQ ID N0:1088 -14.1 -26.2 79.1 -11.6 -0.2 -4
TTTTTTTCCACCTTATATAA
9082 SEQ ID N0:1089 -14.1 -19.3 59.1 -5.2 0 -5
GAGACCTTTCCAGAATCCTC
24 SEQ ID NO:1090 -14 -25.2 72 -11.2 0 -2.9
TTTTTTTTTTTTGACCACAG
102 SEQ ID N0:1091 -14 -19.5 60.3 -5.5 0 -2.3
CTGTTCAGCTTTTTTTTTTT
120 SEQ ID N0:1092 -14 -21 65.7 -7 0 -4.5
AGGGTTGCTCAAGGTCATAA
902 SEQ ID N0:1093 -14 -23.3 69.2 -9.3 0 -3.6
GAGGGTTGCTCAAGGTCATA
903 SEQ ID N0:1094 -14 -24.6 73.1 -9.3 -1.2 -4.1
CAGCACGTAATGTCAACTGG
1638 SEQ ID NO:1095 -14 -22.3 64.4 -8.3 0 -4.8
GGAACTCAACTTTGATGCTT
1931 SEQ ID N0:1096 -14 -21.3 63.3 -7.3 0 -4.8
TGCTCTCTCTGTCTTCTTTT
1984 SEQ ID N0:1097 -14 -24.8 77.1 -10.8 0 -3.6
GTGTTCATCATCAGCAAAGT
2246 SEQ ID N0:1098 -14 '22.1 67.1 -8.1 0 -4.1
CTGTGCATCTTCCCATTTGC
2389 SEQ ID N0:1099 -14 -27.1 77 -12.4 -0.4 -5.4
GAATCCTCCAGCATCTCCAT
2548 SEQ ID N0:1100 -l4 -27.2 75.8 -13.2 0 -4.1
125
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GGAATCCTCCAGCATCTCCA
2549 SEQ ID N0:1101 -14 -28.4 78.4 -13.2 -1.1 -6.5
GCTCACGGCTCTTTGCCTTC
2573 SEQ ID N0:1102 -14 -29.4 82.4 -12.7 -2.7 -7.5
TTGACAGACCAAGCTCCATT
2979 SEQ ID N0:1103 -14 -24.3 68.9 -10.3 0 -5
TTTGACAGACCAAGCTCCAT
2980 SEQ ID N0:1104 -14 -24.3 68.9 -10.3 0 -5
ATTTGACAGACCAAGCTCCA
2981 SEQ ID N0:1105 -14 -24.3 68.9 -10.3 0 -5
CATTTGACAGACCAAGCTCC
2982 SEQ ID N0:1106 -14 -24.3 68.9 -10.3 0 -5
CAGTCTGAATGATCGCAGTA
3017 SEQ ID N0:1107 -14 -22.3 66 -7.6 -0.4 -6.3
CACAAGGTTTCCAATGACCA
3374 SEQ ID N0:1108 -14 -23.4 66.1 -8.5 -0.7 -5
GCAAGGTTGTCTGAGCTAAA
3430 SEQ ID N0:1109 -14 -22.4 66.4 -7.9 -0.1 -5.5
TTATTGCCTTCATGGATTTC
3583 SEQ ID N0:1110 -14 -22.2 66.6 -7.6 -0.3 -4.7
AATGAAAGTCTCAAACCAGT
4088 SEQ ID NO:llll -14 -18.8 57 -4.2 -0.3 -3.4
GGTATGGGTTTCTGAGGTTT
4978 SEQ ID N0:1112 -14 -24.4 74.1 -10.4 0 -2.8
CGAGGTATGGGTTTCTGAGG
4981 SEQ ID N0:1113 -14 -24.4 71.3 -10.4 0 -2.8
TCATGTATTTGCCCTGGTCA
5115 SEQ ID N0:1114 -14 -26.4 75.8 -12.4 0 -4.7
AGTGTCTGAGGGAAACGAGC
5199 SEQ ID N0:1115 -14 -23.3 67.8 -9.3 3 -3.5
ATAAACATGACCAGGAAGAG
5455 SEQ ID N0:1116 -14 -18.4 55.8 -4.4 0 -4.3
AGATAAACATGACCAGGAAG
5457 SEQ 2D NO:lll7 -14 -18.4 55.8 -4.4 0 -5.2
GATGGCATAGATAAACATGA
5465 SEQ ID N0:1118 -14 -18.4 56.4 -4.4 0 -5.2
TCGCATCGGGATCAAACTTT
5865 SEQ ID N0:1119 -14 -22.9 64.7 -8.9 0 -6.9
GTAATAGGCTCATAAGAGAC
6127 SEQ ID N0:1120 -14 -19.3 60 -3.9 -1.3 -4.7
TCAAAGTGGTTGTAATAGGC
6138 SEQ ID N0:1121 -14 -20.3 62.1 -5.6 -0.4 -3.8
GGACCTCCTCTTGAAGTCCA '
6543 SEQ ID N0:1122 -14 -27.8 77.8 -11.4 -2.4 -6.5
CATGGACCTCCTCTTGAAGT
6546 SEQ ID NO:ll23 -14 -25.4 72.3 -11.4 0 -5.1
CTAAAGGTGTTTGGTGTAGT
6765 SEQ ID N0:1124 -14 -21.5 66.1 -7.5 0 -2.2
GCTTTGCTGAGAGCAGAAGA
7334 SEQ ID N0:1125 -14 -23.8 70 -6.7 -3.1 -8.6
CTATCAGCTTTGCTGAGAGC
7340 SEQ ID N0:1126 -14 -24.3 72.5 -6.7 -3.6 -11.3
CAAGACTTGTGAAGAATGGA
7596 SEQ ID N0:1127 -14 -18.6 56.9 -4.6 0.6 -4.1
CCCATTATCTAACTTTTATT
8017 SEQ ID N0:1128 -14 -20 60.3 -6 0 -1.6
TTTGAGTGTTTGACCAATGT
8088 SEQ ID N0:1129 -14 -21.4 64.4 -6.9 -0.2 -3.4
126
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Tntra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATATTTGTAATAGCTTTAGT
8233 SEQ ID N0:1130 -l4 -17.6 57 -3.6 0 -4.6
TTTTCCACCTTATATAATTT
9079 SEQ ID N0:1131 -14 -19.2 58.8 -5.2 0 -5.3
TTTTTCCACCTTATATAATT
9080 SEQ ID N0:1132 -14 -19.2 58.8 -5.2 0 -5.3
TTTTTTCCACCTTATATAAT
9081 SEQ ID N0:1133 -14 -19.2 58.8 -5.2 0 -5.3
TTTTTTCTTTCTTTCTCTGT
59 SEQ ID N0:1134 -13.9 -21.3 68.1 -7.4 0 0
TCAGCTTTTTTTTTTTTTTT
116 SEQ ID NO:1135 -13.9 -19.2 61.4 -5.3 0 -4.5
TTCAGCTTTTTTTTTTTTTT
117 SEQ ID N0:1136 -13.9 -19.2 61.4 -5.3 0 -4.5
GCTTCTTGCATACGAATTAC
422 5EQ ID N0:1137 -13.9 -21.3 63 -6.5 -0.7 -5.1
CATCATTATCTTGTTCCTTT
585 5EQ ID N0:1138 -13.9 -21.8 66.5 -7.9 0 -1.9
TCTTATTGATATAGTAGGGA
714 SEQ ID N0:1139 -13.9 -19.1 60.6 -5.2 0 -2.7
GGAAAATTGCCTTTCCTTTA
753 SEQ TD NO:1140 -13.9 -21.9 63.3 -6 -2 -7.2
CTGCATCTGAGCCATTTCCA
1482 SEQ ID N0:1141 -13.9 -27.1 76 -12.7 -0.1 -4.9
ACACTGGCCTGCATCTGAGC
1490 SEQ ID NO:ll42 -13.9 -28.1 78.9 -14.2 0 -6.5
TTCTGGACACTGGCCTGCAT
1496 SEQ ID N0:1143 -13.9 -27.6 77.2 -13.7 0 -7.2
ATCATGTATGTTTTCCCAGC
1657 SEQ ID N0:1144 -13.9 -24.4 71.9 -10.5 0 -4.7
TAGGCCATGGCCACCACAGC
1732 SEQ ID NO:ll45 -13.9 -30.7 81.7 -12.2 -2.5 -17.4
ACTCCACTGAAATCTCTTGA
1876 SEQ ID N0:1146 -13.9 -21.8 64.4 -7.9 0 -2.5
TGGAACTCAACTTTGATGCT
1932 SEQ ID N0:1147 -13.9 -21.2 62.8 -7.3 0 -5
TTTGCCCGACCTCTGAAACT
2206 SEQ ID N0:1148 -13.9 -26.1 70.1 -12.2 0 -3
CATCAGTAGCAGCAAGGTTG
3441 SEQ ID N0:1149 -13.9 -23.5 70 -9.6 0 -5.4
TGGAAACACTCCCGCATCTT
3532 SEQ ID N0:1150 -13.9 -25.5 69.4 -10.5 -l -4.8
TCACAACCACCCTCATGCCT
4428 SEQ ID N0:1151 -13.9 -29.1 76.9 -15.2 0 -4.4
CAAAGTTTACTTTCACGTTT
4653 SEQ ID N0:1152 -13.9 -19.2 58.9 -3.9 -1.3 -8.7
AGGTATGGGTTTCTGAGGTT
4979 SEQ ID N0:1153 -13.9 -24.3 74 -10.4 0 -2.8
GGGTCATGTATTTGCCCTGG
5118 SEQ ID N0:1154 -13.9 -27.7 78,2 -12.3 -1.4 -6.9
ATGACCAGGAAGAGCAGGAG
5449 SEQ TD N0:1155 -13.9 -23.5 67.9 -9.6 0 -4.1
GATCCAGGGCAGCTGCAAAA
5916 SEQ ID NO:ll56 -13.9 -25.7 70.9 -8.9 -1 -14
TCGAAGGGCATCCATCTCTC
6065 SEQ ID N0:1157 -13.9 -26.1 74.2 -11.3 -0.8 -6.3
TAGGCTCATAAGAGACTTTG
6123 SEQ 2D N0:1158 -13.9 -20.2 62.1 -4.9 -1.3 -5.2
127
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
O
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CCCATTTAGTTTGTCAATAA
6305 SEQ ID N0:1159 -13.9 -20.6 61.5 -6.7 0 -2.9
ACTGTCTTGTATAGGCACTG
6598 SEQ ID N0:1160 -13.9 -23.1 69.9 -8.5 -0.5 -4
TTAGATATATTTTTCTAGAA
7262 SEQ ID N0:1161 -13.9 -15.1 51.1 -1.1 0 -7.4
TACAGGATACATCCCTGTTG
7502 SEQ ID N0:1162 -13.9 -23.6 68.4 -6.7 -3 -8.4
ATACAGGATACATCCCTGTT
7503 SEQ ID N0:1163 -13.9 -23.6 68.5 -6.7 -3 -8.4
CTTGTGAAGAATGGATTGAG
7591 SEQ ID N0:1164 -13.9 -18.5 57.3 -4.6 0 -2.9
ACCAAGACTTGTGAAGAATG
7598 SEQ ID N0:1165 -13.9 -19 57.4 -4.6 -0.2 -5.4
ACATTCTTTAACCAAGACTT
7608 SEQ ID NO:1166 -13.9 -19.5 59.2 -4.6 -0.9 -3.4
CATTTATTCTTACAATATCC
343 SEQ ID N0:1167 -13.8 -18.1 56.9 -4.3 0 -2.6
GGGATCCAGGTCCTCCAGGG
698 SEQ ID N0:1168 -13.8 -31.3 86.2 -15.5 -2 -10.3
ATCGGAAAATTGCCTTTCCT
756 SEQ ID N0:1169 -13.8 -23.2 64.8 -6.9 -2.5 -7.5
GAGACATTGCCCAGGTCCAC
1090 SEQ ID N0:1170 -13.8 -28.4 78.4 -13.9 -0.5 -4.4
TGGACACTGGCCTGCATCTG
1493 SEQ ID NO:ll71 -13.8 -27.5 76.6 -13.7 0 -7.2
TCCTTCTGGACACTGGCCTG
1499 SEQ ID N0:1172 -13.8 -28.4 79 -13.7 -0.8 -8.8
ACCCACCTACTCCACTGAAA
1884 SEQ ID N0:1173 -13.8 -26.2 70.3 -12.4 0 -1.7
ACAGGGAGCCACGGATACTC
2151 SEQ ID NO:1174 -13.8 -26.4 73.5 -l2 -0.3 -4.3
TGCTATTGCGTCTTGGGGAA
2172 SEQ ID N0:1175 -13.8 -25.2 71.5 -9.8 -1.5 -6.6
ATGCTTGTTTTGCTATTGCG
2182 SEQ ID N0:1176 -13.8 -23.4 68.3 -8 -1.5 -5.8
ATGTCTGTGCGGCACAAACA
2303 SEQ ID N0:1177 -13.8 -24.4 68.6 -8.6 0.6 -12.1
AACGTTACTGTTGCGTCGCT
2327 SEQ TD N0:1178 -13.8 -25.4 70.5 -10.6 -0.9 -7.4
TCTCTTTGCTTTCTTCTAGT
3846 SEQ ID N0:1179 -13.8 -23.3 73.2 -9.5 0 -4
CAAACATGTTACCCGTTGTC
4572 SEQ ID N0:1180 -13.8 -23.1 65.6 -8.6 0 -9
CCAACATTATCAAAGTTTAC
4663 SEQ ID N0:1181 -13.8 -17.7 55 -3.9 0 -4.1
ATTTTCTTCATATACAGGCT
4775 SEQ ID N0:1182 -13.8 -21 64.7 -7.2 0 -3.7
TCCTTGGAATTTGTTTGCTG
5003 SEQ ID N0:1183 -13.8 -22.8 67.2 -9 0 -4.3
AGGGTCATGTATTTGCCCTG
5119 SEQ ID N0:1184 -13.8 -26.5 75.9 -10.5 -2.2 -8.4
TTGATCAGACGTAGGATTCG
5359 SEQ ID NO:ll85 -13.8 -21.4 63.3 -7.6 0 -6.6
GCGTGCGGATCCCCTTTGCT
5382 SEQ ID N0:1186 -13.8 -32.4 83.6 -17.9 -0.4 -7.5
GCCAAAGGTCTCAAAGTTGA
5540 SEQ ID N0:1187 -13.8 -22.4 65.2 -8.6 0 -5.1
128
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGTAATAGGCTCATAAGAGA
6128 SEQ ID N0:1188 -13.8 -19.1 59.3 -3.9 -1.3 -4.7
TACGTTTCAAAGTGGTTGTA
6144 SEQ ID N0:1189 -13.8 -20.4 62.1 -5.9 -0.4 -5.6
AAGGTGTTTGGTGTAGTTAC
6762 SEQ ID N0:1190 -13.8 -21.6 67.5 -7.8 0 -2.2
GGAGACTTTACAGGCACATA
7114 SEQ ID N0:1191 -13.8 -22.6 67 -8.8 0 -4
GAGGAGACTTTACAGGCACA
7116 SEQ TD N0:1192 -13.8 -23.5 69.2 -8.8 -0.7 -5.2
AGCTTTGCTGAGAGCAGAAG
7335 SEQ ID N0:1193 -13.8 -23.2 68.9 -6.7 -2.7 -10.2
TATCAGCTTTGCTGAGAGCA
7339 SEQ ID NO:ll94 -13.8 -24.1 71.7 -6.7 -3.6 -11.8
GGCTATATATATATTTGCCC
7421 SEQ TD N0:1195 -13.8 -22.4 65.7 -6.9 -0.9 -11.5
AAAAGGTTATATTGAGGCAA
8134 SEQ ID N0:1196 -13.8 -17.5 54.6 -3.7 0 -4
TATATTTGTAATAGCTTTAG
8234 SEQ ID NO:1197 -13.8 -16.1 53.3 -2.3 0 -4.6
CAATAAGTGAAATGCAATAA
8477 SEQ ID N0:1198 -13.8 -14.2 47.2 0 0 -5.6
AAGATGAGTTTAGATGCTTA
8788 SEQ ID N0:1199 -13.8 -18.7 59 -4.9 0 -3.6
GGTTAGGGTATAACGTGTCT
151 SEQ TD N0:1200 -13.7 -23.2 69.2 -7.5 -2 -5.3
TTAATTACGTGTAGCTTCTT
435 SEQ ID N0:1201 -13.7 -20.2 62 -6.5 0 -5
TTTAATTACGTGTAGCTTCT
436 SEQ ID N0:1202 -13.7 -20.2 62 -6.5 0 -5
GTTCCTTTTTGGGCTTCTTG
573 SEQ ID N0:1203 -13.7 -25.6 75.8 -11.4 -0.2 -3.8
ATGGATCACGAAGAAACGTA
1020 SEQ ID N0:1204 -13.7 -18.9 56 -4.3 -0.8 -6
AACGCTGAGACATTGCCCAG
1096 SEQ ID N0:1205 -13.7 -25.7 69.9 -12 0 -4.l
TGCAAACATTTATTCCTCAG
1288 SEQ ID N0:1206 -13.7 -20.4 61.1 -6.7 0 -4.7
ACATTAACAAATGTCCCATT
1375 SEQ ID N0:1207 -13.7 -19.9 58.6 -4.9 -1.2 -6
CAATAGTCTTGAGTCATGAG
1606 SEQ ID N0:1208 -13.7 -19.8 61.9 -6.1 0 -7.4
TCCCAATAGTCTTGAGTCAT
1609 5EQ ID N0:1209 -13.7 -23.6 69.8 -9.4 -0.2 -5.8
GATGCTTCTGAAGAACTTTC
1918 SEQ ID N0:1210 -13.7 -20.2 61.9 -6 0 -8.3
GATGAGGGGAGCAGAATTTT
2121 SEQ ID N0:1211 -13.7 -22.1 65.5 -8.4 0 -4.1
CTCCTGCTTTCGCCGTCTTC
2275 SEQ ID N0:1212 -13.7 -29.9 82.1 -16.2 0.2 -3.6
TGCCCTCTGGGGGAAGTTGT
2475 SEQ ID N0:1213 -13.7 -29.2 81.1 -13.3 -2.2 -8.7
CCTCCAGCATCTCCATTGAA
2544 SEQ ID N0:1214 -13.7 -26.9 74.4 -13.2 0 -4.1
GCCTTCATGGATTTCTATAA
3578 SEQ ID N0:1215 -13.7 -21.9 65.2 -7.6 -0.3 -4.4
TCAATTCCAGTATTATTGGA
3619 SEQ ID N0:1216 -13.7 -20.2 61.7 -5.5 -0.9 -6.7
129
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GCTGGGGTTGTTTATGAATG
3746 SEQ ID N0:1217 -13.7 -22.6 67.1 -8.9 0 -2.8
TACACCCTTCAGTAAAACAA
3972 SEQ ID NO:1218 -13.7 -19.9 58.5 -6.2 0 -3.1
AATACTGTAGCAGGTTTTTC
4058 SEQ ID NO:1219 -13.7 -20.7 64.4 -6.1 -0.7 -5.3
CAAGAAATCTAGCCAGCACC
4286 SEQ ID N0:1220 -13.7 -23.4 66 -9.7 0 -4.6
GTTTTTCCACCGAGCTTGCT
4637 SEQ TD N0:1221 -13.7 -27.8 77.4 -14.1 0 -5.9
AAGATGTCTTGACCTCCAAA
4903 SEQ ID N0:1222 -13.7 -21.9 63.6 -7.4 -0.6 -5.9
AAAGATGTCTTGACCTCCAA
4904 SEQ 2D N0:1223 -13.7 -21.9 63.6 -7.4 -0.6 -6.8
TTTTTTCTGTTCCTCTGTCA
4925 SEQ ID N0:1224 -13.7 -24 73.6 -10.3 0 -l.7
AAAGCAAAGAGCAGCGTGCG
5395 SEQ ID N0:1225 -13.7 -23.2 64.2 -7.3 -2.2 -8.5
TAGATAAACATGACCAGGAA
5458 SEQ ID N0:1226 -13.7 -18.1 55.2 -4.4 0 -5.2
CAGCCAGCAGAGGTTGTAAT
5584 SEQ ID N0:1227 -13.7 -25 72.3 -10.7 -0.3 -4.7
GGGTCGCATCGGGATCAAAC
5868 SEQ ID N0:1228 -13.7 -25.4 70 -11.7 0 -6.9
AGGGCAGCTGCAAAATCAGA
5911 SEQ ID NO:1229 -13.7 -23.7 67.7 -7.1 -0.7 -14
TTGTAATAGGCTCATAAGAG
6129 SEQ ID N0:1230 -13.7 -18.6 58.3 -3.9 -0.9 -4.4
TGGACCTCCTCTTGAAGTCC
6544 SEQ ID N0:1231 -13.7 -27.1 76.5 -11.4 -2 -5.7
CTGCTTCACAGAGTTGCAGT
6635 SEQ ID NO:1232 -13.7 -25.3 75.4 -9.9 -1.7 -6.6
GGAAGTTAAAAATAGAATGG
6799 SEQ ID N0:1233 -13.7 -14.1 47.4 0 0 -2.6
TTTTTCTAGAATGGATTTAT
7253 SEQ ID N0:1234 -13.7 -17 55.1 -2.8 0 -7.7
ATACTTTAGATATATTTTTC
7267 SEQ ID N0:1235 -13.7 -15.5 52.4 -1.8 0 -4.3
GATACATCCCTGTTGGAAGC
7497 SEQ ID NO:1236 -13.7 -24.7 70.5 -9.9 -1 -5.4
CATTCTTTAACCAAGACTTG
7607 SEQ ID N0:1237 -13.7 -19.3 58.6 -4.6 -0.9 -5.3
AACTTTGCCACTTTGTTCAT
8278 SEQ ID N0:1238 -13.7 -22.8 67.1 -9.1 0 -3.1
AGCTGCTTTTAATTTGCCTT
8653 SEQ ID N0:1239 -13.7 -23.7 69.2 -10 0 -6.7
AGGTGGTTACTACTATTATT
8732 SEQ ID N0:1240 -13.7 -20.1 63 -5.9 -0.1 -3.9
TCTTTCTCTGTGGATAAGAA
50 SEQ ID N0:1241 -13.6 -20 62.1 -5.7 -0.5 -3.8
TTTCTTTCTTTCTCTGTGGA
56 SEQ ID N0:1242 -13.6 -22.8 71.1 -9.2 0 -2.2
TAATTACGTGTAGCTTCTTG
434 SEQ ID N0:1243 -13.6 -20.1 61.6 -6.5 0 -4.7
TGTGCCATCTTTTCATCCTG
460 SEQ ID N0:1244 -13.6 -25.7 74.3 -12.1 0 -3
GGTTTGTTCTCATCATCATT
598 SEQ ID N0:1245 -13.6 -22.6 69.9 -9 0 -1.9
130
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTGGTTTGTTCTCATCATCA
600 SEQ ID N0:1246 -13.6 -22.6 69.7 -9 0 -1.9
CATTAACAAATGTCCCATTT
1374 5EQ ID N0:1247 -13.6 -19.8 58.5 -4.9 -l.2 -5.5
GTTACATTAACAAATGTCCC
1378 SEQ ID N0:1248 -13.6 -20.1 59.8 -4.9 -1.5 -6.6
GCTGTGTTCATCATCAGCAA
2249 SEQ ID N0:1249 -13.6 -24.3 72.2 -7.2 -3.5 -8.5
GCCGTCTTCAAATGTGCTGT
2264 SEQ ID N0:1250 -13.6 -26 73.3 -12.4 0 -3.6
ATGCTCACGGCTCTTTGCCT
2575 SEQ ID N0:1251 -13.6 -28.9 79.9 -12.6 -2.7 -8.3
CCATGCATCACAGCAGTCCC
2690 SEQ ID N0:1252 -13.6 -29.3 80.3 -14.4 -1.2 -7.5
AGTCTGAATGATCGCAGTAC
3016 SEQ ID N0:1253 -13.6 -21.8 65.3 -7.6 -0.3 -6.3
AGACGATGATGGCCAACACC
3132 SEQ ID N0:1254 -13.6 -24.9 67.8 -11.3 0 -6.3
GCCAGCGACCTCCATACAGT
3320 5EQ TD N0:1255 -13.6 -29.7 79.6 -16.1 0 -4.1
GGCCAGCGACCTCCATACAG
3321 SEQ ID N0:1256 -13.6 -29.7 78.7 -16.1 0 -7
CACCAGATCTTCCCTTTGCC
4030 SEQ ID N0:1257 -13.6 -28.9 78.9 -15.3 0 -5.8
CACAACCACCCTCATGCCTT
4427 SEQ ID N0:1258 -13.6 -28.8 75.7 -15.2 0 -4.4
TTTTTCTGTTCCTCTGTCAT
4924 SEQ ID N0:1259 -13.6 -23.9 73.2 -10.3 0 -1.8
AGGGAAACGAGCTTCAGCAC
5197. SEQ ID N0:1260 -13.6 -23.8 67.7 -9.3 -0.7 -6.6
TCAAAGCAAAGAGCAGCGTG
5397 SEQ ID N0:1261 -13.6 -21.7 62.4 -7.2 -0.8 -5.4
ATGGCATAGATAAACATGAC
5464 SEQ ID N0:1262 -13.6 -18 55.6 -4.4 0 -5.2
GCCAGCAGAGGTTGTAATTT
5582 SEQ ID N0:1263 -13.6 -24.5 71.6 -10.9 0 -5.7
TCCCAGCCAGCAGAGGTTGT
5587 SEQ ID N0:1264 -13.6 -30.4 84.6 -15.9 -0.8 -5.2
TCTTGTTTACGTTTCAAAGT
6151 SEQ ID N0:1265 -13.6 -19.8 61.1 -6.2 0 -4.8
CACTTCACTGTCTTGTATAG
6604 SEQ ID NO:1266 -13.6 -21.3 66 -7.7 0 -2.6
GTTCTTGTATACTGTTTCTT
6927 SEQ ID N0:1267 -13.6 -21.2 67.3 -7.6 0 -6.3
AGGAGACTTTACAGGCACAT
7115 SEQ ID N0:1268 -13.6 -22.9 67.8 -8.8 -0.2 -4.3
AGATATATTTTTCTAGAATG
7260 SEQ ID N0:1269 -13.6 -15.3 51.4 -1.1 0 -7.7
CTTTAGATATATTTTTCTAG
7264 SEQ ID N0:1270 -13.6 -16.2 54 -2.6 0 -4.3
ATAGGGTATTTAATTGACAT
7363 SEQ ID N0:1271 -13.6 -17.8 56.3 -4.2 0 -2.9
GCTATATATATATTTGCCCA
7420 SEQ ID N0:1272 -13.6 -21.9 64.4 -7.8 0 -7.9
ACTTGTGAAGAATGGATTGA
7592 SEQ ID N0:1273 -13.6 -18.7 57.6 -4.6 -0.2 -3.1
GACTTGTGAAGAATGGATTG
7593 SEQ ID N0:1274 -13.6 -18.7 57,6 -4.6 -0.2 -3.1
131
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGACTTGTGAAGAATGGATT
7594 SEQ ID N0:1275 -13.6 -18.7 57.8 -4.6 -0.2 -3.1
AGTAGGCAGTATCCAGTGTG
7771 SEQ ID N0:1276 -13.6 -25 75.5 -10.9 -0.2 -3.7
ACTGCTTGGTGAATCATGCA
8622 5EQ ID NO:1277 -13.6 -23.8 69.2 -8.3 -1.9 -6.4
TTTCCACCTTATATAATTTA
9078 SEQ ID NO:1278 -13.6 -18.8 57.9 -5.2 0 -5.3
TTCTTTCTTTCTCTGTGGAT
55 SEQ ID N0:1279 -13.5 -22.7 70.7 -9.2 0 -2.3
TGGTTTGTTCTCATCATCAT
599 SEQ ID N0:1280 -13.5 -22.5 69.3 -9 0 -1.8
TTGGCTTTGGTTTGTTCTCA
606 SEQ ID N0:1281 -13.5 -24.5 74.1 -11 0 -3.7
ATAAGTGACTCAAAGGTATA
964 SEQ ID N0:1282 -13.5 -17.4 55.3 -3.9 0 -3.3
ATCCAGCCAGTTCCATGGAT
1034 SEQ ID N0:1283 -13.5 -27.8 77.5 -12.6 -1.7 -10
CTGAGCCATTTCCACAGAGT
1476 SEQ ID N0:1284 -13.5 -26 74.2 -12.5 0 -3.5
ACAGATGTATCCTTCTGGAC
1508 SEQ ID N0:1285 -13.5 -23.1 69 -8 -1.6 -7.2
GTGGCCTGATTCTGCTCCTC
1753 SEQ ID NO:1286 -13.5 -29.5 84.1 -15.4 -0.3 -7.2
CCATTTGCTGGAAGCCCTGG
2377 SEQ ID N0:1287 -13.5 -28.6 76.5 -12.9 -2.2 -8.6
AATCCTCCAGCATCTCCATT
2547 SEQ ID N0:1288 -13.5 -26.7 74.8 -13.2 0 -4.l
TTTTTGGAAACACTCCCGCA
3536 SEQ ID NO:1289 -13.5 -24.5 67.2 -10.2 -0.6 -4.8
CTTCATGGATTTCTATAACT
3576 SEQ ID N0:1290 -13.5 -19.2 59.7 -5.7 0 -5
CCCATCTCTAAGATAATTAA
3653 SEQ ID N0:1291 -13.5 -19 57.4 -4.8 -0.5 -4.9
GGTTCCATTCCCATCTCTAA
3662 SEQ ID N0:1292 -13.5 -26.4 75 -12.9 0 -3.5
TTTTGATAGTCTTTCGCTGT
4164 SEQ ID N0:1293 -13.5 -22.4 68.1 -8.9 0 -3.4
GTTTTGATAGTCTTTCGCTG
4165 SEQ ID N0:1294 -13.5 -22.4 68.1 -8.9 0 -3.1
TGGTTTTGATAGTCTTTCGC
4167 SEQ ID N0:1295 -13.5 -22.7 68.8 -9.2 0 -2.9
AAAGTTTACTTTCACGTTTT
4652 SEQ ID N0:1296 -13.5 -18.6 58 -3.9 -1.1 -8.6
GATTTTCTTCATATACAGGC
4776 SEQ ID N0:1297 -13.5 -20.7 64.1 -7.2 0 -2.8
TTGACCTCCAAACTTCTTTT
4895 SEQ ID N0:1298 -13.5 -22.3 65 -8.8 0 -2.6
TAGGGTCATGTATTTGCCCT
5120 SEQ ID N0:1299 -13.5 -26.2 75.5 -10.5 -2.2 -8.5
ACGTAGGATTCGGCCAATCC
5351 SEQ ID N0:1300 -13.5 -26.4 71.7 -10.5 -1.7 -12.8
GCAAAGAGCAGCGTGCGGAT
5392 SEQ ID N0:1301 -13.5 -26.4 71.5 -10.7 -2.2 -8.5
~
CATCCCAAAGATGGCATAGA
5474 5EQ ID N0:1302 -13.5 -23 65 -8 -1.4 -6.9
AGCCAGCAGAGGTTGTAATT
5583 SEQ ID N0:1303 -13.5 -24.4 71.5 -10.9 0 -4.6
132
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Tntra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TAACTGAGCTGCCAGGGTGA
5664 SEQ ID N0:1304 -13.5 -26.1 73.8 -11.7 -0.6 -9.3
CACGGTCTCCCTTAACTGAG
5676 SEQ ID N0:1305 -13.5 -25.5 71.2 -11.4 -0.3 -3.8
TCGGGATCAAACTTTTCCCA
5860 SEQ ID N0:1306 -13.5 -24.4 67.8 -8.3 -2.6 -7.9
TCCTCTTGTTTACGTTTCAA
6154 SEQ ID N0:1307 -13.5 -22.6 67.2 -9.l 0 -4.8
GTGTAGTTACAATGTTCACT
6752 SEQ ID NO:1308 -13.5 -20.8 64.7 -6.8 -0.2 -5.4
CAGATATGGAAGTTAAAAAT
6806 SEQ ID N0:1309 -13.5 -14.3 47.8 0 -0.6 -4.9
AGAGACAGGGTTCTTGTATA
6936 SEQ ID N0:1310 -13.5 -21.8 67.4 -7.6 -0.4 -4.5
GACTATCAGCTTTGCTGAGA
7342 SEQ ID N0:1311 -13.5 -23.3 69.7 -6.7 -3.1 -10.3
CTTTAACCAAGACTTGTGAA
7603 SEQ ID N0:1312 -13.5 -19.2 58 -5.7 0 -4.9
CCATTATCTAACTTTTATTT
8016 SEQ ID N0:1313 -13.5 -18.1 56.9 -4.6 0 -1.6
ATAAAAGGTTATATTGAGGC
8136 SEQ ID N0:1314 -13.5 -17.2 54.6 -3.7 0 -2.8
TTTGTAATAGCTTTAGTGCA
8230 SEQ ID NO:1315 -13.5 -20.4 63.2 -6 -0.8 -5.2
CCCCAGAGCCCAATAAGTGA
8487 SEQ ID N0:1316 -13.5 -27.9 73.6 -14.4 0 -3.3
AATCATGCACTAGTTTGTTG
8611 SEQ ID N0:1317 -13.5 -20.4 62.7 -6.9 0 -5.7
TTGGTGAATCATGCACTAGT
8617 SEQ ID N0:1318 -13.5 -22 66 -7.3 -1.1 -6.2
TCCACCTTATATAATTTATT
9076 SEQ ID NO:1319 -13.5 -18.7 57.6 -5.2 0 -5.3
TTCCACCTTATATAATTTAT
9077 SEQ ID N0:1320 -13.5 -18.7 57.6 -5.2 0 -5.3
TATCTCATCCCTGTCAAACC
264 SEQ ID No:1321 -13.4 -24.5 69.7 -11.1 0 -2
TACGTGTAGCTTCTTGCATA
430 SEQ ID N0:1322 -13.4 -23.2 69 -8.2 -1.5 -7.6
CTGCAGCACGTTTTTCGATA
543 SEQ ID N0:1323 -13.4 -24 68.4 -9.6 -0.9 -8.7
GGATCCAGGTCCTCCAGGGG
697 SEQ ID N0:1324 -13.4 -31.3 86.2 -16.5 -1.2 -9.7
TTCTTATTGATATAGTAGGG
715 SEQ ID N0:1325 -13.4 -18.6 59.5 -5.2 0 -2.7
TTGTTTTCAGTGCTCGGAGA
1131 SEQ ID NO:1326 -13.4 -24.2 72 -10.3 -0.1 -6.4
AATCGCTTGGGGGCCACTGC
1305 SEQ ID N0:1327 -13.4 -29.5 79 -15.2 -0.8 -6.8
GCAGCACGTAATGTCAACTG
1639 SEQ ID N0:1328 -13.4 -22.9 65.9 -9.5 0 -4.9
TGTTGCTTTTTAAGCTGTTC
1819 SEQ ID N0:1329 -13.4 -21.8 67.2 -5.8 -2.6 -7.1
TTCTTCCTGTTGCTTTTTAA
1826 SEQ ID NO:1330 -13.4 -22.2 67.2 -8.8 0 -3.6
TGCCTGAGCTTCTTCCTGTT
1835 SEQ ID N0:1331 -13.4 -28.1 80.7 -13.5 -1.1 -5.2
ACTCAACTTTGATGCTTCTG
1928 SEQ ID N0:1332 -13.4 -21.5 64.8 -8.1 0 -5
133
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGTCTGTGCGGCACAAACAG
2302 SEQ ID N0:1333 -13.4 -24.4 68.8 -8.6 -1.1 -12.9
CTAACGTTACTGTTGCGTCG
2329 SEQ ID N0:1334 -13.4 -23.3 65.9 -8.9 -0.9 -7.8
TGTGCATCTTCCCATTTGCT
2388 SEQ ID N0:1335 -13.4 -27.1 77 -12.4 -1.2 -5.4
GAGTGGAAGAAGTCGTTCAT
3247 SEQ ID N0:1336 -13.4 -21.6 64.8 -6.9 -l.2 -4.1
AACTTTTGGCTTTCTAAAAA
3560 SEQ ID N0:1337 -13.4 -17 53.5 -2.8 -0.6 -4.3
GGTTTAAAGTCTTCTTCGGG
3946 SEQ ID N0:1338 -13.4 -22.5 67.2 -8.4 -0.5 -4.7
AATGCACCACTACTGAGAAG
4120 5EQ TD N0:1339 -13.4 -21.1 61.8 -7 -0.4 -6.3
TCAGCATATTCTAGCATGGT
4183 SEQ ID N0:1340 -13.4 -23.3 70.2 -8.9 -0.9 -5
GTCAGCATATTCTAGCATGG
4184 SEQ ID N0:1341 -13.4 -23.3 70.2 -8.9 -0.9 -5
CTGAAGTTTAACATCTCGTG
4757 SEQ ID N0:1342 -13.4 -19.8 60.2 -6.4 0 -3.5
GAGGGAAACGAGCTTCAGCA
5192 SEQ ID N0:1343 -13.4 -24.2 68.4 -9.9 -0.7 -6.6
AGATGGCATAGATAAACATG
5466 SEQ ID N0:1344 -13.4 -17.8 55.3 -4.4 0 -4.7
CAAAGTGGTTGTAATAGGCT
6137 SEQ ID N0:1345 -13.4 -20.8 62.6 -7.4 0 -3.7
ACACCTCCTCTTGTTTACGT
6159 SEQ ID N0:1346 -13.4 -26 74 -12.6 0 -4.6
TTGACACATATACTTTACCT
6522 SEQ ID N0:1347 -13.4 -20 60.6 -6.6 0 -2.4
CCTATAGTCTAGGTAGCCAT
6719 SEQ ID N0:1348 -13.4 -25.1 73.8 -10.8 -0.8 -5.4
ATCCCTATAGTCTAGGTAGC
6722 5EQ ID NO:1349 -13.4 -24.8 74.4 -10 -1.3 -5.2
ATCCTTTAAATATTAGAGGA
7131 SEQ ID N0:1350 -13.4 -17.7 55.7 -2.2 -2.1 -8
CATAGGCAATATTAACATGC
7558 SEQ ID N0:1351 -13.4 -18.9 57.5 -5 -0.1 -5
CATAATGGACAGAGCAGGTT
7653 SEQ ID N0:1352 -13.4 -22 65.2 -8.6 0 -4.1
CATAGTTGGTAGAAAATGAT
8113 SEQ ID NO:1353 -13.4 -16.9 53.8 -3.5 0 -2.5
AGAGCCCAATAAGTGAAATG
8483 SEQ ID N0:1354 -13.4 -19.8 58.3 -6.4 0 -3.3
CCTTTGTTCTGTAGTACTGC
8637 SEQ ID N0:1355 -13.4 -24.4 73.7 -11 0 -6.8
GTTAGGGTATAACGTGTCTT
150 SEQ ID N0:1356 -13.3 -22.1 66.9 -7.5 -1.2 -5.3
TTCTCTAGTAAAAAGGCGGA
512 SEQ ID N0:1357 -13.3 -20.1 60 -6.8 0 -4
TCAGGAGGGTTGCTCAAGGT
907 SEQ ID N0:1358 -13.3 -26.1 76.9 -10.8 -2 -5.7
AAGCAAAACCCTCTTGCCAA
991 SEQ ID N0:1359 -13.3 -24 65.2 -8.7 -2 -6.2
ATTGTTTTCAGTGCTCGGAG
1132 SEQ ID N0:1360 -13.3 -23.6 70.5 -10.3 0 -5.9
ATCCTTCTGGACACTGGCCT
1500 SEQ ID N0:1361 -13.3 -28.4 79.2 -13.7 -1.3 -9.7
134
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTCTTGAGTCATGAGTCGAA
1601 SEQ ID N0:1362 -13.3 -22.4 67.7 -7.6 0 -10.9
TTTTTAAGCTGTTCGAGCAT
1813 SEQ ID N0:1363 -13.3 -21.7 64.8 -6.1 -2.3 -7.3
CTTCTTCCTGTTGCTTTTTA
1827 SEQ ID N0:1364 -13.3 -23.8 71.7 -10.5 0 -3.6
CTGATGCTGCCGCAACTGCC
1851 SEQ ID N0:1365 -13.3 -29.5 77.4 -14.6 -1.6 -8
TGATGCTTCTGAAGAACTTT
1919 SEQ ID N0:1366 -13.3 -19.8 60.4 -6 0 -7.6
TTGATGCTTCTGAAGAACTT
1920 SEQ ID N0:1367 -13.3 -19.8 60.4 -6 0 -8.3
TTTGATGCTTCTGAAGAACT
1921 SEQ ID N0:1368 -13.3 -19.8 60.4 -6 0 -8.3
TGAGGGGAGCAGAATTTTTT
2119 SEQ ID N0:1369 -13.3 -21.7 64.9 -8.4 0 -4.1
GCTCAGTCATGGGGTAGTGC
2811 SEQ ID N0:1370 -13.3 -27.6 82.4 -14.3 0 -4.7
ATCCCAGTAAAGACCAGGTT
2857 SEQ ID N0:1371 -13.3 -24.6 69.6 -11.3 0 -5.9
GAACACAATCAGGAAGGAGT
3263 SEQ ID N0:1372 -13.3 -20.2 60.5 -6.9 0 -2.9
GGAACACAATCAGGAAGGAG
3264 SEQ ID N0:1373 -13.3 -20.2 60 -6.9 0 -2.9
CGTTTTTCCACCGAGCTTGC
4638 SEQ ID N0:1374 -13.3 -27.7 75.2 -14.4 0 -5.5
CACGTTTTTCCACCGAGCTT
4640 SEQ ID NO:1375 -13.3 -26.8 72.9 -13.5 0 -5.2
ATGAGGATCATGATGCTGAT
5059 SEQ TD NO:1376 -13.3 -21.4 64.1 -6.5 -1.5 -8.5
GAAGAGCAGGAGGCCGATGT
5441 SEQ ID NO:1377 -13.3 -26.4 73.4 -12.5 -0.3 -7.7
CCCAACAGATGGGTCCCCAC
5693 SEQ ID N0:1378 -13.3 -30.4 78.9 -14.5 -2.6 -8.8
TTCGAAGGGCATCCATCTCT
6066 SEQ ID N0:1379 -13.3 -25.8 73 -11.3 -1.1 -7.9
CACCTCCTCTTGTTTACGTT
6158 SEQ ID N0:1380 -13.3 -25.9 73.8 -12.6 0 -4.8
GTTTTATAGGTAAGTCAATC
6276 SEQ ID N0:1381 -13.3 -18.3 59 -5 0 -2.3
TAGATATATTTTTCTAGAAT
7261 SEQ ID N0:1382 -13.3 -15 50.8 -1.1 0 -7.7
GCATAGGCAATATTAACATG
7559 SEQ ID N0:1383 -13.3 -18.9 57.5 -4.7 -0.8 -6.3
GACAGAGCAGGTTGAATTCA
7646 SEQ ID N0:1384 -13.3 -22.2 66.4 -8.4 0 -8.1
TTGACATAATGGACAGAGCA
7657 SEQ ID N0:1385 -13.3 -20.4 61.1 -7.1 0 -4.1
GAGGCAACCATAGTTGGTAG
8121 SEQ TD N0:1386 -13.3 -23.6 69.1 -7.9 -2.4 -8.7
GCTCACCATTCTTTTTAGCA
8420 SEQ ID N0:1387 -13.3 -24.7 72.6 -10.7 -0.4 -4.1
AAAGTTGGAACATGTGAACT
g7p2 SEQ ID N0:1388 -13.3 -18.1 55.7 -4.1 -0.3 -8.3
GGTTACTACTATTATTATCA
g72g SEQ ID N0:1389 -13.3 -18.5 59 -5.2 0 -2.3
ATTGAAAGAAGATGAGTTTA
8796 SEQ ID N0:1390 -13.3 -15.5 51 -2.2 0 -2.2
135
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TCTGCTTATGCCTCCGCTTC
4 SEQ ID N0:1391 -13.2 -28.9 80.3 -14.8 -0.8 -5
TAGGGTATAACGTGTCTTCC
148 SEQ ID NO:1392 -13.2 -23.2 68.6 -10 0 -5.3
GAATTATCTCATTTATTCTT
352 SEQ ID N0:1393 -13.2 -17.5 56.6 -4.3 0 -4.1
ACATTTAATTACGTGTAGCT
439 SEQ ID N0:1394 -13.2 -19.7 60.1 -6.5 0 -5
TTTCGACCAGCCTTCACACA
1525 SEQ ID N0:1395 -13.2 -26.6 73.3 -13.4 0 -4.6
CAGCAGCACGTAATGTCAAC
1641 SEQ ID N0:1396 -13.2 -22.7 65.5 -9.5 0 -5.4
GATGCTGCCGCAACTGCCTG
1849 SEQ ID N0:1397 -13.2 -29.5 77.4 -14.7 -1.6 -8
AACTCAACTTTGATGCTTCT
1929 SEQ ID N0:1398 -13.2 -20.8 62.8 -7.6 0 -5
ATGAGGGGAGCAGAATTTTT
2120 SEQ ID N0:1399 -13.2 -21.6 64.6 -8.4 0 -4.1
TCTGTGCGGCACAAACAGTG
2300 SEQ ID N0:1400 -13.2 -24.4 68.8 -8.6 -1.4 -13.2
TGTTGCGTCGCTCTCCATGT
2319 SEQ ID N0:1401 -13.2 -28.6 79.8 -14.8 -0.3 -6.9
GTGCTGTGCATCTTCCCATT
2392 SEQ ID NO:1402 -13.2 -28.2 80.2 -13.9 -1 -5.5
TATGCTCACGGCTCTTTGCC
2576 SEQ ID N0:1403 -13.2 -27.7 77.4 -12.6 -1.9 -7.4
GGCCATAAAGAGGGTATTTA
2786 SEQ ID N0:1404 -13.2 -21.8 64.2 -8.6 0 -7
TGGCCATAAAGAGGGTATTT
2787 SEQ ID N0:1405 -13.2 -22.1 64.6 -8.4 0 -8.3
GCAGTACAGACAATCCCTCC
3003 SEQ ID N0:1406 -13.2 -26.8 74.9 -12.9 -0.4 -5.3
CTGAATGATCGCAGTACAGA
3013 SEQ ID N0:1407 -13.2 -21.5 63.2 -7.6 -0.4 -5.7
AACACCAAGGTGAGGTTTCC
3118 SEQ ID NO:1408 -13.2 -24.4 69.7 -10.1 -0.8 -9.6
GAAGGAGTGGAAGAAGTCGT
3251 SEQ ID N0:1409 -13.2 -21.5 63.8 -7.8 -0.2 -3
AATTCCAGTATTATTGGACA
3617 SEQ ID NO:1410 -13.2 -20 60.8 -5.3 -1.4 -7.2
TTTTCTGTTCCTCTGTCATA
4923 SEQ ID N0:1411 -13.2 -23.5 72.1 -10.3 0 -1.8
GTATGGGTTTCTGAGGTTTC
4977 SEQ TD N0:1412 -13.2 -23.6 73 -10.4 0 -2.8
GCGAGGTATGGGTTTCTGAG
4982 SEQ ID N0:1413 -13.2 -25 73.1 -11.8 0 -3.4
GGAATTTGTTTGCTGGGCGA
4998 5EQ ID N0:1414 -13.2 -25 70.6 -11 -0.6 -4.9
TGTCTGAGGGAAACGAGCTT
5197 SEQ ID N0:1415 -13.2 -23.1 66.6 -9.9 0 -5.7
TTTTACTTTTGATTTTCTCT
6457 SEQ ID N0:1416 -13.2 -18.9 60.6 -5.7 0 -2.2
AATCCTTTAAATATTAGAGG
7132 5EQ ID N0:1417 -13.2 -16.4 52.7 -2.2 -0.9 -5.6
TGACATAATGGACAGAGCAG
7656 SEQ ID N0:1418 -13.2 -20.3 60.9 -7.1 0 -4.1
CATTTAATTACGTGTAGCTT
438 SEQ ID NO:1419 -13.1 -19.6 59.9 -6.5 0 -5
136
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TCCTGCACATTTAATTACGT
445 SEQ ID N0:1420 -13.1 -21.9 63.7 -8.8 0 -4.8
CATCCTGCACATTTAATTAC
447 SEQ ID N0:1421 -13.1 -20.6 61.5 -7.5 0 -4.6
TTTGGCTTTGGTTTGTTCTC
607 SEQ ID N0:1422 -13.1 -23.9 73.3 -10.8 0 -3.7
TCAAAAGCAGAATCGCTTGG
1315 SEQ ID N0:1423 -13.1 -20.6 60 -5.7 -1.8 -9.3
TTACATTAACAAATGTCCCA
1377 SEQ ID N0:1424 -13.1 -19.6 58.1 -4.9 -1.5 -6.6
AATATCATGTATGTTTTCCC
1660 SEQ ID N0:1425 -13.1 -20.9 63.2 -7.8 0 -4.5
TGCTTCTGAAGAACTTTCCA
1916 SEQ ID NO:1426 -13.1 -22.3 65.6 -8.5 -0.4 -8.3
GACTAACGTTACTGTTGCGT
2331 SEQ ID N0:1427 -13.1 -22.9 66.1 -9.3 -0.2 -7.8
AGTGCTGTGCATCTTCCCAT
2393 SEQ ID NO:1428 -13.1 -28.1 80.2 -13.9 -1 -5.5
ACACTCCCGCATCTTATTTT
3527 SEQ ID NO:1429 -13.1 -25.1 70.7 -12 0 -3.6
GGGTTGTTTATGAATGACAT
3742 SEQ ID N0:1430 -13.1 -20.2 61.5 -6.3 -0.6 -5.4
CAGCATATTCTAGCATGGTT
4182 SEQ ID N0:1431 -13.1 -23 68.9 -8.9 -0.9 -5
TCACGTTTTTCCACCGAGCT
4641 SEQ ID N0:1432 -13.1 -27.1 74.1 -14 0 -5
CTTTCACGTTTTTCCACCGA
4644 SEQ ID N0:1433 -13.1 -25.5 70.5 -12.4 0 -4.5
CGCCAACATTATCAAAGTTT
4665 SEQ ID N0:1434 -13.1 -20.4 59.5 -7.3 0 -3.7
TGAAGTTTAACATCTCGTGA
4756 SEQ ID N0:1435 -13.1 -19.5 59.6 -6.4 0 -3.6
GTAGTGTCTGAGGGAAACGA
5201 SEQ ID N0:1436 -13.1 -22.4 66 -9.3 3 -3.5
TTTGATCAGACGTAGGATTC
5360 SEQ ID N0:1437 -13.1 -20.7 63.2 -7.6 0 -6.6
AACTGAGCTGCCAGGGTGAA
5663 SEQ ID N0:1438 -13.1 -25.7 72 -11.7 -0.6 -9.3
CCATGGGCAGATCCATGGCA
5976 SEQ ID N0:1439 -13.1 -29 78.4 -11.5 -4.4 -11.4
ATAGGCTCATAAGAGACTTT
6124 SEQ ID N0:1440 -13.1 -20.2 62.2 -5.9 -1.1 -4.5
ATGGACCTCCTCTTGAAGTC
6545 SEQ ID N0:1441 -13.1 -25.1 72.9 -11.4 -0.3 -5.l
TAGGTAGCCATTGGGTTTCT
6710 SEQ ID N0:1442 -13.1 -25.5 75.4 -11.8 -0.3 -6.3
GAAGTTAAAAATAGAATGGA
6798 SEQ ID N0:1443 -13.1 -13.5 46.2 0 0 -2.8
AGAGGAGACTTTACAGGCAC
7117 SEQ ID N0:1444 -13.1 -22.8 68.3 -8.8 -0.7 -5.2
TCTGCTTGACATAATGGACA
7662 SEQ ID N0:1445 -13.1 -21.3 63.3 -8.2 0 -3.6
GCAACCATAGTTGGTAGAAA
8118 SEQ ID N0:1446 -13.1 -21 62 -5.5 -2.4 -8.6
TTTATATCATGTTAGGTAAT
8303 SEQ ID N0:1447 -13.1 -17.1 55.6 -4 0 -4.7
TGGTTACTACTATTATTATC
g72g SEQ ID N0:1448 -13.1 -17.8 57.6 -4.7 0 -2.3
137
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGTATACATAGGAGTTTATA
8886 SEQ ID N0:1449 -13.1 -17.8 57.4 -4.7 0 -7.4
AGCTTCTTGCATACGAATTA
423 SEQ ID N0:1450 -13 -21.1 62.7 -6.5 -1.5 -5.3
TTTGGTTTGTTCTCATCATC
601 5EQ ID N0:1451 -13 -22 68.9 -9 0 -1.9
CAACGCTGAGACATTGCCCA
1097 SEQ ID N0:1452 -13 -26.4 70.7 -13.4 0 -3.3
CCACTGCAAACATTTATTCC
1292 SEQ ID NO:1453 -13 -22.2 63.6 -9.2 0 -4.9
TACATTAACAAATGTCCCAT
1376 SEQ ID N0:1454 -13 -19.5 57.8 -4.9 -l.5 -6.6
TCCACAGAGTAAAGGGTCTT
1466 SEQ ID N0:1455 -13 -23.1 68.4 -10.1 0 -3.6
TTCCACAGAGTAAAGGGTCT
1467 SEQ ID N0:1456 -13 -23.1 68.4 -10.1 0 -3.6
GGCCTGATTCTGCTCCTCAT
1751 SEQ ID N0:1457 -13 -29 81.6 -15.4 -0.3 -6.4
TGGCCTGATTCTGCTCCTCA
1752 SEQ ID N0:1458 -13 -29 81.4 -15.4 -0.3 -7.2
CGCTGTCTTCAGATTCGGAT
2046 SEQ ID N0:1459 -13 -24.9 71.2 -10.4 -1.4 -5.7
TGATGAGGGGAGCAGAATTT
2122 SEQ ID N0:1460 -13 -22 65.1 -9 0 -4.1
CTGTGTTCATCATCAGCAAA
2248 SEQ ID N0:1461 -13 -21.8 65.4 -8.1 -0.4 -4.1
CCTGACTAACGTTACTGTTG
2334 SEQ ID N0:1462 -13 -22 64.1 -8.5 -0.2 -7.8
GGCCTGACTAACGTTACTGT
2336 SEQ ID N0:1463 -13 -24.9 70.4 -11.4 0 -7.9
TCTGAATGATCGCAGTACAG
3014 SEQ ID N0:1464 -13 -21.3 63.4 -7.6 -0.4 -6.3
GGCCAACACCAAGGTGAGGT
3122 SEQ ID N0:1465 -13 -27.5 75.1 -12.9 -1.3 -10.8
TGGCCAGCGACCTCCATACA
3322 SEQ ID N0:1466 -l3 -29.7 78.2 -16.1 -0.1 -8.3
TCTGAGCTAAATGAACTCAA
3421 SEQ ID N0:1467 -13 -18.3 56.4 -4 -1.2 -5.1
GTAGCAGCAAGGTTGTCTGA
3436 SEQ ID N0:1468 -l3 -24.8 74.2 -10.4 -1.3 -8.2
GACCTCCAAACTTCTTTTTC
4893 SEQ ID N0:1469 -13 -22.7 66.5 -9.7 0 -1.8
ATTTTTTCTGTTCCTCTGTC
4926 SEQ ID N0:1470 -13 -23.3 72.3 -10.3 0 -0.6
TGCTGGGCGAGGTATGGGTT
4988 SEQ ID N0:1471 -13 -28.1 78.8 -14.3 -0.6 -4.3
TTGCTGGGCGAGGTATGGGT
4989 SEQ ID N0:1472 -13 -28.1 78.8 -14.3 -0.6 -4.4
ACAGAATACTTTTCTATCAT
5296 SEQ ID N0:1473 -13 -18 57.2 -4 -0.9 -4.4
ATCAAAGCAAAGAGCAGCGT
5398 SEQ ID N0:1474 -13 -21.7 62.5 -7.1 -1.6 -5.7
ACTGAGCTGCCAGGGTGAAT
5662 SEQ ID N0:1475 -13 -26.4 74.4 -12.5 -0.6 -9.3
TTAACTGAGCTGCCAGGGTG
5665 SEQ TD N0:1476 -13 -25.6 72.9 -11.7 -0.6 -9.3
AAGAGGAGGATCCAGGGCAG
5924 SEQ ID N0:1477 -13 -25.5 72.9 -9.9 -2.6 -9
138
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTCCCATTTAGTTTGTCAAT
6307 SEQ ID N0:1478 -13 -22.1 66 -9.1 0 -2.9
TTTGGCATGGACCTCCTCTT
6551 SEQ ID N0:1479 -13 -27.5 77.4 -14 -0.1 -5.1
GATAGCCTTTAAACTATGTT
7532 5EQ ID NO:1480 -13 -19.6 59.8 -5.9 -0.4 -5.8
ATTTGTAATAGCTTTAGTGC
8231 SEQ ID N0:1481 -13 -19.7 61.9 -6.7 0 -4.6
TTCTTTTTAGCAATAGCAAT
8412 SEQ ID N0:1482 -13 -18.8 58.6 -4.1 -1.7 -4.3
TGCACTAGTTTGTTGTAAAA
8606 SEQ ID N0:1483 -13 -18.8 58.4 -5.3 -0.2 -6.1
GATGAGTTTAGATGCTTATA
8786 SEQ ID N0:1484 -13 -19.1 60.3 -6.1 0 -3.6
TTATATTGAAAGAAGATGAG
8800 SEQ ID N0:1485 -13 -13.9 47.5 -0.7 0 -2.2
GTGAP.TTATCTCATTTATTC
354 SEQ ID N0:1486 -12.9 -17.7 57.3 -4.3 -O.l -4
TTTCATCCTGCACATTTAAT
450 SEQ TD N0:1487 -12.9 -21.2 63.2 -8.3 0 -4.8
GTCAGGAGGGTTGCTCAAGG
908 SEQ ID N0:1488 -12.9 -26.1 76.9 -11.9 -1.2 -5
AGACATTGCCCAGGTCCACA
1089 SEQ ID N0:1489 -12.9 -28.5 78.1 -14.9 -0.5 -4.4
TTGGTTTCAAAAGCAGAATC
1321 SEQ ID N0:1490 -12.9 -18.5 57.3 -5.1 -0.1 -1.1
TCTGAGCCATTTCCACAGAG
1477 SEQ ID N0:1491 -12.9 -25.2 72.5 -11.4 -0.8 -4.6
GCTGTGCATCTTCCCATTTG
2390 SEQ ID N0:1492 -12.9 -27.1 77 -14.2 0 -5.4
TGCATCACAGCAGTCCCAGA
2687 SEQ TD N0:1493 -12.9 -27.9 78.5 -14.1 -0.8 -4.8
ACACAATCAGGAAGGAGTGG
3261 SEQ ID N0:1494 -12.9 -21.5 63.7 -7.8 -0.6 -4.8
GACGGTGAGGCTGGGGTTGT
3755 SEQ ID N0:1495 -12.9 -28.6 80.6 -15.7 0 -3.7
GTGACGGTGAGGCTGGGGTT
3757 SEQ TD N0:1496 -12.9 -28.6 80.6 -15.7 0 -3.7
ATACTGTAGCAGGTTTTTCG
4057 SEQ ID N0:1497 -12.9 -22.2 67 -8.4 -0.7 -5.3
GGTTTTGATAGTCTTTCGCT
4166 SEQ ID N0:1498 -12.9 -23.6 71 -10.7 0 -3.4
TCAAACATGTTACCCGTTGT
4573 SEQ ID N0:1499 -12.9 -23.1 65.6 -9.5 0 -9
ATCCCAAAGATGGCATAGAT
5473 SEQ ID N0:1500 -12.9 -22.3 63.9 -8 -1.3 -5
GACATCCCAAAGATGGCATA
5476 SEQ ID NO:1501 -12.9 -23.2 65.4 -8 -2.3 -8
TAGGCAAAGTTGGACATCCC
5488 SEQ ID N0:1502 -12.9 -24.4 69.1 -11.5 0 -4.9
GCAGATCATGCTGTTGCCAA
5555 SEQ ID N0:1503 -12.9 -26 73.6 -11.5 -1.6 -8.3
TCCCAACAGATGGGTCCCCA
5694 SEQ ID N0:1504 -12.9 -30.6 80 -14.5 -3.2 -8.6
TCTTCCATCTGTATTCGAAG
6079 SEQ ID N0:1505 -12.9 -21.9 65.3 -8.5 -0.2 -7.1
ATATGGAAGTTAAAAATAGA
6803 SEQ ID N0:1506 -12.9 -13.3 46 0 0 -2.8
139
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GATATGGAAGTTAAAAATAG
6804 SEQ ID N0:1507 -12.9 -13.3 46 0 0 -2.8
AGATATGGAAGTTAAAAATA
6805 SEQ ID N0:1508 -12.9 -13.3 46 0 0 -2.8
TTGAGAGACAGGGTTCTTGT
6939 SEQ ID NO:1509 -12.9 -23.1 70.4 -9.7 -0.2 -5
CTTTGCTGAGAGCAGAAGAT
7333 SEQ ID N0:1510 -12.9 -22 65.7 -6.7 -2.4 -8.2
ATAGACTATCAGCTTTGCTG
7345 SEQ ID N0:1511 -12.9 -21.8 66.3 -6.7 -2.2 -8.1
CATAGACTATCAGCTTTGCT
7346 SEQ ID N0:1512 -12.9 -22.5 67.7 -8.9 -0.4 -4.5
TGATAGCCTTTAAACTATGT
7533 SEQ ID N0:1513 -12.9 -19.5 59.4 -5.9 -0.4 -5.8
GTGATAGCCTTTAAACTATG
7534 SEQ ID N0:1514 -12.9 -19.5 59.4 -5.9 -0.4 -5.8
GTTGAATTCATTCTATCACC
7636 SEQ ID N0:1515 -12.9 -20.8 63.4 -7.2 -0.4 -8.4
TTCAAATTATTCTGCTTGAC
7672 SEQ ID N0:1516 -12.9 -18.6 58.1 -5.2 -0.2 -3.6
TGAAGAATAGGTTTTGTCAG
7789 SEQ ID N0:1517 -12.9 -18.5 58.4 -5.6 0 -2.7
TTATATTTGTAATAGCTTTA
8235 SEQ ID N0:1518 -12.9 -16.2 53.5 -3.3 0 -4.6
ACTTTGTTCATGGCTAAAAA
8269 SEQ ID N0:1519 -12.9 -18.5 56.8 -5.6 0 -4.7
CCCAGAGCCCAATAAGTGAA
8486 SEQ ID N0:1520 -12.9 -25.2 68.2 -12.3 0 -3.3
CTGCTTTTAATTTGCCTTTG
8651 SEQ ID NO:1521 -12.9 -22 65 -9.1 0 -3.6
TTTTTTTTTTTTTTTTTTTC
9094 SEQ ID N0:1522 -12.9 -16.2 54.7 -3.3 0 0
CTTTCTTTCTCTGTGGATAA
53 SEQ ID N0:1523 -12.8 -21.2 65.5 -8.4 0 -2.3
ATTTAATTACGTGTAGCTTC
437 SEQ ID N0:1524 -12.8 -19.3 60 -6.5 0 -5
GTGCCTGTGCCATCTTTTCA
465 SEQ ID NO:1525 -12.8 -28.3 80.7 -14.7 -0.6 -3
TCATCATTATCTTGTTCCTT
586 SEQ ID N0:1526 -12.8 -22.1 67.7 -9.3 0 -1.9
GGTTCTTTCCAGCTTCCAAG
633 SEQ ID N0:1527 -12.8 -26.3 76.1 -13.5 0 -4.5
ACCCTCTTGCCAAGATTTTT
984 SEQ ID N0:1528 -12.8 -25.3 71.1 -11.7 -0.6 -6.3
AATGTCCCATTTGAATCCAT
1366 SEQ ID NO:1529 -12.8 -22.8 64.9 -9.5 -0.2 -3.6
CATAGGCCATGGCCACCACA
1734 SEQ ID N0:1530 -12.8 -29.6 78.2 -12.2 -2.5 -17.4
GTGCTCTCTCTGTCTTCTTT
1985 SEQ ID N0:1531 -12.8 -25.9 80.7 -13.1 0 -3.6
TGTGTTCATCATCAGCAAAG
2247 SEQ ID N0:1532 -12.8 -20.9 63.7 -8.1 0 -4.1
TGCATCTTCCCATTTGCTGG
2386 SEQ ID NO:1533 -12.8 -27.1 76.1 -13 -1.2 -5.9
CTATGCTCACGGCTCTTTGC
2577 SEQ ID N0:1534 -12.8 -26.6 75.7 -12.6 -1.1 -4.9
AGACCAAGCTCCATTAAACT
2974 SEQ ID N0:1535 -12.8 -22.1 63.4 -9.3 0 -5
140
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CCTCCACATTTGACAGACCA
2988 SEQ ID N0:1536 -12.8 -26.1 71.9 -13.3 0 -2.4
TGATCGCAGTACAGACAATC
3008 SEQ ID N0:1537 -12.8 -21.3 63.3 -7.8 -0.4 -5.7
CACTCCCGCATCTTATTTTT
3526 SEQ ID N0:1538 -12.8 -25 70.5 -12.2 0 -3.6
AAGCTCTTTGCTTATTTCAA
3635 SEQ ID N0:1539 -12.8 -20.6 63 -5.7 -2.1 -5.8
TGTGACGGTGAGGCTGGGGT
3758 SEQ ID N0:1540 -12.8 -28.5 80 -15.7 0 -3.7
ATTTAATTTCTCTTTGCTTT
3854 SEQ ID N0:1541 -12.8 -19.1 60.4 -6.3 0 -3.6
ACCAGATCTTCCCTTTGCCT
4029 SEQ ID N0:1542 -12.8 -29.1 79.8 -16.3 0 -5.8
GCATATTCTAGCATGGTTTT
4180 SEQ ID N0:1543 -12.8 -22.5 68.2 -9.2 -0.1 -5
AGAAATCTAGCCAGCACCAG
4284 SEQ ID N0:1544 -12.8 -24.1 68.3 -11.3 0 -4.6
TTTACTTTCACGTTTTTCCA
4648 SEQ ID N0:1545 -12.8 -22 65.6 -9.2 0 -4.7
GACCATTCCTTGGAATTTGT
5009 5EQ ID N0:1546 -12.8 -23.5 67.7 -9 -1.7 -8.4
GGTCATGTATTTGCCCTGGT
5117 SEQ ID N0:1547 -12.8 -27.7 79.1 -14.9 0 -4.7
GTTGGACATCCCAAAGATGG
5480 SEQ ID N0:1548 -12.8 -23.5 66.5 -8.4 -2.3 -8.3
GACACCTCCTCTTGTTTACG
6160 SEQ ID N0:1549 -12.8 -25.4 72 -12.6 0 -3
GAAGGAGGAGGGGTGGTAGA
6358 SEQ ID N0:1550 -12.8 -25 73.3 -12.2 0 -0.7
TTGGAAAGCATTTGACCTAA
7222 SEQ ID N0:1551 -12.8 -19.9 59 -6.3 -0.6 -4.1
GATTTAATAGAAGTTGTTTA
7444 SEQ ID N0:1552 -12.8 -15.8 52.5 -3 0 -2.5
AAGACTTGTGAAGAATGGAT
7595 SEQ ID N0:1553 -12.8 -17.9 55.6 -4.6 -0.2 -3.5
TTGAGTGTTTGACCAATGTA
8087 SEQ ID N0:1554 -12.8 -21 63.5 -8.2 0 -3.4
CAGAGCCCAATAAGTGAAAT
8484 SEQ TD N0:1555 -12.8 -20.5 59.5 -7.7 0 -3.3
CCACCTTATATAATTTATTA
9075 SEQ ID N0:1556 -12.8 -18 55.8 -5.2 0 -5.1
TTAGGGTATAACGTGTCTTC
149 SEQ ID N0:1557 -12.7 -21.3 65.1 -8.6 0 -5.3
CCTGCACATTTAATTACGTG
444 SEQ ID N0:1558 -12.7 -21.5 62.3 -8.8 0 -5
TGGCTTTGGTTTGTTCTCAT
605 SEQ ID N0:1559 -12.7 -24.4 73.6 -11.7 0 -3.7
CTTATTGATATAGTAGGGAT
713 SEQ ID N0:1560 -12.7 -18.7 59.1 -6 0 -2.7
TTCCATGGATCACGAAGAAA
1024 SEQ ID N0:1561 -12.7 -20.2 58.9 -6.5 0 -10
TGAGACATTGCCCAGGTCCA
1091 SEQ ID N0:1562 -12.7 -28.2 77.6 -14.8 -0.5 -4.4
CCTCCATTCTTTAGCACCTT
1952 SEQ ID N0:1563 -12.7 -27 76 -14.3 0 -4.1
GCTATTGCGTCTTGGGGAAA
2171 SEQ ID N0:1564 -12.7 -24.5 69.4 -10.9 -0.8 -5.2
141
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTCGCTCTCCATGTCTGTGC
2313 SEQ ID N0:1565 -12.7 -29 83.9 -16.3 0 -4.3
GTGCATCTTCCCATTTGCTG
2387 SEQ ID N0:1566 -12.7 -27.1 77 -13.1 -1.2 -5.4
GTTTTACTTTTAACCATGCA
2703 SEQ ID N0:1567 -12.7 -21 63 -8.3 0 -5.2
GCCATAAAGAGGGTATTTAA
2785 SEQ ID N0:1568 -12.7 -19.9 59.6 -7.2 0 -3.7
AGACAATCCCTCCACATTTG
2996 SEQ ID N0:1569 -12.7 -24.3 68.3 -11.6 0 -2.9
GTTTGGCCAGCGACCTCCAT
3325 SEQ ID N0:1570 -12.7 -30.5 81.2 -17.1 -0.1 -8.8
ATAAGGCACATGGTTTGGCC
3337 SEQ ID N0:1571 -12.7 -25.2 71.6 -10.4 -2.l -6.2
AGCAAGGTTGTCTGAGCTAA
3431 SEQ ID N0:1572 -12.7 -23.1 69 -9.4 -0.9 -5.5
CTTTTTGGAAACACTCCCGC
3537 SEQ ID N0:1573 -12.7 -24.7 67.9 -10.9 -1 -4.6
ACTTTTGGCTTTCTAAAAAA
3559 5EQ ID N0:1574 -12.7 -17 53.5 -3.5 -0.6 -4.3
TTTGATAGTCTTTCGCTGTT
4163 SEQ ID N0:1575 -12.7 -22.4 68.1 -9.7 0 -3.4
CCCGTTGTCATGTTAACACA
4561 SEQ ID N0:1576 -12.7 -24.5 68.8 -11.1 -0.3 -8.7
ACTTTCACGTTTTTCCACCG
4645 SEQ ID N0:1577 -12.7 -25.1 69.8 -12.4 0 -4.7
CAACATTATCAAAGTTTACT
4662 SEQ ID N0:1578 -12.7 -16.6 53.2 -3.9 0 -4.1
ACATAATATCCATCCAGCCT
4722 SEQ ID N0:1579 -12.7 -24.5 68.9 -11.8 0 -3.2
TTGGAATTTGTTTGCTGGGC
5000 SEQ ID N0:1580 -12.7 -23.7 69.4 -11 0 -4.4
AGGATCATGATGCTGATATC
5056 SEQ ID N0:1581 -12.7 -20.9 63.7 -7.3 -0.6 -8.5
ATTTGCCCTGGTCATCCGTT
5109 SEQ ID N0:1582 -12.7 -28.9 79.1 -15 -1.1 -4.4
TGTATTTGCCCTGGTCATCC
5112 SEQ ID N0:1583 -12.7 -27.7 78.3 -15 0 -4.2
ATCATGCTGTTGCCAAAGGT
5551 SEQ ID N0:1584 -12.7 -24.6 70.4 -11.4 -0.1 -4.4
CCATAAACCTGTCTTCCATC
6090 SEQ ID N0:1585 -12.7 -24.2 68.6 -11.5 0 -2
ACCTCCTCTTGTTTACGTTT
6157 SEQ ID N0:1586 -12.7 -25.3 73.1 -12.6 0 -4.8
TGTTTTATAGGTAAGTCAAT
6277 SEQ ID N0:1587 -12.7 -17.9 57.5 -5.2 0 -2.3
TGGTTTTGTTACACTATCAT
6380 SEQ ID N0:1588 -12.7 -20.5 63.5 -7.8 0 -2.7
CTATCCCTATAGTCTAGGTA
6724 SEQ ID N0:1589 -12.7 -23.6 70.9 -l0 -0.8 -5.1
TAATCCTTTAAATATTAGAG
7133 SEQ ID N0:1590 -12.7 -14.9 49.7 -2.2 0 -4.7
ATAATCCTTTAAATATTAGA
7134 SEQ ID N0:1591 -12.7 -14.9 49.6 -2.2 0 -5.3
CTTTGTTCATGGCTAAAAAG
8268 SEQ ID N0:1592 -12.7 -18.3 56.5 -5.6 0 -4.7
ATTTTTTTTCTTTCTTTCTC
62 SEQ ID N0:1593 -12.6 -19.4 63.1 -6.8 0 -0.3
142
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATCCTTGACAGGTATCTCAT
276 SEQ ID N0:1594 -12.6 -23.4 70 -9.8 -0.9 -3.5
TTACGTGTAGCTTCTTGCAT
431 5EQ ID N0:1595 -12.6 -23.6 70 -9.4 -1.5 -7.2
TCTGCAGCACGTTTTTCGAT
544 SEQ ID N0:1596 -12.6 -24.7 70.5 -10.9 -0.9 -9.8
GCCTTTCCTTTATTCATTAC
745 SEQ ID N0:1597 -12.6 -23.3 69.1 -10.7 0 -2
TTCTAAGCAAAACCCTCTTG
995 SEQ TD N0:1598 -12.6 -21.3 61.8 -8.7 0 -4.1
GTTCCTCCATTCTTTAGCAC
1955 SEQ ID N0:1599 -12.6 -25.7 75.6 -13.1 0 -4.1
CGCCGTCTTCAAATGTGCTG
2265 SEQ TD N0:1600 -12.6 -25.6 70.1 -13 0 -3.6
CCAGAGGAATCCTCCAGCAT
2554 SEQ ID N0:1601 -12.6 -27.3 75 -12.5 -2.2 -11.2
TTCCAGAGGAATCCTCCAGC
2556 SEQ ID N0:1602 -12.6 -27.1 76 -12.6 -1.9 -10.4
TGACAGACCAAGCTCCATTA
2978 SEQ ID N0:1603 -12.6 -23.9 68 -11.3 0 -5
CGCGGAACACAATCAGGAAG
3267 SEQ ID N0:1604 -12.6 -21.8 61 -9.2 0 -6.4
TTCAGAACCACAAGGTTTCC
3382 SEQ ID N0:1605 -12.6 -23.2 67.1 -8.6 -2 -6.8
CTGAGCTAAATGAACTCAAT
3420 SEQ 2D N0:1606 -12.6 -17.9 55.1 -4 -1.2 -5.1
CTATCTTATTGCCTTCATGG
3588 SEQ ID NO:1607 -12.6 -22.9 67.9 -10.3 0 -4.7
TAAGCTCTTTGCTTATTTCA
3636 SEQ ID N0:1608 -12.6 -21 64.6 -5.7 -2.7 -6.9
CTTTGCCTTCTTCTGTACTT
4017 SEQ ID N0:1609 -12.6 -24.7 73.6 -12.1 0 -4.8
GATCTTCCCTTTGCCTTCTT
4025 SEQ ID N0:1610 -12.6 -27.7 78.8 -15.1 0 -4.1
TATCAAAGTTTACTTTCACG
4656 SEQ ID N0:1611 -12.6 -17.9 56 -3.9 -1.3 -7.1
TGGAATTTGTTTGCTGGGCG
4999 SEQ ID N0:1612 -12.6 -24.4 69.2 -11 -0.6 -4.9
CATGTATTTGCCCTGGTCAT
5114 SEQ ID N0:1613 -12.6 -26 74 -13.4 0 -4.2
TCCCAAAGATGGCATAGATA
5472 SEQ ID N0:1614 -12.6 -22 63.4 -8 -1.3 -5
GAAGGGCATCCATCTCTCCA
6063 SEQ ID N0:1615 -12.6 -27.6 77.4 -13.8 -1.1 -4.5
CTGGTTTTGTTACACTATCA
6381 SEQ ID N0:1616 -12.6 -21.4 65.6 -8.8 0 -2.7
AATACTTTAGATATATTTTT
7268 SEQ ID N0:1617 -12.6 -14.4 49.3 -1.8 0 -4.3
TAATAGAAGTTGTTTATCAG
7440 SEQ ID N0:1618 -12.6 -16.1 53.3 -3.5 0 -2.5
TACATCCCTGTTGGAAGCTT
7495 SEQ ID N0:1619 -12.6 -25.1 71.5 -11.4 -1 -7.4
TTTAACCAAGACTTGTGAAG
7602 SEQ ID N0:1620 -12.6 -18.3 56.3 -5.7 0 -4.9
AAAATTTATATCATGTTAGG
8307 SEQ ID NO:1621 -12.6 -14.8 49.6 -2.2 0 -5.2
TCACCATTCTTTTTAGCAAT
8418 SEQ ID N0:1622 -12.6 -21.3 63.9 -g.7 0 -4.1
143
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GGAGTTTATATAATGCATTT
8876 SEQ ID N0:1623 -12.6 -18.3 57.6 -5 0 -8.8
AGGAGTTTATATAATGCATT
8877 SEQ ID N0:1624 -12.6 -18.2 57.5 -5 0 -8.6
ATCTCATCCCTGTCAAACCT
263 SEQ ID N0:1625 -12.5 -25.7 72.2 -13.2 0 -2
AATTATCTCATTTATTCTTA
351 SEQ ID N0:1626 -12.5 -16.6 54.7 -4.1 0 -2.3
GCCTGTGCCATCTTTTCATC
463 SEQ ID N0:1627 -12.5 -27.5 79 -15 0 -3
TCTCTAGTAAAAAGGCGGAA
511 SEQ ID N0:1628 -12.5 -19.3 57.8 -6.8 0 -4
AGGTTCTTTCCAGCTTCCAA
634 SEQ ID N0:1629 -12.5 -26.3 76.1 -13.1 -0.4 -4.8.
TGTTTTCAGTGCTCGGAGAA
1130 SEQ ID N0:1630 -12.5 -23.4 69.1 -10.3 -0.3 -6.4
AGCTTCTTTACCGACTGGAT
1192 SEQ ID N0:1631 -12.5 -24.5 70.1 -11.1 -0.7 -5.4
CAAACATTTATTCCTCAGAT
1286 SEQ 2D N0:1632 -12.5 -19.2 58.4 -6.7 0 -2.5
ATCGCTTGGGGGCCACTGCA
1304 SEQ ID N0:1633 -12.5 -30.9 82.5 -16.5 -1.9 -6.9
GCTTTCGCCGTCTTCAAATG
2270 SEQ ID N0:1634 -12.5 -25 69.4 -12.5 0 -3.2
GTTGCGTCGCTCTCCATGTC
2318 SEQ ID N0:1635 -12.5 -29 81.8 -15.9 -0.3 -6.9
CTGACTAACGTTACTGTTGC
2333 SEQ ID NO:1636 -12.5 -21.8 64.5 -8.8 -0.2 -7.6
TCCCATTTGCTGGAAGCCCT
2379 SEQ ID NO:1637 -12.5 -29.8 79.2 -15.1 -2.2 -5.6
TGGCTATGCTCACGGCTCTT
2580 SEQ ID N0:1638 -12.5 -27.7 78 -14 -1.1 ' -5.3
TTTTAACCATGCATCACAGC
2696 SEQ ID N0:1639 -12.5 -22.5 65.6 -10 0 -6.6
AATCCCAGTAAAGACCAGGT
2858 SEQ ID N0:1640 -12.5 -23.8 67.1 -11.3 0 -5.7
CAATAATTCCATCAAAGATA
2946 5EQ ID N0:1641 -12.5 -16.2 51.5 -3.7 0 -3.5
TGAATGATCGCAGTACAGAC
3012 SEQ ID N0:1642 -12.5 -20.8 61.9 -7.6 -0.4 -5.7
CTGTGACGGTGAGGCTGGGG
3759 SEQ TD N0:1643 -12.5 -28.2 78.4 -15.7 , 0 -3.7
AGATCTTCCCTTTGCCTTCT
4026 SEQ ID N0:1644 -12.5 -27.6 78.7 -15.1 0 -5.6
ATGGGTTTCTGAGGTTTCTT
4975 SEQ ID N0:1645 -12.5 -23.7 72.5 -11.2 0 -2.8
AGTAGTGTCTGAGGGAAACG
5202 SEQ ID N0:1646 -12.5 -21.8 64.9 -9.3 3 -3.4
CAGAATACTTTTCTATCATC
5295 SEQ ID N0:1647 -12.5 -18.2 58 -4.7 -0.9 -4.4
CATCAAAGCAAAGAGCAGCG
5399 SEQ ID N0:1648 -12.5 -21.2 60.8 -7.1 -1.6 -5.7
TGATGCCATAAACCTGTCTT
6095 SEQ ID N0:1649 -12.5 -23.1 66 -10.6 0 -3
TTGATGCCATAAACCTGTCT
6096 SEQ ID N0:1650 -12.5 -23.1 66 -10.6 0 -2.8
TCACTTCACTGTCTTGTATA
6605 SEQ ID N0:1651 -12.5 -21.7 67.4 -9.2 0 -2.6
144
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ACTATCCCTATAGTCTAGGT
6725 SEQ ID N0:1652 -12.5 -24.1 72.2 -10 -l.5 -7.8
TGGAAGTTAAAAATAGAATG
6800 5EQ ID N0:1653 -12.5 -12.9 45.1 0 0 -2.8
ATGGAAGTTAAAAATAGAAT
6801 SEQ ID N0:1654 -12.5 -12.9 45.1 0 0 -2.8
AATATGGCAGATATGGAAGT
6813 5EQ ID N0:1655 -12.5 -19.3 58.9 -5.4 -1.3 -5.2
ACACCTTTGTCTGATCATTT
6957 SEQ ID N0:1656 -12.5 -22.6 67.6 -10.1 0 -6.2
CAGGTTGAATTCATTCTATC
7639 SEQ ID N0:1657 -12.5 -19.8 61.8 -6.6 -0.4 -8.1
TTCTGCTTGACATAATGGAC
7663 SEQ ID N0:1658 -12.5 -20.7 62.4 -8.2 0 -3.6
TATTCTGCTTGACATAATGG
7665 SEQ ID N0:1659 -12.5 -19.6 60 -7.1 0 -3.6
AAAGTCCATGTTATATTTGT
8245 SEQ ID N0:1660 -12.5 -19 59.1 -6.5 0 -4.3
TCATTTATTCTTACAATATC
344 SEQ ID N0:1661 -12.4 -16.5 54.2 -4.1 0 -2.6
GTTTTCTTATTGATATAGTA
718 SEQ ID N0:1662 -12.4 -17.6 57.7 -5.2 0 -2.7
TTCAAAAGCAGAATCGCTTG
1316 SEQ ID N0:1663 -12.4 -19.5 58 -5.7 -1.3 -8.8
TGTATGTTTTCCCAGCAGCA
1653 SEQ ID N0:1664 -12.4 -26.5 76.2 -14.1 0 -5.4
ATATCATGTATGTTTTCCCA
1659 SEQ ID N0:1665 -12.4 -22.3 66.6 -9.9 0 -4.7
TCTCCTAACCCACCTACTCC
1891 SEQ ID N0:1666 -12.4 -28.8 77.6 -16.4 0 -0.2
GTTACTGTTGCGTCGCTCTC
2324 SEQ ID N0:1667 -12.4 -26.8 77.7 -13.8 -0.3 -6.9
TGCTGTGCATCTTCCCATTT
2391 SEQ ID NO:1668 -12.4 -27.1 77 -13.9 -0.6 -4.9
TGCTCACGGCTCTTTGCCTT
2574 SEQ ID N0:1669 -12.4 -29 80.3 -13.9 -2.7 -8.3
GCCAATGATCTTAATTAGCA
3080 SEQ ID N0:1670 -12.4 -21.1 62.3 -8.7 0 -4.4
GTGAGGTTTCCTAGAGCCCC
3109 SEQ ID N0:1671 -12.4 -29.8 83.3 -16.7 -0.5 -4.4
ATTCCAGTATTATTGGACAT
3616 SEQ ID N0:1672 -12.4 -20.7 62.9 -6.8 -1.4 -7.2
ACGGTGAGGCTGGGGTTGTT
3754 SEQ ID N0:1673 -12.4 -28.1 79.6 -15.7 0 -3.7
CCTTCTCGGGGTAGAACAAC
3907 SEQ ID N0:1674 -12.4 -24.3 68.7 -11.3 -0.3 -3.8
CCAGCGCCAACATTATCAAA
4669 SEQ ID N0:1675 -12.4 -23.5 64.3 -10.6 0 -7.6
GAAGTTTAACATCTCGTGAA
4755 SEQ ID N0:1676 -12.4 -18.8 57.7 -6.4 0 -3.9
TTTCTGTTCCTCTGTCATAA
4922 SEQ ID N0:1677 -12.4 -22.7 69.2 -10.3 0 -1.8
CTAGGGTCATGTATTTGCCC
5121 SEQ ID N0:1678 -12.4 -26.2 75.5 -12.3 -1.4 -6.9
GGAAACGAGCTTCAGCACAA
5189 SEQ ID N0:1679 -12.4 -22.6 64.1 -9.3 -0.7 -6.6
AAGAGCAGCGTGCGGATCCC
5389 SEQ ID N0:1680 -12.4 -29 77 -14.4 -2.2 -11.1
145
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CGGGATCAAACTTTTCCCAA
5859 SEQ ID N0:1681 -12.4 -23.3 64.4 -8.3 -2.6 -7.9
CCTCTTGTTTACGTTTCAAA
6153 SEQ ID N0:1682 -12.4 -21.5 63.5 -9.1 0 -4.8
TTTTATAGGTAAGTCAATCC
6275 SEQ ID N0:1683 -12.4 -19.1 59.8 -6.7 0 -2.5
TTTTTACTTTTGATTTTCTC
6458 SEQ ID NO:1684 -12.4 -18.1 58.8 -5.7 0 -2.2
ATAGTCTAGGTAGCCATTGG
6716 SEQ ID N0:1685 -12.4 -23.8 71.4 -10.8 -0.3 -5.6
GACTTTACAGGCACATAACT
7111 SEQ ID N0:1686 -12.4 -21.2 63.1 -8.8 0 -4
ACTTTAGATATATTTTTCTA
7265 SEQ ID NO:1687 -12.4 -16.4 54.4 -4 0 -4.3
ACTATCAGCTTTGCTGAGAG
7341 SEQ TD N0:1688 -12.4 -22.7 68.6 -6.7 -3.6 -12
AGACTATCAGCTTTGCTGAG
7343 SEQ ID N0:1689 -12.4 -22.7 68.6 -6.7 -3.6 -10.8
TTGAATTCATTCTATCACCA
7635 SEQ ID N0:1690 -12.4 -20.3 61.5 -7.2 -0.4 -8.4
GCTTGACATAATGGACAGAG
7659 5EQ ID N0:1691 -12.4 -20.6 61.8 -8.2 0 -3.3
TGCTTGACATAATGGACAGA
7660 SEQ ID N0:1692 -12.4 -20.6 61.5 -8.2 0 -3.6
ACCCATTATCTAACTTTTAT
8018 SEQ ID N0:1693 -12.4 -20.1 60.5 -7.7 0 -1.6
TTTGTTCATGGCTAAAAAGA
8267 SEQ TD N0:1694 -12.4 -18 55.9 -5.6 0 -4.7
TTATATCATGTTAGGTAATT
8302 SEQ ID N0:1695 -12.4 -17.1 55.6 -4.7 0 -4.7
ATAAGTGAAATGCAATAAAA
8475 SEQ ID N0:1696 -12.4 -12.8 44.6 0 0 -5.6
AATAAGTGAAATGCAATAAA
8476 SEQ ID N0:1697 -12.4 -12.8 44.6 0 0 -5.6
CTGCTTGGTGAATCATGCAC
8621 SEQ ID N0:1698 -12.4 -23.8 69.2 -9.4 -2 -6.5
TGTAGTACTGCTTGGTGAAT
8628 SEQ ID N0:1699 -12.4 -22 66.7 -9.1 0 -7.8
CTTATGTATACATAGGAGTT
8890 SEQ ID N0:1700 -12.4 -19 60.1 -5.1 -0.1 -10.9
GCTTTTTTTTTTTTTTTTTT
113 SEQ ID N0:1701 -12.3 -18.4 59.4 -6.1 0 -2.8
TGAATTATCTCATTTATTCT
353 SEQ ID N0:1702 -12.3 -17.4 56.2 -4.3 -0.6 -4.8
TGCAGCACGTTTTTCGATAG
542 SEQ ID N0:1703 -12.3 -23.1 66.8 -9.8 -0.9 -7.3
TTTTGGGCTTCTTGGCTTTC
567 SEQ ID N0:1704 -12.3 -25.4 75.7 -12.1 -0.9 -3.7
TTTCTTATTGATATAGTAGG
716 SEQ ID N0:1705 -12.3 -17.5 57.1 -5.2 0 -2.7
TTTTATAAGTGACTCAAAGG
968 SEQ ID N0:1706 -12.3 -16.8 54 -4.5 0 -4.7
CCCTCTTGCCAAGATTTTTA
983 SEQ ID N0:1707 -12.3 -24.8 70 -11.7 -0.6 -6.3
TTTCAAAAGCAGAATCGCTT
1317 SEQ 2D N0:1708 -12.3 -19.6 58.4 -5.7 -1.6 -9
TCGAGCATCTGCTGAAATTC
1801 SEQ ID N0:1709 -12.3 -22 64.5 -8.7 -0.9 -7.9
146
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CTTTTTAAGCTGTTCGAGCA
1814 SEQ ID N0:1710 -12.3 -22.6 66.8 -8 -2.3 -7.l
TCCATCCATGGAGAAAAGGA
2081 SEQ ID N0:1711 -12.3 -22.3 63.6 -8.4 -1.4 -10.4
ACAATAATTCCATCAAAGAT
2947 SEQ ID N0:1712 -12.3 -16.7 52.4 -4.4 0 -3.3
TTGGCCAGCGACCTCCATAC
3323 SEQ ID N0:1713 -12.3 -29.1 77.6 -16.1 -0.1 -8.8
GGTTGTTTATGAATGACATA
3741 SEQ ID N0:1714 -12.3 -18.7 58.4 -5.5 -0.8 -6
CGGTGAGGCTGGGGTTGTTT
3753 SEQ ID NO:1715 -12.3 -28 79.4 -15.7 0 -3.7
CTTTGCTTTCTTCTAGTTCT
3843 SEQ ID N0:1716 -12.3 -23 71.7 -10.7 0 -4
ACCTTCTCGGGGTAGAACAA
3908 SEQ ID N0:1717 -12.3 -24.3 68.7 -11.1 -0.7 -4.7
TTTAAAGTCTTCTTCGGGTT
3944 SEQ ID N0:1718 -12.3 -21.4 64.9 -8.4 -0.5 -4
CAGATCTTCCCTTTGCCTTC
4027 SEQ ID N0:1719 -12.3 -27.4 77.8 -15.1 0 -5.8
GTTTTTCGAAGATTCCACCA
4045 SEQ ID N0:1720 -12.3 -23.4 67 -10.6 -0.1 -6.8
AGGTTTTTCGAAGATTCCAC
4047 SEQ ID N0:1721 -12.3 -21.9 64.9 -8.9 -0.4 -7.4
TGAAAGTCTCAAACCAGTTG
4086 SEQ ID N0:1722 -12.3 -19.6 59.2 -6.8 -0.1 -3.4
TATTTGCCCTGGTCATCCGT
5110 SEQ ID N0:1723 -12.3 -28.5 78.1 -15 -1.l -4.2
GTATTTGCCCTGGTCATCCG
5111 SEQ ID N0:1724 -12.3 -28.5 78.1 -15 -l.1 -4.4
ACATCCCAAAGATGGCATAG
5475 SEQ ID N0:1725 -12.3 -22.6 64.3 -8 -2.3 -8
GGCAAAGTTGGACATCCCAA
5486 SEQ ID N0:1726 -12.3 -24.7 68.3 -10.4 -2 -8
GGTCTCCCTTAACTGAGCTG
5673 SEQ TD N0:1727 -12.3 -26.5 75.6 -14.2 0 -5
TATAAACTGGGTCGCATCGG
5876 SEQ ID N0:1728 -12.3 -22.8 64.5 -10.5 0 -3.6
ATTTTTTAACCTTTGCTTTA
6218 SEQ ID N0:1729 -12.3 -19.4 59.8 -7.1 0 -3.6
TATTTTTTAACCTTTGCTTT
6219 SEQ ID N0:1730 -12.3 -19.4 59.8 -7.1 0 -3.6
ATCCTCCCTTTAATTGCCTC
6259 SEQ ID N0:1731 -12.3 -27 75.1 -14.7 0 -3
GAGGAGGGGTGGTAGAGGAA
6354 SEQ ID N0:1732 -12.3 -25 73.3 -12.7 0 -0.7
GTCACTTCACTGTCTTGTAT
6606 SEQ ID N0:1733 -12.3 -23.2 71.7 -10.9 0 -2.6
TTTGAGAGACAGGGTTCTTG
6940 SEQ ID N0:1734 -12.3 -22 67.2 -9.7 0 -3.6
ATTTGAGAGACAGGGTTCTT
6941 SEQ ID N0:1735 -12.3 -22 67.4 -9.7 0 -3.6
TACTTTTTGGAAAGCATTTG
7228 SEQ ID N0:1736 -12.3 -18.3 56.9 -4.4 -l.6 -5.5
TTTTCTAGAATGGATTTATT
7252 SEQ ID N0:1737 -12.3 -17 55.1 -4.2 0 -7.7
TTTGCTGAGAGCAGAAGATG
7332 SEQ ID N0:1738 -12.3 -21.1 63.6 -6.7 -2.1 -6.9
147
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
totalduplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TAGACTATCAGCTTTGCTGA
7344 SEQ ID N0:1739 -12.3-22.4 67.7 -6.7 -3.4 -10.5
GCTTGCAAAAGACACATACA
7479 SEQ ID N0:1740 -12.3-20.2 59.6 -5.8 -2.1 -6.9
CTGCTTGACATAATGGACAG
7661 SEQ ID N0:1741 -12.3-20.9 62.1 -8.6 0 -3.6
ATGTTATATTTGTAATAGCT
8238 SEQ ID N0:1742 -12.3-17.5 56.4 -5.2 0 -5.7
AAGTTGGAACATGTGAACTT
8701 SEQ ID N0:1743 -12.3-18.9 57.9 -5.6 -0.8 -9.3
CTGAAAGTTGGAACATGTGA
8705 SEQ ID N0:1744 -12.3-19.2 58.2 -6.1 -0.6 -7
GTAGGTGGTTACTACTATTA
8734 SEQ ID N0:1745 -12.3-20.9 65.4 -7.6 -0.9 -4.4
TTTTCTTTCTTTCTCTGTGG
57 SEQ ID N0:1746 -12.2-22.3 70 -10.1 0 -1.3
TTTTTTTTTTTTTTTTTGAC
107 SEQ TD N0:1747 -12.2-16.4 54.6 -4.2 0 -0.1
CTTTTTTTTTTTTTTTTTTT
112 SEQ ID N0:1748 -12.2-16.7 55.4 -4.5 0 0
TGGTTAGGGTATAACGTGTC
l52 5EQ ID N0:1749 -12.2-22.3 67.1 -8.1 -2 -5.3
CTTCTTGCATACGAATTACC
421 SEQ ID N0:1750 -12.2-21.5 62.7 -9.3 0 -4.8
CAGCACGTTTTTCGATAGCA
540 SEQ ID N0:1751 -12.2-23.8 68 -9.8 -1.8 -4.1
ATCATCATTATCTTGTTCCT
587 SEQ ID N0:1752 -12.2-22 67.3 -9.8 0 -1.9
TGTGCCATTAAAGTAGGAAG
1346 SEQ ID N0:1753 -12.2-20.1 60.4 -7.9 0 -3.5
TTTCCACAGAGTAAAGGGTC
1468 SEQ ID N0:1754 -12.2-22.3 66.8 -10.1 0 -3.6
AATGCTTGTTTTGCTATTGC
2183 SEQ ID N0:1755 -12.2-21.9 65.9 -9 -0.4 -4.4
TCCATGTCTGTGCGGCACAA
2306 SEQ ID N0:1756 -12.2-27.3 75.3 -12.5 -1.4 -13.2
CCCAGATCAAGAACACATTG
2673 SEQ ID N0:1757 -12.2-21.5 61.8 -9.3 0 -5.4
ATGGCCATAAAGAGGGTATT
2788 SEQ ID N0:1758 -12.2-22 64.2 -8.8 0 -10
GTGCTTCCTTCAGATGAGCT
3880 SEQ ID N0:1759 -12.2-26.4 77.5 -12.8 -1.3 -5
CTTTTTAATACACCCTTCAG
3980 SEQ ID N0:1760 -12.2-21.2 62.8 -9 0 -2.5
ACAACCACCCTCATGCCTTC
4426 SEQ ID N0:1761 -12.2-28.5 76.3 -16.3 0 -4.4
TTCACAACCACCCTCATGCC
4429 SEQ TD N0:1762 -12.2-28.3 75.5 -16.1 0 -4.4
ACCCGTTGTCATGTTAACAC
4562 SEQ ID N0:1763 -12.2-24 68.2 -11.1 -0.3 -8.7
CATAATATCCATCCAGCCTT
4721 SEQ ID N0:1764 -12.2-24.4 68.6 -12.2 0 -3.2
CTTAACTGAGCTGCCAGGGT
5666 SEQ ID N0:1765 -12.2-26.5 75 -13.8 0.3 -8.4
ATCCCAACAGATGGGTCCCC
5695 SEQ ID N0:1766 -12.2-29.9 79 -14.5 -3.2 -8.6
CTATAAACTGGGTCGCATCG
5877 SEQ ID N0:1767 -12.2-22.5 63.9 -10.3 0 -3.6
148
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mo1
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGGCTCATAAGAGACTTTGG
6122 SEQ ID N0:1768 -12.2 -21.7 65.4 -8.l -1.3 -5
TATGGAAGTTAAAAATAGAA
6802 SEQ ID N0:1769 -12.2 -12.6 44.6 0 0 -2.8
GTATTTAATTGACATAGACT
7358 SEQ ID N0:1770 -12.2 -17.1 55 -4.9 0 -2.9
GGTATTTAATTGACATAGAC
7359 SEQ ID NO:1771 -12.2 -17.4 55.6 -5.2 0 -2.9
ATGATACAGGATACATCCCT
7506 SEQ ID N0:1772 -12.2 -22.9 66.2 -9.7 -0.9 -6.9
ACAAAGTCCATGTTATATTT
8247 SEQ ID N0:1773 -12.2 -18.7 58 -6.5 0 -4.3
GGAACATGTGAACTTGATCC
8696 SEQ ID N0:1774 -12.2 -21.3 62.7 -9.1 0 -7
TGTAGGTGGTTACTACTATT
8735 SEQ TD N0:1775 -12.2 -21.2 65.9 -7.4 -1.6 -5.2
TTTTTTTTTTTTTTTTTTGA
108 SEQ ID N0:1776 -12.1 -16.3 54.4 -4.2 0 -0.1
GTATAACGTGTCTTCCTCTG
144 SEQ ID N0:1777 -12.1 -23.3 69.1 -11.2 0 -4.8
AGTGCCTGTGCCATCTTTTC
466 SEQ ID NO:1778 -12.1 -27.6 79.9 -14.7 -0.6 -3.4
CTCTAGTAAAAAGGCGGAAG
510 SEQ ID N0:1779 -12.1 -18.9 56.7 -6.8 0 -4
GTTTGTTCTCATCATCATTA
597 SEQ ID N0:1780 -12.1 -21.1 66.4 -9 0 -1.9
ACTATTTGGCTTTGGTTTGT
611 SEQ ID N0:1781 -12.1 -22.9 69.3 -10.8 0 -3.7
AATCGGAAAATTGCCTTTCC
757 SEQ ID N0:1782 -12.1 -21.6 61.2 -7.8 -1.7 -6.6
ATCTTGATAGCAATTTTCCT
823 SEQ ID N0:1783 -12.1 -21.1 63.7 -8.4 -0.3 -0.5
AACCCTCTTGCCAAGATTTT
985 SEQ ID N0:1784 -12.1 -24.5 68.5 -11.7 -0.4 -6.1
TATCCTTCTGGACACTGGCC
1501 SEQ ID N0:1785 -12.1 -27.2 76.6 -13.7 -1.3 -8.7
ATAGGCCATGGCCACCACAG
1733 SEQ ID N0:1786 -12.1 -28.9 77.5 -12.2 -2.5 -17.4
GCCTGAGCTTCTTCCTGTTG
1834 SEQ ID N0:1787 -12.1 -28.1 80.7 -15.3 -0.4 -4.6
TTTCGCCGTCTTCAAATGTG
2268 SEQ ID N0:1788 -12.1 -23.5 66.6 -11.4 0 -2.8
GGGGAAGTTGTCCAGTAGGT
2466 SEQ ID N0:1789 -12.1 -26.4 77.7 -12.3 -2 -5.6
CACATTGGCAAATCTATACC
2660 SEQ ID N0:1790 -12.1 -20.9 61.3 -8.8 0 -4.4
ACTTTTAACCATGCATCACA
2698 SEQ ID N0:1791 -12.1 -21.8 63.8 -9.7 0 -6.6
ATAATTCCATCAAAGATATT
2944 SEQ ID N0:1792 -12.1 -16.3 52.2 -3.7 -0.2 -3.5
AAGGAGTGGAAGAAGTCGTT
3250 SEQ ID N0:1793 -12.1 -21 62.8 -8.4 -0.2 -3
CCCGCATCTTATTTTTCACA
3522 5EQ ID N0:1794 -12.1 -24.8 69.7 -12.7 0 -3.6
CATTTAATTTCTCTTTGCTT
3855 SEQ ID N0:1795 -12.1 -19.7 61.3 -7.6 0 -3.6
GCTCTTAGAGGTCTTAAAGC
4393 SEQ ID N0:1796 -12.1 -22.3 68.1 -9.6 -0.3 -5.3
149
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TCCACCGAGCTTGCTTGCCA
4632 5EQ ID N0:1797 -12.1 -30.8 81.3 -18.2 -O.l -5.9
TTCCACCGAGCTTGCTTGCC
4633 SEQ ID N0:1798 -12.1 -30.2 80.7 -17.5 -0.3 -6.4
TTATCAAAGTTTACTTTCAC
4657 SEQ ID N0:1799 -12.1 -17.2 55.6 -3.9 -1.1 -6.9
GTTTAACATCTCGTGAATCA
4752 SEQ ID N0:1$00 -12.1 -20 60.7 -7.9 0 -4.4
CATCATGGTGACCATGTTGA
5084 SEQ ID N0:1801 -12.1 -23.6 68.5 -8.3 -3.2 -11.5
ATAAACTGGGTCGCATCGGG
5875 SEQ ID N0:1802 -12.1 -24.3 67.4 -12.2 0 -3.6
CTGGACTTTGTTGGGTTTTG
5951 SEQ ID N0:1803 -12.1 -23.2 69.5 -11.1 0 -2.6
TATTCGAAGGGCATCCATCT
6068 SEQ TD N0:1804 -12.1 -24.2 68.9 -10.9 -1.1 -8.2
TCTGACCTCTTTTCCTTTGC
6440 SEQ ID N0:1805 -12.1 -25.9 75.6 -13.8 0 -2.6
GGAAAGCATTTGACCTAAAT
7220 SEQ ID N0:1806 -12.1 -19.1 57 -6.3 -0.4 -3.1
CATAGGGTATTTAATTGACA
7364 SEQ ID N0:1807 -12.1 -18.5 57.6 -6.4 0 -2.9
TGATTTAATAGAAGTTGTTT
7445 SEQ ID N0:1808 -12.1 -16.1 53 -4 0 -2.5
GGATACATCCCTGTTGGAAG
7498 SEQ ID N0:1809 -12.1 -24.1 68.9 -10.9 -1 -5.7
GGTTGAATTCATTCTATCAC
7637 SEQ ID N0:1810 -12.1 -20 62.2 -7.2 -0.4 -8.4
TAGGCAGTATCCAGTGTGTT
7769 SEQ ID N0:1811 -12.1 -25.1 75.6 -12.5 -0.2 -4
TTGTAATAGCTTTAGTGCAG
8229 5EQ ID N0:1812 -12.1 -20.3 63.1 -7.3 -0.8 -5.6
GTTATATTTGTAATAGCTTT
8236 SEQ ID N0:1813 -12.1 -17.7 57.2 -5.6 0 -7.1
GAAATTTATTCTTTTGGCTC
8452 SEQ ID N0:1814 -12.1 -19.1 59.6 -6.4 -0.3 -5.2
AGACCTTTCCAGAATCCTCT
23 SEQ ID N0:1815 -12 -25.5 72.6 -13.5 0 -2.9
AGCTTTCAGGTCCTGGGGGT
492 SEQ ID N0:1816 -12 -29.7 85.9 -17 -0.4 -6.8
CATCATCATTATCTTGTTCC
588 SEQ ID N0:1817 -12 -21.8 66.5 -9.8 0 -1.9
CTATTTGGCTTTGGTTTGTT
610 SEQ ID N0:1818 -12 -22.8 69.1 -10.8 0 -3.7
TGATATAGTAGGGATCCAGG
708 SEQ ID N0:1819 -12 -22.2 66.6 -9.4 -0.3 -8.9
TTGATATAGTAGGGATCCAG
709 SEQ ID N0:1820 -12 -21.1 64.3 -8.3 -0.3 -8.9
ATTGATATAGTAGGGATCCA
710 SEQ ID N0:1821 -12 -21.1 64 -8.3 -0.3 -8.9
TGGATCACGAAGAAACGTAA
1019 SEQ ID N0:1822 -12 -18.2 54.4 -5.3 -0.8 -6
TCAACGCTGAGACATTGCCC
1098 SEQ ID N0:1823 -12 -26.1 71.2 -14.1 0 -3.8
GGTTTCAAAAGCAGAATCGC
1319 SEQ ID N0:1824 -12 -21 61.5 -9 0 -5
GTTTCGACCAGCCTTCACAC
1526 SEQ ID N0:1825 -12 -27.1 75.6 -15.1 0 -4.6
150
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTCTTCAGATTCGGATTTGG
2042 SEQ ID N0:1826 -12 -22.8 68.2 -10.8 0 -4.4
TGCGTCTTGGGGAAAACAGG
2166 SEQ ID N0:1827 -12 -23.4 66 -11.4 0 -5.2
CGCTCTCCATGTCTGTGCGG
2311 SEQ ID N0:1828 -12 -29.4 80.3 -16.3 -1 -6.3
AGATCAAGAACACATTGGCA
2670 SEQ ID N0:1829 -12 -20.5 61 -8.5 0 -5.4
TTTAACCATGCATCACAGCA
2695 SEQ ID N0:1830 -12 -23.1 66.4 -10 -1 -6.6
TGTTTTACTTTTAACCATGC
2704 SEQ ID N0:1831 -12 -20.3 61.6 -8.3 0 -4.2
CCAGTAAAGACCAGGTTTCC
2854 SEQ ID N0:1832 -12 -24.7 70 -12.7 0 -5.9
TCCCAGTAAAGACCAGGTTT
2856 SEQ ID N0:1833 -12 -24.7 70 -12.7 0 -5.9
AAGCAGTCTGAATGATCGCA
3020 SEQ ID N0:1834 -12 -22.5 65.3 -9.8 -0.4 -6.3
AATTTCTCTTTGCTTTCTTC
3850 SEQ ID N0:1835 -12 -21 65.9 -9 0 -3.6
CAGCACATTCATGATAGAGG
4469 SEQ TD N0:1836 -12 -21.4 64.2 -9.4 0 -6.4
TTTGTTTGCTGGGCGAGGTA
4994 SEQ ID NO:1837 -12 -26 74.8 -13.2 -0.6 -4.4
GAATTTGTTTGCTGGGCGAG
4997 SEQ ID N0:1838 -12 -23.8 68.3 -11 -0.6 -4.9
CAAAGTTGGACATCCCAAAG
5484 SEQ ID NO:1839 -12 -21 60.4 -7.3 -1.7 -5.2
ATCAATTCCAGCTTCCTTTT
5513 SEQ ID N0:1840 -12 -24 70 -12 0 -4.5
AGCTGCCAGGGTGAATTGTG
5658 SEQ ID N0:1841 -12 -26 74.1 -14 0 -5.6
TGGGTCGCATCGGGATCAAA
5869 SEQ TD N0:1842 -12 -25.2 69.3 -13.2 0 -6.9
TATGAGTATTTGTTAAAACA
6576 SEQ ID N0:1843 -12 -15.2 50.4 -3.2 0 -5.9
AGTGACATAGCATTATGAAT
6882 SEQ ID N0:1844 -12 -18.6 57.9 -5.9 -0.5 -4
GAGAGACAGGGTTCTTGTAT
6937 SEQ ID N0:1845 -12 -22.7 69.5 -10.7 0.2 -5
TGGAAAGCATTTGACCTAAA
7221 SEQ ID N0:1846 -12 -19.1 56.9 -6.3 -0.6 -4.1
CAAAGTCCATGTTATATTTG
8246 SEQ ID N0:1847 -12 -18.5 57.4 -6.5 0 -4.3
TGAAATTTATTCTTTTGGCT
8453 SEQ ID N0:1848 -12 -18.7 58.2 -5.6 -1 -5.2
GTGAAATGCAATAAAAAATG
8471 SEQ ID N0:1849 -12 -12.4 43.7 0 0 -5.6
AGTGAAATGCAATAAAAAAT
8472 SEQ ID N0:1850 -12 -12.4 43.7 0 0 -5.6
CTAGTTTGTTGTAAAATTCA
8602 SEQ ID N0:1851 -12 -17.3 55.5 -4.6 -0.4 -4.4
TCCTTGACAGGTATCTCATC
275 SEQ ID N0:1852 -11.9 -23.8 71.7 -10.9 -0.9 -3.5
GCTTTCAGGTCCTGGGGGTA
491 SEQ ID N0:1853 -11.9 -29.4 84.9 -17 -0.2 -6.2
ATTCTCTAGTAAAAAGGCGG
513 SEQ ID N0:1854 -11.9 -19.5 58.7 -7.6 0 -4
151
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CACGTTTTTCGATAGCAGCA
537 SEQ ID N0:1855 -11.9 -23.8 68 -10.9 -0.9 -6.9
TTCTGCAGCACGTTTTTCGA
545 5EQ ID N0:1856 -11.9 -24.8 70.9 -11.7 -0.9 -9.8
GACATTGCCCAGGTCCACAA
1088 SEQ ID N0:1857 -11.9 -27.8 75.4 -15.9 0 -4
AAACATTTATTCCTCAGATT
1285 SEQ ID N0:1858 -11.9 -18.6 57.'5 -6.7 0 -2.5
CTGTGCGGCACAAACAGTGA
2299 SEQ ID N0:1859 -11.9 -24.6 68.6 -10.1 -1.5 -13.2
TCATCAGTAGCAGCAAGGTT
3442 SEQ ID N0:1860 -11.9 -23.9 71.8 -12 0 -5.4
TTTTGGAAACACTCCCGCAT
3535 SEQ ID N0:1861 -11.9 -24.4 66.9 -11.4 -1 -4.8
TAATTTCTCTTTGCTTTCTT
3851 SEQ ID N0:1862 -11.9 -20.3 63.6 -8.4 0 -3.6
TTAATTTCTCTTTGCTTTCT
3852 SEQ ID NO:1863 -11.9 -20.3 63.6 -8.4 0 -3.6
TTCAGCTTGTTCACCTTCTC
3920 SEQ ID NO:1864 -11.9 -25.3 76.2 -13.4 0 -4.5
TTAAAGTCTTCTTCGGGTTC
3943 SEQ ID N0:1865 -11.9 -21.7 66.1 -9.1 -0.5 -3.8
TGTCAGCATATTCTAGCATG
4185 SEQ ID N0:1866 -11.9 -22.1 67.3 -9.7 -0.1 -4.3
GCGCCAACATTATCAAAGTT
4666 SEQ ID N0:1867 -11.9 -22.1 62.9 -10.2 0 -6.4
TGGGTTTCTGAGGTTTCTTG
4974 SEQ ID N0:1868 -11.9 -23.7 72.4 -11.8 0 -2.8
TTTGCTGGGCGAGGTATGGG
4990 SEQ ID N0:1869 -11.9 -27 75.7 -14.3 -0.6 -4.4
GTTTGCTGGGCGAGGTATGG
4991 SEQ ID NO:1870 -11.9 -27 76.6 -14.3 -0.6 -4.4
TAGTGTCTGAGGGAAACGAG
5200 SEQ ID N0:1871 -11.9 -21.2 63.1 -9.3 3 -3.5
CAAAGCAAAGAGCAGCGTGC
5396 SEQ ID N0:1872 -11.9 -23.1 64.9 -9.6 -1.6 -7.2
CATGCTGTTGCCAAAGGTCT
5549 SEQ ID NO:1873 -11.9 -25.5 72.4 -12.7 -0.8 -4.4
AGCAGATCATGCTGTTGCCA
5556 SEQ ID N0:1874 -11.9 -26.7 76.4 -12.4 -2.4 -9.8
CTCACTCAGGGGCTCTGCAC
5813 SEQ ID N0:1875 -11.9 -28.5 82 -15.6 -0.9 -4.8
CAGGGCAGCTGCAAAATCAG
5912 SEQ ID N0:1876 -11.9 -23.8 67.5 -9 -0.7 -14
TCAATCCTCCCTTTAATTGC
6262 SEQ ID N0:1877 -11.9 -24.1 68.5 -11.6 -0.3 -3.8
AGTCAATCCTCCCTTTAATT
6264 SEQ ID N0:1878 -11.9 -23.5 68 -11.6 0 -2.5
AAGGAGGAGGGGTGGTAGAG
6357 SEQ ID N0:1879 -11.9 -24.4 72.2 -12.5 0 -0.7
TTTCCTTGTCTGGTTTTGTT
6390 SEQ ID N0:1880 -11.9 -24.1 73.4 -12.2 0 -3.2
TTTTCCTTGTCTGGTTTTGT
6391 SEQ ID NO:1881 -11.9 -24.1 73.4 -12.2 0 -3.2
TGACACATATACTTTACCTT
6521 SEQ ID N0:1882 -11.9 -20 60.6 -8.1 0 -2.4
AGTTGACACATATACTTTAC
6524 SEQ ID N0:1883 -11.9 -18.3 58 -5.9 -0.2 -3.6
152
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total dupleacTm target molecularmolecular
of
Positionoligo bindingformationDupleacstructureoligo oligo
TGTAGTTACAATGTTCACTT
6751 SEQ ID N0:1884 -11.9 -19.7 61.7 -7.8 0 -5.6
AACTATGAATTGGGGACCAT
6861 SEQ ID N0:1885 -11.9 -21.2 61.5 -6.9 -2.4 -7.2
ATTACAATTCTTTTTCTGGT
7007 SEQ ID N0:1886 -11.9 -19.5 61.1 -7.6 0 -2.6
GAGACTTTACAGGCACATAA
7113 SEQ ID N0:1887 -11.9 -20.7 62.2 -8.8 0 -4
AAATATAGAGCTCTGAAACT
7199 SEQ ID N0:1888 -11.9 -16.9 53.6 -4 0 -10
TCTTTAACCAAGACTTGTGA
7604 SEQ ID N0:1889 -11.9 -20.3 61.2 -7.6 -0.6 -5.6
ACAAAAATTTATATCATGTT
8310 SEQ ID N0:1890 -11.9 -14.1 47.7 -2.2 0 -5.2
CACCATTCTTTTTAGCAATA
8417 SEQ ID N0:1891 -11.9 -20.6 61.9 -8.7 0 -4.1
TTTATTCTTTTGGCTCAATA
8448 SEQ ID N0:1892 -11.9 -19.6 61.1 -7.7 0 -4.9
GTATACATAGGAGTTTATAT
8885 SEQ ID N0:1893 -11.9 -17.8 57.5 -5.9 0 -6.1
GTCAAACCTTGATGTGGCTT
252 SEQ ID N0:1894 -11.8 -23.9 69 -10.9 -1.1 -5.7
TCTTTGCTCCTTTCCCAGTA
312 SEQ ID N0:1895 -11.8 -27.7 79.5 -15.9 0 -2.9
TATTCTTACAATATCCCTAG
339 SEQ ID N0:1896 -11.8 -19.8 60.3 -8 0 -3.2
TGTGAATTATCTCATTTATT
355 SEQ ID N0:1897 -11.8 -17.3 55.9 -5 -0.1 -3.2
GGCTTTGGTTTGTTCTCATC
604 SEQ ID N0:1898 -11.8 -24.8 75.7 -13 0 -3.7
AGTTGGTCAAAATAGTGCAC
876 SEQ ID N0:1899 -11.8 -20.3 61.9 -7.9 0 -8.6
TAAGTGACTCAAAGGTATAG
963 SEQ ID N0:1900 -11.8 -17.4 55.5 -5.6 0 -3.3
TCGGAGAACTCTGAATGTTC
1118 SEQ ID N0:1901 -11.8 -20.9 62.7 -8.4 -0.4 -7.9
AATTGTTTTCAGTGCTCGGA
1133 SEQ ID N0:1902 -11.8 -22.9 67.9 -11.1 0 -4.5
CTGTTTCCATCCATGGAGAA
2086 SEQ ID N0:1903 -11.8 -24.2 69.4 -10.8 -1.4 -10.4
GGGGAAAACAGGGAGCCACG
2158 SEQ ID N0:1904 -11.8 -25.5 68.5 -13.1 -0.3 -4.3
GCGTCTTGGGGAAAACAGGG
2165 SEQ ID N0:1905 -11.8 -24.6 68.5 -12.8 0 -3.5
GGAAGCCCTGGCACCATCCT
2368 SEQ ID N0:1906 -11.8 -31.7 82.6 -19 -0.7 -9.1
TCTGGGGGAAGTTGTCCAGT
2470 SEQ ID N0:1907 -11.8 -26.8 78 -13 -2 -8.1
CCTTCCAGAGGAATCCTCCA
2558 SEQ ID N0:1908 -11.8 -28.2 76.9 -14.2 -2.2 -11.2
AATAATTCCATCAAAGATAT
2945 SEQ ID N0:1909 -11.8 -15.5 50.2 -3.7 0 -3.5
CCCTCCACATTTGACAGACC
2989 SEQ ID N0:1910 -11.8 -27.4 74.3 -15.6 0 -2.4
GACAATCCCTCCACATTTGA
2995 SEQ ID N0:1911 -11.8 -24.9 69.3 -13.1 0 -3.2
GTTCAGAACCACAAGGTTTC
3383 SEQ ID N0:1912 -11.8 -22.4 66.6 -8 -2.6 -6.8
153
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GCTTTTTGGAAACACTCCCG
3538 SEQ ID N0:1913 -11.8 -24.7 67.9 -11.8 -1 -5.3
CCAACAGCAATTGGCACTGT
3775 SEQ ID N0:1914 -11.8 -24.8 69.2 -11.4 -1.5 -9.3
TTCCCTTTGCCTTCTTCTGT
4021 SEQ TD N0:1915 -11.8 -28.3 80.9 -16.5 0 -3
CTCTTAGAGGTCTTAAAGCT
4392 SEQ ID N0:1916 -11.8 -21.4 65.7 -9.6 0 -4.8
CTTGGAATTTGTTTGCTGGG
5001 SEQ ID N0:1917 -11.8 -22.8 67.1 -ll 0 -4.3
GGTGACCATGTTGAGGCAGA
5078 SEQ ID N0:1918 -11.8 -26.1 74.8 -13.8 -O.l -4.3
AAGATGGCATAGATAAACAT
5467 SEQ ID NO:1919 -11.8 -17.1 53.5 -5.3 0 -4
AGGGCATCCATCTCTCCACT
6061 SEQ ID N0:1920 -11.8 -28.8 81.3 -15.8 -1.1 -4
GGAGGAGGGGTGGTAGAGGA
6355 SEQ ID N0:1921 -11.8 -26.9 78.8 -15.1 0 -0.7
CAGTTGACACATATACTTTA
6525 SEQ ID N0:1922 -11.8 -18.8 58.8 -6.5 -0.2 -3.6
CTGTCTTGTATAGGCACTGA
6597 SEQ ID N0:1923 -11.8 -23.5 70.7 -ll -0.5 -4
AACACCTTTGTCTGATCATT
6958 SEQ ID N0:1924 -11.8 -21.8 65 -9.3 -0.5 -8.3
AAACACCTTTGTCTGATCAT
6959 SEQ ID N0:1925 -11.8 -21 62.5 -8.5 -0.5 -8.3
AATATAGAGCTCTGAAACTT
7198 SEQ TD N0:1926 -11.8 -17.7 55.7 -5 0 -9.7
CTTTTTGGAAAGCATTTGAC
7226 SEQ ID N0:1927 -11.8 -19.2 58.8 -6.5 -0.7 -4.6
ACTTTTTGGAAAGCATTTGA
7227 SEQ ID N0:1928 -11.8 -19.2 58.8 -5.8 -1.6 -5.5
GGATTGAGTAAAATAGAGCA
7579 SEQ TD N0:1929 -11.8 -18.1 56.3 -6.3 0 -4.1
GCACTAGTTTGTTGTAAAAT
8605 SEQ ID N0:1930 -11.8 -18.8 58.5 -6.3 -0.4 -6.3
CAAAGCTGCTTTTAATTTGC
8656 SEQ ID N0:1931 -11.8 -20 60.2 -6.7 -0.3 -10.9
GTTACAATTTTTTTTCTTTC
68 SEQ ID N0:1932 -11.7 -17.8 57.9 -6.1 0 -2.4
GGTATAACGTGTCTTCCTCT
145 SEQ ID N0:1933 -11.7 -24.5 71.9 -12.8 0 -5.3
TCTCATCCCTGTCAAACCTT
262 SEQ ID N0:1934 -11.7 -25.8 72.6 -14.1 0 -2
ATTACGTGTAGCTTCTTGCA
432 SEQ ID NO:1935 -11.7 -23.6 70 -10.3 -1.5 -7.1
AGCACGTTTTTCGATAGCAG
539 SEQ ID N0:1936 -11.7 -23.1 67.1 -9.6 -1.8 -5
TATAGTAGGGATCCAGGTCC
705 SEQ ID N0:1937 -11.7 -25.2 74.4 -12.2 -1.2 -8.9
AATCCAGCCAGTTCCATGGA
1035 SEQ ID N0:1938 -11.7 -27.1 75.1 -14 -1.3 -9.7
ATTAACAAATGTCCCATTTG
1373 SEQ ID N0:1939 -11.7 -19.1 57.2 -4.9 -2.5 -9.5
-
CACGTAATGTCAACTGGTAA
1635 SEQ ID N0:1940 -11.7 -20 59.5 -8.3 0 -4.8
AAAATATCATGTATGTTTTC
1662 SEQ ID N0:1941 -11.7 -15.5 51.4 -3 -0.6 -6.9
154
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TCATAGGCCATGGCCACCAC
1735 SEQ ID N0:1942 -11.7 -29.3 78.8 -13.4 -1.7 -16.6
TTCCATCCATGGAGAAAAGG
2082 SEQ ID N0:1943 -11.7 -21.8 62.7 -8.4 -1.7 -9.9
AACAGGGAGCCACGGATACT
2152 SEQ ID N0:1944 -11.7 -25.3 69.7 -13 -0.3 -3.7
CTTGGGGAAAACAGGGAGCC
2161 SEQ ID N0:1945 -11.7 -24.8 68.8 -13.1 0 -3.6
CGTCGCTCTCCATGTCTGTG
2314 SEQ ID NO:1946 -11.7 -28 78.7 -16.3 0 -4.3
CTGGGGGAAGTTGTCCAGTA
2469 SEQ ID N0:1947 -11.7 -26.1 75.6 -13 -1.3 -7.5
CTTTCTGACTTCCGTTTCAG
2501 SEQ TD N0:1948 -11.7 -23.9 70.4 -11.3 -0.8 -5.4
TCCAGAGGAATCCTCCAGCA
2555 SEQ ID N0:1949 -11.7 -27.7 76.7 -13.8 -2.2 -11.2
AATTCCATCAAAGATATTCC
2942 SEQ ID N0:1950 -11.7 -19 57.6 -6.6 -0.4 -3.9
TGCCAATGATCTTAATTAGC
3081 SEQ ID N0:1951 -11.7 -20.4 61.1 -8.7 0 -4.9
AATGAAGACGATGATGGCCA
3137 SEQ ID N0:1952 -11.7 -21.7 61.5 -9.3 0 -8.8
TCAGAACCACAAGGTTTCCA
3381 SEQ ID N0:1953 -11.7 -23.8 67.9 -9.5 -2.6 -7.6
TTAAGCTCTTTGCTTATTTC
3637 SEQ TD N0:1954 -11.7 -20.4 63.7 -5.7 -3 -7.4
TGACGGTGAGGCTGGGGTTG
3756 5EQ ID N0:1955 -11.7 -27.4 76.8 -15.7 0 -3.7
TTCTCTTTGCTTTCTTCTAG
3847 SEQ ID N0:1956 -11.7 -22.2 69.8 -10.5 0 -3.6
TTTAATTTCTCTTTGCTTTC
3853 SEQ ID N0:1957 -11.7 -19.5 61.9 -7.8 0 -3.6
ATTATCAAAGTTTACTTTCA
4658 SEQ ID N0:1958 -11.7 -17 55.1 -3.9 -1.3 -7.1
CATTATCAAAGTTTACTTTC
4659 SEQ ID N0:1959 -11.7 -17 55.1 -3.9 -1.3 -7.1
ACATTATCAAAGTTTACTTT
4660 SEQ ID N0:1960 -11.7 -16.8 54.3 -3.9 -1.1 -6.9
AGATTTTCTTCATATACAGG
4777 5EQ ID N0:1961 -11.7 -18.9 59.9 -7.2 0 -2.6
TGTACAGATTTTCTTCATAT
4782 SEQ ID N0:1962 -11.7 -18.9 60.1 -7.2 , 0 -5.9
ATGTACAGATTTTCTTCATA
4783 SEQ ID N0:1963 -11.7 -18.9 60.1 -7.2 0 -6.7
CATTCCTTGGAATTTGTTTG
5006 SEQ ID NO:1964 -11.7 -20.9 62.7 -7.5 -1.7 -8.4
AGACCATTCCTTGGAATTTG
5010 SEQ ID N0:1965 -11.7 -22.3 64.8 -9 -1.5 -8.2
CAGCCTATAGTGAAGTAGTA
5218 SEQ ID N0:1966 -11.7 -21.7 66 -10 0 -5.1
ACCATGGGCAGATCCATGGC
5977 SEQ ID N0:1967 -11.7 -28.5 78 -11.5 -5.3 -13.1
CTCCTCTTGTTTACGTTTCA
6155 SEQ ID N0:1968 -11.7 -24.2 71.6 -12.5 0 -4.8
CTTTTCCTTGTCTGGTTTTG
6392 SEQ ID N0:1969 -11.7 -23.8 71.9 -12.1 0 -3.2
CACATATACTTTACCTTCAT
6518 SEQ ID N0:1970 -11.7 -20.3 61.4 -8.6 0 -2.4
155
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Position oligo bindingformationDuplexstructureoligo oligo
GTGACATAGCATTATGAATA
6881 SEQ ID N0:1971 -11.7 -18.3 57.1 -5.1 -1.4 -4.9
GATCATTTGAGAGACAGGGT
6945 SEQ ID N0;1972 -11.7 -22.2 67.1 -10.5 0 -4.7
GTTGGAAGCTTGCAAAAGAC
7486 SEQ ID NO:1973 -11.7 -20.4 60.6 -6.6 -2.1 -7
AGTGATAGCCTTTAAACTAT
7535 SEQ ID N0:1974 -11.7 -19.5 59.6 -7.3 -0.2 -5.8
CAATATTAACATGCATTAGT
7552 SEQ TD NO:1975 -11.7 -17.2 54.3 -5.5 0 -6.7
ACAGAGCAGGTTGAATTCAT
7645 SEQ ID N0:1976 -11.7 -21.6 65 -9.3 0 -8.4
ATGAAGAATAGGTTTTGTCA
7790 SEQ TD N0:1977 -11.7 -18.5 58.2 -6.8 0 -3
TAAGTGAAATGCAATAAAAA
8474 SEQ TD N0:1978 -11.7 -12.1 43.2 0 0 -5.6
CCTTATGTATACATAGGAGT
8891 SEQ ID N0:1979 -11.7 -20.9 63.7 -7.6 -0.2 -ll.l
TTTTTTTTTTTGACCACAGA
101 SEQ ID N0:1980 -11.6 -20 61.2 -8.4 0 -2.3
TTTTTTTTTTTTTTTTTTTG
109 SEQ ID N0:1981 -11.6 -15.8 53.3 -4.2 0 0
CTTGCATACGAATTACCTTA
418 SEQ ID N0:1982 -11,6 -20.8 60.8 -9.2 0 -5.1
TGCCTGTGCCATCTTTTCAT
464 SEQ TD N0:1983 -11.6 -27.1 77 -14.7 -0.6 -3
AAGGTTCTTTCCAGCTTCCA
635 SEQ ID N0:1984 -11,6 -26.3 76.1 -14 -0.4 -4.8
AGGGATCCAGGTCCTCCAGG
699 SEQ ID N0:1985 -11,6 -30.1 83.9 -16.5 -2 -10.3
CACAGTTGGTCAAAATAGTG
879 SEQ ID N0:1986 -11.6 -19.2 59 -7.6 0 -3.8
AAATGTCCCATTTGAATCCA
1367 SEQ ID NO:1987 -11.6 -22.1 62.9 -9.2 -1.2 -5.7
TGTTACATTAACAAATGTCC
1379 SEQ ID N0:1988 -11.6 -18.1 56.1 -4.9 -1.5 -6.6
GCCGCAACTGCCTGAGCTTC
1843 SEQ ID N0:1989 -11.6 -30 80.1 -17.2 -1.1 -5.8
TCAAGGTGCTCTCTCTGTCT
1990 SEQ ID N0:1990 -11.6 -25.9 78.7 -14.3 0 -3.6
TCTGTTTCCATCCATGGAGA
2087 SEQ ID NO:1991 -11.6 -25.3 73.4 -12 -1.7 -10.4
CTGATGAGGGGAGCAGAATT
2123 SEQ TD N0:1992 -I1.6 -22.8 66.7 -11.2 0 -4.1
CATTTGCTGGAAGCCCTGGC
2376 SEQ ID N0:1993 -11.6 -28.4 77.3 -15.2 -1.5 -8.6
CGGCTCTTTGCCTTCCAGAG
2568 SEQ ID N0:1994 -11.6 -28.7 79.I -14.4 -2.7 -7.3
TAATTCCATCAAAGATATTC
2943 SEQ ID N0:1995 -11.6 -16.7 53.4 -4.4 -0.4 -3.5
GGTGAGGTTTCCTAGAGCCC
3110 SEQ ID N0:1996 -11.6 -29 82.4 -16.7 -0.5 -4.4
ATGAAGACGATGATGGCCAA
3136 SEQ TD N0:1997 -11.6 -21.7 61.5 -9.3 0 -9.2
AGGTTTCCAATGACCATGAC
3370 SEQ ID N0:1998 -11.6 -23.3 67.1 -10.1 -1.5 -5.8
CCGCATCTTATTTTTCACAT
3521 SEQ ID N0:1999 -11.6 -22.8 66.1 -11.2 0 -3.6
156
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GAGGCTGGGGTTGTTTATGA
3749 SEQ ID N0:2000 -11.6 -25.1 74.1 -13.5 0 -3.7
GCTAACCAAAGAAACATCAA
4310 SEQ ID N0:2001 -11.6 -17.7 53.6 -6.1 0 -2.9
ATAATATCCATCCAGCCTTT
4720 SEQ ID N0:2002 -11.6 -23.8 67.9 -12.2 0 -3.2
AACGAGCTTCAGCACAAATT
5186 SEQ ID N0:2003 -11.6 -20.9 60.8 -9.3 0.1 -5.8
AAGAGCAGGAGGCCGATGTT
5440 SEQ ID N0:2004 -11.6 -25.9 72.4 -13.4 -0.8 -7.7
TCATGCTGTTGCCAAAGGTC
5550 SEQ ID N0:2005 -11.6 -25 72.1 -12.5 -0.8 -4.4
TAAACTGGGTCGCATCGGGA
5874 SEQ ID N0:2006 -11.6 -24.9 68.6 -13.3 0 -3.6
GAAGAGGAGGATCCAGGGCA
5925 SEQ ID N0:2007 -11.6 -26.1 73.9 -12.7 -1.8 -9
CTGTTTTTTCTGGAGTGGAG
6327 5EQ ID N0:2008 -11.6 -22.7 69.5 -11.1 0 -2.7
AGGAGGGGTGGTAGAGGAAC
6353 SEQ ID N0:2009 -11.6 -24.6 72.6 -13 0 -1.9
ACATATACTTTACCTTCATA
6517 SEQ ID N0:2010 -11.6 -19.3 59.6 -7.7 0 -2.4
CCAGTTGACACATATACTTT
6526 SEQ ID N0:2011 -11.6 -21.1 63.2 -9 -0.2 -3.6
AGCCATTGGGTTTCTCCTCA
6705 SEQ ID N0:2012 -11.6 -28.1 80.5 -15.6 -0.8 -6.3
AGCTTGCAAAAGACACATAC
7480 SEQ ID N0:2013 -11.6 -19.5 58.6 -5.8 -2.1 -6.9
ATATTAACATGCATTAGTGA
7550 SEQ ID N0:2014 -11.6 -17.8 56.2 -6.2 0 -6.7
GATTGAGTAAAATAGAGCAG
7578 SEQ ID N0:2015 -11.6 -16.9 54 -5.3 0 -4.1
TCAGTAGGCAGTATCCAGTG
7773 SEQ ID N0:2016 -11.6 -24.9 75 -12.8 -0.2 -4
TTGTTCATGGCTAAAAAGAA
8266 SEQ ID N0:2017 -11.6 -17.2 53.8 -5.6 0 -4.1
TCTTTTTAGCAATAGCAATT
8411 SEQ 2D N0:2018 -11.6 -18.8 58.6 -5.5 -1.7 -4.6
AAATTTATTCTTTTGGCTCA
8451 SEQ ID N0:2019 -11.6 -19.2 59.6 -7.6 0 -4.3
TTATGTATACATAGGAGTTT
8889 SEQ TD N0:2020 -11.6 -18.2 58.4 -5.1 -0.1 -10.9
CATTAATACCTTATGTATAC
8899 SEQ ID N0:2021 -11.6 -17.2 54.7 -5 -0.3 -5.3
TTTTTTTTTTTTTTTTTTCC
9093 SEQ ID N0:2022 -11.6 -18.1 58.6 -6.5 0 0
ATTTGGCTTTGGTTTGTTCT
608 SEQ ID N0:2023 -11.5 -23.5 71.4 -12 0 -2.9
GCCTTCACACAGATGTATCC
1516 SEQ ID N0:2024 -11.5 -25.6 73.6 -7:3.4 -0.5 -3.7
GCTTCTTCCTGTTGCTTTTT
1828 SEQ ID N0:2025 -11.5 -25.9 77 -14.4 0 -3.6
CTCCACTGAAATCTCTTGAA
1875 SEQ ID N0:2026 -11.5 -20.9 61.8 -9.4 0 -2.5
TCAACTTTGATGCTTCTGAA
1926 SEQ ID N0:2027 -11.5 -20.3 61.5 -8.8 0 -5
CCATCCATGGAGAAAAGGAA
2080 SEQ ID N0:2028 -11.5 -21.2 60.4 -8.4 -0.4 -10.4
157
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GAGCCACGGATACTCAAGAG
2146 SEQ ID N0:2029 -11.5 -23.7 67.3 -11.5 -0.4 -4.9
TCTTTCTGACTTCCGTTTCA
2502 SEQ ID N0:2030 -11.5 -24.3 71.7 -12.8 0 -3.8
CTGGCTATGCTCACGGCTCT
2581 SEQ ID N0:2031 -11.5 -28.5 79.6 -15.8 -1.1 -5.3
TGAGCTAAATGAACTCAATA
3419 SEQ ID N0:2032 -11.5 -16.7 52.8 -4 -1.1 -5.1
CGCATCTTATTTTTCACATA
3520 SEQ ID N0:2033 -11.5 -20.5 61.8 -9 0 -3.6
CATCAACGATCAAGAAATCT
4296 SEQ ID N0:2034 -11.5 -17.6 54 -6.1 0 -4.9
AGTGCAAGATAGCCAGCGCC
4681 SEQ ID N0:2035 -11.5 -28.2 76.8 -15.5 -1.1 -7.7
TTTTCTTCATATACAGGCTG
4774 5EQ ID N0:2036 -11.5 -21 64.6 -9.5 0 -3.8
CGTAGGATTCGGCCAATCCT
5350 SEQ ID N0:2037 -11.5 -27.1 72.9 -11.9 -3.3 -15.2
CCCAAAGATGGCATAGATAA
5471 SEQ TD N0:2038 -11.5 -20.9 60.2 -8 -1.3 -5
GTCACCACTGACCATGGGCA
5987 SEQ ID N0:2039 -11.5 -28.7 78.5 -15.7 -1.4 -8.9
GTGGATCCGGTCACCACTGA
5996 SEQ ID N0:2040 -11.5 -28.3 77.6 -14.5 -2.2 -12
TGCCATAAACCTGTCTTCCA
6092 SEQ ID N0:2041 -11.5 -25.6 71 -14.1 0 -3
AGGAGGAGGGGTGGTAGAGG
6356 SEQ ID N0:2042 -11.5 -26.3 77.7 -14.8 0 -0.7
ATCATAGGAAGGAGGAGGGG
6365 SEQ ID N0:2043 -11.5 -23.1 68 -11.6 0 -3.4
CTTTCTTTTTCTGGTTTGTC
6421 SEQ ID N0:2044 -11.5 -22.3 70.2 -10.8 0 -1.5
AATAAACTATGAATTGGGGA
6865 5EQ ID N0:2045 -11.5 -16.6 52.2 -5.1 0 -3.1
GAATAAACTATGAATTGGGG
6866 SEQ ID N0:2046 -11.5 -16.6 52.2 -5.1 0 -3.1
AGACTTTACAGGCACATAAC
7112 SEQ ID N0:2047 -11.5 -20.3 61.4 -8.8 0 -4
GGCAATATTAACATGCATTA
7554 SEQ ID N0:2048 -11.5 -19 57.7 -5.5 -2 -6.8
CATTCTATCACCAATATGTG
7628 SEQ ID N0:2049 -11.5 -20 60.5 -8.5 0 -3.8
AGGCAGTATCCAGTGTGTTT
7768 SEQ TD N0:2050 -11.5 -25.5 76.7 -13.5 -0.2 -4
GTTTTAGACATATTTTTAGC
7815 5EQ ID N0:2051 -11.5 -18.3 58.9 -6.8 0 -2.8
TATTTAAACAAGTTTTAGAC
7826 SEQ ID N0:2052 -11.5 -14.4 49 -2.9 0 -5.2
CCAGAGCCCAATAAGTGAAA
8485 SEQ ID N0:2053 -11.5 -22.5 62.9 -11 0 -2.4
ACTAGTTTGTTGTAAAATTC
8603 SEQ ID N0:2054 -11.5 -16.8 54.7 -4.6 -0.4 -6
TGAAAGTTGGAACATGTGAA
8704 SEQ ID N0:2055 -11.5 -17.6 54.6 -5.3 -0.6 -7
ATGTATACATAGGAGTTTAT
gg87 SEQ ID N0:2056 -11.5 -18.1 58 -5.9 0 -9.1
TCTTTCTTTCTCTGTGGATA
54 SEQ ID N0:2057 -11.4 -22.3 69.6 -10.9 0 -2.3
158
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TACAATTTTTTTTCTTTCTT
66 SEQ ID N0:2058 -11.4 -17.5 56.8 -6.1 0 -2.6
TTACAATTTTTTTTCTTTCT
67 SEQ ID N0:2059 -11.4 -17.5 56.8 -6.1 0 -2.6
TTTGGGCTTCTTGGCTTTCT
566 SEQ ID N0:2060 -11.4 -26.2 77.4 -14.3 -0.1 -3.7
AATCTTGATAGCAATTTTCC
824 SEQ ID N0:2061 -11.4 -19.5 59.7 -7.5 -0.3 -0.5
CTTCTTTACCGACTGGATCA
1190 SEQ ID N0:2062 -11.4 -23.8 68.4 -11.5 -0.7 -5.3
GCAGAATCGCTTGGGGGCCA
1309 SEQ ID N0:2063 -11.4 -29.7 79.3 -17.6 -0.5 -7.6
TTGTGCCATTAAAGTAGGAA
1347 SEQ ID N0:2064 -11.4 -20.2 60.5 -8.8 0 -3.5
ATGTATGTTTTCCCAGCAGC
1654 SEQ ID N0:2065 -11.4 -25.8 75 -14.4 0 -4.1
GCTGCTTCTTTTGACGCTGT
2060 SEQ ID N0:2066 -11.4 -26.6 76.3 -13.2 -2 -6.3
TGTTCATCATCAGCAAAGTC
2245 SEQ ID N0:2067 -11.4 -21.3 65.3 -9.9 0 -4.1
ATTCCATCAAAGATATTCCA
2941 SEQ ID N0:2068 -11.4 -20.4 60.7 -8.3 -0.4 -3.9
AGCTAAATGAACTCAATAAT
3417 SEQ ID N0:2069 -11.4 -15.4 50 -4 0 -4.3
CTTATTGCCTTCATGGATTT
3584 SEQ ID N0:2070 -11.4 -22.7 67 -10.7 -0.3 -4.7
GGTGGTTCCATTCCCATCTC
3665 SEQ ID N0:2071 -11.4 -28.9 82.3 -16.8 -0.4 -5.5
CCAGATCTTCCCTTTGCCTT
4028 SEQ ID N0:2072 -11.4 -29 79.5 -17.6 0 -5.8
GAAAGTCTCAAACCAGTTGT
4085 SEQ ID N0:2073 -11.4 -20.8 62.2 -8.7 -0.4 -3.4
GCCAGCACCAGGCATTAGTG
4275 SEQ ID N0:2074 -11.4 -28.6 79.4 -15.3 -1.9 -7.5
CTCATGCCTTCAAACCGGGA
4417 SEQ ID N0:2075 -11.4 -26.5 71.2 -15.1 0 -7.1
AACATTATCAAAGTTTACTT
4661 SEQ ID N0:2076 -11.4 -16 52.2 -3.9 -0.4 -5.5
ACAGATTTTCTTCATATACA
4779 SEQ ID N0:2077 -11.4 -18.6 58.9 -7.2 0 -2.6
ATCATGGTGACCATGTTGAG
5083 SEQ ID N0:2078 -11.4 -22.9 67.6 -8.3 -3.2 -11.5
TAGTAGTGTCTGAGGGAAAC
5203 SEQ ID N0:2079 -11.4 -20.7 64 -9.3 0 -3.2
AGTTGGACATCCCAAAGATG
5481 SEQ ID N0:2080 -11.4 -22.3 64.3 -8.7 -2.2 -8
CCAGCAGAGGTTGTAATTTG
5581 SEQ ID N0:2081 -11.4 -22.7 67.1 -11.3 0 -5.7
ATCCCAGCCAGCAGAGGTTG
5588 SEQ TD N0:2082 -11.4 -29.2 80.9 -17.1 -0.5 -4.9
AGTCATCCTCACTCAGGGGC
5820 SEQ ID N0:2083 -11.4 -28.3 82.6 -16 -0.8 -7.6
GATGCCATAAACCTGTCTTC
6094 SEQ TD N0:2084 -11.4 -23.5 67.6 -12.1 0 -3
GCCTCTTTGTTATAGTTACT
6244 SEQ ID N0:2085 -11.4 -23 70.1 -11.6 0 -2.5
GTCAATCCTCCCTTTAATTG
6263 SEQ ID N0:2086 -11.4 -23.5 67.6 -11.6 -O.l -3.7
159
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTTCCCATTTAGTTTGTCAA
6308 SEQ ID N0:2087 -11.4 -23.3 69.4 -11.9 0 -2.7
ACTTTTCCTTGTCTGGTTTT
6393 SEQ ID N0:2088 -11.4 -24 72.7 -12.6 0 -3.2
AAACTATGAATTGGGGACCA
6862 SEQ ID N0:2089 -11.4 -20.5 59.7 -6.9 -2.2 -7.2
ATAAACTATGAATTGGGGAC
6864 SEQ ID N0:2090 -11.4 -17.5 54.4 -6.1 0 -3.1
CTTTACAGGCACATAACTGT
7109 SEQ ID N0:2091 -11.4 -21.6 64.3 -8.8 -1.3 -5
AATAATCCTTTAAATATTAG
7135 SEQ ID N0:2092 -11.4 -13.6 46.8 -2.2 0 -5.3
CTTGACATAATGGACAGAGC
7658 SEQ ID N0:2093 -11.4 -20.6 61.8 -9.2 0 -3.l
TTATTCTGCTTGACATAATG
7666 SEQ ID N0:2094 -11.4 -18.5 57.8 -7.1 0 -3.6
TCTAACTTTTATTTTAGGAA
8010 5EQ ID N0:2095 -11.4 -16.5 53.8 -5.l 0 -3.2
CAACTTTGCCACTTTGTTCA
8279 SEQ ID N0:2096 -11.4 -23.5 68.2 -12.1 0 -3.1
CAAAAATTTATATCATGTTA
8309 SEQ ID N0:2097 -11.4 -13.6 46.8 -2.2 0 -5.2
AGCTCACCATTCTTTTTAGC
8421 SEQ ID N0:2098 -11.4 -24 71.7 -12.1 -0.1 -4.3
TGAAATGCAATAAAAAATGA
8470 SEQ ID N0:2099 -11.4 -11.8 42.6 0 0 -5.1
ACCTTTCCAGAATCCTCTCT
21 SEQ ID N0:2100 -11.3 -26.2 74.6 -14.9 0 -3.5
AGAGACCTTTCCAGAATCCT
25 SEQ 2D N0:2101 -11.3 -24.8 70.7 -13.5 0 -2.9
AGTTACAATTTTTTTTCTTT
69 SEQ ID NO:2102 -11.3 -17.4 56.7 -6.1 0 -2.6
CTGCACATTTAATTACGTGT
443 SEQ ID N0:2103 -11.3 -20.7 61.6 -8.8 -0.3 -5.2
AGTCACTATTTGGCTTTGGT
615 SEQ ID NO:2104 -11.3 -23.8 72 -11.8 -0.4 -3.7
GAACAGCTGCAGCCCAATGA
1259 SEQ ID N0:2105 -11.3 -26.4 71.9 -13 0 -12.4
GTAAAGATTTTCCCAATAGT
1619 SEQ ID N0:2106 -11.3 -19.7 59.6 -8.4 0 -3.2
TCCTAACCCACCTACTCCAC
1889 SEQ ID N0:2107 -11.3 -28.4 75.7 -17.1 0 -0.3
CAAGGTGCTCTCTCTGTCTT
1989 SEQ ID N0:2108 -11.3 -25.6 77.2 -14.3 0 -3.6
GATCAAGAACACATTGGCAA
2669 SEQ ID N0:2109 -11.3 -19.8 58.9 -8.5 0 -4.7
CCCAGTAAAGACCAGGTTTC
2855 SEQ ID N0:2110 -11.3 -24.7 70 -13.4 0 -5.9
GAGCTAAATGAACTCAATAA
3418 SEQ ID NO:2111 -11.3 -16 51.2 -4 -0.4 -5.1
TTCAATTCCAGTATTATTGG
3620 SEQ ID N0:2112 -11.3 -19.7 60.7 -7.7 -0.4 -5
ATTAAGCTCTTTGCTTATTT
3638 SEQ ID N0:2113 -11.3 -20 62.2 -5.7 -3 -7.5
,
TGAGGCTGGGGTTGTTTATG
3750 SEQ ID N0:2114 -11.3 -24.5 72.5 -13.2 0 -3.7
TTCACGTTTTTCCACCGAGC
4642 SEQ ID N0:2115 -11.3 -26.3 72.6 -15 0 -4.7
160
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TAATATCCATCCAGCCTTTA
4719 SEQ ID N0:2116 -11.3 -23.5 67.4 -12.2 0 -3.2
CCTTGGAATTTGTTTGCTGG
5002 SEQ ID N0:2117 -11.3 -23.6 68.3 -12.3 0 -4.3
CCAAAGGTCTCAAAGTTGAA
5539 SEQ ID N0:2118 -11.3 -19.9 59.3 -8.6 0 -5.4
TGCCAAAGGTCTCAAAGTTG
5541 SEQ TD N0:2119 -11.3 -21.8 63.8 -10.5 0 -4
AGGAGGATCCAGGGCAGCTG
5921 SEQ ID N0:2120 -11.3 -28.3 80 -14.3 -2.6 -12.5
AGTGGATCCGGTCACCACTG
5997 SEQ ID N0:2121 -11.3 -27.7 76.6 -13.3 -3 -13.5
GGCTCATAAGAGACTTTGGA
6121 SEQ ID N0:2122 -11.3 -22.3 66.5 -9.6 -1.3 -5
TGCCTCTTTGTTATAGTTAC
6245 SEQ ID N0:2123 -11.3 -22.1 67.8 -10.8 0 -3
GGTTTTGTTACACTATCATA
6379 SEQ ID N0:2124 -11.3 -20.2 63 -8.9 0 -2.7
TACTTTTGATTTTCTCTGAC
6454 SEQ ID N0:2125 -11.3 -19.4 61.4 -8.1 0 -2.4
TCTTTTTACTTTTGATTTTC
6460 SEQ ID N0:2126 -11.3 -7.8.1 58.8 -6.8 0 -2
TATCCCTATAGTCTAGGTAG
6723 SEQ ID N0:2127 -11.3 -22.7 69.1 -10 -1.3 -4.6
TCTTCAACGTAAACCTCATT
6911 SEQ ID N0:2128 -11.3 -20.6 60.7 -9.3 0 -5.3
TTCTTCAACGTAAACCTCAT
6912 SEQ ID N0:2129 -11.3 -20.6 60.7 -9.3 0 -5.3
CATTTGAGAGACAGGGTTCT
6942 SEQ ID N0:2130 -11.3 -22.6 68.2 -11.3 0 -3.6
ATTAAATATAGAGCTCTGAA
7202 SEQ ID N0:2131 -11.3 -16.3 52.7 -4 0 -10
ATTCATTCTATCACCAATAT
7631 SEQ ID N0:2132 -11.3 -19.3 59.4 -8 0 -2.4
ATTCTGCTTGACATAATGGA
7664 SEQ ID N0:2133 -11.3 -20.5 61.8 -9.2 0 -3.3
CTTCAAATTATTCTGCTTGA
7673 SEQ ID N0:2134 -11.3 -19.3 59.5 -8 0 -3.6
AAGTGAAATGCAATAAAAAA
8473 SEQ ID N0:2135 -11.3 -11.7 42.4 0 0 -5.6
ATTAATACCTTATGTATACA
8898 SEQ ID N0:2136 -11.3 -17.2 54.7 -5 -0.8 -7.9
TTTATTATGGGAGAATTATG
9062 SEQ ID N0:2137 -11.3 -16.4 53.2 -5.1 0 -3.2
ATTTATTATGGGAGAATTAT
9063 SEQ ID N0:2138 -11.3 -16.4 53.2 -5.1 0 -3.2
GACCTTTCCAGAATCCTCTC
22 SEQ ID N0:2139 -11.2 -25.9 74 -14.7 0 -3.5
ACAGGTATCTCATCCCTGTC
269 SEQ ID N0:2140 -11.2 -26.3 77.4 -12.6 -2.5 -7.5
GTCACTATTTGGCTTTGGTT
614 SEQ ID N0:2141 -11.2 -23.9 72 -12.7 0 -3.7
TTTTCTTATTGATATAGTAG
717 SEQ ID N0:2142 -11.2 -16.4 54.7 -5.2 0 -2.7
GTTTTCAGTGCTCGGAGAAC
1129 SEQ ID N0:2143 -11.2 -23.6 69.9 -11.8 -0.3 -6.4
GTGTAGCCATAGTTGGGGTT
1543 SEQ ID N0:2144 -11.2 -26.5 78.3 -13.8 -1.4 -4.8
161
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGAGGAATCCTCCAGCATCT
2552 SEQ ID N0:2145 -11.2 -25.9 74 -12.5 -2.2 -11.2
CCATAAAGAGGGTATTTAAG
2784 5EQ ID N0:2146 -11.2 -18.1 55.9 -6.9 0 -3.1
CAAGGTGAGGTTTCCTAGAG
3113 5EQ ID N0:2147 -11.2 -23.2 69.2 -11.3 -0.5 -4.4
ACAAGGTTTCCAATGACCAT
3373 SEQ ID N0:2148 -11.2 -22.7 64.9 -9.9 -1.5 -5.8
AACACTCCCGCATCTTATTT
3528 SEQ ID N0:2149 -11.2 -24.3 68.1 -13.1 0 -3.6
CATCGATTACGTATTTTTCA
3711 SEQ ID N0:2150 -11.2 -19.7 59.5 -7.6 -0.7 -6.3
ACACCCTTCAGTAAAACAAG
3971 SEQ ID N0:2151 -11.2 -20.2 59.2 -9 0 -2.9
AACAATACTGTAGCAGGTTT
4061 SEQ ID N0:2152 -11.2 -20.3 61.8 -8.2 -0.7 -5.3
GGGATAAGGCTCTTAGAGGT
4401 SEQ ID N0:2153 -11.2 -24 71.5 -12.2 -0.3 -6.1
TTTTTCCACCGAGCTTGCTT
4636 SEQ ID N0:2154 -11.2 -26.7 74.3 -15 -0.2 -6.1
CAGATTTTCTTCATATACAG
4778 SEQ ID N0:2155 -11.2 -18.4 58.5 -7.2 0 -2.6
ATTTGTTTGCTGGGCGAGGT
4995 SEQ ID N0:2156 -11.2 -26.3 75.3 -14.3 -0.6 -4.4
GGATCATGATGCTGATATCA
5055 SEQ ID N0:2157 -11.2 -21.6 64.7 -9.5 -0.6 -8.5
TTGGACATCCCAAAGATGGC
5479 SEQ ID N0:2158 -11.2 -24.1 67.4 -11.2 -1.7 -7.8
TCATCAATTCCAGCTTCCTT
5515 SEQ ID N0:2159 -11.2 -24.9 72 -13.7 0 -4.5
ATCGGGATCAAACTTTTCCC
5861 SEQ TD N0:2160 -11.2 -23.7 66.7 -10.9 -1.5 -6.5
ACTCCCATCTGTTTTTTCTG
6335 SEQ ID N0:2161 -11.2 -24.5 72.3 -13.3 0 -2.l
TCCTTGTCTGGTTTTGTTAC
6388 SEQ ID N0:2162 -11.2 -23.8 72.6 -12.6 0 -3.2
GTTTGGCATGGACCTCCTCT
6552 SEQ ID N0:2163 -11.2 -28.6 80.6 -16.9 -0.1 -5.l
ATAGAATGGATGCAAGGACT
6788 SEQ ID N0:2164 -11.2 -20.1 60.2 -8.9 0 -5.6
AGGCACATAACTGTTCAGAT
7103 SEQ ID N0:2165 -11.2 -21.7 65 -10 -0.2 -5.6
ACATAGACTATCAGCTTTGC
7347 SEQ ID N0:2166 -11.2 -21.8 66.2 -10.6 0 -4.5
TGTTGGAAGCTTGCAAAAGA
7487 SEQ ID N0:2167 -11.2 -20.2 60 -6.9 -2.1 -7
ATAGCCTTTAAACTATGTTT
7531 SEQ ID N0:2168 -11.2 -19.1 58.8 -7.3 -0.3 -5
ACCATTCTTTTTAGCAATAG
8416 SEQ ID N0:2169 -11.2 -19.9 60.9 -8.7 0 -4.1
TTGAAAGAAGATGAGTTTAG
8795 SEQ ID N0:2170 -11.2 -15.5 51.2 -4.3 0 -2.2
TTAATACCTTATGTATACAT
8897 SEQ ID N0:2171 -11.2 -17.2 54.7 -5 -0.8 -9.3
AGCTTTTTTTTTTTTTTTTT
114 SEQ ID N0:2172 -11.1 -18.3 59.3 -7.2 0 -4.3
CGTGTCTTCCTCTGGCAGCT
138 SEQ ID N0:2173 -11.1 -29.6 83.9 -18.5 0 -5
162
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TCATCCCTGTCAAACCTTGA
260 SEQ ID N0:2174 -11.1 -25.1 70.3 -13 -0.9 -4.3
TCCAGGTCCCTTCTGTGAAT
368 SEQ ID N0:2175 -11.1 -27.3 77.1 -15.7 -0.2 -4.2
TAGTAAAAAGGCGGAAGCTT
507 SEQ ID N0:2176 -11.1 -19.5 57.8 -6 -2.4 -7
GTCATAAATACACAGTTGGT
889 SEQ ID N0:2177 -11.1 -19.8 60.9 -8.7 0 -2.6
GGTCATAAATACACAGTTGG
890 SEQ ID N0:2178 -11.1 -19.8 60.4 -8.7 0 -2.8
GGGTTGCTCAAGGTCATAAA
901 SEQ ID N0:2179 -11.1 -22.6 66.7 -11.5 0 -3.4
TGTGTAGCCATAGTTGGGGT
1544 SEQ ID N0:2180 -ll.l -26.4 77.6 -13.8 -1.4 -4.8
TAACCCACCTACTCCACTGA
1886 SEQ ID N0:2181 -11.1 -26.6 72 -15.5 0 -1.6
CCATGTCTGTGCGGCACAAA
2305 SEQ ID N0:2182 -11.1 -26.2 71.5 -12.5 -1.4 -13.2
TACTTTTAACCATGCATCAC
2699 SEQ ID N0:2183 -11.1 -20.8 62 -9.7 0 -6.6
GAATTGCTCAGTCATGGGGT
2816 SEQ ID N0:2184 -11.1 -24.9 73.2 -13.8 0 -4.7
TTTCCAATGACCATGACCAA
3367 SEQ ID N0:2185 -11.1 -22.9 64 -11.8 0 -4.5
GTTTCCAATGACCATGACCA
3368 SEQ ID N0:2186 -11.1 -24.8 69 -13.7 0 -4.5
TTTGGAAACACTCCCGCATC
3534 SEQ ID N0:2187 -11.1 -24.7 68 -12.5 -1 -5.7
CTCTAAGATAATTAAGCTCT
3648 SEQ ID N0:2188 -11.1 -17.9 56.6 -6.8 0 -5.1
GGTGAGGCTGGGGTTGTTTA
3752 SEQ ID N0:2189 -11.1 -26.9 79.2 -15.8 0 -3.7
CAACAGCAATTGGCACTGTG
3774 SEQ ID N0:2190 -11.1 -22.8 65.5 -10.1 -1.6 -9.6
TCTCGGGGTAGAACAACATC
3904 SEQ ID N0:2191 -11.1 -22.4 65.5 -11.3 0 -3.7
CTTCTCGGGGTAGAACAACA
3906 SEQ ID N0:2192 -11.1 -23 66.2 -11.3 -0.3 -3.8
TACTGTAGCAGGTTTTTCGA
4056 SEQ ID N0:2193 -11.1 -22.8 68.4 -10.8 -0.7 -5.5
AGCACATTCATGATAGAGGG
4468 SEQ ID N0:2194 -11.1 -21.9 65.7 -10.8 0 -6.4
TATGGGTTTCTGAGGTTTCT
4976 SEQ ID N0:2195 -11.1 -23.3 71.5 -12.2 0 -2.8
GGCGAGGTATGGGTTTCTGA
4983 SEQ ID N0:2196 -11.1 -26.2 75.5 -15.1 0 -4
TTTGCCCTGGTCATCCGTTT
5108 SEQ ID N0:2197 -11.1 -29 79.5 -16.7 -1.1 -4.4
GCTTCAGCACAAATTCTCCA
5181 SEQ ID N0:2198 -11.1 -24.4 70 -13.3 0 -5.g
CATCCCAGCCAGCAGAGGTT
5589 SEQ ID N0:2199 -11.1 -29.9 82.1 -18.8 0 -4.6
GCTGGACTTTGTTGGGTTTT
5g52 SEQ ID N0:2200 -11.1 -25 74.2 -13.9 0 -28
TCCTCCCTTTAATTGCCTCT
6258 SEQ ID N0:2201 -ll.l -27.9 77.1 -16.8 0 -3
AAGTCAATCCTCCCTTTAAT
6265 SEQ ID N0:2202 -ll.l -22.7 65.5 -11.6 0 -2.5
163
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTTATAGGTAAGTCAATCCT
6274 SEQ ID N0:2203 -11.1 -19.9 61.5 -8.8 0 -3.8
CCTCTTTTCCTTTGCTTTCT
6435 5EQ ID N0:2204 -11.1 -26.2 76.6 -15.1 0 -3.6
TAGTTACAATGTTCACTTTG
6749 SEQ ID N0:2205 -11.1 -18.6 58.9 -7.5 0 -5.6
AAAACACCTTTGTCTGATCA
6960 SEQ ID N0:2206 -11.1 -20.3 60.5 -8.5 -0.5 -6.8
ACTTTACAGGCACATAACTG
7110 SEQ ID N0:2207 -11.1 -20.6 61.8 -8.8 -0.5 -4
AAGCAATACTTTAGATATAT
7272 SEQ ID N0:2208 -11.1 -15.8 51.7 -4.7 0 -4.1
TTGATTTAATAGAAGTTGTT
7446 SEQ ID N0:2209 -11.1 -16.1 53 -5 0 -2.5
AGCATAGGCAATATTAACAT
7560 SEQ ID N0:2210 -11.1 -18.9 57.8 -6.2 -1.6 -6.7
AGGTTGAATTCATTCTATCA
7638 SEQ ID N0:2211 -11.1 -19.8 61.8 -8.2 0.3 -8.4
CCATATGATACTCATGTTGA
7728 SEQ ID N0:2212 -11.1 -20.8 62.5 -8.8 -0.8 -6
TATCCAGTGTGTTTCCTTGA
7762 SEQ TD N0:2213 -11.1 -24.6 73.1 -13.5 0 -3.7
TTTAGGAAATTATCCATTGA
7998 SEQ ID N0:2214 -11.1 -17.9 55.8 -4.6 -2.2 -7.2
TATCTAACTTTTATTTTAGG
8012 SEQ ID N0:2215 -11.1 -16.3 53.8 -5.2 0 -3.2
TGAGTGTTTGACCAATGTAT
8086 SEQ ID N0:2216 -11.1 -20.9 63.1 -9.8 0 -3.4
CATGTTATATTTGTAATAGC
8239 SEQ ID N0:2217 -11.1 -17.3 55.7 -6.2 0 -3.5
AACAAAAATTTATATCATGT
8311 SEQ ID N0:2218 -ll.l -13.3 45.9 -2.2 0 -4.7
ATGAAATTTATTCTTTTGGC
8454 SEQ ID N0:2219 -11.1 -17.8 56.2 -5.6 -1 -5.2
GAGTTTATATAATGCATTTA
8875 SEQ ID N0:2220 -ll.l -16.8 54.4 -5 0 -8.8
AGAGTTTGGTTTTGACCTCA
8974 SEQ ID N0:2221 -ll.l -23.5 70.6 -10.1 -2.3 -6.3
CTTTCTCTGTGGATAAGAAA
49 SEQ ID N0:2222 -11 -18.9 58.6 -6.8 -1 -4.5
TTTTTTTTTTTTTTTTTTTT
111 SEQ ID N0:2223 -11 -15.9 53.7 -4.9 0 0
ATTCTTTGCTCCTTTCCCAG
314 SEQ ID N0:2224 -11 -26.9 76.8 -15.9 0 -3.6
TGTAGCTTCTTGCATACGAA
426 SEQ TD N0:2225 -11 -22.2 65.4 -9.4 -1.8 -5.2
GTTGGTCAAAATAGTGCACA
875 SEQ ID N0:2226 -11 -21 62.9 -9 0 -9.9
AGCAAAACCCTCTTGCCAAG
990 SEQ ID N0:2227 -11 -24.7 67.4 -11.7 -2 -6.2
TTAACAAATGTCCCATTTGA
1372 SEQ ID N0:2228 -11 -19.7 58.4 -4.9 -3.8 -10.4
CCTAACCCACCTACTCCACT
lggg SEQ ID N0:2229 -11 -28.9 75.9 -17.9 0 -0.3
TTGGAACTCAACTTTGATGC
1933 SEQ ID N0:2230 -1l -20.4 61.3 -9.4 0 -5
AAGGTGCTCTCTCTGTCTTC
1988 SEQ ID N0:2231 -11 -25.3 77.9 -14.3 0 -2.9
164
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg koal/molkcal/molkcal/mol
C
Intra- Tnter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGGGGAAAACAGGGAGCCAC
2159 SEQ ID N0:2232 -11 -24.7 68.2 -13.1 -0.3 -4.3
TCGCTCTCCATGTCTGTGCG
2312 SEQ ID N0:2233 -11 -28.6 79.6 -16.3 -l.2 -6.7
TGGAAGCCCTGGCACCATCC
2369 SEQ ID N0:2234 -11 -30.8 80.6 -18.2 -1.4 -10.4
CAGAGGAATCCTCCAGCATC
2553 SEQ ID N0:2235 -11 -25.7 73.1 -12.5 -2.2 -11.2
AAATGAAGACGATGATGGCC
3138 SEQ ID N0:2236 -11 -20.3 58.6 -9.3 0 -6.2
AACAGCAATTGGCACTGTGA
3773 SEQ ID N0:2237 -11 -22.7 65.7 -10.1 -1.6 -9.6
TTTCAGCTTGTTCACCTTCT
3921 SEQ ID N0:2238 -11 -25 74.8 -14 0 -4.5
TCCCTTTGCCTTCTTCTGTA
4020 SEQ ID N0:2239 -11 -27.9 79.9 -16.9 0 -3
AGAAACATCAACGATCAAGA
4301 SEQ ID N0:2240 -11 -17.1 52.9 -6.1 0 -4.9
ATGTCAAACATGTTACCCGT
4576 SEQ ID N0:2241 -11 -23 65.2 -11.1 -0.6 -9
AGAATACTTTTCTATCATCT
5294 SEQ ID N0:2242 -11 -18.4 58.7 -6.5 -0.8 -3.4
CTCCCTTAACTGAGCTGCCA
5670 SEQ ID N0:2243 -11 -28.2 76.8 -17.2 0 -5.6
AGGTAAGTCAATCCTCCCTT
6269 SEQ ID N0:2244 -11 -25.7 73.4 -14.7 0 -4.7
TTTCTGGAGTGGAGTTCCCA
6321 SEQ ID N0:2245 -11 -26.7 77.5 -14.6 -1 -8.7
GGAGGGGTGGTAGAGGAACT
6352 SEQ ID N0:2246 -11 -25.5 74.3 -13.8 -0.5 -3.1
TTCTTTTTACTTTTGATTTT
6461 SEQ ID N0:2247 -11 -17.8 57.7 -6.8 0 -2.2
CAACGTTGATACCCTGCTTC
6648 SEQ ID N0:2248 -11 -24.9 69.3 -13 0 -9.8
TACAATGTTCACTTTGCACA
6745 SEQ ID N0:2249 -11 -21 63 -10 0 -5.4
ATTGGGGACCATGGAAATGC
6853 SEQ ID N0:2250 -11 -23.4 65.9 -10 -2.4 -8.8
CAAAACACCTTTGTCTGATC
6961 SEQ ID NO:2251 -11 -20.3 60.5 -8.5 -0.6 -5.1
GAAAGCATTTGACCTAAATT
7219 SEQ ID N0:2252 -11 -18 54.9 -6.3 -0.4 -4
TTACTTTTTGGAAAGCATTT
7229 SEQ ID N0:2253 -11 -18.4 57.3 -5.8 -1.6 -5.5
TTATTAGATTACTTTTTGGA
7237 SEQ ID N0:2254 -11 -17.3 56 -6.3 0 -2.4
GGATTTATTAGATTACTTTT
7241 SEQ ID N0:2255 -11 -17.3 56.1 -6.3 0 -2.4
GATACAGGATACATCCCTGT
7504 SEQ ID N0:2256 -11 -24.1 69.5 -10.3 -2.8 -8.2
AATATTAACATGCATTAGTG
7551 SEQ ID N0:2257 -11 -16.5 53 -5.5 0 -6.7
GCAATATTAACATGCATTAG
7553 SEQ ID N0:2258 -11 -17.8 55.4 -5.5 -1.2 -6.7
ATAGGCAATATTAACATGCA
7557 SEQ ID N0:2259 -11 -18.9 57.5 -5.9 -2 -6.8
GACATTCTTTAACCAAGACT
7609 SEQ ID N0:2260 -11 -20 60.1 -8.2 -0.6 -3.3
165
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTTTAGACATATTTTTAGCA
7814 SEQ TD N0:2261 -11 -17.8 57.1 -6.8 0 -4.l
TAGTTACAATTTTTTTTCTT
70 SEQ ID N0:2262 -10.9 -17 55.7 -6.1 0 -2.6
TTAGTTACAATTTTTTTTCT
71 SEQ ID N0:2263 -10.9 -17 55.7 -6.1 0 -2.6
ATTCTTACAATATCCCTAGA
338 SEQ ID NO:2264 -10.9 -20.7 62.2 -9.8 0 -3.8
AGGCGGAAGCTTTCAGGTCC
499 SEQ ID N0:2265 -10.9 -27.7 77.9 -14.4 -2.4 -7.6
TTTGTTCTCATCATCATTAT
596 SEQ ID N0:2266 -10.9 -19.9 62.9 -9 0 -1.9
TCTTGATAGCAATTTTCCTA
822 SEQ ID N0:2267 -10.9 -20.8 63.2 -9.3 -0.3 -0.5
TGGTTTCAAAAGCAGAATCG
1320 SEQ ID N0:2268 -10.9 -19.2 57.6 -8.3 0.4 -0.6
TGAGCCATTTCCACAGAGTA
1475 SEQ ID N0:2269 -10.9 -24.8 71.7 -13.9 0 -3.2
TTCGACCAGCCTTCACACAG
1524 SEQ ID N0:2270 -10.9 -26.5 73.3 -15.6 0 -4.6
AAGGTGGCCTGATTCTGCTC
1756 SEQ ID N0:2271 -10.9 -26.7 76.8 -15.1 -0.4 -6.5
GCTTTTTAAGCTGTTCGAGC
1815 SEQ ID N0:2272 -10.9 -23.7 70 -10.9 -1.9 -8.7
TTGGGGAAAACAGGGAGCCA
2160 SEQ ID N0:2273 -10.9 -24.6 68 -13.1 -0.3 -4.7
TTGCGTCTTGGGGAAAACAG
2167 SEQ TD N0:2274 -10.9 -22.3 63.9 -11.4 0 -5.2
TTCGCCGTCTTCAAATGTGC
2267 SEQ ID N0:2275 -10.9 -25.2 70.2 -14.3 0 -2.8
GGGAAGTTGTCCAGTAGGTG
2465 SEQ ID N0:2276 -10.9 -25.2 74.8 -12.3 -2 -5.6
CAGTAAAGACCAGGTTTCCT
2853 SEQ ID N0:2277 -10.9 -23.6 68.3 -12.7 0 -5.9
CAGACCAAGCTCCATTAAAC
2975 SEQ ID N0:2278 -10.9 -21.9 62.8 -11 0 -5
GACAGACCAAGCTCCATTAA
2977 SEQ ID N0:2279 -10.9 -23.2 66 -12.3 0 -5
TGCTTCCTTCAGATGAGCTG
3879 SEQ ID N0:2280 -10.9 -25.2 73.7 -12.9 -1.3 -5.3
CTTCTGTACTTACTTGACAG
4008 SEQ ID N0:2281 -10.9 -20.8 64.3 -8.8 -1 -4.6
TCTTCTGTACTTACTTGACA
4009 SEQ ID N0:2282 -10.9 -21.2 65.6 -10.3 0 -4.8
CAGGTTTTTCGAAGATTCCA
4048 SEQ ID N0:2283 -10.9 -22.4 65.5 -10.8 -0.4 -7.4
CAATGAAAGTCTCAAACCAG
4089 SEQ ID N0:2284 -10.9 -18.3 55.5 -6.8 -0.3 -3.4
CCCTCATGCCTTCAAACCGG
4419 SEQ ID N0:2285 -10.9 -28.7 74.2 -17.8 0 -6.6
CATAAAGATGTCTTGACCTC
4907 SEQ ID N0:2286 -10.9 -20.3 61.4 -8.6 -0.6 -6.8
AACTAGGGTCATGTATTTGC
5123 SEQ ID N0:2287 -10.9 -21.7 66 -10.8 0 -4.7
TCATCAAAGCAAAGAGCAGC
5400 SEQ ID N0:2288 -10.9 -20.8 61.7 -8.3 -1.6 -5.5
CACCACTGACCATGGGCAGA
5985 SEQ ID N0:2289 -10.9 -27.7 75 -15.7 -1 -8.9
166
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGGAAGGAGGAGGGGTGGTA
6360 SEQ ID N0:2290 -10.9 -25.6 74.7 -14.7 0 -0.6
TAGGAAGGAGGAGGGGTGGT
6361 SEQ ID N0:2291 -10.9 -25.6 74.7 -14.7 0 -0.2
AACTTTTCCTTGTCTGGTTT
6394 SEQ ID N0:2292 -10.9 -23.2 69.7 -12.3 0 -3.2
GGCACTGACTATGAGTATTT
6585 SEQ ID N0:2293 -10.9 -21.9 66.1 -10.5 -0.1 -4.1
TGTTCACTTTGCACAACTAT
6740 SEQ ID N0:2294 -10.9 -21.2 63.8 -10.3 0 -5
ATGTTCACTTTGCACAACTA
6741 SEQ ID N0:2295 -10.9 -21.2 63.8 -10.3 0 -5
GTTACAATGTTCACTTTGCA
6747 SEQ ID N0:2296 -10.9 -21.4 64.8 -10.5 0 -5.4
ACTATGAATTGGGGACCATG
6860 SEQ ID N0:2297 -10.9 -21.9 63.4 -8.6 -2.4 -,7.2
GGCACATAACTGTTCAGATA
7102 SEQ ID N0:2298 -10.9 -21.4 64.2 -10 -0.2 -5.6
TTTTTGGAAAGCATTTGACC
7225 SEQ ID N0:2299 -10.9 -20.3 60.6 -8.7 -0.4 -4.1
TGGATTTATTAGATTACTTT
7242 SEQ TD N0:2300 -10.9 -17.2 55.7 -6.3 0 -2.4
ATTATTCTGCTTGACATAAT
7667 SEQ ID N0:2301 -10.9 -18.5 57.8 -7.1 -0.2 -4.2
TCCTCTCTGCTTATGCCTCC
9 SEQ ID N0:2302 -10.8 -29.5 83.4 -17.8 -0.8 -4.6
TTTTTTTTTTTTTTTTTTTT
110 SEQ ID N0:2303 -10.8 -15.9 53.7 -5.1 0 0
TTGACAGGTATCTCATCCCT
272 SEQ ID N0:2304 -10.8 -25.4 73.8 -14.6 0 -3.1
GATTCTTTGCTCCTTTCCCA
315 SEQ ID N0:2305 -10.8 -27.5 77.9 -16.7 0 -3.6
CCAGGTCCCTTCTGTGAATT
367 SEQ TD N0:2306 -10.8 -27 75.8 -15.7 -0.2 -4.2
TCTCATCATCATTATCTTGT
591 SEQ ID N0:2307 -10.8 -21 65.8 -10.2 0 -1.9
TATTTGGCTTTGGTTTGTTC
609 SEQ ID N0:2308 -10.8 -22.3 68.7 -11.5 0 -3.7
ATATAGTAGGGATCCAGGTC
706 SEQ ID N0:2309 -10.8 -23.2 70.4 -11.6 -0.3 -8.9
TTTGTCCAGTCAGGAGGGTT
916 SEQ ID N0:2310 -10.8 -26.3 78.4 -14.1 , -1.3 -5.3
TCGCTTGGGGGCCACTGCAA
1303 SEQ ID N0:2311 -10.8 -30.2 80 -17.5 -1.9 -6.9
CCTGAGCTTCTTCCTGTTGC
1833 SEQ ID N0:2312 -10.8 -28.1 80.7 -17.3 0 -5.2
GCTTCTGAAGAACTTTCCAA
1915 SEQ ID N0:2313 -10.8 -21.6 63.6 -10.1 -0.4 -8.3
CTCCATTCTTTAGCACCTTT
1951 SEQ ID N0:2314 -10.8 -25.1 72.7 -14.3 0 -4.1
TTCAAGGTGCTCTCTCTGTC
1991 SEQ ID N0:2315 -10.8 -25.1 76.9 -14.3 0 -3.6
TCTCTCCTTTGTTGTTTCCT
2010 SEQ ID N0:2316 -10.8 -26.1 78.1 -15.3 0 0
CTCTCTCCTTTGTTGTTTCC
2011 SEQ ID N0:2317 -10.8 -26.1 78.1 -15.3 0 0
TTGCCCGACCTCTGAAACTG
2205 SEQ ID N0:2318 -10.8 -26 69.6 -15.2 0 -3
167
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CTCCATGTCTGTGCGGCACA
2307 SEQ ID N0:2319 -10.8 -28.9 79.7 -15.6 -1.3 -13
TTCCCATTTGCTGGAAGCCC
2380 SEQ ID N0:2320 -10.8 -29 77.8 -16 -2.2 -6.6
CATTGCAATCCACAGTGCTG
2406 SEQ ID N0:2321 -10.8 -24.5 69.7 -12.1 -1.5 -9
GGTTTCCTAGAGCCCCCACA
3105 SEQ ID N0:2322 -10.8 -31.6 84.2 -20.8 0 -3.8
ATCATCAGTAGCAGCAAGGT
3443 SEQ ID N0:2323 -10.8 -23.8 71.4 -13 0 -5.4
GGCTTTTTGGAAACACTCCC
3539 SEQ ID N0:2324 -10.8 -25.1 70.2 -13.2 -1 -5.8
ACTGTGACGGTGAGGCTGGG
3760 SEQ ID N0:2325 -10.8 -27.2 76.4 -16.4 0 -3.7
ATTTCTCTTTGCTTTCTTCT
3849 SEQ ID N0:2326 -10.8 -22.6 70.5 -11.8 0 -3.6
CATTTCCAGAATGAATATAT
4217 SEQ ID N0:2327 -10.8 -17.2 53.9 -5.4 -0.9 -5.7
ACATCAACGATCAAGAAATC
4297 SEQ ID N0:2328 -10.8 -16.9' 52.7 -6.1 0 -4.9
ACGTTTTTCCACCGAGCTTG
4639 SEQ ID N0:2329 -10.8 -26.1 71.7 -15.3 0 -5.3
ATTCTCCAGTGAACAGAACA
5169 SEQ ID N0:2330 -10.8 -21.3 63.3 -10 -0.2 -4.8
GCAGAGGTTGTAATTTGGAA
5578 SEQ ID N0:2331 -10.8 -21.1 63.6 -10.3 0 -5.7
GATGACCGCGATGTACATGT
5762 5EQ ID N0:2332 -10.8 -24.4 67.7 -12.9 0 -8.9
GGGCATCCATCTCTCCACTC
6060 5EQ ID N0:2333 -10.8 -29.2 82.9 -17.8 -0.3 -4
ATGCCATAAACCTGTCTTCC
6093 SEQ ID N0:2334 -10.8 -24.9 69.9 -14.1 0 -3
TTTTCTGGAGTGGAGTTCCC
6322 SEQ ID N0:2335 -10.8 -26.1 76.8 -14.6 -0.5 -4.5
AGTTACAATGTTCACTTTGC
6748 SEQ ID N0:2336 -10.8 -20.7 63.8 -9.9 0 -5.3
AAGTTAAAAATAGAATGGAT
6797 SEQ ID N0:2337 -10.8 -12.9 45.1 -2.1 0 -2.8
TAAACTATGAATTGGGGACC
6863 SEQ ID N0:2338 -10.8 -19.5 58 -7.5 -1.1 -5.7
GCATTATGAATAAACTATGA
6873 SEQ ID N0:2339 -10.8 -15.9 51.2 -5.1 0 -3.5
ACAATTCTTTTTCTGGTTTT
7004 SEQ ID N0:2340 -10.8 -20 62.5 -9.2 0 -2.5
TTGGAAGCTTGCAAAAGACA
7485 SEQ ID N0:2341 -10.8 -19.9 59 -7 -2.1 -7
CCATAGTTGGTAGAAAATGA
8114 SEQ ID N0:2342 -10.8 -18.9 57.5 -7.3 -0.6 -3.5
CCATGTTATATTTGTAATAG
8240 SEQ ID N0:2343 -10.8 -17.5 55.6 -6.7 0 -4.3
ATTCTTTTTAGCAATAGCAA
8413 SEQ ID N0:2344 -10.8 -18.8 58.6 -6.3 -1.7 -4.5
CATTCTTTTTAGCAATAGCA
8414 SEQ ID N0:2345 -10.8 -20.2 61.9 -7.7 -1.7 -4.5
AATTTATTCTTTTGGCTCAA
8450 SEQ ID N0:2346 -10.8 -19.2 59.6 -8.4 0 -4.6
ACCCCAGAGCCCAATAAGTG
8488 SEQ ID N0:2347 -10.8 -27.5 72.9 -16.7 0 -3.2
168
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTATATATATTTTAAACTGC
8533 SEQ ID N0:2348 -10.8 -14.4 48.9 -3.6 0 -5.2
TTGTAGGTGGTTACTACTAT
8736 SEQ ID N0:2349 -10.8 -21.2 65.9 -8.8 -1.6 -5.2
ATGAGTTTAGATGCTTATAG
8785 SEQ ID N0:2350 -10.8 -18.5 59.1 -7.7 0 -3.6
TACATAGGAGTTTATATAAT
8882 SEQ ID N0:2351 -10.8 -15.9 52.5 -5.1 0 -5.5
ATACATAGGAGTTTATATAA
8883 SEQ TD N0:2352 -10.8 -15.9 52.5 -5.1 0 -5.2
AATTTTTTTTCTTTCTTTCT
63 SEQ ID N0:2353 -10.7 -18.3 59.3 -7.6 0 -2.3
GCTGTTCAGCTTTTTTTTTT
121 SEQ ID N0:2354 -10.7 -22.7 69.9 -10.9 -0.9 -9.3
GGGTATAACGTGTCTTCCTC
146 SEQ ID N0:2355 -10.7 -24.8 72.6 -14.1 0 -5.3
CCCTGTCAAACCTTGATGTG
256 SEQ ID N0:2356 -10.7 -24.8 69 -13.3 -0.6 -4.5
CTTTGCTCCTTTCCCAGTAA
311 SEQ ID N0:2357 -10.7 -26.6 75.1 -15.9 0 -3.6
TTTCCGGAAAAGCTCCAGGT
381 SEQ ID N0:2358 -10.7 -25.3 69.7 -12.5 -1.9 -11.8
CAGTGCCTGTGCCATCTTTT
467 SEQ ID N0:2359 -10.7 -27.9 79.1 -16.4 -0.6 -5.2
TATTGATATAGTAGGGATCC
711 SEQ ID N0:2360 -10.7 -20.1 62.2 -8.9 0 -7.7
TTATTGATATAGTAGGGATC
712 SEQ ID N0:2361 -10.7 -18.2 58.5 -7.5 0 -4.1
AGAGCAAACACGCTCAGACA
1240 SEQ ID N0:2362 -10.7 -22.9 65.3 -8.9 -3.3 -8.5
AGCAGAATCGCTTGGGGGCC
1310 SEQ ID N0:2363 -10.7 -29 78.7 -17.6 -0.5 -7.1
CCTTCACACAGATGTATCCT
1515 SEQ ID N0:2364 -10.7 -24.7 71.2 -13.4 -0.3 -3.7
TGTAGCCATAGTTGGGGTTT
1542 SEQ TD N0:2365 -10.7 -25.4 74.9 -13.8 -0.7 -4.8
CAAGGTGGCCTGATTCTGCT
1757 SEQ ID N0:2366 -10.7 -27 76.2 -15.6 -0.4 -7.2
GTCACTGGTCAGTCTGTTTC
2099 SEQ ID N0:2367 -10.7 -25.2 78.8 -14.5 0 -6.6
AGCCACGGATACTCAAGAGA
2145 SEQ ID N0:2368 -10.7 -23.7 67.3 -13 0 -5.4
GACAATAATTCCATCAAAGA
2948 SEQ ID N0:2369 -10.7 -17.3 53.6 -6.6 0 -2.9
AACACAATCAGGAAGGAGTG
3262 SEQ ID N0:2370 -10.7 -19.6 59.2 -8.4 -0.2 -4.7
AAGGTTTCCAATGACCATGA
3371 SEQ ID N0:2371 -10.7 -22.4 64.4 -10.1 -1.5 -5.8
AACCACAAGGTTTCCAATGA
3377 SEQ ID N0:2372 -10.7 -22 62.9 -9.3 -2 -6.7
GGCCAATGCACCACTACTGA
4124 SEQ ID N0:2373 -10.7 -26.9 73.1 -14.7 -1.4 -7
AGCATATTCTAGCATGGTTT
4181 SEQ ID N0:2374 -10.7 -22.4 68.1 -10.7 -0.9 -5
GAAATCTAGCCAGCACCAGG
4283 SEQ ID N0:2375 -10.7 -25.3 70.6 -14.6 0 -4.6
TGAGGTTTCTTGGATCCAAG
4966 SEQ ID N0:2376 -10.7 -22.8 67.7 -8.7 -1 -14.9
169
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CACAGAATACTTTTCTATCA
5297 SEQ ID N0:2377 -10.7 -18.7 58.5 -7 -0.9 -4.6
GCAGGAGGCCGATGTTAAAC
5436 SEQ ID NO:2378 -10.7 -24.5 68.4 -13.2 -0.3 -7.7
TCAATTCCAGCTTCCTTTTT
5512 SEQ ID N0:2379 -10.7 -24.1 70.4 -13.4 0 -4.5
TCTCCCTTAACTGAGCTGCC
5671 SEQ ID N0:2380 -10.7 -27.9 77.5 -17.2 0 -5.6
AAGGGCATCCATCTCTCCAC
6062 SEQ TD N0:2381 -10.7 -27.2 76.7 -15.3 -1.1 -4
AATAGGCTCATAAGAGACTT
6125 SEQ TD NO:2382 -10.7 -19.4 59.8 -7.3 -1.3 -5.2
TCTGGAGTGGAGTTCCCATT
6319 SEQ ID N0:2383 -10.7 -26.6 77.1 -14.6 -1.2 -6.7
TTCTGGAGTGGAGTTCCCAT
6320 SEQ ID NO:2384 -10.7 -26.6 77.1 -14.6 -1.2 -8.7
TTCTGGTTTGTCTTTCTCAA
6413 5EQ TD N0:2385 -10.7 -22.4 69.4 -11.7 0 -2.7
CTTTTTACTTTTGATTTTCT
6459 SEQ ID N0:2386 -10.7 -18.6 59.5 -7.9 0 -2.2
AGGCACTGACTATGAGTATT
6586 SEQ ID N0:2387 -10.7 -21.8 66 -10.5 -0.3 -4.1
TGCTTCACAGAGTTGCAGTG
6634 SEQ ID N0:2388 -10.7 -24.4 73.1 -13 -0.4 -'S.3
CAGGCACATAACTGTTCAGA
7104 SEQ ID N0:2389 -10.7 -22.4 66.3 -11.7 0 -5.6
AAATAATCCTTTAAATATTA
7136 SEQ ID N0:2390 -10.7 -12.9 45.2 -2.2 0 -5
TAAATATAGAGCTCTGAAAC
7200 SEQ ID N0:2391 -10.7 -15.7 51.2 -4 0 -10
TATTTAATTGACATAGACTA
7357 SEQ ID N0:2392 -10.7 -15.6 51.5 -4.9 0 -2.7
TAGTGATAGCCTTTAAACTA
7536 SEQ ID N0:2393 -10.7 -19.2 59.1 -8.5 0 -4.2
TTAACCAAGACTTGTGAAGA
7601 SEQ ID N0:2394 -10.7 -18.8 57.2 -7.6 -0.2 -5.4
ATCCAGTGTGTTTCCTTGAA
7761 SEQ TD N0:2395 -10.7 -24.2 71.2 -13.5 0 -3.7
GTCAGTAGGCAGTATCCAGT
7774 SEQ ID N0:2396 -10.7 -26.1 79.1 -14.9 -0.2 -4
TGTTCATGGCTAAAAAGAAC
8265 SEQ ID N0:2397 -10.7 -17.3 54 -5.6 -0.9 -5.3
AAAAATTTATATCATGTTAG
8308 SEQ ID N0:2398 -10.7 -12.9 45.5 -2.2 0 -5.2
GAAATGCAATAAAAAATGAA
8469 SEQ TD NO:2399 -10.7 -11.1 41.3 0 0 -5.6
AACCCCAGAGCCCAATAAGT
8489 SEQ ID N0:2400 -10.7 -26.8 70.9 -16.1 0 -3.2
CCTGAAAGTTGGAACATGTG
8706 SEQ ID N0:2401 -10.7 -20.6 60.6 -9.1 -0.6 -7
ATGGTTAGGGTATAACGTGT
153 SEQ ID N0:2402 -10.6 -21.9 65.5 -9.3 -2 -5.3
TTCTTTGCTCCTTTCCCAGT
313 SEQ ID N0:2403 -10.6 -28.1 80.5 -17.5 0 -3.6
AAGCTCCAGGTCCCTTCTGT
372 SEQ ID NO:2404 -10.6 -29.4 82.9 -18.3 -0.2 -6.6
GGCGGAAGCTTTCAGGTCCT
4gg SEQ TD N0:2405 -10.6 -28.6 79.6 -15.6 -2.4 -7.9
170
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GATCCAGGTCCTCCAGGGGC
696 SEQ ID N0:2406 -10.6 -31.9 88.2 -20 -1.2 -8.4
GGTCAAAATAGTGCACATGA
872 SEQ ID N0:2407 -10.6 -20.3 60.8 -8.7 0 -9.9
ACATAAAAGTGACTGTCATC
1432 SEQ ID N0:2408 -10.6 -18.1 56.8 -6.8 -0.1 -8.8
TCGCCGTCTTCAAATGTGCT
2266 SEQ ID N0:2409 -10.6 -26 71.7 -15.4 0 -3.6
ACATACTGGCCTGACTAACG
2343 SEQ ID N0:2410 -10.6 -23.3 65.5 -12.7 0 -7.2
CTCTGGGGGAAGTTGTCCAG
2471 SEQ ID N0:2411 -10.6 -26.5 76.4 -13.9 -2 -7.8
AGAACACATTGGCAAATCTA
2664 SEQ ID N0:2412 -10.6 -19.1 57.8 -8.5 0 -4.4
CCAATGATCTTAATTAGCAT
3079 SEQ ID N0:2413 -10.6 -19.3 58.4 -8.7 0 -4.2
TCCAATGACCATGACCAACA
3365 SEQ ID N0:2414 -10.6 -23.6 64.9 -13 0 -4.5
CAGCAAGGTTGTCTGAGCTA
3432 SEQ ID N0:2415 -10.6 -24.5 72.7 -12.8 -1 -7.1
ACTCCCGCATCTTATTTTTC
3525 SEQ ID N0:2416 -10.6 -24.7 70.9 -14.1 0 -3.6
GGCTTTCTAAAAAAGGCTTT
3553 SEQ ID N0:2417 -10.6 -19.7 59.1 -7.6 -1.4 -6.2
CCTTCATGGATTTCTATAAC
3577 SEQ ID N0:2418 -10.6 -20.3 61.6 -9.7 0 -5
TTCCAGTATTATTGGACATG
3615 SEQ ID N0:2419 -10.6 -20.7 62.8 -8.6 -1.4 -7.5
TCTCTAAGATAATTAAGCTC
3649 SEQ ID N0:2420 -10.6 -17.4 55.9 -6.8 0 -5.1
TTGATAGTCTTTCGCTGTTC
4162 SEQ ID N0:2421 -10.6 -22.7 69.4 -12.1 ~ 0 -3.4
TTGTCAGCATATTCTAGCAT
4186 SEQ ID N0:2422 -10.6 -22.2 67.8 -10.6 -0.9 -4.1
AGCCAGCACCAGGCATTAGT
4276 SEQ ID N0:2423 -10.6 -28.6 79.9 -15.3 -2.7 -7.4
AACGATCAAGAAATCTAGCC
4292 SEQ ID N0:2424 -10.6 -19.3 57.3 -8.7 0 -4.9
CAACCACCCTCATGCCTTCA
4425 SEQ ID N0:2425 -10.6 -29 76.7 -18.4 0 -4.4
CCGTTGTCATGTTAACACAG
4560 SEQ ID N0:2426 -10.6 -22.5 65.4 -11.1 -0.5 -8.7
TTTCTTCATATACAGGCTGA
4773 SEQ ID N0:2427 -10.6 -21.5 65.6 -10.9 0 -4.l
TCTGTTCCTCTGTCATAAAG
4920 SEQ ID N0:2428 -10.6 -21.8 66.3 -11.2 0 -1.8
AATTTGTTTGCTGGGCGAGG
4996 SEQ ID N0:2429 -10.6 -24.4 69.6 -13 -0.6 -4.4
GTGACCATGTTGAGGCAGAT
5077 SEQ ID N0:2430 -10.6 -24.9 72.1 -13.8 -0.1 -4
TTCTCCAGTGAACAGAACAA
5168 SEQ ID N0:2431 -10.6 -20.6 61.3 -10 0 -3.9
AGAGCAGGAGGCCGATGTTA
5439 SEQ ID N0:2432 -10.6 -26.3 74.2 -14.8 -0.8 -7.7
GATCATGCTGTTGCCAAAGG
5552 SEQ ID N0:2433 -10.6 -24 68.5 -12.5 -0.8 -5.9
ACAGATGGGTCCCCACGGTC
5689 SEQ ID N0:2434 -10.6 -30 80.9 -18.7 -0.3 -8.3
171
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GGATGACCGCGATGTACATG
5763 SEQ ID N0:2435 -10.6 -24.4 67.1 -12.9 -0.5 -9.4
TCTGCACTTTCTTCAGTAGC
5800 SEQ ID N0:2436 -10.6 -24.3 74.4 -13.1 -0.3 -4.8
CATGGGCAGATCCATGGCAA
5975 SEQ ID N0:2437 -10.6 -26.3 72.6 -12.9 -2.8 -9.7
TTTGATGCCATAAACCTGTC
6097 SEQ TD N0:2438 -10.6 -22.3 64.5 -11.7 0 -3
CTTTAATTGCCTCTTTGTTA
6252 SEQ ID N0:2439 -10.6 -21.4 64.7 -10.8 0 -3
GGAAGGAGGAGGGGTGGTAG
6359 SEQ ID N0:2440 -10.6 -25.6 74.7 -15 0 -0.7
TTCCTTGTCTGGTTTTGTTA
6389 SEQ ID N0:2441 -10.6 -23.7 72.4 -13.1 0 -3.2
CTCCTCTTGAAGTCCAGTTG
6539 SEQ ID N0:2442 -10.6 -25.1 73.6 -14.5 0 -3
TAGCCATTGGGTTTCTCCTC
6706 SEQ ID N0:2443 -10.6 -27.1 78.8 -15.6 -0.8 -6.3
ACAATGTTCACTTTGCACAA
6744 SEQ ID N0:2444 -10.6 -20.6 61.5 -10 0 -5.4
TTAAATATAGAGCTCTGAAA
7201 SEQ ID No:2445 -10.6 -15.6 51 -4 0 -10
CTATATATATATTTGCCCAA
7419 SEQ ID N0:2446 -10.6 -19.4 58.4 -8.8 0 -6.7
AATAGAAGTTGTTTATCAGG
7439 SEQ ID N0:2447 -10.6 -17.6 56.5 -7 0 -2.9
AATGATACAGGATACATCCC
7507 SEQ ID N0:2448 -10.6 -21.3 62.3 -9.7 -0.9 -6.9
GCATTAGTGATAGCCTTTAA
7540 SEQ ID N0:2449 -10.6 -21.7 64.9 -11.1 0 -3.5
AACCCATTATCTAACTTTTA
8019 SEQ ID N0:2450 -10.6 -19.4 58.6 -8.8 0 -1.6
CAACCATAGTTGGTAGAAAA
8117 SEQ ID N0:2451 -10.6 -18.5 56.2 -5.5 -2.4 -6.3
AACAAAGTCCATGTTATATT
8248 SEQ ID N0:2452 -10.6 -17.9 55.8 -6.5 -0.6 -4.3
GAACAAAGTCCATGTTATAT
8249 SEQ ID N0:2453 -10.6 -18.4 56.7 -6.5 -1.2 -4.7
AGAACAAAGTCCATGTTATA
8250 SEQ ID N0:2454 -10.6 -18.4 56.9 -6.5 -1.2 -4.7
AATTTATTATGGGAGAATTA
9064 SEQ ID N0:2455 -10.6 -15.7 51.4 -5.1 0 -3.4
TAATTTATTATGGGAGAATT
9065 SEQ ID N0:2456 -10.6 -15.7 51.4 -5.1 0 -3.5
TTTTTTTTTTTTTTTTTCCA
9092 SEQ ID N0:2457 -10.6 -18.7 59.5 -8.1 0 0
CAGTTTTCTTGCTCCATAAT
227 SEQ TD N0:2458 -10.5 -22.4 66.9 -11.9 0 -4.4
CCTTGACAGGTATCTCATCC
274 SEQ ID N0:2459 -10.5 -25.4 73.8 -14.3 -0.3 -2.9
CTCATCATCATTATCTTGTT
590 SEQ ID N0:2460 -10.5 -20.7 64.6 -10.2 0 -1.9
GATATAGTAGGGATCCAGGT
707 SEQ ID N0:2461 -10.5 -23.4 70.1 -12.1 -0.3 -8.9
CTTCTAAGCAAAACCCTCTT
996 SEQ ID N0:2462 -10.5 -22.2 63.7 -11.7 0 -4.1
GGATCACGAAGAAACGTAAA
1018 SEQ ID N0:2463 -10.5 -17.5 52.8 -6.2 -0.6 -6
172
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CAAAAGCAGAATCGCTTGGG
1314 SEQ ID N0:2464 -10.5 -21.4 61.1 -9.1 -1.8 -9.3
ATTGTGCCATTAAAGTAGGA
1348 SEQ ID N0:2465 -10.5 -20.9 62.5 -10.4 0 -3.5
GTAGCCATAGTTGGGGTTTC
1541 SEQ ID N0:2466 -10.5 -25.8 77 -13.8 -1.4 -4.8
TTCACCAAATAAAATGAGCC
1702 SEQ ID N0:2467 -10.5 -18.7 55.5 -8.2 0 -3.2
CTCTCCTTTGTTGTTTCCTT
2009 SEQ ID N0:2468 -10.5 -25.8 76.6 -15.3 0 0
CTCTCTCTCCTTTGTTGTTT
2013 SEQ ID N0:2469 -10.5 -25 76.3 -14.5 0 0
GAGGGGAGCAGAATTTTTTG
2118 SEQ ID N0:2470 -10.5 -21.7 64.9 -11.2 0 -4.1
ATGCATCACAGCAGTCCCAG
2688 SEQ ID N0:2471 -10.5 -27.3 77.1 -15.5 -l.2 -7.5
TGCTCAGTCATGGGGTAGTG
2812 SEQ ID N0:2472 -10.5 -25.8 77.3 -15.3 0 -4.7
CAAGCTCCATTAAACTGAGG
2970 SEQ ID N0:2473 -10.5 -21.1 61.7 -10.1 -0.1 -5
TGAAGACGATGATGGCCAAC
3135 SEQ ID N0:2474 -10.5 -21.9 62 -10.6 0 -9.2
AGTGGAAGAAGTCGTTCATG
3246 SEQ ID N0:2475 -10.5 -21 63.4 -9.2 -1.2 -4.3
ACGCGGAACACAATCAGGAA
3268 SEQ ID N0:2476 -10.5 -22 61.3 -11 0 -7.9
TGGCTTTCTAAAAAAGGCTT
3554 SEQ ID N0:2477 -10.5 -19.6 58.7 -7.6 -1.4 -5.9
TTGGCTTTCTAAAAAAGGCT
3555 SEQ ID N0:2478 -10.5 -19.6 58.7 -7.6 -1.4 -5.9
AATTAAGCTCTTTGCTTATT
3639 SEQ ID N0:2479 -10.5 -19.2 59.7 -5.7 -3 -7.8
GGGGTTGTTTATGAATGACA
3743 SEQ ID N0:2480 -10.5 -21.4 64.1 -10.1 -0.6 -4.3
GCCAATGCACCACTACTGAG
4123 SEQ ID N0:2481 -10.5 -25.7 70.9 -14.4 -0.6 -5
GGCATTAGTGAAATATGTTT
4265 SEQ ID N0:2482 -10.5 -19 58.9 -8.5 0 -4.1
TCAACGATCAAGAAATCTAG
4294 SEQ ID N0:2483 -10.5 -16.6 52.4 -6.1 0 -4.4
ATCAACGATCAAGAAATCTA
4295 SEQ ID N0:2484 -10.5 -16.6 52.3 -6.1 0 -4.9
TTACCCGTTGTCATGTTAAC
4564 SEQ ID N0:2485 -10.5 -22.9 66.3 -12.4 0 -5.8
TTTAACATCTCGTGAATCAA
4751 SEQ ID N0:2486 -10.5 -18.1 55.9 -7.6 0 -4.6
CATGTACAGATTTTCTTCAT
4784 SEQ ID N0:2487 -10.5 -19.9 62 -9.4 0 -6.7
GGTTTCTTGGATCCAAGTTT
4963 SEQ ID N0:2488 -10.5 -23.6 70.4 -9.7 -0.7 -14.9
GACCATGTTGAGGCAGATGA
5075 SEQ TD N0:2489 -10.5 -24.3 70.1 -13.8 0 -4.3
TCTCCAGTGAACAGAACAAT
5167 SEQ ID N0:2490 -10.5 -20.5 60.9 -10 0 -3.9
GAAACGAGCTTCAGCACAAA
5188 SEQ ID N0:2491 -10.5 -20.7 59.9 -9.3 -0.7 -6.6
CTTTTCTATCATCTCAGCCA
5288 SEQ ID N0:2492 -10.5 -24.2 72.1 -13.7 0 -3.2
173
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Tnter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CGTGCGGATCCCCTTTGCTC
5381 SEQ TD N0:2493 -10.5 -3l 81.3 -19.8 -0.4 -7.3
CCCTTAACTGAGCTGCCAGG
5668 SEQ ID N0:2494 -10.5 -28.1 76.1 -16.7 -0.6 -9.3
TTCTCCAGGATGACCGCGAT
5770 SEQ ID N0:2495 -10.5 -27.1 73 -15.2 -1.3 -6.7
GGGCAGCTGCAAAATCAGAG
5910 5EQ ID N0:2496 -10.5 -23.7 67.7 -10.3 -0.7 -14
GGCATCCATCTCTCCACTCT
6059 SEQ TD N0:2497 -10.5 -28.9 82.2 -18.4 0 -4
AGACACCTCCTCTTGTTTAC
6161 SEQ ID N0:2498 -10.5 -24.6 72.3 -14.1 0 -3
CTATCATAGGAAGGAGGAGG
6367 SEQ ID N0:2499 -10.5 -21.3 64.2 -10.8 0 -3.4
CATATACTTTACCTTCATAG
6516 SEQ ID N0:2500 -10.5 -19.1 59.3 -8.6 0 -2.4
AGGTAGCCATTGGGTTTCTC
6709 SEQ ID N0:2501 -10.5 -26.2 77.9 -15.1 -0.3 -6.3
TGATCATTTGAGAGACAGGG
6946 SEQ TD N0:2502 -10.5 -21 63.7 -10.5 0 -6
TTTATTAGATTACTTTTTGG
7238 SEQ TD N0:2503 -10.5 -16.8 55 -6.3 0 -2.4
TTTCTAGAATGGATTTATTA
7251 SEQ ID N0:2504 -10.5 -16.6 54.2 -5.6 0 -7.7
CAGGCTATATATATATTTGC
7423 SEQ ID N0:2505 -10.5 -19.1 59.5 -7.9 0 -8.7
TATTAACATGCATTAGTGAT
7549 SEQ ID N0:2506 -10.5 -17.8 56.2 -7.3 0 -6.7
GGCAGTATCCAGTGTGTTTC
7767 SEQ ID N0:2507 -10.5 -25.9 78.3 -15.4 0 -4
AATACCTTATGTATACATAG
8895 SEQ ID N0:2508 -10.5 -17.1 54.5 -5 -0.8 -10.9
CAGGAGGGTTGCTCAAGGTC
906 SEQ TD N0:2509 -10.4 -26.1 76.9 -13.7 -2 -4.5
CTTTGTCCAGTCAGGAGGGT
917 SEQ ID N0:2510 -10.4 -27.1 80.2 -15.8 -0.8 -5.3
ATTTTTATAAGTGACTCAAA
970 SEQ ID N0:2511 -10.4 -15.7 51.6 -5.3 0 -4.7
ATTCCTCAGATTGCCCATGA
1277 SEQ TD N0:2512 -10.4 -26.3 73.6 -15.9 0 -4.5
CCTTCCAGTTAAATGTGCTC
1401 SEQ ID N0:2513 -10.4 -24 69.6 -13.6 0 -5.1
AGGTGGCCTGATTCTGCTCC
1755 5EQ ID N0:2514 -10.4 -29.4 83.2 -19 0 -7.2
CAGAATTTTTTGTCACTGGT
2110 SEQ ID N0:2515 -10.4 -20.9 63.9 -10.5 0 -3.5
TGGCCTGACTAACGTTACTG
2337 SEQ ID N0:2516 -10.4 -23.7 67.1 -12.8 0 -7.9
ACTGGCCTGACTAACGTTAC
2339 SEQ ID N0:2517 -10.4 -23.9 67.8 -13 0 -7.9
GTGCCCTCTGGGGGAAGTTG
2476 SEQ ID N0:2518 -10.4 -29.2 81.1 -16.6 -2.2 -8.7
GAGGGTATTTAAGACAATGC
2777 SEQ ID N0:2519 -10.4 -19.7 60.2 -9.3 0 -2.9
TCCCGCATCTTATTTTTCAC
3523 SEQ ID N0:2520 -10.4 -24.5 70.1 -14.1 0 -3.6
CACCCTTCAGTAAAACAAGC
3970 SEQ ID N0:2521 -10.4 -21.8 62.5 -11.4 0 -2.9
174
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGCCTTCTTCTGTACTTACT
4014 SEQ ID N0:2522 -10.4 -24.4 72.9 -14 0 -4.8
TTGCCTTCTTCTGTACTTAC
4015 SEQ ID N0:2523 -10.4 -23.6 71.2 -13.2 0 -4.8
AGGCATTAGTGAAATATGTT
4266 SEQ ID N0:2524 -10.4 -18.9 58.7 -8.5 0 -4
CAAAGAAACATCAACGATCA
4304 SEQ ID N0:2525 -10.4 -16.5 51.2 -6.1 0 -4.9
GGATAAGGCTCTTAGAGGTC
4400 SEQ ID N0:2526 -10.4 -23.2 70.5 -12.2 -0.3 -6.1
ATGGTGACCATGTTGAGGCA
5080 SEQ ID N0:2527 -10.4 -25.5 73 -14 -1 -7.l
GTAGTAGTGTCTGAGGGAAA
5204 SEQ ID N0:2528 -10.4 -21.7 66.8 -11.3 0 -2.9
CATCAATTCCAGCTTCCTTT
5514 SEQ ID N0:2529 -10.4 -24.6 70.7 -14.2 0 -4.5
GCTGCCAGGGTGAATTGTGT
5657 SEQ ID N0:2530 -10.4 -27.2 77.3 -16.8 0 -4.4
GTTCACCACAACCAGGAAGG
5744 SEQ ID N0:2531 -10.4 -24.7 69.1 -13.8 -0.2 -4
TCACTCAGGGGCTCTGCACT
5812 SEQ TD N0:2532 -10.4 -28.5 82 -17.5 -0.3 -4.8
ATGGGCAGATCCATGGCAAT
5974 SEQ ID N0:2533 -10.4 -25.6 71.5 -14 -1.1 -8
CTGGAGTGGAGTTCCCATTT
6318 SEQ ID N0:2534 -10.4 -26.3 75.7 -14.6 -1.2 -6.7
ACCTCTTTTCCTTTGCTTTC
6436 SEQ ID N0:2535 -10.4 -25.5 75.2 -15.1 0 -3.6
TGACCTCTTTTCCTTTGCTT
6438 SEQ ID N0:2536 -10.4 -25.6 74.2 -15.2 0 -3.6
TCCAGTTGACACATATACTT
6527 SEQ ID N0:2537 -10.4 -21.4 64.3 -10.5 -0.2 -3.6
GCCATCTAGAAAATGGAAGT
7043 SEQ ID N0:2538 -10.4 -20.3 60 -8.3 -1.6 -8.3
AATTAAATATAGAGCTCTGA
7203 5EQ ID N0:2539 -10.4 -16.3 52.7 -4.9 0 -10
TGCATTAGTGATAGCCTTTA
7541 SEQ ID N0:2540 -10.4 -22.4 67.1 -12 0 -4.7
ATATTTAAACAAGTTTTAGA
7827 SEQ ID N0:2541 -10.4 -14.2 48.5 -3.8 0 -5.5
AATAAAAGGTTATATTGAGG
8137 SEQ TD N0:2542 -10.4 -14.7 49 -3.7 -0.3 -2.8
CTACAGTAAATAGTTTTGTA
8367 SEQ ID N0:2543 -10.4 -17.1 55.4 -6.7 0 -4.1
ATTTATTCTTTTGGCTCAAT
8449 SEQ ID N0:2544 -10.4 -19.9 61.6 -9.5 0 -4.9
GTTACTACTATTATTATCAA
8727 SEQ ID N0:2545 -10.4 -16.6 54.3 -6.2 0 -1.7
TAATACCTTATGTATACATA
ggg6 SEQ ID N0:2546 -10.4 -16.8 53.8 -5 -0.8 -10.5
TATCATTAATACCTTATGTA
gg02 SEQ ID N0:2547 -10,4 -17.4 55.4 -7 0 -4.2
CAGCTTTTTTTTTTTTTTTT
115 SEQ ID N0:2548 -10.3 -18.9 60.3 -8.6 0 -4.5
TGTCAAACCTTGATGTGGCT
253 SEQ ID N0:2549 -10.3 -23.8 68.5 -12.3 -1.1 -5.8
GTAGCTTCTTGCATACGAAT
425 SEQ ID N0:2550 -10.3 -22.2 65.5 -10.3 -1.5 -5.7
175
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATCCTGCACATTTAATTACG
446 SEQ ID N0:2551 -10.3 -20.7 60.8 -10.4 0 -4.8
ACAGTTGGTCAAAATAGTGC
878 SEQ ID N0:2552 -10.3 -20.3 61.9 -10 0 -3.8
TCATAAATACACAGTTGGTC
888 SEQ ID N0:2553 -10.3 -19 59.2 -8,7 0 -2.8
CCTCTTGCCAAGATTTTTAT
982 SEQ ID N0:2554 -10.3 -22.8 66.3 -11.7 -0.6 -6.3
AAATCCAGCCAGTTCCATGG
1036 SEQ ID N0:2555 -10.3 -25.8 71.5 -14.8 -0.4 -7.7
TGAACAGCTGCAGCCCAATG
1260 SEQ ID N0:2556 -10.3 -25.8 70.5 -13 0 -13.2
CACAGATGTATCCTTCTGGA
1509 SEQ ID N0:2557 -10.3 -23.6 69.6 -11.7 -1.6 -5.9
ACGTAATGTCAACTGGTAAA
1634 SEQ ID N0:2558 -10.3 -18.6 56.5 -8.3 0 -4.4
TATCATGTATGTTTTCCCAG
1658 SEQ ID N0:2559 -10.3 -22.3 66.9 -12 0 -4.7
CTTTGATGCTTCTGAAGAAC
1922 SEQ ID N0:2560 -10.3 -19.8 60.4 -9 0 -8.3
TGTCACTGGTCAGTCTGTTT
2100 SEQ TD N0:2561 -10.3 -24.8 76.5 -14.5 0 -6.6
TTGTCACTGGTCAGTCTGTT
2101 5EQ ID NO:2562 -10.3 -24.8 76.5 -14.5 0 -6.4
TTTGTCACTGGTCAGTCTGT
2102 SEQ ID N0:2563 -10.3 -24.8 76.5 -14.5 0 -6.6
AGAATTTTTTGTCACTGGTC
2109 SEQ ID N0:2564 -10.3 -20.6 64.2 -10.3 0 -3.3
CCAGCATCTCCATTGAAATC
2541 SEQ ID N0:2565 -10.3 -23.3 66.7 -13 0 -4.1
TTTGGCTTTCTAAAAAAGGC
3556 5EQ ID N0:2566 -10.3 -18.8 57.2 -7.6 -0.7 -4.5
TCTATCTTATTGCCTTCATG
3589 SEQ ID N0:2567 -10.3 -22.1 66.8 -11.8 0 -4.1
TCTAAGATAATTAAGCTCTT
3647 SEQ ID N0:2568 -10.3 -17.1 55 -6.8 0 -5.9
TTCTCGGGGTAGAACAACAT
3905 SEQ ID N0:2569 -10.3 -22.1 64.4 -11.3 -0.1 -3.7
TTCTGTACTTACTTGACAGA
4007 SEQ ID N0:2570 -10.3 -20.5 63.6 -8.2 -2 -6.5
GAAACATCAACGATCAAGAA
4300 SEQ ID N0:2571 -10.3 -16.4 51.2 -6.1 0 -4.9
AGAGCATTCACAACCACCCT
4435 SEQ ID N0:2572 -10.3 -26.5 72.5 -15.6 -0.3 -4.1
ACAGCACATTCATGATAGAG
4470 SEQ ID N0:2573 -10.3 -20.4 62.2 -10.1 0 -6.4
AATATCCATCCAGCCTTTAA
4718 SEQ ID N0:2574 -10.3 -23.1 65.8 -12.8 0 -3.2
CTGACCATGGGCAGATCCAT
5980 SEQ ID N0:2575 -10.3 -27 74.4 -15.5 -1.1 -8.8
TCACCACTGACCATGGGCAG
5986 SEQ ID N0:2576 -10.3 -27.5 75.4 -15.7 -1.4 -8.9
ATGATAGCGGCAGACACCTC
6172 SEQ ID N0:2577 -10.3 -25.6 71.9 -15.3 0 -6.6
TGTATAGGCACTGACTATGA
6591 SEQ ID N0:2578 -10.3 -21.4 64.6 -10.5 -0.3 -4.8
AATAGAATGGATGCAAGGAC
6789 SEQ ID N0:2579 -10.3 -18.5 56.4 -8.2 0 -5.6
176
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGAATAAACTATGAATTGGG
6867 SEQ ID N0:2580 -10.3 -15.4 49.9 -5.1 0 -3.1
GTATACTGTTTCTTCAACGT
6921 SEQ ID N0:2581 -10.3 -21.1 64.3 -9.7 -1 -7
TACAATTCTTTTTCTGGTTT
7005 SEQ ID N0:2582 -10.3 -19.6 61.5 -9.3 0 -2.6
AGCCATCTAGAAAATGGAAG
7044 SEQ ID N0:2583 -10.3 -19.1 57.4 -7.2 -1,6 -8.3
ATTAGAGGAGACTTTACAGG
7120 SEQ ID N0:2584 -10.3 -19.9 61.8 -9.1 -O.l -5.5
AAAATAATCCTTTAAATATT
7137 SEQ ID N0:2585 -10.3 -12.5 44.3 -2.2 0 -4.4
ATATAGAGCTCTGAAACTTA
7197 SEQ ID N0:2586 -10.3 -18.1 57 -6.8 0 -10
AAAGCATTTGACCTAAATTA
7218 SEQ ID N0:2587 -10.3 -17.1 53.2 -6.3 -0.1 -4
CTGTTGGAAGCTTGCAAAAG
7488 SEQ ID N0:2588 -10.3 -20.5 60.6 -8.5 -1.7 -7
TGATACAGGATACATCCCTG
7505 SEQ ID N0:2589 -10.3 -22.9 66.2 -11.4 -1.1 -6.9
TTAGGAAATTATCCATTGAA
7997 SEQ ID N0:2590 -10.3 -17.1 53.7 -4.6 -2.2 -7.2
CTAACTTTTATTTTAGGAAA
8009 SEQ ID N0:2591 -10.3 -15.4 50.8 -5.1 0 -2.8
ATCTAACTTTTATTTTAGGA
8011 SEQ ID N0:2592 -10.3 -17.2 55.7 -6.9 0 -3.2
TGTAATAGCTTTAGTGCAGC
8228 SEQ ID N0:2593 -10.3 -22 67.2 -10.8 -0.8 -5.6
GTTCTTCAATACACTACAGT
8380 SEQ ID N0:2594 -10.3 -20.6 63.7 -10.3 0 -3.1
GAAAGTTGGAACATGTGAAC
8703 SEQ ID N0:2595 -10.3 -17.8 55.1 -6.7 -0.6 -7
AAGCTATTGTAGGTGGTTAC
8742 SEQ TD N0:2596 -10.3 -21.5 66.2 -11.2 0 -5.1
AAGCTTTCAGGTCCTGGGGG
493 SEQ ID N0:2597 -10.2 -27.8 79.2 -16.8 -0.4 -9
AAGTGACTCAAAGGTATAGA
962 SEQ ID N0:2598 -10.2 -18.3 57.4 -8.1 0 -3.1
GCAAAACCCTCTTGCCAAGA
989 SEQ ID N0:2599 -10.2 -25.3 68.3 -13.8 -1.2 -6.9
AACAGCTGCAGCCCAATGAG
1258 SEQ ID N0:2600 -10.2 -25.8 70.9 -13.1 0 -13.2
TAACAAATGTCCCATTTGAA
1371 SEQ ID N0:2601 -10.2 -18.9 56.4 -4.9 -3.8 -10.4
TCTTGAGTCATGAGTCGAAA
1600 SEQ ID N0:2602 -10.2 -20.5 62.2 -8.6 0 -11.6
CCCAATAGTCTTGAGTCATG
1608 SEQ ID N0:2603 -10.2 -23.2 68 -12.5 -0.2 -5.8
AGCTGCTTCTTTTGACGCTG
2061 SEQ ID N0:2604 -10.2 -25.4 73.2 -13.2 -2 -7.5
CAGATCCAACATCCTTTGCC
2220 SEQ ID N0:2605 -10.2 -25.9 71.8 -15.2 -0.1 -4.5
AAGAACACATTGGCAAATCT
2665 SEQ ID N0:2606 -10.2 -18.7 56.5 -8.5 0 -4.4
ATGATCGCAGTACAGACAAT
3009 SEQ ID N0:2607 -10.2 -20.9 61.9 -10 -0.4 -5.7
CTGTACTTACTTGACAGAAT
4005 SEQ ID N0:2608 -10.2 -19.3 59.6 -8.2 -0.8 -4.8
177
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TCTCAAACCAGTTGTGCTCA
4080 SEQ ID N0:2609 -10.2 -24.2 70.6 -13.3 -0.4 -5.2
AGTCTCAAACCAGTTGTGCT
4082 SEQ ID N0:2610 -10.2 -24.3 71.5 -14.1 0.2 -4.9
AGTGGTAGAACTTGCCAGCA
4542 SEQ ID N0:2611 -10.2 -25.4 73.3 -13.9 -l.2 -6.4
CTTTGATCAGACGTAGGATT
5361 SEQ ID N0:2612 -10.2 -21.2 63.7 -11 0 -6.5
AAAGAGCAGCGTGCGGATCC
5390 SEQ ID N0:2613 -10.2 -26.3 71.4 -14.4 -1.4 -11.1
CAAAGAGCAGCGTGCGGATC
5391 SEQ ID N0:2614 -10.2 -25 69.1 -12.6 -2.2 -8.5
AGCAGGAGGCCGATGTTAAA
5437 SEQ ID NO:2615 -10.2 -24.3 68.1 -13.2 -0.8 -7.7
TGGACTTTGTTGGGTTTTGC
5950 SEQ ID N0:2616 -10.2 -24.1 71.9 -13.9 0 -2.6
TTTAATTGCCTCTTTGTTAT
6251 SEQ ID N0:2617 -10.2 -20.5 62.7 -10.3 0 -3
GGTAAGTCAATCCTCCCTTT
6268 SEQ ID N0:2618 -10.2 -25.8 73.5 -15.6 0 -2.5
TTACTTTTGATTTTCTCTGA
6455 SEQ ID N0:2619 -10.2 -19.3 61.2 -9.l 0 -2.2
GTATAGGCACTGACTATGAG
6590 SEQ ID NO:2620 -10.2 -21.4 65 -10.5 -0.4 -5.5
GTTCACTTTGCACAACTATC
6739 SEQ ID N0:2621 -10.2 -21.6 65.4 -11.4 0 -5
AGCATTATGAATAAACTATG
6874 SEQ ID N0:2622 -10.2 -15.3 50.1 -5.1 0 -4.1
CATAGCATTATGAATAAACT
6877 SEQ ID N0:2623 -10.2 -16 51.4 -5.1 -0.5 -4.2
CTTGTATACTGTTTCTTCAA
6924 SEQ ID N0:2624 -10.2 -19.9 62.3 -9.7 0 -6.3
CTGATCATTTGAGAGACAGG
6947 SEQ TD N0:2625 -10.2 -20.7 63.1 -10.5 0 -6.2
ATTACTTTTTGGAAAGCATT
7230 SEQ ID N0:2626 -10.2 -18.3 57 -6.5 -l.6 -5.5
TATTAGATTACTTTTTGGAA
7236 SEQ ID N0:2627 -10.2 -16.5 53.7 -6.3 0 -2.4
GACATAGACTATCAGCTTTG
7348 SEQ ID N0:2628 -10.2 -20.6 63.2 -10.4 0 -4.5
TGACATAGACTATCAGCTTT
7349 SEQ ID N0:2629 -10.2 -20.6 63.2 -10.4 0 -4.5
TTGACATAGACTATCAGCTT
7350 SEQ ID N0:2630 -10.2 -20.6 63.2 -10.4 0 -4.5
TGGAAGCTTGCAAAAGACAC
7484 SEQ ID N0:2631 -10.2 -20 59.1 -7.7 -2.1 -7
CCTGTTGGAAGCTTGCAAAA
7489 SEQ ID N0:2632 -10.2 -22.5 64 -12.3 0 -7.2
TTTAGACATATTTTTAGCAA
7813 SEQ ID N0:2633 -10.2 -17 54.8 -6.8 0 -4.1
AAGAACAAAGTCCATGTTAT
8251 SEQ ID N0:2634 -10.2 -18 55.6 -6.5 -l.2 -4.7
TTTTAGCAATAGCAATTCCC
8408 SEQ ID N0:2635 -10.2 -21.8 63.8 -10.6 -0.9 -4.5
ATTATATTGAAAGAAGATGA
8801 SEQ ID N0:2636 -10.2 -13.9 47.4 -3.7 0 -2.2
CCTCACATAAATCCAAGGGT
8959 SEQ ID N0:2637 -10.2 -23.2 65.7 -13 0 -3.6
178
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGTGGCTTGGCTTCAGTTTT
240 SEQ ID N0:2638 -10.1 -25.8 76.9 -15 -0.4 -6
CTGTGAATTATCTCATTTAT
356 SEQ ID N0:2639 -10.1 -18.1 57.5 -8 0.4 -2.8
TAAAAGTTTTCTTATTGATA
723 SEQ ID N0:2640 -10.1 -14.6 49.5 -3.4 -1 -6.3
CCAAAATCTTGATAGCAATT
828 SEQ ID N0:2641 -10.1 -18.2 55.3 -7.5 -0.3 -4.4
AGCCCAATGAGAGCAAACAC
1249 SEQ ID N0:2642 -10.1 -23.2 65 -12.3 -0.6 -4.1
AACATTTATTCCTCAGATTG
1284 SEQ ID N0:2643 -10.1 -19.3 59.4 -9.2 0 -2.5
AACATAAAAGTGACTGTCAT
1433 SEQ ID N0:2644 -10.1 -17 53.7 -6.2 -O.l -8.8
CGTAATGTCAACTGGTAAAG
1633 SEQ ID N0:2645 -10.1 -18.4 56.2 -8.3 0 -3.2
GGTGCTCTCTCTGTCTTCTT
1986 SEQ ID N0:2646 -10.1 -27 83.3 -16.9 0 -3.6
AAGCTGCTTCTTTTGACGCT
2062 SEQ ID N0:2647 -10.1 -24.7 70.9 -13.2 -1.3 -8.6
GGTCAGTCTGTTTCCATCCA
2093 SEQ ID N0:2648 -10.1 -27.6 81.1 -17.5 0 -3.6
TCTTGGGGAAAACAGGGAGC
2162 SEQ ID N0:2649 -10.1 -23.2 66.7 -13.1 0 -2.8
CTATTGCGTCTTGGGGAAAA
2170 SEQ ID N0:2650 -10.1 -22 63.3 -7.1.9 0 -4.5
TCTCCTGCTTTCGCCGTCTT
2276 SEQ ID N0:2651 -10.1 -29.9 82.1 -19.1 -0.5 -3.6
GCATCTTCCCATTTGCTGGA
2385 SEQ ID N0:2652 -10.1 -27.7 77.6 -16.5 -l -5.2
CAGCATCTCCATTGAAATCT
2540 SEQ ID N0:2653 -10.1 -22.2 65 -12.1 0 -4.1
CTTTTAACCATGCATCACAG
2697 SEQ ID N0:2654 -10.1 -21.6 63.4 -11.5 0 -6.6
CTCCACATTTGACAGACCAA
2987 SEQ ID N0:2655 -10.1 -23.4 66.3 -13.3 0 -2.7
AGGTTTCCTAGAGCCCCCAC
3106 SEQ ID N0:2656 -10.1 -30.9 83.6 -20.8 0 -3.8
TCACATAATCAATTCCCTTT
3507 SEQ ID N0:2657 -10.1 -21 62 -10.9 0 -2.5
TTCACATAATCAATTCCCTT
3508 SEQ ID N0:2658 -10.1 -21 62 -10.9 , 0 -2.5
TAATTAAGCTCTTTGCTTAT
3640 SEQ ID N0:2659 -10.1 -18.8 58.8 -5.7 -3 -8
TTGCTTTCTTCTAGTTCTGA
3841 SEQ ID N0:2660 -10.1 -22.6 70.4 -12.5 0 -4
TTTCTCTTTGCTTTCTTCTA
3848 SEQ TD N0:2661 -10.1 -22.3 69.9 -12.2 0 -3.6
CTTCTTCGGGTTCAGTTTCA
3936 SEQ ID N0:2662 -10.1 -24.9 74.6 -14.8 0 -3
ACCCTTCAGTAAAACAAGCT
3969 SEQ ID N0:2663 -10.1 -22 63.2 -11.9 0 -4.8
TCATATACAGGCTGAAGTTT
4768 SEQ ID N0:2664 -10.1 -20.6 63 -10.5 0 -4.1
TTCATATACAGGCTGAAGTT
4769 SEQ ID N0:2665 -10.1 -20.6 63 -10.5 0 -4.1
AGGTTTCTTGGATCCAAGTT
4964 SEQ ID N0:2666 -10.1 -23.5 70.3 -9.7 -1.3 -15.5
179
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTTCTATCATCTCAGCCAGA
5286 SEQ ID N0:2667 -10.1 -23.8 71.4 -13.7 0 -3,4
CAGCAGAGGTTGTAATTTGG
5580 SEQ ID N0:2668 -10.1 -21.9 65.9 -11.8 0 -5.7
AAACTGGGTCGCATCGGGAT
5873 SEQ ID N0:2669 -10.1 -25.2 69.1 -15.1 0 -3.6
CCTCCTCTTGTTTACGTTTC
6156 SEQ ID N0:2670 -10.1 -25.5 74.2 -15.4 0 -4.8
TAGGTAAGTCAATCCTCCCT
6270 SEQ ID N0:2671 -10.1 -25.3 72.4 -14.7 -0.2 -4.8
GCTTTCTTTTTCTGGTTTGT
6422 SEQ ID N0:2672 -10.1 -23.7 73.2 -13.6 0 -2.8
CCTTTAAATATTAGAGGAGA
7129 SEQ ID N0:2673 -10.1 -17.9 55.9 -6.9 -0.7 -5.2
ACCATATGATACTCATGTTG
7729 SEQ TD N0:2674 -10.1 -20.4 61.7 -9.6 -0.5 -6
AATTACGTGTAGCTTCTTGC
433 SEQ ID N0:2675 -10 -22.2 66.4 -11.5 -0.4 -5.8
GTTCTTTCCAGCTTCCAAGT
632 SEQ ID N0:2676 -10 -26.3 77 -16.3 0 -4.5
TCATTACTATAAAAGTTTTC
732 SEQ ID N0:2677 -10 -15.2 51 -5.2 0 -6.3
ATACACAGTTGGTCAAAATA
882 SEQ ID N0:2678 -10 -17.9 55.9 -7.9 0 -3.8
AAGATTTTTATAAGTGACTC
973 SEQ ID N0:2679 -10 -16.3 53.6 -6.3 0 -4.1
TGGGGGCCACTGCAAACATT
1298 SEQ ID N0:2680 -10 -26.5 72 -15.7 -0.6 -7.7
TTGTGTAGCCATAGTTGGGG
1545 SEQ ID N0:2681 -10 -25.3 74.4 -13.8 -1.4 -4.8
TGTCAACTGGTAAAGATTTT
1628 SEQ ID N0:2682 -10 -18.3 57.2 -8.3 0 -2.7
TGTTCTGCTTCTTCCAAGGT
1771 SEQ ID N0:2683 -l0 -25.6 75.7 -15.1 -0.1 -3.6
GTCTCTCTCTCCTTTGTTGT
2015 5EQ ID N0:2684 -10 -26.4 81.5 -16.4 0 0
GTCTGTTTCCATCCATGGAG
2088 5EQ ID N0:2685 -10 -25.9 75.5 -14.2 -l.7 -10.4
TCTCCATGTCTGTGCGGCAC
2308 SEQ ID N0:2686 -10 -28.6 80.5 -17.1 -0.2 -10.9
TGGGGGAAGTTGTCCAGTAG
2468 SEQ ID N0:2687 -10 -25.2 73.9 -13.2 -2 -6.1
TTTCTGACTTCCGTTTCAGT
2500 SEQ ID N0:2688 -10 -24.2 71.8 -13 -1.1 -5.7
CAAGAACACATTGGCAAATC
2666 SEQ ID N0:2689 -10 -18.5 55.9 -8.5 0 -4.4
TCAAGAACACATTGGCAAAT
2667 SEQ ID N0:2690 -10 -18.5 55.9 -8.5 0 -4.4
ATCAAGAACACATTGGCAAA
2668 SEQ ID N0:2691 -10 -18.5 55.9 -8.5 0 -4.4
TTAACCATGCATCACAGCAG
2694 SEQ ID N0:2692 -10 -23 66.3 -11.7 -1.2 -6.6
AGGGTATTTAAGACAATGCA
2776 SEQ ID N0:2693 -10 -19.8 60.1 -9.3 -0.1 -52
ATTGCTCAGTCATGGGGTAG
2814 SEQ ID N0:2694 -10 -24.7 74.1 -14.7 0 -4.7
AATAAGGCACATGGTTTGGC
3338 SEQ ID N0:2695 -10 -22.5 65.7 -11.9 -0.3 -5,2
180
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTCCAATGACCATGACCAAC
3366 SEQ ID N0:2696 -10 -23 64.2 -13 0 -4.5
TTCCCTTTTGCATTCTTCCT
3495 SEQ ID N0:2697 -10 -27 76.9 -17 0 -5.l
CTTTTGGCTTTCTAAAAAAG
3558 SEQ ID N0:2698 -10 -16.8 53.2 -5.7 -1 -5.7
ACTTTTTAATACACCCTTCA
3981 SEQ TD N0:2699 -10 -21.4 63.2 -11.4 0 -2.2
CTTCCCTTTGCCTTCTTCTG
4022 SEQ ID N0:2700 -10 -28 79.2 -18 0 -3
CCAGCACCAGGCATTAGTGA
4274 SEQ ID N0:2701 -10 -27.4 76.3 -15.8 -1.5 -5.4
ACGATCAAGAAATCTAGCCA
4291 SEQ ID N0:2702 -10 -20.7 60.2 -10.7 0 -4.9
CTAACCAAAGAAACATCAAC
4309 SEQ ID N0:2703 -10 -16.1 50.6 -6.1 0 -2.9
AATGTCCGTAATGATTTGAT
4369 SEQ ID N0:2704 -10 -19.3 58.1 -9.3 0 -2.6
TAAGGCTCTTAGAGGTCTTA
4397 SEQ ID N0:2705 -10 -22.1 68.1 -11.5 -0.3 -5.4
CATTCACAACCACCCTCATG
4431 SEQ ID N0:2706 -10 -25.2 69.2 -15.2 0 -4.l
CTCCAACAAGAGCATTCACA
4443 SEQ ID N0:2707 -10 -22.7 65.4 -12.1 -0.3 -4.1
GTCAAACATGTTACCCGTTG
4574 SEQ ID N0:2708 -10 -23.1 65.6 -12.4 0 -9
TTAACATCTCGTGAATCAAC
4750 SEQ TD N0:2709 -10 -18.2 56.1 -8.2 0 -4.6
TTGTTTGCTGGGCGAGGTAT
4993 SEQ ID N0:2710 -10 -25.9 74.3 -15.1 -0.6 -4.4
CCATTCCTTGGAATTTGTTT
5007 SEQ ID N0:2711 -10 -22.9 66.6 -11.2 -1.7 -8.4
AAGACCATTCCTTGGAATTT
5011 SEQ ID N0:2712 -10 -21.6 62.9 -9.9 -1.7 -8.4
ACTTTTCTATCATCTCAGCC
5289 SEQ ID NO:2713 -10 -23.7 71.6 -13.7 0 -3.2
TGGACATCCCAAAGATGGCA
5478 SEQ ID N0:2714 -10 -24.7 68.2 -12.4 -2.3 -8
AGGATGACCGCGATGTACAT
5764 SEQ ID N0:2715 -10 -24.4 67.5 -12.9 -1.3 -10.1
CTGCACTTTCTTCAGTAGCA
5799 SEQ ID N0:2716 -10 -24.6 73.8 -13.1 -1.4 -5.5
TCTCAAAGTCATCCTCACTC
5826 SEQ ID NO:2717 -10 -23.2 69.7 -13.2 0 -2.6
ATTCGAAGGGCATCCATCTC
6067 SEQ ID N0:2718 -10 -24.9 71 -13.7 -1.1 -8.2
CTCTTGTTTACGTTTCAAAG
6152 SEQ TD N0:2719 -10 -19.5 60 -9.5 0 -4.8
TATCATAGGAAGGAGGAGGG
6366 SEQ ID N0:2720 -10 -21.6 64.8 -11.6 0 -3.4
CACCTTTGTCTGATCATTTG
6956 SEQ ID N0:2721 -l0 -22.4 66.9 -12.4 0 -6.2
CAATTCTTTTTCTGGTTTTG
7003 SEQ ID N0:2722 -10 -19.8 61.8 -9.8 0 -2.5
ATGCATTAGTGATAGCCTTT
7542 SEQ ID N0:2723 -10 -22.7 67.7 -12.7 0 -6.6
TTCTTTAACCAAGACTTGTG
7605 SEQ ID N0:2724 -10 -19.8 60.3 -8.8 -0.9 -5.4
181
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Tnter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTATCTAACTTTTATTTTAG
8013 SEQ ID N0:2725 -10 -15.2 51.5 -5.2 0 -3
CCATTCTTTTTAGCAATAGC
8415 5EQ ID N0:2726 -10 -21.5 64.5 -10.7 -0.6 -4.1
CTCACCATTCTTTTTAGCAA
8419 SEQ ID N0:2727 -10 -22.2 65.9 -12.2 0 -4.l
AGTTGGAACATGTGAACTTG
8700 SEQ ID N0:2728 -10 -19.6 59.8 -8.8 -0.6 -7.8
TTATTATGGGAGAATTATGA
9061 SEQ ID N0:2729 -10 -16.9 54.1 -6.9 0 -3.2
TATAACGTGTCTTCCTCTGG
143 SEQ ID N0:2730 -9.9 -23.3 68.4 -13.4 0 -5.3
TCAGTTTTCTTGCTCCATAA
228 SEQ ID N0:2731 -9.9 -22.8 68.5 -12.9 0 -4.4
CATTACTATAAAAGTTTTCT
731 SEQ ID N0:2732 -9.9 -15.7 51.7 -5.2 -0.3 -6.3
AGGTCATAAATACACAGTTG
891 SEQ ID N0:2733 -9.9 -18.6 58 -8.7 0 -2.8
TTTATTCCTCAGATTGCCCA
1280 SEQ ID N0:2734 -9.9 -25.6 72.6 -15.7 0 -3
CAAATGTCCCATTTGAATCC
1368 SEQ ID N0:2735 -9.9 -22.1 62.9 -9.3 -2.9 -8.9
ATGTCAACTGGTAAAGATTT
1629 SEQ ID N0:2736 -9.9 -18.2 56.9 -8.3 0 -3.2
GTAATGTCAACTGGTAAAGA
1632 SEQ TD N0:2737 -9.9 -18.2 56.7 -8.3 0 -3.2
CTCATAGGCCATGGCCACCA
1736 SEQ ID N0:2738 -9.9 -30 80.1 -15.5 -2.5 -17.4
GTTCTGCTTCTTCCAAGGTG
1770 SEQ ID N0:2739 -9.9 -25.6 75.7 -15.2 -0.1 -3.6
GTTCATCATCAGCAAAGTCA
2244 SEQ ID N0:2740 -9.9 -22 66.7 -12.1 0 -4.1
GCGTCGCTCTCCATGTCTGT
2315 SEQ ID N0:2741 -9.9 -29.8 83.4 -19.9 0 -6.1
TACTGGCCTGACTAACGTTA
2340 SEQ ID N0:2742 -9.9 -23.4 66.7 -13 0 -7.8
CTGGAAGCCCTGGCACCATC
2370 SEQ ID N0:2743 -9.9 -29.7 79.2 -18.2 -1.5 -10.6
ATTGCAATCCACAGTGCTGT
2405 SEQ ID N0:2744 -9.9 -25 71.9 -13.5 -1.5 -9
TTACTTTTAACCATGCATCA
2700 SEQ ID N0:2745 -9.9 -20.7 61.8 -10.8 0 -6.6
GAATTGCCAATGATCTTAAT
3085 SEQ ID N0:2746 -9.9 -18.8 56.9 -8.9 0 -4.9
AGAATTGCCAATGATCTTAA
3086 5EQ ID N0:2747 -9.9 -18.8 57 -8.9 0 -4.9
GAAGACGATGATGGCCAACA
3134 5EQ ID N0:2748 -9.9 -22.6 63.2 -12.7 0 -6
GTGGAAGAAGTCGTTCATGT
3245 SEQ ID N0:2749 -9.9 -22.2 66.4 -11 -1.2 -4.9
TGTGCTTCCTTCAGATGAGC
3881 SEQ ID N0:2750 -9,9 -25.5 75.2 -14.9 -0.5 -4
TCTTCGGGTTCAGTTTCAGC
3934 SEQ ID N0:2751 -9.9 -25.7 77.1 -15.8 0 -3
TAACCAAAGAAACATCAACG
4308 SEQ ID N0:2752 -9.9 -16 49,8 -6.1 0 -3
GGCTAACCAAAGAAACATCA
4311 SEQ ID N0:2753 -9.9 -19.6 57.5 -9 -0.5 -3.9
182
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ACCCTCATGCCTTCAAACCG
4420 SEQ ID N0:2754 -9.9 -27.7 72.4 -17.8 0 -3.8
AGTTTAACATCTCGTGAATC
4753 SEQ ID N0:2755 -9.9 -19.3 59.7 -9.4 0 -3.9
TGACCATGTTGAGGCAGATG
5076 SEQ ID N0:2756 -9.9 -23.7 68.7 -13.8 0 -4.3
AAACGAGCTTCAGCACAAAT
5187 5EQ 2D N0:2757 -9.9 -20.1 58.7 -9.3 -0.7 -6.6
GCAAAGTTGGACATCCCAAA
5485 SEQ ID N0:2758 -9.9 -22.8 64 -10.7 -2.2 -7.6
GGTGAATTGTGTCAGGGTCA
5649 SEQ ID N0:2759 -9.9 -24.6 73.6 -14.7 0 -3.1
GTCTCCCTTAACTGAGCTGC
5672 SEQ ID N0:2760 -9.9 -27.1 77.4 -17.2 0 -5.2
CAGGATGACCGCGATGTACA
5765 SEQ ID N0:2761 -9.9 -25.1 68.5 -13.8 -1.3 -8.1
ACTGACCATGGGCAGATCCA
5981 SEQ ID N0:2762 -9.9 -27.2 75 -15.5 -1.8 -8.5
CTGAATGATAGCGGCAGACA
6176 SEQ ID N0:2763 -9.9 -22.9 65.3 -13 0 -6.6
TATAGGTAAGTCAATCCTCC
6272 SEQ ID N0:2764 -9.9 -22.1 66.1 -11.7 -0.2 -3.5
TTTCTTTTTACTTTTGATTT
6462 SEQ ID N0:2765 -9.9 -17.8 57.7 -7.9 0 -2.2
AATGTTCACTTTGCACAACT
6742 SEQ ID N0:2766 -9.9 -20.8 62.2 -10.9 0 -5
ACTAAAGGTGTTTGGTGTAG
6766 SEQ ID N0:2767 -9.9 -20.5 63.4 -9.9 -0.5 -4.7
TTTCTTCAACGTAAACCTCA
6913 SEQ ID N0:2768 -9.9 -20.7 61 -10.8 0 -5.3
GATTTATTAGATTACTTTTT
7240 SEQ ID N0:2769 -9.9 -16.2 53.7 -6.3 0 -2.3
TTGCTGAGAGCAGAAGATGG
7331 SEQ ID N0:2770 -9.9 -22.2 65.8 -10.2 -2.1 -6.9
TTAGTGATAGCCTTTAAACT
7537 SEQ ID N0:2771 -9.9 -19.6 60 -9.7 0 -4.2
TAGGCAATATTAACATGCAT
7556 SEQ ID N0:2772 -9.9 -18.9 57.5 -7 -2 -6.8
AATTGTGATGTCATCAACCT
7910 SEQ ID N0:2773 -9.9 -21 62.7 -10.4 -0.5 -7.2
GCTTTAGTGCAGCAGGAATT
8221 SEQ ID N0:2774 -9.9 -24 70.8 -13.2 -0.7 -6.6
ATATATATTTTAAACTGCCA
8531 5EQ ID N0:2775 -9.9 -17.3 54.3 -7.4 0 -4.8
TATATATATTTTAAACTGCC
8532 SEQ ID N0:2776 -9.9 -16.3 52.5 -6.4 0 -5.2
GAACATGTGAACTTGATCCT
8695 SEQ ID N0:2777 -9.9 -21 62.1 -11.1 0 -7
ACCTGAAAGTTGGAACATGT
8707 SEQ ID N0:2778 -9.9 -20.8 61.2 -10.1 -0.6 -6.7
AGTTTAGATGCTTATAGCCA
8782 SEQ ID N0:2779 -9.9 -22.4 67.5 -11.2 -1.2 -4.6
ATCATTAATACCTTATGTAT
8901 SEQ ID N0:2780 -9.9 -17.7 56 -7 -0.6 -4.2
ATATCATTAATACCTTATGT
8903 SEQ ID N0:2781 -9.9 -17.7 56 -7.8 0 -4
ATAATTTATTATGGGAGAAT
9066 SEQ ID N0:2782 -9.9 -15.6 51.1 -5.1 -0.3 -4.3
183
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTTTTTTTTTGACCACAGAG
100 5EQ ID N0:2783 -9.8 -19.9 61.1 -10.1 0 -2.3
GTGTCTTCCTCTGGCAGCTG
137 SEQ ID N0:2784 -9.8 -28.8 84.4 -18.5 0 -8.2
ATGTGGCTTGGCTTCAGTTT
241 SEQ ID N0:2785 -9.8 -25.7 76.4 -15.9 0.4 -4.4
AGATTCTTTGCTCCTTTCCC
316 SEQ ID N0:2786 -9.8 -26.8 77.1 -17 0 -3.6
GAAGCTTTCAGGTCCTGGGG
494 SEQ ID N0:2787 -9.8 -27.2 77.9 -16 -0.4 -10.8
CTTTCTCTTCTGCAGCACGT
552 SEQ ID N0:2788 -9.8 -26.3 76.6 -16 0 -8.3
GGGCTTCTTGGCTTTCTCTT
563 SEQ ID N0:2789 -9.8 -27.4 81.3 -16.6 -0.9 -3.7
ATAAATGGAAGGTTCTTTCC
643 SEQ ID N0:2790 -9.8 -19.8 60.2 -8.4 -1.6 -6.5
AGTGACTCAAAGGTATAGAT
961 SEQ ID N0:2791 -9.8 -19 59.4 -9.2 0 -3.1
CCAATGAGAGCAAACACGCT
1246 SEQ ID N0:2792 -9.8 -22.9 63.4 -12.2 -0.7 -4.7
TTATTCCTCAGATTGCCCAT
1279 5EQ ID N0:2793 -9.8 -25.5 72.2 -15.7 0 -3
TCTCTCTCTCCTTTGTTGTT
2014 SEQ ID N0:2794 -9.8 -25.3 77.9 -15.5 0 0
TGCAATCCACAGTGCTGTGC
2403 SEQ ID N0:2795 -9.8 -26.7 75.7 -14.7 -1.7 -12.4
TAACCTTCTCTTTCTGACTT
2510 SEQ ID N0:2796 -9.8 -22.1 66.7 -12.3 0 -2.6
CTTCCAGAGGAATCCTCCAG
2557 SEQ ID N0:2797 -9.8 -26.2 73.7 -14.2 -2.2 -11.2
CATAAAGAGGGTATTTAAGA
2783 SEQ ID N0:2798 -9.8 -16.7 53.4 -6.9 0 -3
TCCACATTTGACAGACCAAG
2986 SEQ ID N0:2799 -9.8 -22.5 64.7 -12.7 0 -2.9
GAAGTCGTTCATGTGCCACC
3239 SEQ ID N0:2800 -9.8 -26.6 74.6 -16.1 -0.4 -4.7
GGTTCAGAACCACAAGGTTT
3384 SEQ ID N0:2801 -9.8 -23.2 67.7 -10.8 -2.6 -11.3
ATAATCAATTCCCTTTTGCA
3503 SEQ ID N0:2802 -9.8 -21.6 63.1 -11.8 0 -4.8
CAGTTTCAGCTTGTTCACCT
3924 SEQ ID N0:2803 -9.8 -25.5 75.6 -15.7 0 -4.5
ATATCTTCAAAGGCCAATGC
4135 SEQ ID N0:2804 -9.8 -21.6 63.1 -11.2 -0.3 -7.7
ATAAGGCTCTTAGAGGTCTT
4398 SEQ ID N0:2805 -9.8 -22.4 68.7 -12 -0.3 -6.1
CGTTGTCATGTTAACACAGT
4559 SEQ ID N0:2806 -9.8 -21.7 64.9 -11.1 -0.5 -8.7
AGCGCCAACATTATCAAAGT
4667 SEQ ID N0:2807 -9.8 -22 62.8 -11.7 0 -7.6
TGGGCGAGGTATGGGTTTCT
4985 SEQ ID N0:2808 -9.8 -26.8 76.8 -17 0 -4
CTGGGCGAGGTATGGGTTTC
4986 SEQ ID N0:2809 -9.8 -26.8 76.8 -17 0 -4
ACCATTCCTTGGAATTTGTT
5008 SEQ ID N0:2810 -9.8 -23 66.8 -11.5 -1.7 -8.4
ATGTATTTGCCCTGGTCATC
5113 SEQ ID N0:2811 -9.8 -25.7 74.6 -15.9 0 -4~2
184
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Tntra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ACGAGCTTCAGCACAAATTC
5185 SEQ TD N0:2812 -9.8 -22 64.2 -11.3 -0.7 -6.6
CCAGCCTATAGTGAAGTAGT
5219 SEQ ID N0:2813 -9.8 -24 70.5 -14.2 0 -4.6
CGGATCCCCTTTGCTCCTTT
5377 SEQ ID N0:2814 -9.8 -30.3 80.3 -19.8 -0.4 -7.5
GAGAACTCTATAAACTGGGT
5884 SEQ ID N0:2815 -9.8 -19.6 59.7 -9.8 0 -4.9
AGAGAACTCTATAAACTGGG
5885 SEQ ID N0:2816 -9.8 -18.4 57 -8.6 0 -6.4
AACTCCCATCTGTTTTTTCT
6336 SEQ ID N0:2817 -9.8 -23.8 70 -14 0 -3.1
TTGTCTTTCTCAAACTTTTC
6406 SEQ ID N0:2818 -9.8 -19.6 61.9 -9.8 0 -2.6
CCTTTGCTTTCTTTTTCTGG
6427 SEQ ID N0:2819 -9.8 -24.2 71.9 -14.4 0 -2.9
ATGAGTATTTGTTAAAACAG
6575 SEQ ID N0:2820 -9.8 -15.5 51.1 -5.7 0 -6.1
TTGGGTTTCTCCTCAGCAGT
6700 SEQ ID N0:2821 -9.8 -27.3 8l -16.6 -0.8 -4.9
TGACATAGCATTATGAATAA
6880 SEQ ID N0:2822 -9.8 -16.4 52.4 -5.1 -1.4 -4.9
TAGTGACATAGCATTATGAA
6883 SEQ TD N0:2823 -9.8 -18.3 57.3 -7 -1.4 -4.9
ATTAGATTACTTTTTGGAAA
7235 SEQ ID N0:2824 -9.8 -16.1 52.5 -6.3 0 -2.3
AATTATTCTGCTTGACATAA
7668 SEQ ID N0:2825 -9.8 -17.8 55.9 -8 0 -3.8
GAATAAAAGGTTATATTGAG
8138 SEQ ID N0:2826 -9.8 -14.1 47.9 -3.7 -0.3 -3
TGAATAAAAGGTTATATTGA
8139 SEQ ID N0:2827 -9.8 -14.1 47.8 -3.7 -0.3 -3
TGTTATATTTGTAATAGCTT
8237 SEQ ID N0:2828 -9.8 -17.6 56.8 -7.8 0 -7.1
TTTAGCAATAGCAATTCCCT
8407 SEQ ID N0:2829 -9.8 -22.6 65.4 -11.1 -1.7 -4.6
CTTGGTGAATCATGCACTAG
8618 SEQ TD N0:2830 -9.8 -21.7 64.8 -10.7 -1.1 -6.2
GAGTTTAGATGCTTATAGCC
8783 SEQ ID N0:2831 -9.8 -22.3 67.6 -11.2 -1.2 -4.6
GTTTATATAATGCATTTAAG
8873 SEQ TD N0:2832 -9.8 -15.5 51.3 -5 0 -8.8
AGTTTATATAATGCATTTAA
8874 SEQ ID N0:2833 -9.8 -15.5 51.3 -5 0 -8.8
CTAGTAAAAAGGCGGAAGCT
508 SEQ ID N0:2834 -9.7 -20.3 59.2 -8.2 -2.4 -6.9
ACGTTTTTCGATAGCAGCAA
536 SEQ ID N0:2835 -9.7 -22.4 64.7 -11.7 -0.9 -6.9
CAAGATTTTTATAAGTGACT
974 SEQ ID N0:2836 -9.7 -16.6 53.6 -6.9 0 -4.1
GCTCGGAGAACTCTGAATGT
1120 SEQ ID N0:2837 -9.7 -23.1 66.9 -12.7 -0.4 -8.2
TATTCCTCAGATTGCCCATG
1278 SEQ ID N0:2838 -9.7 -25.4 71.7 -15.7 0 -3.9
ACATTTATTCCTCAGATTGC
1283 SEQ ID N0:2839 -9.7 -21.8 65.8 -12.1 0 -2.6
TTTCCATCCATGGAGAAAAG
2083 SEQ ID N0:2840 -9.7 -20.7 60.6 -9.1 -1.7 -11.5
185
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/mo1deg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGTTTCCATCCATGGAGAAA
2085 SEQ ID N0:2841 -9.7 -22.6 65.3 -10.8 -1.7 -12.1
AAACAGGGAGCCACGGATAC
2153 SEQ ID N0:2842 -9.7 -23.7 65.8 -14 0.5 -4.3
TTGCGTCGCTCTCCATGTCT
2317 SEQ ID N0:2843 -9.7 -28.7 80.2 -18.4 -0.3 -6.9
TTTGCTGGAAGCCCTGGCAC
2374 SEQ ID N0:2844 -9.7 -28.6 77.9 -16.7 -2.2 -8.6
ACCATTGCAATCCACAGTGC
2408 SEQ ID N0:2845 -9.7 -25.8 72.1 -15.2 -0.7 -9
GGGGGAAGTTGTCCAGTAGG
2467 SEQ TD N0:2846 -9.7 -26.4 76.8 -14.7 -2 -5.5
TTTGGCCAGCGACCTCCATA
3324 SEQ TD N0:2847 -9.7 -29 77.4 -18.6 -0.1 -8.8
TAGCAGCAAGGTTGTCTGAG
3435 SEQ TD N0:2848 -9.7 -23.6 70.9 -12.5 -l.3 -8.2
GTTGTTTATGAATGACATAT
3740 SEQ ID N0:2849 -9.7 -17.5 55.8 -6.7 -1 -6
TTGGCACTGTGACGGTGAGG
3765 SEQ ID N0:2850 -9.7 -25.9 73.3 -14.4 -1.8 -7.6
ACTGTAGCAGGTTTTTCGAA
4055 SEQ ID N0:2851 -9.7 -22.4 66.7 -11.8 -0.7 -7.5
AACATCAACGATCAAGAAAT
4298 SEQ ID N0:2852 -9.7 -15.8 50 -6.1 0 -4.9
AAGAAACATCAACGATCAAG
4302 SEQ ID N0:2853 -9.7 -15.8 50.2 -6.1 0 -4.9
ATTGCATTGTAATATTTTTT
4939 SEQ ID N0:2854 -9.7 -17.1 55 -7.4 0 -5.2
GGTCATCCGTTTCCACCATC
5100 SEQ ID N0:2855 -9.7 -28.5 79 -18.1 -0.4 -4.1
CAGATCATGCTGTTGCCAAA
5554 SEQ TD N0:2856 -9.7 -23.5 67.1 -12.9 -0.8 -6.6
CCTTAACTGAGCTGCCAGGG
5667 SEQ ID N0:2857 -9.7 -27.3 75.1 -16.7 -0.6 -9.3
TGTTCACCACAACCAGGAAG
5745 SEQ ID N0:2858 -9.7 -23.5 66.5 -13.8 0 -5.5
GGACTTTGTTGGGTTTTGCT
5949 SEQ ID N0:2859 -9.7 -25 74.2 -15.3 0 -3.6
GCGGCAGACACCTCCTCTTG
6166 SEQ ID NO:2860 -9.7 -29.6 80.2 -19.4 -0.1 -5.9
AGCGGCAGACACCTCCTCTT
6167 SEQ ID N0:2861 -9.7 -29.6 80.8 -19.4 -0.1 -6.6
TGTTTTTTCTGGAGTGGAGT
6326 SEQ ID N0:2862 -9,7 -23 71 -13.3 0 -2.7
CTATGAGTATTTGTTAAAAC
6577 SEQ ID N0:2863 -9.7 -15.4 51 -5.7 0 -3.3
GCACTGACTATGAGTATTTG
6584 SEQ TD N0:2864 -9.7 -20.7 63.3 -10.5 -0.1 -3.5
TTGTATAGGCACTGACTATG
6592 SEQ ID N0:2865 -9.7 -20.9 63.6 -10.5 -0.4 -4.8
GGTAGCCATTGGGTTTCTCC
6708 SEQ ID N0:2866 -9.7 -28.2 81.3 -18 -0.2 -5.6
CTGTACTAAAGGTGTTTGGT
6770 SEQ ID N0:2867 -9.7 -21.4 65.2 -10.9 -0.6 -5.1
AGTTAAAAATAGAATGGATG
6796 SEQ ID N0:2868 -9.7 -13.6 46.6 -3.9 0 -2.8
TTCTTGTATACTGTTTCTTC
6926 SEQ ID N0:2869 -9.7 -20.4 65.4 -10.7 0 -5.6
186
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GCACATAACTGTTCAGATAG
7101 SEQ ID N0:2870 -9.7 -20.2 61.8 -l0 -0.2 -5.6
TTATTTTAGGAAATTATCCA
8002 5EQ ID N0:2871 -9.7 -17.1 54.3 -5.2 -2.2 -7.2
AAACCCATTATCTAACTTTT
8020 SEQ ID N0:2872 -9.7 -19 57.3 -9.3 0 -1.6
TCCATGTTATATTTGTAATA
8241 SEQ TD N0:2873 -9.7 -17.9 56.7 -8.2 0 -4.3
TACACTACAGTAAATAGTTT
8371 SEQ ID N0:2874 -9.7 -16.9 54.6 -6.7 -0.1 -3.3
TTTATTAGCCACCAAGTAAT
8836 SEQ ID N0:2875 -9.7 -20.6 61.1 -10.9 0 -3.2
TGTCTTCCTCTGGCAGCTGT
136 SEQ ID N0:2876 -9.6 -28.8 84.4 -18.5 0 -8.7
GGCTTGGCTTCAGTTTTCTT
237 SEQ ID N0:2877 -9.6 -26 78 -15.7 -0.4 -6
CACTATTTGGCTTTGGTTTG
612 SEQ ID N0:2878 -9.6 -22.4 67.1 -12.8 0 -3.7
GAAGGTTCTTTCCAGCTTCC
636 SEQ ID N0:2879 -9.6 -26.2 76.3 -15.9 -0.5 -4.7
CCTTTCCTTTATTCATTACT
744 SEQ ID N0:2880 -9.6 -22.4 66.7 -12.8 0 -0.7
AATACACAGTTGGTCAAAAT
883 SEQ ID N0:2881 -9.6 -17.5 54.6 -7.9 0 -3.8
TTTTTATAAGTGACTCAAAG
969 SEQ TD N0:2882 -9.6 -15.7 51.7 -6.1 0 -4.7
GCTTCTTTACCGACTGGATC
1191 SEQ ID N0:2883 -9.6 -24.9 71.5 -14.4 -0.7 -4.1
GAATCGCTTGGGGGCCACTG
1306 SEQ ID N0:2884 -9.6 -28.3 76.1 -18 -0.4 -6.8
CCCATTTGAATCCATTGTGC
1361 SEQ ID N0:2885 -9.6 -25 69.7 -15.4 0 -2.6
GAACTCAACTTTGATGCTTC
1930 SEQ ID N0:2886 -9.6 -20.5 62.1 -10.9 0 -5
TTCCTCCATTCTTTAGCACC
1954 SEQ ID N0:2887 -9.6 -26.5 75.8 -16.9 0 -4.1
TTGCTGGAAGCCCTGGCACC
2373 SEQ ID N0:2888 -9.6 -30.5 80.9 -18.7 -2.2 -8.7
GGAAGTTGTCCAGTAGGTGA
2464 SEQ ID N0:2889 -9.6 -24.6 73.4 -13.7 -1.2 -4.8
TAAGCAGTCTGAATGATCGC
3021 SEQ ID N0:2890 -9.6 -21.5 63.6 -11.2 -0.4 -6.3
GTTTCCTAGAGCCCCCACAG
3104 SEQ ID N0:2891 -9.6 -30.4 82.1 -20.8 0 -3.3
ACCTCCATACAGTCCCACAT
3313 SEQ ID N0:2892 -9.6 -28 76.5 -18.4 0 -2.8
TCCCTTTTGCATTCTTCCTA
3494 SEQ ID N0:2893 -9.6 -26.6 75.9 -17 0 -5.1
ATCTCTAAGATAATTAAGCT
3650 5EQ ID N0:2894 -9.6 -17 54.6 -6.8 -0.3 -5.4
TTTGCTTTCTTCTAGTTCTG
3842 SEQ ID N0:2895 -9.6 -22.1 69.4 -12.5 0 -4
TTCTTCGGGTTCAGTTTCAG
3935 SEQ ID N0:2896 -9.6 -24 72.8 -14.4 0 -2.4
TCTGTACTTACTTGACAGAA
4006 SEQ ID N0:2897 -9.6 -19.7 61 -8.2 -1.9 -6.3
TTTGCCTTCTTCTGTACTTA
4016 SEQ ID N0:2898 -9.6 -23.5 70.9 -13.9 0 -4.8
187
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATCTTCCCTTTGCCTTCTTC
4024 SEQ ID N0:2899 -9.6 -27.5 79.2 -17.9 0 -3
CAACAATACTGTAGCAGGTT
4062 SEQ ID N0:2900 -9.6 -20.9 62.7 -10.4 -0.7 -5.3
GCATTCACAACCACCCTCAT
4432 SEQ ID N0:2901 -9.6 ~ -27 73.3 -17.4 0 -3.4
TTACTTTCACGTTTTTCCAC
4647 SEQ ID NO:2902 -9.6 -22.1 65.8 -12.5 0 -4.7
ACATGTACAGATTTTCTTCA
4785 SEQ ID N0:2903 -9.6 -20.1 62.6 -10.5 0 -6.7
TTCCACCATCATGGTGACCA
5090 SEQ ID N0:2904 -9.6 -27.1 74.7 -13.8 -3.7 -11.1
TGGTCATCCGTTTCCACCAT
5101 SEQ ID N0:2905 -9.6 -28.1 77.1 -17.3 -1.1 -5.4
TTCAGCACAAATTCTCCAGT
5179 SEQ ID N0:2906 -9.6 -22.9 67.4 -13.3 0 -4.1
TTTTCTATCATCTCAGCCAG
5287 SEQ ID N0:2907 -9.6 -23.3 70.4 -13.7 0 -3.2
GGATCCCCTTTGCTCCTTTG
5376 SEQ ID N0:2908 -9.6 -29.5 80.5 -19.9 0 -6.9
CAGGAGGCCGATGTTAAACA
5435 SEQ ID N0:2909 -9.6 -23.4 65.6 -13.2 -0.3 -6.9
AAAGATGGCATAGATAAACA
5468 SEQ ID N0:2910 -9.6 -16.4 51.9 -6.8 0 -4
CCATCCCAGCCAGCAGAGGT
5590 SEQ ID N0:2911 -9.6 -31.8 85.1 -22.2 0 -4.6
AGCTGGACTTTGTTGGGTTT
5953 SEQ ID N0:2912 -9.6 -24.9 74.1 -15.3 0 -4.3
GGTCACCACTGACCATGGGC
5988 SEQ ID N0:2913 -9.6 -29.2 80 -15.7 -3.9 -10.6
TATATTTTTTAACCTTTGCT
6221 SEQ ID NO:2914 -9.6 -18.9 58.6 -9.3 0 -3.6
TGGAGTGGAGTTCCCATTTA
6317 SEQ ID N0:2915 -9.6 -25.1 73.1 -14.6 -0.7 -6.7
GACCTCTTTTCCTTTGCTTT
6437 SEQ ID N0:2916 -9.6 -25.7 74.8 -16.1 0 -3.6
ACACATATACTTTACCTTCA
6519 SEQ TD N0:2917 -9.6 -20.5 62 -10.9 0 -2.2
CACTGACTATGAGTATTTGT
6583 SEQ ID N0:2918 -9.6 -20.1 62.2 -10.5 0.5 -4
GGTCACTTCACTGTCTTGTA
6607 SEQ ID N0:2919 -9.6 -24.4 74.7 -14.8 0 -2.6
GTTAAAAATAGAATGGATGC
6795 SEQ ID N0:2920 -9.6 -15.4 50.1 -5.8 0 -2.8
AAATATGGCAGATATGGAAG
6814 SEQ ID N0:2921 -9.6 -17.4 54.2 -6.4 -1.3 -5.2
AATTGGGGACCATGGAAATG
6854 SEQ ID N0:2922 -9.6 -20.9 60.2 -8.9 -2.4 -8.8
CATTACAATTCTTTTTCTGG
7008 SEQ ID N0:2923 -9.6 -19 59.3 -9.4 0 -2.5
AAGCCATCTAGAAAATGGAA
7045 SEQ ID N0:2924 -9.6 -18.4 55.5 -7.2 -1.6 -8.3
AGAATGGATTTATTAGATTA
7246 SEQ ID N0:2925 -9.6 -15.8 52.1 -6.2 0 -2.4
TTTGATTTAATAGAAGTTGT
7447 SEQ ID N0:2926 -9.6 -16.1 53 -6.5 0 -2.5
ATAATGGACAGAGCAGGTTG
7652 SEQ ID N0:2927 -9.6 -21.3 63.9 -11.7 0 -4.1
188
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GCTTCAAATTATTCTGCTTG
7674 SEQ ID N0:2928 -9.6 -20.5 62.3 -10.9 0 -3.6
TATTTTAGGAAATTATCCAT
8001 SEQ ID N0:2929 -9.6 -17 54 -5.2 -2.2 -7.2
ATACACTACAGTAAATAGTT
8372 5EQ ID N0:2930 -9.6 -16.8 54.2 -6.7 -0.1 -3.6
ACGTGTCTTCCTCTGGCAGC
139 SEQ ID N0:2931 -9.5 -28.9 82.6 -19.4 0 -4.4
TGGCTTGGCTTCAGTTTTCT
238 SEQ ID N0:2932 -9.5 -25.9 77.3 -15.7 -0.4 -6
TTTTCCGGAAAAGCTCCAGG
382 SEQ ID N0:2933 -9.5 -24.2 67.1 -11.9 -1.6 -13.8
CTTCTGCAGCACGTTTTTCG
546 SEQ ID N0:2934 -9.5 -25.1 71.5 -14.7 -0.5 -9.3
AAGTCACTATTTGGCTTTGG
616 SEQ ID N0:2935 -9.5 -21.9 66 -11 -1.3 -4.7
AGTCAGGAGGGTTGCTCAAG
909 SEQ ID N0:2936 -9.5 -24.9 74.4 -13.4 -2 -4.6
ATTGCCCAGGTCCACAAACT
1085 SEQ ID N0:2937 -9.5 -26.7 72.6 -17.2 0 -3.6
TCTCAACGCTGAGACATTGC
1100 SEQ ID N0:2938 -9.5 -23.4 67.5 -11.4 -2.5 -8.4
CTCGGAGAACTCTGAATGTT
1119 SEQ ID N0:2939 -9.5 -21.4 63.2 -11.2 -0.4 -8.2
CCTCAGATTGCCCATGAACA
1274 SEQ ID N0:2940 -9.5 -26 71.1 -16.5 0 -4.5
CATAAAAGTGACTGTCATCT
1431 SEQ ID N0:2941 -9.5 -18.8 58.2 -8.6 -0.1 -8.8
GCTGATGCTGCCGCAACTGC
1852 SEQ TD N0:2942 -9.5 -29.3 78.2 -18.6 -1.1 -7.5
ATTTGCTGGAAGCCCTGGCA
2375 SEQ ID N0:2943 -9.5 -28.4 77.3 -16.7 -2.2 -8.6
TTGCTCAGTCATGGGGTAGT
2813 SEQ ID N0:2944 -9.5 -25.9 77.9 -16.4 0 -4.7
ACACACTACTGAATTGCTCA
2826 SEQ ID N0:2945 -9.5 -21.5 63.8 -12 0 -3.6
GAGGTTTCCTAGAGCCCCCA
3107 SEQ ID N0:2946 -9.5 -31.3 84.3 -21.1 -0.5 -4.4
GCAGCAAGGTTGTCTGAGCT
3433 SEQ ID N0:2947 -9.5 -26.6 77.9 -15.7 -1.3 -8.2
CATAATCAATTCCCTTTTGC
3504 SEQ ID N0:2948 -9.5 -21.6 63.1 -12.1 0 -2.7
GCATCTTATTTTTCACATAA
3519 SEQ ID N0:2949 -9.5 -19 59.3 -9.5 0 -3.4
GCTTTCTAAAAAAGGCTTTT
3552 SEQ ID N0:2950 -9.5 -18.6 57 -7.6 -1.4 -7.2
CTAAGATAATTAAGCTCTTT
3646 SEQ ID N0:2951 -9.5 -16.8 54 -6.8 -0.1 -6.1
TCCAACAGCAATTGGCACTG
3776 SEQ ID N0:2952 -9.5 -24 67.6 -12.9 -1.5 -8.l
TGATTTGATGGCACCGAGTT
4358 SEQ ID N0:2953 -9.5 -24 68.2 -14.5 0 -4
CGGGATAAGGCTCTTAGAGG
4402 SEQ ID N0:2954 -9.5 -23.6 68.2 -13.5 -0.3 -5.6
GTGGTAGAACTTGCCAGCAA
4541 SEQ ID N0:2955 -9.5 -24.7 70.6 -13.9 -1.2 -7.3
CCACCGAGCTTGCTTGCCAA
4631 SEQ ID N0:2956 -9.5 -29.7 77.2 -19.6 -0.3 -6.4
189
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATATCCATCCAGCCTTTAAA
4717 SEQ ID N0:2957 -9.5 -23.1 65.8 -13.6 0 -4
TCCACCATCATGGTGACCAT
5089 SEQ ID N0:2958 -9.5 -27 74.3 -13.8 -3.7 -11.1
ACTAGGGTCATGTATTTGCC
5122 SEQ ID N0:2959 -9.5 -24.4 72.3 -14.9 0 -4.7
CAAAGGTCTCAAAGTTGAAC
5538 SEQ ID N0:2960 -9.5 -18.1 56.1 -8.6 0 -5.4
AATCCCAACAGATGGGTCCC
5696 SEQ ID N0:2961 -9.5 -27.2 73.4 -14.5 -3.2 -8.6
TTCACCACAACCAGGAAGGA
5743 SEQ ID N0:2962 -9.5 -24.1 67.3 -13.8 -0.6 -4.3
GGATCAAACTTTTCCCAAAC
5857 SEQ ID N0:2963 -9.5 -20.8 60.4 -11.3 0 -5.3
ACCACTGACCATGGGCAGAT
5984 SEQ ID N0:2964 -9.5 -27 74 -15.7 -1.8 -8.8
TCCATCTCTCCACTCTCACA
6055 SEQ ID N0:2965 -9.5 -27.2 78.5 -17.7 0 -0.5
CAAACTTTTCCTTGTCTGGT
6396 SEQ ID N0:2966 -9.5 -23 67.8 -13.5 0 -3.2
CTGACCTCTTTTCCTTTGCT
6439 SEQ ID N0:2967 -9.5 -26.4 75.8 -16.9 0 -3.6
GTCCAGTTGACACATATACT
6528 SEQ ID N0:2968 -9.5 -22.5 67.2 -11.9 -1 -4.4
TTAAAAATAGAATGGATGCA
6794 SEQ ID N0:2969 -9.5 -14.9 48.7 -5.4 0 -5.2
TTGTATACTGTTTCTTCAAC
6923 SEQ TD N0:2970 -9.5 -19.2 60.9 -9.7 0 -6.3
AAAAATAATCCTTTAAATAT
7138 SEQ ID N0:2971 -9.5 -11.7 42.7 -2.2 0 -4.3
TTTTGGAAAGCATTTGACCT
7224 SEQ ID N0:2972 -9.5 -21.1 62.1 -10.8 -0.6 -4.1
ACATCCCTGTTGGAAGCTTG
7494 SEQ ID N0:2973 -9.5 -25.4 71.9 -14.8 -1 -7.2
TGTCAGTAGGCAGTATCCAG
7775 SEQ ID N0:2974 -9.5 -24.9 75 -14.9 -0.2 -4
TAGGAAATTATCCATTGAAA
7996 SEQ ID N0:2975 -9.5 -16.3 51.7 -4.6 -2.2 -7.2
GAGTGTTTGACCAATGTATC
8085 SEQ ID N0:2976 -9.5 -21.3 64.7 -11.8 0 -3.4
AAAGAACAAAGTCCATGTTA
8252 SEQ ID N0:2977 -9.5 -17.3 53.8 -6.5 -1.2 -4.7
ACAACTTTGCCACTTTGTTC
8280 SEQ ID N0:2978 -9.5 -23 67.7 -13.5 0 -3.8
TATATCATGTTAGGTAATTG
8301 SEQ ID N0:2979 -9.5 -17 55.2 -7.5 0 -4.1
CACTACAGTAAATAGTTTTG
8369 SEQ ID N0:2980 -9.5 -17.1 54.9 -7.1 -0.1 -3.3
ATGCAATAAAAAATGAAATT
8466 SEQ ID N0:2981 -9.5 -11.3 41.7 -1.8 0 -5.6
AATGCAATAAAAAATGAAAT
8467 SEQ ID N0:2982 -9.5 -10.5 40.3 -0.9 0 -5.6
CACTAGTTTGTTGTAAAATT
8604 SEQ ID N0:2983 -9.5 -17.1 54.8 -6.9 -0.4 -6.3
CAAACCTGAAAGTTGGAACA
8710 SEQ ID N0:2984 -9.5 -18.9 56.1 -8.7 -0.4 -4.8
TATGTATACATAGGAGTTTA
ggg8 SEQ ID N0:2985 -9.5 -17.8 57.4 -7.1 0 -10.3
190
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CCTCTCTGCTTATGCCTCCG
8 SEQ ID N0:2986 -9.4 -29.9 81 -19.6 -0.8 -4.6
TTCTTACAATATCCCTAGAA
337 SEQ ID N0:2987 -9.4 -20 60.2 -10.6 0 -3.8
AGCTCCAGGTCCCTTCTGTG
371 SEQ ID N0:2988 -9.4 -30.1 85.5 -20.7 0.3 -6.3
CTTTCAGGTCCTGGGGGTAC
490 SEQ ID N0:2989 -9.4 -27.8 80.8 -17.7 -0.4 -6.8
GAATCGGAAAATTGCCTTTC
758 SEQ ID N0:2990 -9.4 -20.2 59 -10.3 -0.2 -3.9
CAGTTGGTCAAAATAGTGCA
877 SEQ ID N0:2991 -9.4 -20.8 62.6 -11.4 0 -5.2
ACACAGTTGGTCAAAATAGT
880 SEQ ID N0:2992 -9.4 -19.4 59.6 -l0 0 -3.8
CAGCCCAATGAGAGCAAACA
1250 SEQ ID N0:2993 -9.4 -23.7 65.5 -13.5 -0.6 -4.l
GGGGGCCACTGCAAACATTT
1297 SEQ ID N0:2994 -9.4 -26.6 72.5 -15.7 -1.4 -7.7
AAAAATATCATGTATGTTTT
1663 SEQ ID N0:2995 -9.4 -14.4 48.6 -4 -0.9 -7.5
CCATGGCCACCACAGCCAGG
1728 SEQ ID N0:2996 -9.4 -31.9 82.3 -19.7 -2.8 -9.1
CTTCAAGGTGCTCTCTCTGT
1992 SEQ ID N0:2997 -9.4 -25.6 77.2 -16.2 0 -3.6
TGCCCGACCTCTGAAACTGA
2204 SEQ ID N0:2998 -9.4 -26.5 70.5 -17.1 0 -3
AGTCTCTCCTGCTTTCGCCG
2280 SEQ TD N0:2999 -9.4 -29.8 82 -19.7 -0.5 -3.6
ATTCACAAGATGTTTTACTT
2714 SEQ ID N0:3000 -9.4 -18.4 58.1 -9 0 -3
AATTGCCAATGATCTTAATT
3084 SEQ ID N0:3001 -9.4 -18.3 56 -8.9 0 -4.9
AAGACGATGATGGCCAACAC
3133 SEQ TD N0:3002 -9.4 -22.2 62.5 -12.8 0 -6.3
AGTCCCACATGGTCTCTATC
3303 SEQ ID N0:3003 -9.4 -26.3 77.4 -16.9 0 -5.2
CAGAACCACAAGGTTTCCAA
3380 SEQ ID N0:3004 -9.4 -22.7 64.4 -10.7 -2.6 -7.6
AGCAGCAAGGTTGTCTGAGC
3434 SEQ ID N0:3005 -9.4 -25.7 76.2 -14.9 -1.3 -8.2
ATTGGCACTGTGACGGTGAG
3766 SEQ ID N0:3006 -9.4 -24.7 70.7 -14.1 -1.1 -6.9
TGCTTTCTTCTAGTTCTGAC
3840 SEQ ID N0:3007 -9.4 -22.7 70.7 -13.3 0 -4
GCATTTAATTTCTCTTTGCT
3856 5EQ ID N0:3008 -9.4 -21.4 65.3 -11.5 -0.2 -4
CCCTTCAGTAAAACAAGCTT
3968 SEQ ID N0:3009 -9.4 -21.9 63 -12.5 0 -6.2
TTCTTCTGTACTTACTTGAC
4010 SEQ ID N0:3010 -9.4 -20.6 64.7 -11.2 0 -4.8
ATGATTTGATGGCACCGAGT
4359 SEQ ID N0:3011 -9.4 -23.9 67.9 -14.5 0 -4
ATTCACAACCACCCTCATGC
4430 SEQ ID N0:3012 -9.4 -26.3 72.1 -16.9 0 -4.4
CTTGCCAGCAAACAAATTCA
4532 SEQ ID N0:3013 -9.4 -21.3 61.1 -11.9 0 -7.4
TTTTCCACCGAGCTTGCTTG
4635 SEQ ID N0:3014 -9.4 -26.6 73.8 -16.7 -0.2 -6.2
191
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TACATAATATCCATCCAGCC
4723 SEQ ID N0:3015 -9.4 -23.3 66.5 -13.9 0 -3.2
CTTCATATACAGGCTGAAGT
4770 SEQ ID N0:3016 -9.4 -21.4 64.6 -10.5 -1.4 -5.9
GTTTCTTGGATCCAAGTTTC
4962 SEQ ID N0:3017 -9.4 -22.8 69.3 -9.7 -1.3 -15.5
GAGGTTTCTTGGATCCAAGT
4965 SEQ ID N0:3018 -9.4 -24 71.3 -10.9 -1.3 -15.5
AATTCTCCAGTGAACAGAAC
5170 SEQ ID N0:3019 -9.4 -19.9 60 -10 -0.2 -4.8
GAATACTTTTCTATCATCTC
5293 SEQ ID N0:3020 -9.4 -18.8 60 -9.4 0 -2.6
ATAGGCAAAGTTGGACATCC
5489 SEQ ID N0:3021 -9.4 -22.4 65.5 -13 0 -4.5
GTCATCAATTCCAGCTTCCT
5516 SEQ ID N0:3022 -9.4 -26 75.1 -16.6 0 -4.5
TCACCACAACCAGGAAGGAT
5742 SEQ ID N0:3023 -9.4 -24 66.9 -13.8 -0.6 -4.3
ATGACCGCGATGTACATGTT
5761 SEQ ID N0:3024 -9.4 -23.9 66.8 -13.8 0 -8.9
AGTTTGGCATGGACCTCCTC
6553 SEQ ID N0:3025 -9.4 -27.7 78.9 -18.3 0.1 -5.1
AAATAGAATGGATGCAAGGA
6790 SEQ ID N0:3026 -9.4 -17.6 54.2 -8.2 0 -5.6
ATAGTGACATAGCATTATGA
6884 SEQ TD N0:3027 -9.4 -19 59.3 -8.1 -l.4 -4.9
CTTCAACGTAAACCTCATTT
6910 SEQ ID N0:3028 -9.4 -20.3 59.7 -10.9 0 -4.8
TGAGAGACAGGGTTCTTGTA
6938 5EQ ID N0:3029 -9.4 -22.7 69.4 -12.6 -0.4 -5
ATAACTGTTCAGATAGAAAC
7097 SEQ ID N0:3030 -9.4 -16.2 52.6 -6.1 -0.5 -5.6
GGAAGCTTGCAAAAGACACA
7483 SEQ ID N0:3031 -9.4 -20.7 60.4 -9.8 -1.4 -7
ATTCTTTAACCAAGACTTGT
7606 SEQ ID N0:3032 -9.4 -19.8 60.3 -9.4 -0.9 -5.4
AATTCATTCTATCACCAATA
7632 SEQ ID N0:3033 -9.4 -18.6 57.4 -9.2 0 -2.3
TATGAAGAATAGGTTTTGTC
7791 SEQ ID N0:3034 -9.4 -17.5 56.3 -8.1 0 -1.9
TTAGACATATTTTTAGCAAA
7812 SEQ ID N0:3035 -9.4 -16.2 52.6 -6.8 0 -4.1
CTTTTATTTTAGGAAATTAT
8005 SEQ ID N0:3036 -9.4 -15.1 50.5 -5.1 -0.3 -4.6
ACTTTTATTTTAGGAAATTA
8006 SEQ ID N0:3037 -9.4 -15.3 51 -5.1 -0.6 -4.6
AAATGCAATAAAAAATGAAA
8468 SEQ ID N0:3038 -9.4 -9.8 39.1 0 0 -5.6
GTTGGAACATGTGAACTTGA
g6g9 SEQ ID N0:3039 -9.4 -20.2 60.9 -10 -0.6 -7
TCAAACCTGAAAGTTGGAAC
8711 SEQ ID N0:3040 -9.4 -18.6 56.1 -8.7 -O.l -4.6
AAAGCTATTGTAGGTGGTTA
8743 SEQ ID N0:3041 -9.4 -20.6 63.3 -11.2 0 -5.1
CTCACATAAATCCAAGGGTT
8958 SEQ ID N0:3042 -9.4 -21.3 62.4 -11.9 0 -4.1
GTTTGGTTTTGACCTCACAT
8971 SEQ ID N0:3043 -9.4 -23.8 70.4 -12.1 -2.3 -6.5
192
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TATAATTTATTATGGGAGAA
9067 SEQ ID N0:3044 -9.4 -15.3 50.6 -5.1 -0.6 -4.9
AATCCTTGACAGGTATCTCA
277 5EQ ID N0:3045 -9.3 -22.7 67.6 -12.4 -0.9 -3.4
TTGCTCCTTTCCCAGTAAGC
309 SEQ ID N0:3046 -9.3 -27.4 77.5 -17.4 -0.4 -4.1
TCACTATTTGGCTTTGGTTT
613 SEQ ID N0:3047 -9.3 -22.8 68.9 -13.5 0 -3.7
ACCAAAATCTTGATAGCAAT
829 SEQ ID N0:3048 -9.3 -18.3 55.5 -8.4 -0.3 -0.5
CCAGTCAGGAGGGTTGCTCA
911 SEQ ID N0:3049 -9.3 -28.3 81.8 -l7 -2 -5.1
CATTGCCCAGGTCCACAAAC
1086 SEQ ID N0:3050 -9.3 -26.5 71.8 -17.2 0 -3.6
CGGAGAACTCTGAATGTTCT
1117 SEQ ID N0:3051 -9.3 -21.4 63.2 -9.8 -2.3 -8.4
GCTGCAGCCCAATGAGAGCA
1254 SEQ TD N0:3052 -9.3 -28.7 78 -17.4 -1 -12
GAGCCATTTCCACAGAGTAA
1474 SEQ ID N0:3053 -9.3 -24.1 69.5 -14.8 0 -3.2
GACACTGGCCTGCATCTGAG
1491 5EQ ID N0:3054 -9.3 -26.9 75.9 -17.6 0 -7.2
CGAGCATCTGCTGAAATTCG
1800 SEQ ID N0:3055 -9.3 -22.4 63.5 -12.1 -0.9 -7.9
ACTTTGATGCTTCTGAAGAA
1923 SEQ ID N0:3056 -9.3 -19.8 60.4 -10 0 -8.3
ACCATGCATCACAGCAGTCC
2691 SEQ ID N0:3057 -9.3 -27.5 77.4 -16.9 -1.2 -7.5
AATTGCTCAGTCATGGGGTA
2815 SEQ ID NO:3058 -9.3 -24 71.2 -14.7 0 -4.7
TGAATTGCTCAGTCATGGGG
2817 SEQ ID N0:3059 -9.3 -23.7 69.6 -14.4 0 -4.7
CCACATTTGACAGACCAAGC
2985 SEQ ID N0:3060 -9.3 -23.9 67.2 -14.6 0 -2.9
GTCCCACATGGTCTCTATCC
3302 SEQ ID N0:3061 -9.3 -28.3 80.8 -19 0 -5.2
CCTCCATACAGTCCCACATG
3312 SEQ ID NO:3062 -9.3 -27.8 75.8 -18.5 0 -4.7
ACATAATCAATTCCCTTTTG
3505 SEQ ID N0:3063 -g.3 -20 59.7 -10.7 0 -2.6
CATCTCTAAGATAATTAAGC
3651 SEQ ID N0:3064 -9.3 -16.8 54 -6.8 -0.5 -4.9
CTCGGGGTAGAACAACATCA
3903 SEQ ID N0:3065 -9.3 -22.7 65.2 -13.4 0 -3.5
TCAGTTTCAGCTTGTTCACC
3925 SEQ ID N0:3066 -9.3 -25 75.4 -15.7 0 -4.5
ACCAACAGCACATTCATGAT
4474 SEQ ID N0:3067 -9.3 -22.3 64.4 -13 0 -6.4
TCCATCCAGCCTTTAAATGT
4714 SEQ ID N0:3068 -9.3 -24.6 69.3 -15.3 0 -4.3
CCTCTGTCATAAAGATGTCT
4914 SEQ ID N0:3069 -9.3 -21.9 65.7 -11.9 -0.4 -4.5
CTTCAGCACAAATTCTCCAG
5180 SEQ ID N0:3070 -9.3 -22.6 66.1 -13.3 0 -3.3
AACAGATGGGTCCCCACGGT
5690 SEQ ID N0:3071 -g,3 -28.9 76.8 -18.7 -0.6 -8.8
GTACATGTTCACCACAACCA
5750 5EQ ID N0:3072 -g,3 -24.2 68.6 -14.9 0.1 -6.5
193
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CCATCTCTCCACTCTCACAC
6054 SEQ TD N0:3073 -9.3 -27 77.3 -17.7 0 -0.5
GCATCCATCTCTCCACTCTC
6058 SEQ ID N0:3074 -9.3 -28.1 81.4 -18.8 0 -3.4
TTATAGGTAAGTCAATCCTC
6273 SEQ ID N0:3075 -9.3 -20.2 62.6 -10.4 -0.2 -3.5
TCTGGTTTTGTTACACTATC
6382 SEQ ID N0:3076 -9.3 -21.1 65.9 -11.8 0 -2.7
CCTTGTCTGGTTTTGTTACA
6387 SEQ ID N0:3077 -9.3 -24.1 72 -14.8 0 -2.7
TTACAATTCTTTTTCTGGTT
7006 SEQ ID N0:3078 -9.3 -19.6 61.5 -10.3 0 -2.6
TGACCTAAATTAAATATAGA
7210 SEQ ID N0:3079 -9.3 -14.4 48 -5.1 0 -3.2
ATTTATTAGATTACTTTTTG
7239 SEQ TD N0:3080 -9.3 -15.6 52.3 -6.3 0 -2.4
TAGAATGGATTTATTAGATT
7247 SEQ ID N0:3081 -9.3 -15.8 52.1 -6.5 0 -2.4
ACATAGGGTATTTAATTGAC
7365 SEQ ID N0:3082 -9.3 -18 56.9 -8.7 0 -2.9
TAGCCTTTAAACTATGTTTA
7530 SEQ ID N0:3083 -9.3 -18.8 58.3 -8.5 -0.9 -5.7
AGGCAATATTAACATGCATT
7555 SEQ ID N0:3084 -9.3 -19.3 58.4 -8 -2 -6.8
AGCAGGTTGAATTCATTCTA
7641 SEQ ID N0:3085 -9.3 -21.2 64.9 -11.2 -0.4 -8.4
TGTTGAATTAAAAGTGCAAA
7714 5EQ TD N0:3086 -9.3 -15.2 49.5 -5.9 0 -5.4
TCCAGTGTGTTTCCTTGAAA
7760 SEQ TD N0:3087 -9.3 -23.5 68.8 -13.5 -0.4 -4.5
GCAGTATCCAGTGTGTTTCC
7766 SEQ ID N0:3088 -9.3 -26.7 79.3 -17.4 0 -3.7
ATTTTAGGAAATTATCCATT
8000 SEQ ID N0:3089 -9.3 -17.4 54.9 -5.9 -2.2 -7.2
ATTATCTAACTTTTATTTTA
8014 SEQ ID N0:3090 -9.3 -15.2 51.3 -5.9 0 -l.6
AATACACTACAGTAAATAGT
8373 SEQ ID N0:3091 -9.3 -16 52.1 -6.7 0 -3.6
ATAGCAATTCCCTGCATGCA
8400 SEQ ID N0:3092 -9.3 -25.9 72.1 -14.7 -1.9 -10.8
AGCAATAGCAATTCCCTGCA
8404 SEQ ID N0:3093 -9.3 -25.2 70.3 -14.2 -1.7 -7.5
TGAAAGAAGATGAGTTTAGA
8794 SEQ ID N0:3094 -9.3 -16 52.7. -6.7 0 -2.2
GACCTCACATAAATCCAAGG
8961 SEQ ID N0:3095 -9.3 -21.6 62.1 -12.3 0 -3.7
CCTTATATAATTTATTATGG
9072 SEQ ID N0:3096 -9.3 -16.3 52.6 -6.2 -0.6 -5.3
TAAATGGAAGGTTCTTTCCA
642 SEQ ID N0:3097 -9.2 -20.5 61.4 -8.4 -2.9 -9.1
AAAAGTTTTCTTATTGATAT
722 SEQ ID N0:3098 -9.2 -14.9 50.1 -4.6 , -1 -5.7
ATAAAAGTTTTCTTATTGAT
724 SEQ ID N0:3099 -9.2 -14.9 50.1 -4.6 -1 -6.3
ATATACAAGGCAGAGGTGGC
781 SEQ ID N0:3100 -9.2 -23.3 68.6 -14.1 0 -4
TTGGTCAAAATAGTGCACAT
874 SEQ ID N0:3101 -9.2 -19.8 59.8 -9.6 0 -9.9
194
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GATTTTTATAAGTGACTCAA
971 SEQ ID N0:3102 -9.2 -l7 54.7 -7.8 0 -4.4
CCAAGATTTTTATAAGTGAC
975 SEQ ID N0:3103 -9.2 -17.7 55.6 -8.5 0 -4.1
ATTTATTCCTCAGATTGCCC
1281 SEQ ID N0:3104 -9.2 -24.9 71.5 -15.7 0 -3
TCCCATTTGAATCCATTGTG
1362 SEQ TD N0:3105 -9.2 -23.6 67.2 -14.4 0 -2.3
CAGATGTATCCTTCTGGACA
1507 5EQ ID N0:3106 -9.2 -23.6 69.6 -13 -1.3 -6.6
TTTTTGTTCTGCTTCTTCCA
1775 SEQ ID N0:3107 -9.2 -24.3 73.2 -15.1 0 -3.6
TGCTTTCGCCGTCTTCAAAT
2271 SEQ ID N0:3108 -9.2 -25 69.4 -15.1 -0.5 -3.6
CTCTCCTGCTTTCGCCGTCT
2277 SEQ ID N0:3109 -9.2 -30.7 83.6 -20.8 -0.5 -3.6
GAGTCTCTCCTGCTTTCGCC
2281 5EQ ID N0:3110 -9.2 -29.6 84 -19.7 -0.5 -4.1
CATCTTCCCATTTGCTGGAA
2384 SEQ TD N0:3111 -9.2 -25.2 71 -14.9 -1 -4.4
ATCCACAGTGCTGTGCATCT
2399 SEQ 2D N0:3112 -9.2 -26.9 77.8 -15.5 -l.7 -12.4
CCATTGCAATCCACAGTGCT
2407 SEQ ID N0:3113 -9.2 -26.5 73.4 -16.3 -0.8 -9
ATTGGCAAATCTATACCAGC
2657 SEQ ID N0:3114 -9.2 -21.8 63.8 -11.9 -0.4 -4.4
CATGGCCATAAAGAGGGTAT
2789 SEQ ID N0:3115 -9.2 -22.6 65.1 -12.2 0 -10.4
AAATCCCAGTAAAGACCAGG
2859 SEQ ID N0:3116 -9.2 -21.9 62.2 -12.7 0 -3.6
GACCTCCATACAGTCCCACA
3314 SEQ ID N0:3117 -9.2 -28.6 77.9 -19.4 0 -3.3
CAATAAGGCACATGGTTTGG
3339 SEQ ID N0:3118 -9.2 -21.4 62.8 -12.2 0 -5.2
TCCAGTATTATTGGACATGC
3614 SEQ ID N0:3119 -9.2 -22.4 66.7 -12 -1.1 -7.9
GCAGGTTTTTCGAAGATTCC
4049 SEQ ID N0:3120 -9.2 -23.5 68.6 -13.6 -0.4 -6.8
ACAATGAAAGTCTCAAACCA
4090 SEQ ID N0:3121 -9.2 -18.5 55.8 -8.7 -0.3 -3.1
TTTGTCAGCATATTCTAGCA
4187 SEQ ID N0:3122 -9.2 -22.3 68.2 -12.1 -0.9 -4.1
GCTCCAACAAGAGCATTCAC
4444 SEQ ID N0:3123 -9.2 -23.8 68.4 -12.1 -2.5 -7.8
TTCTGTTCCTCTGTCATAAA
4921 SEQ ID N0:3124 -9.2 -21.9 66.4 -12.7 0 -1.8
AAAGGTCTCAAAGTTGAACA
5537 SEQ ID N0:3125 -9.2 -18.1 56.1 -8 -0.8 -6.5
AGCAGAGGTTGTAATTTGGA
5579 SEQ ID N0:3126 -9.2 -21.8 66.1 -12.6 0 -5.7
AGTTTAGAGAACTCTATAAA
5g90 SEQ ID N0:3127 -9.2 -16 52.6 -5.6 -1.1 -8
GAGTGGAGTTCCCATTTAGT
6315 SEQ ID N0:3128 -9.2 -25.1 74.4 -14.6 -1.2 -6.4
GGAGTGGAGTTCCCATTTAG
6316 SEQ ID N0:3129 -9.2 -25.1 73.5 -14.6 -l.2 -6
GTCTGGTTTTGTTACACTAT
6383 SEQ ID N0:3130 -9.2 -21.9 67.8 -12.7 0 -2.7
195
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAACTTTTCCTTGTCTGGTT
6395 SEQ ID N0:3131 -9.2 -22.4 67 -13.2 0 -3.5
CTCTTTTCCTTTGCTTTCTT
6434 5EQ ID N0:3132 -9.2 -24.3 73.2 -15.1 0 -3.6
GCTTCACAGAGTTGCAGTGA
6633 SEQ TD N0:3133 -9.2 -25 74.7 -14.5 -1.2 -7.2
CTGTTTCTTCAACGTAAACC
6916 SEQ ID N0:3134 -9.2 -20.8 61.4 -10.5 -1 -6.6
TAAAAATAATCCTTTAAATA
7139 SEQ ID N0:3135 -9.2 -11.4 42.2 -2.2 0 -4.3
GATTACTTTTTGGAAAGCAT
7231 SEQ ID N0:3136 -9.2 -18.8 57.9 -8.7 -0.7 -4.6
GCTGAGAGCAGAAGATGGCA
7329 SEQ ID N0:3137 -9.2 -24.6 71.1 -14 -1.3 -6.5
CAGCATAGGCAATATTAACA
7561 SEQ ID N0:3138 -9.2 -19.6 59 -8.8 -l.6 -6.7
GAATTCATTCTATCACCAAT
7633 SEQ ID N0:3139 -9.2 -19.5 59.2 -10.3 0 -6.7
GCAGGTTGAATTCATTCTAT
7640 SEQ ID N0:3140 -9.2 -21.2 64.6 -11.3 -0.4 -8.4
AAATTATTCTGCTTGACATA
7669 SEQ ID N0:3141 -9.2 -17.8 55.9 -8.6 0 -3.6
GCAAAATATGAAGAATAGGT
7797 SEQ ID N0:3142 -9.2 -16 51.1 -6.8 0 -3.4
AAACAAAAATTTATATCATG
8312 SEQ ID N0:3143 -9.2 -11.4 42.2 -2.2 0 -5.2
GTTTAGATGCTTATAGCCAA
8781 5EQ ID NO:3144 -9.2 -21.7 64.9 -11.2 -1.2 -4.6
TATACATAGGAGTTTATATA
8884 SEQ ID N0:3145 -9.2 -16.3 53.8 -7.1 0 -3.2
GCTTGGCTTCAGTTTTCTTG
236 SEQ ID N0:3146 -9.1 -24.8 74.9 -15.7 0 -4.4
CTCATCCCTGTCAAACCTTG
261 SEQ ID N0:3147 -9.1 -25.4 70.9 -16.3 0 -2.5
CTCCAGGTCCCTTCTGTGAA
369 SEQ ID N0:3148 -9.1 -28.2 79.2 -18.6 -0.2 -4.2
GCTTTGGTTTGTTCTCATCA
603 SEQ TD N0:3149 -9.1 -24.3 74 -15.2 0 -2.8
TGTCTCCATAAATAAATGGA
654 SEQ ID N0:3150 -9.1 -18 55.3 -6.8 -2.1 -7.5
TTCATTACTATAAAAGTTTT
733 SEQ ID N0:3151 -9.1 -14.9 50.1 -5.2 -0.3 -5.9
AAATATACAAGGCAGAGGTG
783 SEQ ID N0:3152 -9.1 -18.9 57.7 -9.8 0 -4
ACATTGCCCAGGTCCACAAA
1087 SEQ ID N0:3153 -9.1 -26.5 71.8 -17.4 0 -3.6
GCCACTGCAAACATTTATTC
1293 SEQ ID N0:3154 -9.1 -22 64 -12.1 -0.6 -4.7
TTGGGGGCCACTGCAAACAT
1299 SEQ ID N0:3155 -9.1 -26.5 72 -15.9 -1.4 -6.9
CTTCCAGTTAAATGTGCTCA
1400 SEQ ID N0:3156 -9.1 -22.7 67 -13.6 0 -5.6
AATGTCAACTGGTAAAGATT
1630 SEQ ID N0:3157 -9.1 -17.4 54.7 -8.3 0 -3.2
CATGTCTGTGCGGCACAAAC
2304 SEQ ID N0:3158 -9.1 -24.4 68.6 -12.7 -1.4 -13.2
GTTGTCCAGTAGGTGACGTT
2460 SEQ ID N0:3159 -9.1 -25.8 76 -15.6 -1 -5.4
196
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/mol'kcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CTTAACCTTCTCTTTCTGAC
2512 SEQ ID N0:3160 -9.1 -22.1 66.7 -13 0 -2.6
CTCCAGCATCTCCATTGAAA
2543 SEQ ID N0:3161 -9.1 -24.2 68.6 -15.1 0 -3.3
CACTGGTGGTTCCATTCCCA
3669 SEQ ID N0:3162 -9.1 -29 80 -18.7 -1.1 -6.4
ATCATTTTCATCGATTACGT
3719 SEQ ID N0:3163 -9.1 -20.3 61.1 -10.3 -0.7 -6.3
GCCTTCTTCTGTACTTACTT
4013 SEQ ID N0:3164 -9.1 -24.5 73.4 -15.4 0 -4.8
CTCAAACCAGTTGTGCTCAA
4079 SEQ ID N0:3165 -9.l -23.1 66.8 -13.3 -0.5 -6.4
TAGCCAGCACCAGGCATTAG
4277 SEQ ID N0:3166 -9.1 -27.1 75.8 -15.3 -2.7 -7.4
CCAACAGCACATTCATGATA
4473 SEQ ID N0:3167 -9.1 -21.8 63.3 -12.7 0 -6.4
GACCAACAGCACATTCATGA
4475 SEQ ID N0:3168 -9.1 -22.9 65.7 -13.8 0 -6.1
ACAGACCAACAGCACATTCA
4478 SEQ ID N0:3169 -9.l -23.2 66.4 -14.1 0 -4.1
TTTCTTGGATCCAAGTTTCT
4961 SEQ ID N0:3170 -9.1 -22.5 67.9 -9.7 -1.3 -15.5
GCTGGGCGAGGTATGGGTTT
4987 SEQ ID N0:3171 -9.1 -28.2 79.4 -19.1 0 -3.7
CAATTCCAGCTTCCTTTTTA
5511 SEQ ID N0:3172 -9.1 -23.4 68.2 -14.3 0 -4.5
GTTCTCCAGGATGACCGCGA
5771 SEQ ID N0:3173 -9.1 -28.3 76.2 -17.8 -1.3 -7.2
CTCTGCACTTTCTTCAGTAG
5801 SEQ ID N0:3174 -9.1 -23.4 71.8 -13.8 -0.1 -4.8
ATCTCAAAGTCATCCTCACT
5827 SEQ ID N0:3175 -9.1 -22.8 68 -13.7 0 -2.6
CGGCAGACACCTCCTCTTGT
6165 SEQ ID N0:3176 -9.1 -29 79.4 -19.4 -0.1 -4
ATATTTTTTAACCTTTGCTT
6220 SEQ ID N0:3177 -9.1 -19.3 59.5 -10.2 0 -3.6
TTGCCTCTTTGTTATAGTTA
6246 SEQ ID N0:3178 -9.1 -22 67.6 -12.9 0 -3
GTTTTTTCTGGAGTGGAGTT
6325 SEQ ID N0:3179 -9.1 -23.1 71.6 -14 0 -2.7
TTCCTTTGCTTTCTTTTTCT
6429 SEQ ID N0:3180 -9.1 -23.5 71.5 -14.4 0 -3.6
TGAGTATTTGTTAAAACAGT
6574 SEQ ID N0:3181 -9.1 -16.7 54 -7.6 0 -6.1
ATGAATAAACTATGAATTGG
6868 SEQ ID N0:3182 -9.1 -14.2 47.6 -5.1 0 -3.1
GACATAGCATTATGAATAAA
6879 SEQ ID N0:3183 -9.1 -15.7 50.8 -5.1 -1.4 -5
TGTATACTGTTTCTTCAACG
6922 SEQ ID N0:3184 -9.1 -19.9 61 -9.7 -1 -7.3
TCATTTGAGAGACAGGGTTC
6943 SEQ ID N0:3185 -9.1 -22.1 67.8 -13 0 -3.1
TTTCAAAATTAAAGCCATCT
7056 SEQ ID N0:3186 -9.1 -17.4 53.9 -8.3 0 -3.2
CTTTCAAAATTAAAGCCATC
7057 SEQ ID N0:3187 -9.1 -17.4 53.9 -8.3 0 -3.9
ATTGACATAGACTATCAGCT
7351 SEQ ID N0:3188 -9.1 -20.5 62.9 -11.4 0 -4.3
197
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATTAACATGCATTAGTGATA
7548 SEQ ID N0:3189 -9.1 -17.8 56.2 -8.7 0 -6.8
GAGCAGGTTGAATTCATTCT
7642 SEQ ID N0:3190 -9.1 -22.1 66.9 -12.3 -0.4 -8.4
ATTTAAACAAGTTTTAGACA
7825 SEQ ID N0:3191 -9.l -15.4 50.8 -5.6 -0.4 -5.5
AGGAAATTATCCATTGAAAA
7995 SEQ ID N0:3192 -9.1 -15.9 50.6 -4.6 -2.2 -7.2
AGCTTTAGTGCAGCAGGAAT
8222 SEQ ID N0:3193 -9.1 -23.9 70.7 -13.2 -1.5 -6.6
GCTCAATAATGACGTAGCTC
8436 SEQ ID N0:3194 -9.1 -21.7 64.1 -11.9 -0.5 -6.7
TCTCTTCTGCAGCACGTTTT
549 SEQ ID N0:3195 -9 -25.5 74.9 -16 0 -8.3
TTCTCTTCTGCAGCACGTTT
550 SEQ ID N0:3196 -9 -25.5 74.9 -16 0 -8.3
TTTCTCTTCTGCAGCACGTT
551 SEQ ID N0:3197 -9 -25.5 74.9 -16 0 -8.3
TTCTCATCATCATTATCTTG
592 SEQ ID N0:3198 -9 -19.9 62.8 -10.9 0 -1.6
CCATAAATAAATGGAAGGTT
649 SEQ ID N0:3199 -9 -16.9 52.4 -6.8 -1 -5.3
ATTACTATAAAAGTTTTCTT
730 SEQ ID N0:3200 -9 -15.1 50.7 -5.2 -0.8 -6.3
ATTCATTACTATAAAAGTTT
734 SEQ ID N0:3201 -9 -14.8 49.8 -5.2 -0.3 -4.3
CTTGGGGGCCACTGCAAACA
1300 SEQ ID N0:3202 -9 -27.4 73.8 -16.9 -1.4 -7.6
CATGGCCACCACAGCCAGGA
1727 SEQ ID N0:3203 -9 -30.5 80.3 -18.7 -2.8 -9.1
AGCTTCTTCCTGTTGCTTTT
1829 SEQ ID N0:3204 -9 -25.8 76.9 -16.3 -0.2 -4.3
TCCACTGAAATCTCTTGAAG
1874 SEQ ID N0:3205 -9 -20 60.2 -ll 0 -2.7
CTAACCCACCTACTCCACTG
1887 SEQ ID N0:3206 -9 -26.9 72.5 -17.9 0 -1.4
TTCTTTTGACGCTGTCTTCA
2055 SEQ ID N0:3207 -9 -23.7 70.6 -13.8 -0.8 -7.6
GAAGCTGCTTCTTTTGACGC
2063 SEQ ID N0:3208 -9 -24.4 70.3 -13.2 -1.2 -12.4
GGAAAACAGGGAGCCACGGA
2156 SEQ ID N0:3209 -9 -24.9 67.4 -15.3 -0.3 -4.3
TCCAGCATCTCCATTGAAAT
2542 SEQ ID N0:3210 -9 -23.3 66.7 -14.3 0 -4.1
GCAAAI~ATGAAGACGATGAT
3142 SEQ ID N0:3211 -9 -16.4 50.9 -7.4 0 -3.5
AGTCGTTCATGTGCCACCGT
3237 SEQ ID N0:3212 -9 -28.7 78.9 -19.7 0 -4.7
CACGCGGAACACAATCAGGA
3269 SEQ ID N0:3213 -9 -23.4 64.2 -13.9 0 -7.9
TTATTTTTCACATAATCAAT
3514 SEQ ID N0:3214 -9 -15.6 51.4 -6.6 0 -2.1
TAAAGTCTTCTTCGGGTTCA
3942 SEQ ID N0:3215 -9 -22.3 67 -12.6 -0.5 -3.8
TGATAGTCTTTCGCTGTTCA
4161 SEQ ID N0:3216 -9 -23.3 70.3 -14.3 0 -3.4
AAACATCAACGATCAAGAAA
4299 SEQ ID N0:3217 -9 -15.1 48.6 -6.1 0 -4.9
198
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAAGAAACATCAACGATCAA
4303 5EQ ID N0:3218 -9 -15.1 48.6 -6.1 0 -4.9
GGCTCTTAGAGGTCTTAAAG
4394 SEQ TD N0:3219 -9 -21.7 66.3 -12.1 -0.3 -5.3
GCACATTCATGATAGAGGGA
4467 SEQ ID N0:3220 -9 -22.5 66.8 -13.5 0 -6.4
TACTTTCACGTTTTTCCACC
4646 SEQ TD N0:3221 -9 -24 69.2 -15 0 -4.7
CCTCCAAACTTCTTTTTCTG
4891 SEQ ID N0:3222 -9 -22.8 66.5 -13.8 0 -1.8
CAGATGAGGATCATGATGCT
5062 SEQ ID N0:3223 -9 -22.1 65.6 -11 -2.1 -8.5
TTTCCACCATCATGGTGACC
5091 SEQ ID N0:3224 -9 -26.5 74 -13.8 -3.7 -11.1
TCAGCACAAATTCTCCAGTG
5178 5EQ ID N0:3225 -9 -22.8 66.9 -13.3 -0.2 -4.5
CCTTTGATCAGACGTAGGAT
5362 SEQ ID N0:3226 -9 -23.1 67.1 -14.1 0 -6.5
GAGCAGGAGGCCGATGTTAA
5438 SEQ ID N0:3227 -9 -25.6 71.6 -15.7 -0.8 -7.7
GGACATCCCAAAGATGGCAT
5477 SEQ ID N0:3228 -9 -24.7 68.3 -13.4 -2.3 -8
AGATCATGCTGTTGCCAAAG
5553 5EQ ID N0:3229 -9 -22.8 66.2 -12.9 -0.8 -6.6
TTAATTGCCTCTTTGTTATA
6250 SEQ ID N0:3230 -9 -20.1 61.8 -11.1 0 -3
TCCTTTGCTTTCTTTTTCTG
6428 5EQ ID N0:3231 -9 -23.4 70.9 -14.4 0 -3.6
TGGGTTTCTCCTCAGCAGTG
6699 SEQ ID N0:3232 -9 -27.2 80.3 -17.3 -0.8 -5.7
TTGGGGACCATGGAAATGCA
6852 SEQ ID N0:3233 -9 -24.1 67 -12.7 -2.4 -9.9
GAATTGGGGACCATGGAAAT
6855 SEQ ID N0:3234 -9 -21.5 61.4 -10.1 -2.4 -8.8
CAATACTTTAGATATATTTT
7269 SEQ ID N0:3235 -9 -15 50.4 -6 0 -4.3
TGCTGAGAGCAGAAGATGGC
7330 SEQ ID N0:3236 -9 -23.9 69.8 -13 -1.9 -6.5
GTCCATGTTATATTTGTAAT
8242 SEQ ID N0:3237 -9 -19.4 60.4 -10.4 0 -4.3
TTTTTAGCAATAGCAATTCC
8409 SEQ ID N0:3238 -9 -19.9 60.5 -9.2 , -1.7 -4.6
AGCTATTGTAGGTGGTTACT
8741 SEQ ID N0:3239 -9 -23.1 70.8 -13.6 -O.l -4.4
TGACAGGTATCTCATCCCTG
271 SEQ ID N0:3240 -8.9 -25.3 73.2 -14.6 -1.8 -6.1
CACATTTAATTACGTGTAGC
440 SEQ ID N0:3241 -8.9 -19.5 59.4 -10.6 0 -5
AGTAAAAAGGCGGAAGCTTT
506 5EQ ID N0:3242 -8.9 -19.9 58.6 -8.6 -2.4 -7.2
TCATCATCATTATCTTGTTC
589 SEQ ID N0:3243 -8.9 -20.2 64.1 -11.3 0 -1.9
AGCTTCCAAGTCACTATTTG
623 SEQ ID N0:3244 -8.9 -22.5 67.4 -13.6 0 -4.3
AATATACAAGGCAGAGGTGG
7g2 SEQ ID N0:3245 -8.9 -20.8 62.2 -11.9 0 -4
AAATACACAGTTGGTCAAAA
884 SEQ ID N0:3246 -8.9 -16.8 52.9 -7.9 0 -3.8
199
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GGTTGCTCAAGGTCATAAAT
900 SEQ ID N0:3247 -8.9 -21.4 64 -12.5 0 -3.6
AGGAGGGTTGCTCAAGGTCA
905 SEQ TD N0:3248 -8.9 -26.1 76.9 -15.2 -2 -4.7
GTCCAGTCAGGAGGGTTGCT
913 SEQ ID N0:3249 -8.9 -28.8 84.6 -18.4 -1.4 -5.9
GTGACTCAAAGGTATAGATT
960 SEQ ID N0:3250 -8.9 -19.1 59.5 -10.2 0 -3.1
AAATTGTTTTCAGTGCTCGG
1134 SEQ ID N0:3251 -8.9 -21.6 64.3 -12.7 0 -4.5
GAGCAAACACGCTCAGACAG
1239 SEQ ID N0:3252 -8.9 -22.9 65.3 -11.5 -2.5 -7.8
ACACAGATGTATCCTTCTGG
1510 SEQ ID N0:3253 -8.9 -23.2 68.8 -12.7 -1.6 -5.3
TTGTTCTGCTTCTTCCAAGG
1772 SEQ ID N0:3254 -8.9 -24.5 72.5 -15.1 -0.1 -3.6
GAAGCCCTGGCACCATCCTG
2367 SEQ ID N0:3255 -8.9 -30.5 80 -20.7 -0.7 -8.2
ACACATTGGCAAATCTATAC
2661 SEQ ID N0:3256 -8.9 -19.1 58.2 -10.2 0 -4.4
AACCATGCATCACAGCAGTC
2692 SEQ ID N0:3257 -8.9 -24.8 71.3 -15 -0.7 -7.5
CACAAGATGTTTTACTTTTA
2711 SEQ ID N0:3258 -8.9 -17.8 56.5 -8.9 0 -3
AAACTCTAAGCAGTCTGAAT
3027 SEQ ID N0:3259 -8.9 -18.9 58.2 -10 0 -4.1
TCCTAGAGCCCCCACAGAAT
3101 SEQ ID N0:3260 -8.9 -28.9 76.7 -20 0 -3.8
AAGGTGAGGTTTCCTAGAGC
3112 SEQ ID N0:3261 -8.9 -24.3 72.5 -14.7 -0.5 -4.4
ACTGGTGGTTCCATTCCCAT
3668 SEQ ID N0:3262 -8.9 -28.3 79 -18.2 -1.1 -6.6
CTGGGGTTGTTTATGAATGA
3745 SEQ ID N0:3263 -8.9 -21.4 64.2 -12.5 0 -1.8
CTTCAAAGGCCAATGCACCA
4131 SEQ ID N0:3264 -8.9 -25.1 68.5 -14.7 -1.4 -7.7
CAACGATCAAGAAATCTAGC
4293 SEQ ID N0:3265 -8.9 -18 54.9 -9.1 0 -4.9
ATGTCCGTAATGATTTGATG
4368 SEQ ID N0:3266 -8.9 -20 59.9 -11.1 0 -2.3
CAGACCAACAGCACATTCAT
4477 SEQ ID N0:3267 -8.9 -23 65.9 -14.1 0 -4.1
ACTTGCCAGCAAACAAATTC
4533 SEQ ID N0:3268 -8.9 -20.8 60.5 -11.9 0 -7.4
GTACAGATTTTCTTCATATA
4781 SEQ ID NO:3269 -8.9 -18.6 59.6 -9.7 0 -4.6
TGTTTGCTGGGCGAGGTATG
4992 SEQ ID N0:3270 -8.9 -25.8 73.8 -16.9 0.1 -4
GATGAGGATCATGATGCTGA
5060 SEQ ID N0:3271 -8.9 -22 65.4 -11 -2.1 -8.5
CATGGTGACCATGTTGAGGC
5081 SEQ ID N0:3272 -8.9 -25.5 73 -14 -2.6 -10.3
GCTCTGCACTTTCTTCAGTA
5802 SEQ ID N0:3273 -8.9 -25.2 76.3 -15.8 -0.1 -4.8
AGAACTCTATAAACTGGGTC
5883 SEQ ID N0:3274 -8.9 -19.4 59.8 -10.5 0 -2.6
ATCAGAGAGTTTAGAGAACT
5897 SEQ ID N0:3275 -8.9 -19 60.2 -8.6 -1.4 -5.5
200
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Tntra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGGGCAGATCCATGGCAATA
5973 SEQ ID N0:3276 -8.9 -25.3 71 -15.4 -0.9 -8
AATGATAGCGGCAGACACCT
6173 SEQ ID N0:3277 -8.9 -24.5 68.2 -15.6 0 -6.6
ATAGGTAAGTCAATCCTCCC
6271 SEQ ID N0:3278 -8.9 -24.4 70.5 -15 -0.2 -3.5
TAGAATGGATGCAAGGACTG
6787 SEQ ID N0:3279 -8.9 -20.1 60.1 -11.2 0 -5.6
CCATTACAATTCTTTTTCTG
7009 SEQ TD N0:3280 -8.9 -19.8 60.5 -10.9 0 -2.5
CTGTTCAGATAGAAACAAAC
7093 SEQ ID N0:3281 -8.9 -16.5 52.7 -6.8 -0.6 -4.1
ACTGTTCAGATAGAAACAAA
7094 SEQ ID N0:3282 -8.9 -16.5 52.7 -6.8 -0.6 -5.6
AACTGTTCAGATAGAAACAA
7095 SEQ TD N0:3283 -8.9 -16.5 52.7 -6.8 -0.6 -5.6
TTAGAGGAGACTTTACAGGC
7119 SEQ ID N0:3284 -8.9 -21.7 66.2 -11.9 -0.7 -5.4
CTTTAAATATTAGAGGAGAC
7128 SEQ ID N0:3285 -8.9 -16.1 52.6 -7.2 0 -4.3
TTTGACCTAAATTAAATATA
7212 SEQ ID N0:3286 -8.9 -14 47.3 -5.1 0 -3.2
GTTCATGGCTAAAAAGAACA
8264 SEQ ID N0:3287 -8.9 -18 55.2 -7.7 -1.3 -5.7
ATTCTTTTGGCTCAATAATG
8445 SEQ ID N0:3288 -8.9 -19 58.8 -10.1 0 -5.3
AATTATATTGAAAGAAGATG
8802 SEQ ID N0:3289 -8.9 -12.6 44.7 -3.7 0 -2.3
CAATTATATTGAAAGAAGAT
8803 SEQ ID N0:3290 -8.9 -13.3 46 -3.7 -0.4 -3.4
TTTCTCTGTGGATAAGAAAA
48 SEQ TD N0:3291 -8.8 -17.3 54.8 -7.4 -1 -4.5
GCTCCAGGTCCCTTCTGTGA
370 SEQ ID N0:3292 -8.8 -30.7 86.5 -21.4 -0.2 -4
GATTCTCTAGTAAAAAGGCG
514 SEQ ID N0:3293 -8.8 -18.9 57.5 -10.1 0 -4
TTGGGCTTCTTGGCTTTCTC
565 SEQ ID N0:3294 -8.8 -26.5 78.9 -16.7 -0.9 -3.7
GCTTCCAAGTCACTATTTGG
622 SEQ ID N0:3295 -8.8 -23.7 69.8 -13.6 -1.2 -5.2
TATACAAGGCAGAGGTGGCA
780 SEQ ID N0:3296 -8.8 -24 69.8 -14.3 -0.8 -4.1
AAATCTTGATAGCAATTTTC
825 SEQ ID N0:3297 -8.8 -16.8 54 -7.5 -0.1 -0.3
CTCAGATTGCCCATGAACAG
1273 SEQ ID N0:3298 -8.8 -24 67.9 -15.2 0 -4.5
CCAAGGTGGCCTGATTCTGC
1758 SEQ ID N0:3299 -8.8 -28.1 77.8 -18.6 -0.4 -7.2
TTTTTTGTCACTGGTCAGTC
2105 SEQ ID N0:3300 -8.8 -23 71.8 -14.2 0 -6.6
ACTGATGAGGGGAGCAGAAT
2124 SEQ ID N0:3301 -8.8 -22.9 66.9 -13.4 -0.5 -4.1
AAATGCTTGTTTTGCTATTG
2184 SEQ ID N0:3302 -8.8 -19.4 59.6 -9.9 -0.4 -4.3
GCTATGCTCACGGCTCTTTG
2578 SEQ ID N0:3303 -8.8 -26.6 75.7 -17.1 -0.4 -4.7
TAACCATGCATCACAGCAGT
2693 SEQ ID N0:3304 -8.8 -24.1 69.1 -14 -1.2 -6.4
201
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ACATTTGACAGACCAAGCTC
2983 SEQ ID N0:3305 -8.8 -22.5 65.8 -13.7 0 -5
CACATTTGACAGACCAAGCT
2984 SEQ ID N0:3306 -8.8 -22.8 65.5 -14 0 -4.8
AATGATCGCAGTACAGACAA
3010 SEQ ID N0:3307 -8.8 -20.2 59.9 -10.7 -0.4 -5.7
TGAGGTTTCCTAGAGCCCCC
3108 SEQ ID N0:3308 -8.8 -30.6 83.1 -21.1 -0.5 -4.4
TAATCAATTCCCTTTTGCAT
3502 SEQ ID N0:3309 -8.8 -21.6 63.1 -12.8 0 -5.1
ATAATTAAGCTCTTTGCTTA
3641 SEQ ID N0:3310 -8.8 -18.8 58.8 -7.5 -2.5 -8
CATTTTCATCGATTACGTAT
3717 SEQ ID N0:3311 -8.8 -19.6 59.2 -9.9 -0.7 -6.3
ACAGCAATTGGCACTGTGAC
3772 SEQ ID N0:3312 -8.8 -23.6 68.4 -13.2 -1.5 -8.7
TCTTAGAGGTCTTAAAGCTC
4391 SEQ TD N0:3313 -8.8 -20.9 65.2 -12.1 0.7 -5
AACAGCACATTCATGATAGA
4471 SEQ ID N0:3314 -8.8 -19.7 59.9 -10.9 0 -6.4
AATGTCAAACATGTTACCCG
4577 SEQ ID N0:3315 -8.8 -21.1 60.4 -11.1 -1.1 -9
CAGTGCAAGATAGCCAGCGC
4682 SEQ TD N0:3316 -8.8 -26.9 74.4 -17.2 -0.7 -7.3
TCCTCTGTCATAAAGATGTC
4915 SEQ ID N0:3317 -8.8 -21.4 65.2 -11.9 -0.4 -3.1
CTGGTCATCCGTTTCCACCA
5102 SEQ TD N0:3318 -8.8 -29 79 -19 -1.1 -5.4
TGCCCTGGTCATCCGTTTCC
5106 SEQ ID N0:3319 -8.8 -31.2 83.9 -21.2 -1.1 -4.4
AGTAGTAGTGTCTGAGGGAA
5205 SEQ ID N0:3320 -8.8 -22.4 69.6 -13.6 0 -2.9
CAACAGATGGGTCCCCACGG
5691 SEQ ID N0:3321 -8.8 -28.4 74.6 -18.7 -0.6 -8.8
CCACAACCAGGAAGGATATG
5739 SEQ ID N0:3322 -8.8 -22.4 63.3 -12.8 -0.6 -4.4
GAGTTTAGAGAACTCTATAA
5891 SEQ ID N0:3323 -8.8 -17.3 55.9 -5.6 -2.9 -8.5
GCCATAAACCTGTCTTCCAT
6091 SEQ ID N0:3324 -8.8 -25.6 71.1 -16.8 0 -2
ATAGGAAGGAGGAGGGGTGG
6362 SEQ ID N0:3325 -8.8 -24.4 71.1 -15.6 0 -0.9
TCTGGTTTGTCTTTCTCAAA
6412 SEQ ID N0:3326 -8.8 -21.6 66.6 -12.3 -0.2 -6.4
TACTAAAGGTGTTTGGTGTA
6767 SEQ ID N0:3327 -8.8 -20.2 62.5 -10.5 -0.8 -6.2
ACTGTACTAAAGGTGTTTGG
6771 SEQ ID N0:3328 -8.8 -20.4 62.5 -11.6 0 -5.1
TATACTGTTTCTTCAACGTA
6920 SEQ ID N0:3329 -8.8 -19.6 60,5 -9.7 -1 -5.3
TAACTGTTCAGATAGAAACA
7096 SEQ ID N0:3330 -8.8 -16.9 53.9 -7.4 -0.5 -5.6
TTGACCTAAATTAAATATAG
7211 SEQ ID N0:3331 -8.8 -13.9 47.1 -5.1 0 -3.2
GCATTTGACCTAAATTAAAT
7215 SEQ ID N0:3332 -8.8 -17.1 53.1 -7,7 -0.3 -4.8
CTAGAATGGATTTATTAGAT
7248 SEQ ID N0:3333 -8.8 -16.6 53.7 -7.8 0 -3
202
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ACCAATATGTGACATTCTTT
7619 SEQ ID N0:3334 -8.8 -20.2 61 -11.4 0 -3.9
ATGTTGAATTAAAAGTGCAA
7715 SEQ ID N0:3335 -8.8 -15.9 51.1 -7.1 0 -5.4
TAGCTTTAGTGCAGCAGGAA
8223 SEQ ID N0:3336 -8.8 -23.6 70.1 -13.,2 -l.5 -6.6
TACAGTAAATAGTTTTGTAA
8366 SEQ ID N0:3337 -8.8 -15.5 51.6 -6.7 0 -4.1
TTCTTCAATACACTACAGTA
8379 SEQ ID N0:3338 -8.8 -19.1 59.9 -10.3 0 -3.4
AAACCCCAGAGCCCAATAAG
8490 SEQ ID N0:3339 -8.8 -24.9 66.1 -16.1 0 -3.2
TTATTAGCCACCAAGTAATT
8835 SEQ ID N0:3340 -8.8 -20.6 61.1 -11.8 0 -3.2
TGGGAGAATTATGAAATACA
9055 SEQ ID NO:3341 -8.8 -16.5 52.3 -7.7 0 -3.2
TCTGTGAATTATCTCATTTA
357 SEQ ID N0:3342 -8.7 -18.5 58.9 -9.8 0.4 -3.2
TTCCGGAAAAGCTCCAGGTC
380 SEQ ID NO:3343 -8.7 -25.6 70.9 -15 -1.9 -9.8
ATAAATAAATGGAAGGTTCT
647 SEQ ID NO:3344 -8.7 -15.5 50.5 -6.8 0 -4.2
ATCCAGGTCCTCCAGGGGCT
695 SEQ ID N0:3345 -8.7 -32.2 88.8 -22.1 -1.3 -8.4
TTATTCATTACTATAAAAGT
736 SEQ ID N0:3346 -8.7 -14.4 49 -5.2 -0.1 -2.7
TTGTCCAGTCAGGAGGGTTG
915 SEQ ID N0:3347 -8.7 -26.2 77.8 -16.1 -1.3 -5.3
TCTTCTAAGCAAAACCCTCT
997 SEQ ID N0:3348 -8.7 -22.5 64.7 -13.8 0 -4.1
GAGAGCAAACACGCTCAGAC
1241 SEQ ID N0:3349 -8.7 -22.8 65.4 -10.8 -3.3 -8.5
AGATGTATCCTTCTGGACAC
1506 SEQ ID N0:3350 -8.7 -23.1 69 -13 -1.3 -5.8
CTTCACACAGATGTATCCTT
1514 SEQ ID N0:3351 -8.7 -22.8 67.8 -13.4 -0.5 -3.7
CTTGAGTCATGAGTCGAAAT
1599 SEQ ID N0:3352 -8.7 -20.1 60.7 -9.7 0 -11.6
TAATGTCAACTGGTAAAGAT
1631 SEQ ID N0:3353 -8.7 -17 53.9 -8.3 0 -3.2
CTCCTTTGTTGTTTCCTTCA
2007 SEQ ID NO:3354 -8.7 -25.6 75.7 -16.9 0 -1.7
TCTCTCTCCTTTGTTGTTTC
2012 SEQ ID N0:3355 -8.7 -24.5 76.1 -15.8 0 0
CAGTCTGTTTCCATCCATGG
2090 SEQ ID N0:3356 -8.7 -26 75.3 -16.6 -0.5 -7.7
GTCAGTCTGTTTCCATCCAT
2092 SEQ ID N0:3357 -8.7 -26.4 78.2 -17.7 0 -3.6
GGTGCCCTCTGGGGGAAGTT
2477 SEQ ID NO:3358 -8.7 -30.4 83.9 -19.5 -2.2 -8.7
AGCTTAACCTTCTCTTTCTG
2514 SEQ ID N0:3359 -8.7 -23.1 69.4 -14.4 0 -4.3
TTGGCAAATCTATACCAGCA
2656 SEQ ID N0:3360 -8.7 -22.5 64.9 -13.1 -0.5 -4.6
GGGTATTTAAGACAATGCAA
2775 SEQ ID NO:3361 -8.7 -19.1 58 -9.9 -0.1 -5.6
ACCAGGTTTCCTACAGTCAA
2845 SEQ ID NO:3362 -8.7 -25 72.4 -15.8 -0.1 -4.9
203
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGTAAAGACCAGGTTTCCTA
2852 SEQ ID N0:3363 -8.7 -22.6 66.6 -13.4 -0.1 -5.9
CCATCAAAGATATTCCAGCC
2938 SEQ ID N0:3364 -8.7 -23.7 66.7 -14.3 -0.4 -3.8
ACTTGAAAACTCTAAGCAGT
3033 SEQ ID N0:3365 -8.7 -18.8 57.8 -10.1 0 -4.1
CCACAGAATTGCCAATGATC
3090 SEQ ID N0:3366 -8.7 -22.4 63.7 -13.7 0 -3.9
GCTAAATGAACTCAATAATA
3416 SEQ ID N0:3367 -8.7 -15.1 49.4 -6.4 0 -3.9
ATAGTCTTTCGCTGTTCAAT
4159 SEQ TD N0:3368 -8.7 -22 66.6 -13.3 0 -3.1
CACCCTCATGCCTTCAAACC
4421 SEQ TD N0:3369 -8.7 -27.6 73.5 -18.9 0 -4.4
GGAATTGCTCCAACAAGAGC
4450 SEQ ID N0:3370 -8.7 -22.9 65.6 -12.1 -2.1 -7.7
TTTCACGTTTTTCCACCGAG
4643 SEQ ID N0:3371 -8.7 -24.6 68.9 -15.9 0 -4.7
TGATGCTGATATCAAAGACT
5049 SEQ ID N0:3372 -8.7 -l9 58.2 -9.6 -0.4 -7.7
GTTTCCACCATCATGGTGAC
5092 SEQ ID N0:3373 -8.7 -25.7 73.8 -13.8 -3.2 -10.6
AGAGTTTAGAGAACTCTATA
5892 SEQ ID N0:3374 -8.7 -18 58.1 -5.6 -3.7 -9.1
TCAGAGAGTTTAGAGAACTC
5896 SEQ ID N0:3375 -8.7 -19.4 61.7 -8.6 -2.1 -7.6
GAGGATCCAGGGCAGCTGCA
5919 SEQ ID N0:3376 -8.7 -29.6 82.5 -18 -1 -14
TAATAGGCTCATAAGAGACT
6126 SEQ ID N0:3377 -8.7 -19 58.9 -8.9 -1.3 -5.2
TAGCGGCAGACACCTCCTCT
6168 SEQ ID N0:3378 -8.7 -29.2 79.8 -20 -0.1 -6.6
TCAAACTTTTCCTTGTCTGG
6397 SEQ ID N0:3379 -8.7 -22.2 66.1 -13.5 0 -2.9
TTTACTTTTGATTTTCTCTG
6456 SEQ ID N0:3380 -8.7 -18.8 60.1 -10.1 0 -2.2
GTTTCTTTTTACTTTTGATT
6463 SEQ TD N0:3381 -8.7 -18.9 60.6 -10.2 0 -2.2
CTCTTGAAGTCCAGTTGACA
6536 SEQ ID N0:3382 -8.7 -23.3 69.2 -12.8 -1.8 -5.1
TCCTCTTGAAGTCCAGTTGA
6538 SEQ ID N0:3383 -8.7 -24.8 72.9 -16.1 0 -3
TAGGCACTGACTATGAGTAT
6587 SEQ ID N0:3384 -8.7 -21.4 65 -10.5 -2.2 -7.3
ATAGGCACTGACTATGAGTA
6588 SEQ ID N0:3385 -8.7 -21.4 65 -10.5 -2.2 -7.3
TATAGGCACTGACTATGAGT
6589 SEQ ID N0:3386 -8.7 -21.4 65 -10.5 -2.2 -7.3
TGTCTTGTATAGGCACTGAC
6596 SEQ TD N0:3387 -8.7 -22.8 69.3 -13.2 -0.8 -4.7
CATTGGGTTTCTCCTCAGCA
6702 SEQ ID N0:3388 -8.7 -26.8 77.9 -17.6 -0.1 -4.1
AACTATCCCTATAGTCTAGG
6726 SEQ ID N0:3389 -8.7 -22.2 66.3 -11.5 -2 -7.6
ACATAGCATTATGAATAAAC
6878 SEQ ID N0:3390 -8.7 -15.3 50.1 -5.1 -1.4 -5
TTCAAAATTAAAGCCATCTA
7055 SEQ ID N0:3391 -8.7 -17 53.1 -8.3 0 -3.2
204
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGTTCAGATAGAAACAAACA
7092 SEQ ID N0:3392 -8.7 -16.3 52.1 -6.9 -0.5 -4.4
TAACCAAGACTTGTGAAGAA
7600 SEQ ID N0:3393 -8.7 -18 55.1 -8.8 -0.2 -5.4
ATTTATATTTAAACAAGTTT
7831 SEQ ID N0:3394 -8.7 -13.7 47.4 -4.4 -0.3 -5.3
ATTTTCTTATGTACAAAATG
7883 SEQ ID N0:3395 -8.7 -15.1 50.2 -6.4 0 -6.8
TTTTATTTTAGGAAATTATC
8004 SEQ ID N0:3396 -8.7 -14.6 49.7 -5.1 -0.6 -4.4
TAACTTTTATTTTAGGAAAT
8008 SEQ ID N0:3397 -8.7 -14.5 49 -5.1 -0.4 -4.6
CATTATCTAACTTTTATTTT
8015 SEQ ID N0:3398 -8.7 -16.2 53.3 -7.5 0 -1.6
CTTTAGTGCAGCAGGAATTA
8220 SEQ ID N0:3399 -8.7 -21.9 65.8 -13.2 0 -6.6
TTCTTTTGGCTCAATAATGA
8444 SEQ ID N0:3400 -8.7 -19.6 60.1 -10.3 -0.3 -5
TAGTTTGTTGTAAAATTCAT
8601 SEQ ID N0:3401 -8.7 -16.4 53.6 -7 -0.4 -4.4
AAACCTGAAAGTTGGAACAT
8709 SEQ ID N0:3402 -8.7 -18.2 54.9 -8.7 -0.6 -4.8
ATAACGTGTCTTCCTCTGGC
142 SEQ ID N0:3403 -8.6 -25.4 73.3 -16.8 0 -5.3
TGGCTTCAGTTTTCTTGCTC
233 SEQ ID N0:3404 -8.6 -25.1 76.4 -15.8 -0.4 -3.7
GACAGGTATCTCATCCCTGT
270 SEQ ID N0:3405 -8.6 -26.5 77 -15 -2.9 -8.3
AAAGTTTTCTTATTGATATA
721 SEQ ID N0:3406 -8.6 -15.3 51.3 -5.6 -1 -4.6
TATTCATTACTATAAAAGTT
735 SEQ ID N0:3407 -8.6 -14.4 49 -5.2 -0.3 -2.8
CCCCCACAATGGTCTTTAAA
1167 SEQ ID N0:3408 -8.6 -25.1 67.9 -15.6 -0.7 -5.2
GCCTGATTCTGCTCCTCATA
1750 SEQ ID N0:3409 -8.6 -27.5 78.3 -18.9 0 -3.6
ATAATTAAGCTCTTTGCTTA
1832 SEQ ID N0:3410 -8.6 -27 79 -17.7 -0.5 -5.2
TCAGTCTGTTTCCATCCATG
2091 SEQ ID N0:3411 -8.6 -25.2 74.3 -16.6 0 -3.9
GAATTTTTTGTCACTGGTCA
2108 SEQ ID N0:3412 -8.6 -21.3 65.2 -12.7 0 -3.3
CAGTGCTGTGCATCTTCCCA
2394 SEQ ID N0:3413 -8.6 -28.8 81.3 -19.1 -1 -5.9
TTAACCTTCTCTTTCTGACT
2511 SEQ ID N0:3414 -8.6 -22.1 66.7 -13.5 0 -2.6
GAGCTTAACCTTCTCTTTCT
2515 SEQ ID N0:3415 -8.6 -23.7 70.9 -15.1 0 -5.2
AATTCACAAGATGTTTTACT
2715 SEQ TD N0:3416 -8.6 -17.6 55.8 -9 0 -4
TTCCATCAAAGATATTCCAG
2940 5EQ ID N0:3417 -8.6 -20.4 60.9 -11.1 -0.4 -3.9
TTGCCAATGATCTTAATTAG
3082 SEQ ID N0:3418 -8.6 -18.7 57.4 -10.1 0 -4.9
CTTATTTTTCACATAATCAA
3515 SEQ ID N0:3419 -8.6 -16.5 53.3 -7.9 0 -2.2
GTCTATCTTATTGCCTTCAT
3590 SEQ ID N0:3420 -8.6 -23.3 70.5 -14.7 0 -3
205
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TAAGATAATTAAGCTCTTTG
3645 SEQ ID N0:3421 -8.6 -15.9 52.1 -6.8 -0.1 -6.1
ACTACTGAGAAGGATCATGA
4112 SEQ ID N0:3422 -8.6 -19.9 60.7 -10.4 -0.8 -7.8
TCTTTCGCTGTTCAATGTAT
4155 SEQ ID N0:3423 -8.6 -22 66.2 -13.4 0 -3.1
CTTAAAGCTCTTAATGTCCG
4381 SEQ ID N0:3424 -8.6 -20.8 61.3 -12.2 0 -5.9
CAAGAGCATTCACAACCACC
4437 SEQ ID N0:3425 -8.6 -23.6 66.2 -14.4 -0.3 -3.3
GGTAGAACTTGCCAGCAAAC
4539 SEQ ID N0:3426 -8.6 -23 65.9 -13.9 -O.l -7.5
TGATAAAGATGACAAAGTAT
4809 SEQ TD N0:3427 -8.6 -14.5 48.4 -5.9 0 -2.8
TCTTCATTGCATTGTAATAT
4944 SEQ ID N0:3428 -8.6 -19.1 59.7 -10.5 0 -6.2
ACCATCATGGTGACCATGTT
5086 SEQ ID N0:3429 -8.6 -25.2 71.6 -14 -2.6 -10.9
CACCATCATGGTGACCATGT
5087 SEQ ID N0:3430 -8.6 -25.8 72.3 -14 -3.2 -11.5
ATCCGTTTCCACCATCATGG
5096 SEQ ID N0:3431 -8.6 -26.9 73.8 -17.4 -0.8 -5.5
GTCTCAAAGTTGAACATGTC
5533 SEQ ID N0:3432 -8.6 -19.9 61.6 -11.3 0 -7
AAGCAGATCATGCTGTTGCC
5557 SEQ ID N0:3433 -8.6 -25.3 72.7 -13.9 -2.8 -10.6
GGGGCTCTGCACTTTCTTCA
5805 SEQ ID N0:3434 -8.6 -27.9 81.2 -19.3 ~ 4.6 -4.8
ACTTTTCCCAAACCTCATAG
5850 SEQ ID N0:3435 -8.6 -23 65.6 -14.4 0 -1.7
TTGGGTTTTGCTATGAGAAG
5941 5EQ ID N0:3436 -8.6 -20.9 63.6 -12.3 0 -3.6
AGGAACTCCCATCTGTTTTT
6339 SEQ ID N0:3437 -8.6 -24.2 70.3 -14.6 -0.9 -5.1
TTGTCTGGTTTTGTTACACT
6385 SEQ TD N0:3438 -8.6 -22.3 68.7 -13.7 0 -2.9
TTCTCAAACTTTTCCTTGTC
6400 SEQ ID N0:3439 -8.6 -21.5 65.5 -12.9 0 -2.8
TCTCCTCAGCAGTGTCAGCT
6693 SEQ ID N0:3440 -8.6 -28.4 84.6 -19 -0.6 -4.6
TTCTCCTCAGCAGTGTCAGC
6694 SEQ ID N0:3441 -8.6 -27.6 82.8 -l9 0 -4.2
ATTGGGTTTCTCCTCAGCAG
6701 SEQ ID N0:3442 -8.6 -26.1 77.1 -16.6 -0.8 -4.9
GCAAAACACCTTTGTCTGAT
6962 SEQ ID N0:3443 -8.6 -21.7 63.1 -11.7 -1.3 -5.9
ATTAAAGCCATCTAGAAAAT
7049 SEQ ID N0:3444 -8.6 -16.4 51.8 -7.8 0 -6.2
TATAGAGCTCTGAAACTTAG
7196 SEQ ID N0:3445 -8.6 -18.1 57.2 -8.5 0 -10
TTCTAGAATGGATTTATTAG
7250 SEQ ID N0:3446 -8.6 -16.5 54 -7.9 0 -7.2
GTTGAATTAAAAGTGCAAAA
7713 SEQ ID N0:3447 -8.6 -14.5 48 -5.9 0 -5,4
AACTTTTATTTTAGGAAATT
8007 SEQ ID N0:3448 -8.6 -14.9 49.8 -5.5 -0.6 -4.6
AATGAAATTTATTCTTTTGG
8455 SEQ ID N0:3449 -8.6 -15.3 50.6 -5.6 -1 -5.2
206
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Tnter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ACATAGGAGTTTATATAATG
8881 SEQ TD N0:3450 -8.6 -16.2 53 -7.6 0 -5.5
AAGAGACCTTTCCAGAATCC
26 SEQ ID N0:3451 -8.5 -23.2 66.6 -14.7 0 -2.9
GTCCCTTCTGTGAATTATCT
363 SEQ ID N0:3452 -8.5 -24.1 71.1 -15.1 -O.l -3.2
CATAAATAAATGGAAGGTTC
648 SEQ ID N0:3453 -8.5 -15.3 49.9 -6.8 0 -3.3
TTACTATAAAAGTTTTCTTA
729 SEQ TD N0:3454 -8.5 -14.8 50.1 -5.2 -1 -6.3
TGTCCAGTCAGGAGGGTTGC
914 SEQ ID N0:3455 -8.5 -27.9 82.2 -18 -1.3 -5.3
CACATATGCCATCACAATGA
1061 SEQ ID N0:3456 -8.5 -21.7 62.7 -12.5 -0.5 -8.3
TTTTCAGTGCTCGGAGAACT
1128 SEQ ID N0:3457 -8.5 -23.3 68.5 -14 -0.6 -6.4
CCATTTCCACAGAGTAAAGG
1471 SEQ ID N0:3458 -8.5 -22.2 64.4 -13.7 0 -3.3
ATGTATCCTTCTGGACACTG
1504 SEQ ID N0:3459 -8.5 -23.4 69.2 -14.9 1.5 -5.8
GATGTATCCTTCTGGACACT
1505 SEQ ID N0:3460 -8.5 -24 70.7 -15.5 l.5 -5.9
GGTAAAGATTTTCCCAATAG
1620 SEQ TD N0:3461 -8.5 -19.7 59.1 -11.2 0 -3.3
CATGTATGTTTTCCCAGCAG
1655 SEQ ID N0:3462 -8.5 -24.7 71.7 -16.2 0 -4.1
TCACCAAATAAAATGAGCCC
1701 SEQ ID N0:3463 -8.5 -20.6 58.6 -12.1 0 -3.2
TCCTCCATTCTTTAGCACCT
1953 SEQ ID N0:3464 -8.5 -27.3 77.4 -18.8 0 -4.1
AATCCACAGTGCTGTGCATC
2400 SEQ ID N0:3465 -8.5 -25.3 73.2 -14.6 -1.7 -12.4
GAAGTTGTCCAGTAGGTGAC
2463 SEQ ID N0:3466 -8.5 -23.6 71.2 -14.5 -0.3 -4.6
GCTTAACCTTCTCTTTCTGA
2513 SEQ ID N0:3467 -8.5 -23.7 70.5 -15.2 0 -2.8
GCTGGCTATGCTCACGGCTC
2582 SEQ ID N0:3468 -8.5 -29.4 82 -19.7 -1.1 -6.7
ACAATCCCTCCACATTTGAC
2994 SEQ TD N0:3469 -8.5 -24.5 68.6 -16 0 -3.2
CAGAATTGCCAATGATCTTA
3087 SEQ ID N0:3470 -8.5 -20.2 60.1 -11.7 0 -4.9
CCCACAGAATTGCCAATGAT
3091 SEQ ID N0:3471 -8.5 -24 65.8 -15.5 0 -4.3
TCTTATTTTTCACATAATCA
3516 SEQ TD N0:3472 -8.5 -17.6 56.5 -9.1 0 -2.2
CAGTAAAACAAGCTTCCGGT
3963 SEQ ID N0:3473 -8.5 -22.1 63 -13.6 0 -6.6
TGTACTTACTTGACAGAATG
4004 SEQ ID N0:3474 -8.5 -18.4 57.6 -9.9 0 -4.8
CTTCTTCTGTACTTACTTGA
4011 SEQ ID N0:3475 -8.5 -21.3 66.2 -12.8 0 -4.8
TATATAGGTAAAGACTTTGT
4202 SEQ ID N0:3476 -8.5 -16.9 54.7 -7.9 -0.1 -4.8
GCATTTCCAGAATGAATATA
4218 SEQ ID N0:3477 -8.5 -19 57.8 -8.9 -1.6 -6.4
AGAGCATTGGCTACCAGGCT
4327 SEQ ID N0:3478 -8.5 -27.6 78 -17.3 -1.8 -8.4
207
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGCATTCACAACCACCCTCA
4433 5EQ ID N0:3479 -8.5 -27 73.6 -18.5 0 -4.1
TAACATCTCGTGAATCAACA
4749 SEQ ID N0:3480 -8.5 -18.8 57 -10.3 0 -4.6
TTCCTCTGTCATAAAGATGT
4916 SEQ ID N0:3481 -8.5 -21.1 64.1 -11.9 -0.4 -3.1
AGTTTCTTCATTGCATTGTA
4948 SEQ ID N0:3482 -8.5 -21.5 66.9 -l3 0 -6.2
AAGGTCTCAAAGTTGAACAT
5536 SEQ ID N0:3483 -8.5 -18.8 58 -9.4 -0.8 -6.5
GGCAGCTGCAAAATCAGAGA
5909 SEQ ID N0:3484 -8.5 -23.1 66.5 -11.7 -0.7 -14
TTTTTTAACCTTTGCTTTAA
6217 SEQ ID N0:3485 -8.5 -18.7 57.9 -10.2 0 -3.6
GAGGAACTCCCATCTGTTTT
6340 SEQ ID N0:3486 -8.5 -24.7 71.3 -14.6 -1.6 -5.7
GGGGTGGTAGAGGAACTCCC
6349 SEQ ID N0:3487 -8.5 -28.1 79 -17.2 -2.4 -7.2
GTTTTGTTACACTATCATAG
6378 SEQ ID N0:3488 -8.5 -19 60.5 -10.5 0 -3.1
CTTTACCTTCATAGGCTGTA
6510 SEQ ID N0:3489 -8.5 -23.6 70.2 -14.6 -0.2 -3.7
ACTGACTATGAGTATTTGTT
6582 SEQ ID N0:3490 -8.5 -19.5 61.3 -10.5 -0.1 -3.8
TCAACGTTGATACCCTGCTT
6649 SEQ ID N0:3491 -8.5 -24.9 69.3 -14.5 0 -l2
AAAGCCATCTAGAAAATGGA
7046 SEQ ID N0:3492 -8.5 -18.4 55.5 -8.3 -1.6 -8.3
TGATACTCATGTTGAATTAA
7723 SEQ ID N0:3493 -8.5 -16.8 53.8 -8.3 0 -4.7
ATGATACTCATGTTGAATTA
7724 SEQ ID N0:3494 -8.5 -17.5 55.7 -8.3 -0.5 -4.7
AAAACAAAAATTTATATCAT
8313 SEQ ID N0:3495 -8.5 -10.7 40.8 -2.2 0 -5.2
GACGTAGCTCACCATTCTTT
8426 SEQ ID N0:3496 -8.5 -24.8 71.6 -16.3 0 -5.3
TATATTTTAAACTGCCAACA
8528 SEQ ID N0:3497 -8.5 -17.8 54.8 -9.3 0 -4.1
TATTAATTATATATATTTTA ?
8539 SEQ ID N0:3498 -8.5 -11.7 43.5 -3.2 0 -5.2
TCATTAATACCTTATGTATA
8900 SEQ ID N0:3499 -8.5 -17.4 55.4 -8 -0.8 -4.2
TCCCTGTCAAACCTTGATGT
257 SEQ ID N0:3500 -8.4 -25.2 70.7 -15.6 -1.1 -4.5
TACTATAAAAGTTTTCTTAT
728 SEQ ID N0:3501 -8.4 -14.7 49.8 -5.2 -1 -6.3
AAAAGTGACTGTCATCTCCA
1428 SEQ ID N0:3502 -8.4 -21.5 63.9 -12.5 0.1 -8.6
CAGCCTTCACACAGATGTAT
1518 SEQ ID N0:3503 -8.4 -23.9 69.7 -14.8 -0.5 -4.2
TTTTGTTCTGCTTCTTCCAA
1774 5EQ ID N0:3504 -8.4 -23.5 70.3 -15.1 0 -3.6
TTTTTGTCACTGGTCAGTCT
2104 SEQ ID N0:3505 -8.4 -23.8 73.6 -15.4 0 -6.6
ATTTTTTGTCACTGGTCAGT
2106 SEQ ID N0:3506 -8.4 -22.6 70 -14.2 0 -6.4
TGACAATAATTCCATCAAAG
2949 SEQ ID N0:3507 -8.4 -16.7 52.4 -8.3 0 -2.9
208
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGGTGAGGTTTCCTAGAGCC
3111 SEQ ID N0:3508 -8.4 -27 79.1 -18.1 -0.1 -3.9
GAGCTGCATGCCGACCACAG
3161 SEQ TD N0:3509 -8.4 -28.8 76.8 -19.5 -0.8 -8.4
CAGTCCCACATGGTCTCTAT
3304 SEQ ID N0:3510 -8.4 -26.6 76.7 -18.2 0 -5.2
CCAATGACCATGACCAACAT
3364 5EQ ID N0:3511 -8.4 -23.2 63.6 -14.3 -O.l -4.5
TGGTGGTTCCATTCCCATCT
3666 SEQ ID N0:3512 -8.4 -28.5 80.1 -19 -1 -6.4
TGGGGTTGTTTATGAATGAC
3744 SEQ ID N0:3513 -8.4 -20.7 62.8 -12.3 0 -3.1
GTTTCAGCTTGTTCACCTTC
3922 SEQ ID N0:3514 -8.4 -25.3 76.4 -16.9 0 -4.3
TCTTCAAAGGCCAATGCACC
4132 SEQ ID N0:3515 -8.4 -24.8 68.9 -14.9 -1.4 -7.7
GGTCTTAAAGCTCTTAATGT
4384 SEQ ID N0:3516 -8.4 -20.4 62.7 -12 0 -5.9
TCCAACAAGAGCATTCACAA
4442 SEQ ID N0:3517 -8.4 -21.1 61.6 -12.1 -0.3 -4.1
GGGAATTGCTCCAACAAGAG
4451 SEQ ID N0:3518 -8.4 -22.3 64 -12.1 -1.8 -5.3
AGGGAATTGCTCCAACAAGA
4452 SEQ ID N0:3519 -8.4 -22.3 64 -12.1 -1.8 -5.2
TATCCATCCAGCCTTTAAAT
4716 SEQ ID N0:3520 -8.4 -23.1 65.8 -14.7 0 -4.3
TTCTTCATATACAGGCTGAA
4772 SEQ ID N0:3521 -8.4 -20.7 63 -12.3 0 -4.1
AAACTAGGGTCATGTATTTG
5124 SEQ ID N0:3522 -8.4 -19.2 59.6 -10.8 0 -4.7
ACACAGAATACTTTTCTATC
5298 SEQ ID N0:3523 -8.4 -18.2 57.8 -8.8 -0.9 -4.4
CAACGCAGGAAGGGACATCA
5417 SEQ ID N0:3524 -8.4 -23.6 66 -15.2 0 -3.6
GGAGGCCGATGTTAAACAAC
5433 SEQ ID N0:3525 -8.4 -22.2 62.8 -13.2 -0.2 -8.l
ATGTTCACCACAACCAGGAA
5746 SEQ ID N0:3526 -8.4 -23.5 66.3 -14.4 -0.4 -5.7
TGCACTTTCTTCAGTAGCAA
5798 SEQ ID N0:3527 -8.4 -23 69.2 -13.1 -1.4 -5.5
TGATAGCGGCAGACACCTCC
6171 SEQ ID N0:3528 -8.4 -27.6 75.4 -19.2 0 -5.8
TTTGTCTTTCTCAAACTTTT
6407 SEQ ID N0:3529 -8.4 -19.3 60.8 -10.2 -0.4 -3.6
GTTAAAACAGTCAGTTTGGC
6565 SEQ ID N0:3530 -8.4 -20.5 62.7 -10.5 -1.6 -6.1
TCTTGTATACTGTTTCTTCA
6925 SEQ ID N0:3531 -8.4 -21 66.3 -12.6 0 -6.3
AACCAAGACTTGTGAAGAAT
7599 SEQ ID N0:3532 -8.4 -18.3 55.6 -9.4 -0.2 -5.4
TGACATTCTTTAACCAAGAC
7610 SEQ ID N0:3533 -8.4 -19.1 58.2 -9.7 -0.9 -5
CATGTTGAATTAAAAGTGCA
7716 SEQ ID N0:3534 -8.4 -17.3 54 -8.9 0 -5.2
CATATGATACTCATGTTGAA
7727 SEQ ID N0:3535 -8.4 -18.1 56.7 -8.8 -0.8 -5.2
CAGTATCCAGTGTGTTTCCT
7765 SEQ ID N0:3536 -8.4 -25.8 76.6 -17.4 0 -3.7
209
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TATATTTAAACAAGTTTTAG
7828 SEQ ID N0:3537 -8.4 -13.3 46.6 -4.9 0 -5.5
TTTTAGGAAATTATCCATTG
7999 SEQ ID N0:3538 -8.4 -17.4 54.8 -7.5 -1.4 -6.4
TTTATTTTAGGAAATTATCC
8003 SEQ ID N0:3539 -8.4 -16.5 53.4 -6.9 -1.1 -5.9
ATGAATAAAAGGTTATATTG
8140 SEQ ID N0:3540 -8.4 -13.5 46.6 -4.5 -0.3 -3
TGACGTAGCTCACCATTCTT
8427 SEQ ID N0:3541 -8.4 -24.7 71.1 -16.3 0 -5.3
AACATGTGAACTTGATCCTT
8694 SEQ ID N0:3542 -8.4 -20.5 61.1 -12.1 0 -7
ATTTATTAGCCACCAAGTAA
8837 SEQ ID N0:3543 -8.4 -20.6 61.1 -12.2 0 -3.2
TTACAACTGGAGTTTTCCAC
9002 SEQ ID N0:3544 -8.4 -21.7 64.8 -11.2 -2.1 -5.6
TTTGCTCCTTTCCCAGTAAG
310 SEQ ID N0:3545 -8.3 -25.7 73.5 -17.4 0 -3.6
TTCTGTGAATTATCTCATTT
358 SEQ ID N0:3546 -8.3 -18.9 59.9 -10.6 0.9 -3.2
TCCATAAATAAATGGAAGGT
650 SEQ ID N0:3547 -8.3 -17.2 53.2 -6.8 -2.1 -7.5
ATGTCTCCATAAATAAATGG
655 SEQ ID N0:3548 -8.3 -17.4 54.1 -7.8 -1.2 -5.7
TATAAAAGTTTTCTTATTGA
725 SEQ TD N0:3549 -8.3 -14.6 49.5 -5.6 -0.5 -6.3
ATAAATACACAGTTGGTCAA
886 SEQ ID N0:3550 -8.3 -17.9 55.9 -9.6 0 -3.6
TTCTTTACCGACTGGATCAG
1189 SEQ ID N0:3551 -8.3 -22.9 66.7 -13.7 -0.7 -5.3
CGCTTGGGGGCCACTGCAAA
1302 SEQ ID N0:3552 -8.3 -29.1 76.1 -18.9 -1.9 -6.9
ATGGCCACCACAGCCAGGAT
1726 SEQ ID N0:3553 -8.3 -29.8 79.3 -18.7 -2.8 -9.1
TTTGTTCTGCTTCTTCCAAG
1773 SEQ ID N0:3554 -8.3 -23.4 70.2 -15.1 0 -3.6
GTTTCCATCCATGGAGAAAA
2084 SEQ ID N0:3555 -8.3 -21.9 63.3 -11.4 -1.7 -12.3
AGGGGAGCAGAATTTTTTGT
2117 SEQ ID N0:3556 -8.3 -22.3 66.9 -14 0 -4.1
TGCGTCGCTCTCCATGTCTG
2316 SEQ ID N0:3557 -8.3 -28.6 79.6 -19.7 -0.3 -6.9
CTGGCCTGACTAACGTTACT
2338 SEQ ID N0:3558 -8.3 -24.6 69.1 -15.8 0 -7.9
TTTACTTTTAACCATGCATC
2701 SEQ ID N0:3559 -8.3 -20.1 60.9 -11.8 0 -6.6
CATCAAAGATATTCCAGCCT
2937 SEQ ID N0:3560 -8.3 -22.6 65 -14.3 0,1 -3.5
TGATCTTAATTAGCATATTT
3075 SEQ TD N0:3561 -8.3 -17.2 55.3 -8.9 0 -4.9
TTTCCTAGAGCCCCCACAGA
3103 5EQ ID N0:3562 -8.3 -29.8 79.9 -21.5 0 -3.8
TTTTCATCGATTACGTATTT
3715 SEQ ID N0:3563 -8.3 -19.1 58.6 -9.9 -0.7 -6.1
CTGTAGCAGGTTTTTCGAAG
4054 SEQ ID N0:3564 -8.3 -22.2 66.4 -13.9 0 -6.8
TAATGTCCGTAATGATTTGA
4370 SEQ ID N0:3565 -8.3 -19 57.6 -10.7 0 -2.6
210
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Tnter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGCTCCAACAAGAGCATTCA
4445 SEQ ID N0:3566 -8.3 -23.6 67.7 -12.1 -3.2 -9.1
GACAGACCAACAGCACATTC
4479 SEQ ID N0:3567 -8.3 -23.1 66.6 -14.8 0 -4.1
GAACTTGCCAGCAAACAAAT
4535 SEQ ID N0:3568 -8.3 -20.2 58.3 -11.9 0 -7.4
TACCCGTTGTCATGTTAACA
4563 SEQ ID N0:3569 -8.3 -23.5 67.1 -14.7 0.2 -8.4
CTTCATTGCATTGTAATATT
4943 SEQ ID N0:3570 -8.3 -18.8 58.6 -10.5 0 -6.2
GGGCGAGGTATGGGTTTCTG
4984 SEQ ID N0:3571 -8.3 -26.8 76.8 -18.5 0 -4
AGATGAGGATCATGATGCTG
5061 SEQ ID N0:3572 -8.3 -21.4 64.3 -l1 -2.1 -8.5
ACATGTCATCAATTCCAGCT
5520 SEQ ID N0:3573 -8.3 -23.5 68.9 -15.2 0 -6.1
TTCTTCAGTAGCAACACTGA
5792 SEQ ID N0:3574 -8.3 -21.9 66.3 -11.6 -2 -7.8
GCTGAATGATAGCGGCAGAC
6177 SEQ ID N0:3575 -8.3 -24 68.1 -14.4 -1.2 -6.6
CCTCTTTGTTATAGTTACTT
6243 SEQ ID N0:3576 -8.3 -21.3 65.9 -13 0 -2.5
GTAGAGGAACTCCCATCTGT
6343 SEQ ID N0:3577 -8.3 -25.3 73.3 -14.6 -2.4 -6.7
GGTAGAGGAACTCCCATCTG
6344 SEQ ID N0:3578 -8.3 -25.3 72.5 -14.6 -2.4 -7.3
GTCTTTCTCAAACTTTTCCT
6404 SEQ ID N0:3579 -8.3 -22.4 67.6 -14.1 0 -1.9
TGTCTTTCTCAAACTTTTCC
6405 SEQ ID N0:3580 -8.3 -21.5 65.5 -13.2 0 -2.4
ACTTTACCTTCATAGGCTGT
6511 SEQ ID N0:3581 -8.3 -24.1 71.4 -14.6 -1.1 -4.1
CTTGAAGTCCAGTTGACACA
6534 SEQ ID N0:3582 -8.3 -22.9 67.4 -12.8 -1.8 -5.7
CATTATGAATAAACTATGAA
6872 SEQ ID N0:3583 -8.3 -13.4 46 -5.1 0 -3.5
GTAGCCATTACAATTCTTTT
7013 SEQ ID N0:3584 -8.3 -21.1 63.8 -12.3 -0.1 -3.2
TTAGATTACTTTTTGGAAAG
7234 SEQ ID N0:3585 -8.3 -16.1 52.6 -6.3 -1.4 -4.9
GAATGGATTTATTAGATTAC
7245 SEQ ID N0:3586 -8.3 -16 52.5 -7.7 0 -2.4
ATTAGTGATAGCCTTTAAAC
7538 SEQ ID N0:3587 -8.3 -18.7 58 -10.4 0 -4.2
ATGGATTGAGTAAAATAGAG
7581 SEQ ID N0:3588 -8.3 -15.6 51.1 -7.3 0 -2.3
CCAATATGTGACATTCTTTA
7618 SEQ ID N0:3589 -8.3 -19.7 59.9 -11.4 0 -3.9
TAATGGACAGAGCAGGTTGA
7651 SEQ ID N0:3590 -8.3 -21.9 65.2 -13.6 0 -4.1
AGCTTCAAATTATTCTGCTT
7675 SEQ ID N0:3591 -8.3 -20.5 62.6 -12.2 0 -4.3
TATTTATATTTAAACAAGTT
7832 SEQ ID N0:3592 -8.3 -13.3 46.6 -4.4 -0.3 -4.9
TTATTTATATTTAAACAAGT
7833 SEQ ID N0:3593 -8.3 -13.3 46.6 -4.4 -0.3 -4.9
CAAAAGTTTGGAATTGTGAT
7963 SEQ ID N0:3594 -8.3 -17 53.5 -8.7 0 -4.9
211
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTAACATTAAACTTTTGGTT
8340 SEQ ID N0:3595 -8.3 -16.3 52.6 -7.4 -0.3 -3.9
TAGCAATTCCCTGCATGCAG
8399 SEQ ID N0:3596 -8.3 -25.9 72.4 -14.7 -1.9 -13.9
TAGCAATAGCAATTCCCTGC
8405 SEQ ID N0:3597 -8.3 -24.2 68.6 -14.2 -1.7 -6.2
ATTACAACTGGAGTTTTCCA
9003 SEQ ID N0:3598 -8.3 -21.5 64.3 -11.2 -2 -5.5
GGGAGAATTATGAAATACAT
9054 SEQ ID N0:3599 -8.3 -16.5 52.4 -7.7 -0.2 -3.8
CAATTTTTTTTCTTTCTTTC
64 SEQ ID N0:3600 -8.2 -18.1 58.6 -9.9 0 -2.6
GATGGTTAGGGTATAACGTG
154 SEQ TD N0:3601 -8.2 -21.3 63.6 -11.1 -2 -5.3
AAAGCTCCAGGTCCCTTCTG
373 SEQ TD N0:3602 -8.2 -27.5 76.7 -19.3 0 -5
ACAGTGCCTGTGCCATCTTT
468 SEQ ID N0:3603 -8.2 -28 79.4 -18.7 -1 -7.8
TCTTTCCAGCTTCCAAGTCA
630 SEQ ID N0:3604 -8.2 -26.1 75.9 -17.9 0 -4.5
GTCTCCATAAATAAATGGAA
653 SEQ ID N0:3605 -8.2 -17.3 53.7 -6.8 -2.3 -7.8
CAAAATCTTGATAGCAATTT
827 SEQ ID N0:3606 -8.2 -16.3 52 -7.5 -0.3 -0.5
TAAATACACAGTTGGTCAAA
885 SEQ ID N0:3607 -8.2 -17.2 54.1 -9 0 -3.8
AGCAAACACGCTCAGACAGA
1238 SEQ ID N0:3608 -8.2 -22.9 65.3 -14 -0.4 -4.3
CATTTATTCCTCAGATTGCC
1282 SEQ ID N0:3609 -8.2 -23.6 69 -15.4 0 -3
AAACATAAAAGTGACTGTCA
1434 SEQ ID N0:3610 -8.2 -16.3 52 -7.5 0 -8.6
CCAGCCTTCACACAGATGTA
1519 SEQ ID N0:3611 -8.2 -25.9 73.4 -17 -0.5 -4.2
GTGCGGCACAAACAGTGAGT
2297 SEQ ID N0:3612 -8.2 -24.9 70.3 -14.8 -1.5 -11.7
TGTGCGGCACAAACAGTGAG
2298 SEQ ID N0:3613 -8.2 -23.7 67 -13 -l.5 -13
CTCTCCATGTCTGTGCGGCA
2309 SEQ ID N0:3614 -8.2 -29.3 81.9 -20.6 0 -7.7
CCAGATCAAGAACACATTGG
2672 SEQ ID N0:3615 -8.2 -20.7 60.7 -12.5 0 -5.4
TCACAAGATGTTTTACTTTT
2712 SEQ ID N0:3616 -8.2 -18.5 58.5 -10.3 0 -3
ACTCTAAGCAGTCTGAATGA
3025 SEQ ID N0:3617 -8.2 -20.9 63.6 -12.7 0 -6.3
AACTCTAAGCAGTCTGAATG
3026 SEQ ID N0:3618 -8.2 -19.6 60.1 -11.4 0 -5.8
ATGATCTTAATTAGCATATT
3076 SEQ ID N0:3619 -8.2 -17.1 55 -8.9 0 -4.9
ACAATAAGGCACATGGTTTG
3340 SEQ ID N0:3620 -8.2 -20.4 60.9 -12.2 0 -5.2
ATTTTCATCGATTACGTATT
3716 SEQ ID N0:3621 -8.2 -19 58.3 -9.9 -0.7 -6.3
GATAGTCTTTCGCTGTTCAA
4160 SEQ ID N0:3622 -8.2 -22.6 68 -14.4 0 -3.1
TCTTAAAGCTCTTAATGTCC
4382 SEQ ID N0:3623 -8.2 -20.4 62.2 -12.2 0 -5.9
212
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Tnter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AACCACCCTCATGCCTTCAA
4424 SEQ ID N0:3624 -8.2 -27.6 73.5 -19.4 0 -4.4
AGACCAACAGCACATTCATG
4476 SEQ ID N0:3625 -8.2 -22.3 64.6 -14.1 0 -4,1
CTCCAAACTTCTTTTTCTGC
4890 SEQ ID N0:3626 -8.2 -22.6 66.9 -14.4 0 -2.6
ACCTCCAAACTTCTTTTTCT
4892 SEQ ID N0:3627 -8.2 -23 67.1 -14.8 0 -1.8
GCATTGTAATATTTTTTCTG
4936 SEQ TD N0:3628 -8.2 -18.3 58 -10.1 0 -4.2
TTCTTGGATCCAAGTTTCTT
4960 SEQ ID N0:3629 -8.2 -22.5 67.9 -10.6 -1.3 -15.5
GATGCTGATATCAAAGACTT
5048 SEQ ID N0:3630 -8.2 -19.1 58.5 -10.4 0 -7.5
CGAGCTTCAGCACAAATTCT
5184 SEQ ID N0:3631 -8.2 -22.7 65.5 -13.6 -0.7 -6.6
AAGTAGTAGTGTCTGAGGGA
5206 SEQ ID N0:3632 -8.2 -22.4 69.6 -14.2 0 -2.9
TCCTTTGATCAGACGTAGGA
5363 SEQ ID N0:3633 -8.2 -23.5 68.7 -14.8 -0.1 -7.5
CATGTCATCAATTCCAGCTT
5519 SEQ ID N0:3634 -8.2 -23.4 68.7 -15.2 0 -4.5
CACAACCAGGAAGGATATGA
5738 SEQ ID N0:3635 -8.2 -21 61 -12.8 0.1 -3.7
AATCAGAGAGTTTAGAGAAC
5898 SEQ ID N0:3636 -8.2 -17.4 56.1 -8.6 -0.3 -3.2
GCAGATCCATGGCAATAAGC
5970 SEQ ID N0:3637 -8.2 -24 68.2 -15.1 -0.5 -8
TGGTAGAGGAACTCCCATCT
6345 5EQ TD N0:3638 -8.2 -25.3 72.5 -14.6 -2.5 -7.9
TGTCTGGTTTTGTTACACTA
6384 SEQ ID N0:3639 -8.2 -21.9 67.7 -13.7 0 -2.7
CACTTTGCACAACTATCCCT
6736 SEQ ID N0:3640 -8.2 -24.8 69.6 -16.6 0 -4.7
AGAATGGATGCAAGGACTGT
6786 SEQ ID N0:3641 -8.2 -21.6 63.7 -13.4 0 -5.6
TTCAACGTAAACCTCATTTA
6909 SEQ ID N0:3642 -8.2 -19.1 57.4 -10.4 -0.2 -5.3
AAGTAACTGAAACTGTAGCC
7027 SEQ ID N0:3643 -8.2 -19.6 59.1 -11.4 0 -3.3
AAATTAAATATAGAGCTCTG
7204 SEQ ID N0:3644 -8.2 -15 49.8 -5.8 0 -10
TACCATATGATACTCATGTT "
7730 SEQ ID N0:3645 -8.2 -20.1 61.2 -11 -0.8 -6
AATTTTCTTATGTACAAAAT
7884 SEQ ID N0:3646 -8.2 -14.4 48.6 -5.6 -0.3 -6.8
ATATCATGTTAGGTAATTGC
8300 SEQ ID N0:3647 -8.2 -19.1 60 -10.9 0 -4.7
GAAAGAAGATGAGTTTAGAT
8793 SEQ ID N0:3648 -8.2 -16 52.2 -7.8 0 -2.2
TTGACCTCACATAAATCCAA
8.963 SEQ ID N0:3649 -8.2 -20.5 59.8 -12.3 0 -2.9
TATTATGGGAGAATTATGAA
9060 SEQ ID N0:3650 -8.2 -16.1 52 -7.9 0 -3.2
CTTATATAATTTATTATGGG
9071 SEQ ID N0:3651 -8.2 -15.5 51.3 -6.7 -0.3 -5.3
GTCTTCCTCTGGCAGCTGTT
135 SEQ ID N0:3652 -8.1 -28.9 85.1 -20.1 0 -8.9
213
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CAGCATAACAAAGCCCAGCA
179 SEQ ID N0:3653 -8.1 -24.7 67.6 -15.7 -0.7 -5
TCCAGGTCCTCCAGGGGCTC
694 SEQ TD N0:3654 -8.1 -32.6 91 -23.2 -1.2 -8.4
TTTATTCATTACTATAAAAG
737 SEQ ID N0:3655 -8.1 -13.3 46.6 -5.2 0 -3.2
TCTTTGTCCAGTCAGGAGGG
918 SEQ ID N0:3656 -8.1 -26.3 78.3 -16.8 -1.3 -5
CTCAACGCTGAGACATTGCC
1099 SEQ TD N0:3657 -8.1 -25 69.6 -15.4 -1.4 -5.8
CTGCAGCCCAATGAGAGCAA
1253 SEQ ID N0:3658 -8.1 -26.2 71.6 -17.4 -0.5 -7.2
GTCATCTCCAATGTAATCCT
1418 SEQ ID N0:3659 -8.l -23.5 68.7 -14.8 -0.3 -3
TTGCTTTTTAAGCTGTTCGA
1817 SEQ ID N0:3660 -8.l -22 65.6 -11.3 -2.6 -9
AGGTGCTCTCTCTGTCTTCT
1987 SEQ ID N0:3661 -8.1 -26.9 83.3 -18.8 0 -3.6
GCTTCTTTTGACGCTGTCTT
2057 SEQ ID N0:3662 -8.1 -25.3 74.2 -15.8 -1.3 -7.6
TGCTGGAAGCCCTGGCACCA
2372 SEQ ID N0:3663 -8.1 -31.1 81.5 -20.8 -2.2 -10.4
ACAGTGCTGTGCATCTTCCC
2395 SEQ ID N0:3664 -8.1 -28.3 80.9 -19.1 -1 -8.5
TTCTGACTTCCGTTTCAGTG
2499 SEQ ID N0:3665 -8.1 -24.1 71.3 -14.8 -1.1 -5.7
ACACTACTGAATTGCTCAGT
2824 SEQ ID N0:3666 -8.1 -21.8 65.4 -11.4 -2.3 -7.5
CACACTACTGAATTGCTCAG
2825 SEQ ID N0:3667 -8.1 -21.3 63.4 -11.4 -1.8 -6.2
CTGCAGATTATTCATTTCAT
3467 SEQ ID N0:3668 -8.1 -20.3 62.5 '12.2 0.6 -7.6
AATCATTTTCATCGATTACG
3720 SEQ ID N0:3669 -8.1 -18.4 56.3 -9.6 -0.4 -6.3
CTTCAGATGAGCTGGTTGCA
3873 5EQ ID N0:3670 -8.1 -25 73.5 -15.3 -1.5 -6.8
AACTTTTTAATACACCCTTC
3982 SEQ ID N0:3671 -8.1 -20 60 -11.9 0 -2.5
AAGTCTCAAACCAGTTGTGC
4083 SEQ ID N0:3672 -8.1 -22.7 67.2 -13.9 -0.4 -3.4
GTCTTTCGCTGTTCAATGTA
4156 SEQ ID N0:3673 -8.1 -23.2 69.6 -15.1 0 -3.1
ATCTAGCCAGCACCAGGCAT
4280 SEQ ID N0:3674 -8.1 -28.6 79.3 -18.6 -1.9 -7.4
CCTCATGCCTTCAAACCGGG
4418 5EQ ID N0:3675 -8.1 -27.9 73.3 -19.8 0 -7.l
AACTTGCCAGCAAACAAATT
4534 SEQ ID N0:3676 -8.1 -19.7 57.5 -11.6 0 -7.4
CAGTGGTAGAACTTGCCAGC
4543 SEQ ID N0:3677 -8.1 -25.4 73.3 -16 -1.2 -4.8
AAATTCTCCAGTGAACAGAA
5171 SEQ ID N0:3678 -8.1 -19 57.6 -10.9 0 -4.5
AATACTTTTCTATCATCTCA
5292 SEQ ID N0:3679 -8.1 -18.9 59.9 -10.8 0 -1.4
AGGAGGCCGATGTTAAACAA
5434 SEQ ID N0:3680 -8.1 -22 62.5 -13.2 -0.5 -8.1
CTTTTCCCAAACCTCATAGA
5849 SEQ ID N0:3681 -8.1 -23.4 66.4 -15.3 0 -2.4
214
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTGGTAGAGGAACTCCCATC
6346 5EQ ID N0:3682 -8.1 -25.6 73.9 -14.6 -2.9 -8.2
TTGAAGTCCAGTTGACACAT
6533 SEQ ID N0:3683 -8.1 -22 65.4 -12.8 -1 -5.7
ATCATTTGAGAGACAGGGTT
6944 SEQ ID N0:3684 -8.1 -21.7 66.1 -13.6 0 -4
AGTAACTGAAACTGTAGCCA
7026 SEQ ID N0:3685 -8.1 -21 62.2 -12.9 0 -3.3
CATAACTGTTCAGATAGAAA
7098 SEQ ID N0:3686 -8.1 -16.7 53.4 -7.9 -0.5 -5
CATTAGTGATAGCCTTTAAA
7539 SEQ ID N0:3687 -8.1 -19.2 58.8 -11.1 0 -4
ACTACAGTAAATAGTTTTGT
8368 SEQ ID NO:3688 -8.1 -17.6 56.6 -9.5 0 -3.6
CTTTTTAGCAATAGCAATTC
8410 SEQ ID N0:3689 -8.1 -18.8 58.6 -9 -l.7 -4.6
GTAGCTCACCATTCTTTTTA
8423 SEQ ID N0:3690 -8.1 -23.1 69.8 -15 0 -4.8
AAAACCCCAGAGCCCAATAA
8491 SEQ TD N0:3691 -8.1 -24.2 64.1 -16.1 0 -3.2
ATTAATTATATATATTTTAA
8538 SEQ ID NO:3692 -8.1 -11.3 42.5 -3.2 0 -6.8
ATTGTAGGTGGTTACTACTA
8737 SEQ ID N0:3693 -8.1 -21.2 65.9 -11.5 -1.6 -5.2
GCATCAATTATATTGAAAGA
8807 SEQ ID N0:3694 -8.1 -16.3 52.3 -6.2 -2 -7.9
CATTTATTAGCCACCAAGTA
8838 SEQ ID NO:3695 -8.1 -22 64.3 -13.9 0 -3.2
TGACCTCACATAAATCCAAG
8962 SEQ ID N0:3696 -8.1 -20.4 59.7 -12.3 0 -2.6
TTTTGACCTCACATAAATCC
8965 SEQ ID N0:3697 -8.1 -20.7 61.2 -12.6 0 -2.9
ACAGCATAACAAAGCCCAGC
180 SEQ ID N0:3698 -8 -24.2 67.1 -15.7 -0.2 -4.1
TAGCTTCTTGCATACGAATT
424 SEQ ID N0:3699 -8 -21.1 62.7 -11.5 -1.5 -5.2
GCGGAAGCTTTCAGGTCCTG
497 SEQ ID N0:3700 -8 -27.4 76.8 -17.7 -1.6 -10.7
CCAAGTCACTATTTGGCTTT
618 SEQ ID N0:3701 -8 -23.4 68.5 -13.8 -1.5 -5
CTCTTGCCAAGATTTTTATA
981 SEQ TD N0:3702 -8 -20.5 62.1 -11.7 -0.6 -6.3
CAGGGCCCCCACAATGGTCT '
1172 SEQ ID N0:3703 -8 -31.5 82.2 -21.7 -0.7 -11.8
ATTGCCCATGAACAGCTGCA
1268 SEQ ID N0:3704 -8 -26.6 72.8 -17.9 -0.2 -8.9
TGTATCCTTCTGGACACTGG
1503 SEQ ID N0:3705 -8 -24.6 71.9 -16.6 1.5 -5.9
ACTGGTAAAGATTTTCCCAA
1623 SEQ ID N0:3706 -8 -21.1 61.8 -13.1 0 -4.8
TCCATTCTTTAGCACCTTTG
1950 SEQ ID N0:3707 -8 -24.2 70.6 -16.2 0 -4.l
GGAAGCTGCTTCTTTTGACG
2064 SEQ ID N0:3708 -8 -23.8 68.7 -13.2 -1.8 -13.3
AGTCTGTTTCCATCCATGGA
2089 SEQ ID N0:3709 -8 -25.9 75.5 -16.3 -1.5 -10.1
GATCTTAATTAGCATATTTA
3074 SEQ ID N0:3710 -8 -16.9 54.8 -8.9 0 -4.1
215
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CATCATCAGTAGCAGCAAGG
3444 SEQ ID N0:3711 -8 -23.3 69.1 -15.3 0 -5.4
TTTCACATAATCAATTCCCT
3509 SEQ ID N0:3712 -8 -2l 62 -13 0 -2.5
AAACACTCCCGCATCTTATT
3529 SEQ ID N0:3713 -8 -23.5 65.7 -15.5 0 -3.6
CTTTCTAAAAAAGGCTTTTT
3551 SEQ ID N0:3714 -8 -16.9 53.5 -7.6 -1.2 -8.2
CCAGTATTATTGGACATGCA
3613 SEQ ID N0:3715 -8 -22.7 66.4 -14.7 0 -5.2
CCATCTCTAAGATAATTAAG
3652 SEQ ID N0:3716 -8 -17 53.9 -8.3 -0.5 -4.9
GGGTTCAGTTTCAGCTTGTT
3929 SEQ TD N0:3717 -8 -25.4 77.7 -17.4 0 -4.5
AAAGTCTCAAACCAGTTGTG
4084 SEQ ID N0:3718 -8 -20.2 60.9 -11.5 -0.4 -3.4
AGGCCAATGCACCACTACTG
4125 SEQ ID N0:3719 -8 -26.3 72.1 -16.8 -1.4 -7.7
GTTCAATGTATATATCTTCA
4146 SEQ ID N0:3720 -8 -18.5 59.2 -10.5 0 -3.9
AAGAGCATTGGCTACCAGGC
4328 5EQ ID N0:3721 -8 -26 73.6 -16.2 -1.8 -8.4
TGGTAGAACTTGCCAGCAAA
4540 SEQ ID N0:3722 -8 -22.8 65.3 -13.9 -0.8 -7.5
CAGGCTGAAGTTTAACATCT
4761 SEQ ID N0:3723 -8 -21.1 63.4 -13.1 0 -4.6
TCCAGCCTATAGTGAAGTAG
5220 5EQ ID N0:3724 -8 -23.2 68.7 -15.2 0 -5.1
AAGATGTTCCAGCCTATAGT
5227 SEQ ID N0:3725 -8 -23.6 69.4 -15.6 0 -5.1
ATCATCAAAGCAAAGAGCAG
5401 SEQ ID N0:3726 -8 -l9 57.7 -9.4 -1.6 -4.4
CAGAGGTTGTAATTTGGAAC
5577 SEQ ID N0:3727 -8 -19.5 60 -11.5 0 -3
ACCACAACCAGGAAGGATAT
5740 SEQ ID N0:3728 -8 -22.6 63.9 -13.8 -0.6 -4.3
TTTCTTCAGTAGCAACACTG
5793 SEQ ID N0:3729 -8 -21.4 65.3 -12.3 -1 -5.8
AGGGGCTCTGCACTTTCTTC
5806 SEQ ID N0:3730 -8 -27.2 80.5 -19.2 4.6 -4.8
CGCATCGGGATCAAACTTTT
5864 SEQ ID N0:3731 -8 -22.6 63.7 -14.6 0 -5.3
CTTGTCTGGTTTTGTTACAC
6386 SEQ ID N0:3732 -8 -22.3 68.7 -14.3 0 -2.9
TCTTGAAGTCCAGTTGACAC
6535 SEQ ID N0:3733 -8 -22.6 67.8 -12.8 -1.8 -5.1
ATGGATGCAAGGACTGTACT
6783 SEQ ID N0:3734 -8 -22.5 66.2 -14.5 0 -5.1
AAAATATGGCAGATATGGAA
6815 SEQ ID N0:3735 -8 -16.7 52.4 -7.3 -1.3 -5.2
GACCTAAATTAAATATAGAG
7209 SEQ ID NO:3736 -8 -14.4 48.1 -6.4 0 -3.2
AGCAAAATATGAAGAATAGG
7798 SEQ ID N0:3737 -8 -14.8 48.7 -6.8 0 -4.1
ATTGTGATGTCATCAACCTG
7909 SEQ ID N0:3738 -8 -21.7 64.7 -12.6 -1 -7.2
ACGTAGCTCACCATTCTTTT
8425 SEQ ID N0:3739 -8 -24.3 70.7 -16.3 0 -4.8
216
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATTATATATATTTTAAACTG
8534 SEQ ID N0:3740 -8 -12.6 45.1 -4.6 0 -5.2
GTTTTGACCTCACATAAATC
8966 SEQ ID N0:3741 -8 -19.9 60.5 -11.9 0 -2.9
CAGGTCCCTTCTGTGAATTA
366 SEQ ID N0:3742 -7.9 -24.7 71.6 -16.8 0 -4.2
GCTTTCTCTTCTGCAGCACG
553 SEQ ID N0:3743 -7.9 -26.9 77.5 -18.3 -0.4 -8.3
GTTCTCATCATCATTATCTT
593 SEQ ID N0:3744 -7.9 -21.1 66.4 -13.2 0 -0.9
CAGTCAGGAGGGTTGCTCAA
910 SEQ ID N0:3745 -7.9 -25.6 75.3 -15.7 -2 -5
CAAAACCCTCTTGCCAAGAT
988 SEQ ID N0:3746 -7.9 -23.5 64.6 -14.8 -0.6 -6.3
GGGGCCACTGCAAACATTTA
1296 SEQ ID N0:3747 -7.9 -25.1 69.5 -15.7 -1.4 -7.6
ATTTCCACAGAGTAAAGGGT
1469 SEQ ID N0:3748 -7.9 -21.9 65.2 -14 0 -3.6
CTTTTTGTTCTGCTTCTTCC
1776 SEQ ID N0:3749 -7.9 -24.5 74.1 -16.6 0 -3.6
CTCTCCTAACCCACCTACTC
1892 SEQ ID N0:3750 -7.9 -27.7 76.1 -19.8 0 -0.3
GGATACTCAAGAGAGACTGA
2139 SEQ ID N0:3751 -7.9 -20.5 62.4 -11.8 -0.6 -4.5
CGTCTTGGGGAAAACAGGGA
2164 SEQ ID N0:3752 -7.9 -23.4 65.8 -15.5 0 -2.7
GAAAATCCCAGTAAAGACCA
2861 SEQ ID N0:3753 -7.9 -20.6 59.1 -12.7 0 -2.1
GAATGATCGCAGTACAGACA
3011 SEQ ID N0:3754 -7.9 -21.5 63.2 -12.9 -0.4 -5.7
CCATACAGTCCCACATGGTC
3309 SEQ ID N0:3755 -7.9 -27.3 76.3 -18.7 -0.5 -5.2
TATTTTTCACATAATCAATT
3513 SEQ ID N0:3756 -7.9 -15.6 51.4 -7.7 0 -2.3
TGGCACTGTGACGGTGAGGC
3764 SEQ ID N0:3757 -7.9 -27.6 77.3 -17.9 -1.8 -7.6
AGTAAAACAAGCTTCCGGTT
3962 SEQ ID N0:3758 -7.9 -21.5 62.2 -13.6 0 -6.6
TCTTCCCTTTGCCTTCTTCT
4023 SEQ TD N0:3759 -7.9 -28.4 81.3 -20.5 0 -3
ATCAAGAAATCTAGCCAGCA
4288 SEQ ID N0:3760 -7.9 -21.6 63.3 -13.7 0 -4.6
CCAAGAGCATTGGCTACCAG
4330 SEQ ID N0:3761 -7.9 -25.7 71.5 -16.2 -1.6 -7.2
TACAGATTTTCTTCATATAC
4780 SEQ ID N0:3762 -7.9 -17.6 57 -9.7 0 -2.6
TATTTTTTCTGTTCCTCTGT
4927 SEQ ID N0:3763 -7.9 -22.6 69.9 -14.7 0 -0.7
AAAGACCATTCCTTGGAATT
5012 SEQ ID N0:3764 -7.9 -20.8 60.6 -11.2 -1.7 -8.4
TGGTGACCATGTTGAGGCAG
5079 SEQ ID N0:3765 -7.9 -25.5 73.3 -17.1 -0.2 -5.5
TGAAGTAGTAGTGTCTGAGG
5208 SEQ ID N0:3766 -7.9 -21.2 66.5 -13.3 0 -2.9
GTGAAGTAGTAGTGTCTGAG
5209 SEQ ID N0:3767 -7.9 -21.2 67.3 -13.3 0 -2.9
AGTGAAGTAGTAGTGTCTGA
5210 SEQ ID N0:3768 -7,g -21.2 67.3 -13.3 0 -2.8
217
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATGTCATCAATTCCAGCTTC
5518 SEQ ID N0:3769 -7.9 -23.1 69.1 -15.2 0 -4.5
CCAGGGTGAATTGTGTCAGG
5653 SEQ ID N0:3770 -7.9 -25 72.4 -17.1 0 -3.3
TGTACATGTTCACCACAACC
5751 SEQ TD NO:3771 -7.9 -23.5 67.4 -14.9 -0.4 -7.1
AGCAACACTGAAGTTCTCCA
5783 SEQ ID N0:3772 -7.9 -23.4 68.1 -15.5 0 -6.3
CTTTCTTCAGTAGCAACACT
5794 SEQ ID N0:3773 -7.9 -22.3 67.5 -13.7 -0.5 -0.8
GACCATGGGCAGATCCATGG
5978 SEQ ID N0:3774 -7.9 -27.3 75 -14.3 -5.1 -12.8
TTTTTAACCTTTGCTTTAAA
6216 SEQ ID N0:3775 -7.9 -17.9 55.7 -10 0 -4
TGCTTTCTTTTTCTGGTTTG
6423 SEQ ID N0:3776 -7.9 -22.5 69.3 -14.6 0 -3.6
TTAAAACAGTCAGTTTGGCA
6564 SEQ ID N0:3777 -7.9 -20 60.8 -10.5 -1.6 -7.7
TCTGATCATTTGAGAGACAG
6948 SEQ ID N0:3778 -7.9 -19.9 61.9 -11.5 -0.1 -6.2
TCTAGAAAATGGAAGTAACT
7039 SEQ ID N0:3779 -7.9 -15.9 51.4 -8 0 -5.2
AATTAAAGCCATCTAGAAAA
7050 SEQ ID N0:3780 -7.9 -15.7 50.2 -7.8 0 -6.2
AAATTAAAGCCATCTAGAAA
7051 SEQ ID N0:3781 -7.9 -15.7 50.2 -7.8 0 -6.2
CACATAACTGTTCAGATAGA
7100 SEQ ID N0:3782 -7.9 -19 59 -10.6 -0.2 -5.6
TATTAGAGGAGACTTTACAG
7121 SEQ ID N0:3783 -7.9 -18.4 58.5 -9.6 -0.7 -5.5
CATTTGACCTAAATTAAATA
7214 SEQ ID N0:3784 -7.9 -15 49 -6.5 -0.3 -5
TTTGGAAAGCATTTGACCTA
7223 SEQ ID N0:3785 -7.9 -20.7 61.2 -12 -0.6 -4.1
GCAATACTTTAGATATATTT
7270 SEQ.ID N0:3786 -7.9 -16.7 54 -8.8 0 -4.3
AAAGCAATACTTTAGATATA
7273 SEQ ID N0:3787 -7.9 -15.1 50 -6.l -1 -4.7
AATGGATTGAGTAAAATAGA
7582 SEQ ID N0:3788 -7.9 -14.9 49.3 -7 0 -2.1
CACCAATATGTGACATTCTT
7620 SEQ ID N0:3789 -7.9 -20.8 61.9 -12.9 0 -4
TTCATTCTATCACCAATATG
7630 SEQ ID N0:3790 -7.9 -19.3 59.3 -11.4 0 -2.7
TAGACATATTTTTAGCAAAA
7811 SEQ ID N0:3791 -7.9 -15.4 50.6 -6.8 -0.4 -5
TTTAAACAAGTTTTAGACAT
7824 SEQ ID N0:3792 -7.9 -15.4 50.8 -6.8 -0.4 -5.5
GCAATAGCAATTCCCTGCAT
8403 SEQ ID N0:3793 -7.9 -25.2 70 -15.6 -1.7 -6.8
TTTTGGCTCAATAATGACGT
8441 SEQ ID N0:3794 -7.9 -20.4 60.6 -11.8 -0.5 -5.3
ACAAAGCTGCTTTTAATTTG
8657 SEQ ID N0:3795 -7.9 -18.4 56.8 -9 -0.5 -10.9
CTATTGTAGGTGGTTACTAC
g739 SEQ ID N0:3796 -7.9 -21.2 65.9 -12.8 -0.1 -4.3
CATAGGAGTTTATATAATGC
8880 SEQ ID N0:3797 -7.9 -17.8 56.6 -9.9 0 -5.5
218
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTGGTTTTGACCTCACATAA
8969 SEQ ID N0:3798 -7.9 -21.5 63.9 -11.3 -2.3 -5
AGTTTGGTTTTGACCTCACA
8972 5EQ ID N0:3799 -7.9 -23.8 70.7 -13.6 -2.3 -5.7
TTTTTTTTTTTTTTTTCCAC
9091 SEQ ID N0:3800 -7.9 -18.8 59.8 -10.9 0 0
AGCTGTTCAGCTTTTTTTTT
122 SEQ ID N0:3801 -7.8 -22.6 69.8 -13 -1.7 -10.8
GGCTTCAGTTTTCTTGCTCC
232 SEQ ID N0:3802 -7.8 -27.1 80.5 -18.6 -0.4 -3.7
GAATCCTTGACAGGTATCTC
278 SEQ ID N0:3803 -7.8 -22.6 67.8 -13.8 -0.9 -3.6
TCTTACAATATCCCTAGAAG
336 SEQ ID N0:3804 -7.8 -19.9 60 -12.1 0 -3.8
TCTTCTGCAGCACGTTTTTC
547 SEQ ID N0:3805 -7.8 -24.7 73.3 -16.4 0 -8.3
TAAATAAATGGAAGGTTCTT
646 SEQ TD N0:3806 -7.8 -15.6 50.7 -7.8 0 -4.2
CTCCATAAATAAATGGAAGG
651 SEQ ID N0:3807 -7.8 -16.9 52.4 -6.8 -2.3 -7.8
GGAATGTCTCCATAAATAAA
658 SEQ ID N0:3808 -7.8 -17.3 53.7 -8.4 -1 -4
AGGAATGTCTCCATAAATAA
659 SEQ ID N0:3809 -7.8 -18 55.5 -8.4 -1.8 -4.8
CATCTCTGGAGGAATGTCTC
668 SEQ ID N0:3810 -7.8 -23.1 69.8 -14.6 -0.4 -6.1
CTTGATAGCAATTTTCCTAA
821 SEQ ID N0:3811 -7.8 -19.7 59.7 -11.3 -0.3 -0.5
AGATTTTTATAAGTGACTCA
972 SEQ ID N0:3812 -7.8 -17.7 56.9 -9.9 0 -4.7
GGTTTCGACCAGCCTTCACA
1527 SEQ ID N0:3813 -7.8 -28.1 77.5 -18.4 -1.9 -7.2
TAGCCATAGTTGGGGTTTCG
1540 5EQ ID N0:3814 -7.8 -25.4 73.2 -16.1 -1.4 -5.1
AAAAAATATCATGTATGTTT
1664 SEQ ID N0:3815 -7.8. -13.6 46.7 -5.3 -0.1 -5.8
ATTCACCAAATAAAATGAGC
1703 SEQ ID N0:3816 -7.8 -16.7 52.1 -8.9 0 -3
TCCTTTGTTGTTTCCTTCAA
2006 5EQ ID N0:3817 -7.8 -24 71.1 -16.2 0 -2.9
GAAAACAGGGAGCCACGGAT
2155 SEQ ID N0:3818 -7.8 -23.7 65.1 -15.3 -0.3 -4.3
GCCCGACCTCTGAAACTGAA
2203 SEQ ID N0:3819 -7.8 -25.8 68.6 -18 0 -2.8
CAATCCACAGTGCTGTGCAT
2401 SEQ ID N0:3820 -7.8 -25.6 72.6 -15.9 -1.2 -11.9
CATGCATCACAGCAGTCCCA
2689 SEQ ID N0:3821 -7.8 -28 77.8 -18.9 -1.2 -7.5
ATTAAATTCACAAGATGTTT
271g SEQ ID N0:3822 -7.8 -15.8 51.6 -8 0 -3.2
TCCCTCCACATTTGACAGAC
2gg0 SEQ TD N0:3823 -7.8 -25.8 72.4 -18 0 -2.4
CCAGCGACCTCCATACAGTC
3319 SEQ ID N0:3824 -7.8 -28.3 77.1 -20.5 0 0
CAAGGTTTCCAATGACCATG
3372 SEQ ID N0:3825 -7.8 -22.5 64.3 -13.1 -1.5 -5.8
AGGTTCAGAACCACAAGGTT
3385 SEQ ID N0:3826 -7.8 -23.1 67.6 -12.6 -2.7 -12
219
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mot kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CGGTTTAAAGTCTTCTTCGG
3947 SEQ ID N0:3827 -7.8 -22.1 64.9 -13.6 -0.5 -4.7
TATATCTTCAAAGGCCAATG
4136 SEQ ID N0:3828 -7.8 -19.5 58.7 -11.2 0 -7.7
CAGGCTAACCAAAGAAACAT
4313 SEQ ID N0:3829 -7.8 -19.2 56.5 -10 -1.3 -3.7
GATTTGATGGCACCGAGTTC
4357 SEQ ID N0:3830 -7.8 -24.4 69.9 -16.6 0 -4
GAGGTCTTAAAGCTCTTAAT
4386 SEQ ID N0:3831 -7.8 -19.8 61.2 -11.5 -0.1 -5.9
GATAAGGCTCTTAGAGGTCT
4399 SEQ ID N0:3832 -7.8 -22.9 69.8 -14.5 -0.3 -6.1
CCGGGATAAGGCTCTTAGAG
4403 SEQ ID N0:3833 -7.8 -24.4 69.3 -16.1 -0.2 -6.1
TGTCAAACATGTTACCCGTT
4575 SEQ ID N0:3834 -7.8 -23.1 65.6 -14.7 0 -8.5
GTTTCTTCATTGCATTGTAA
4947 SEQ ID N0:3835 -7.8 -20.8 64.3 -13 0 -6.2
GAGGCAGATGAGGATCATGA
5066 SEQ ID N0:3836 -7.8 -23 68 -13.1 -2.1 -7.8
CCATCATGGTGACCATGTTG
5085 SEQ ID N0:3837 -7.8 -25 70.9 -14 -3.2 -11.5
GATGTTCCAGCCTATAGTGA
5225 SEQ ID N0:3838 -7.8 -24.9 72.8 -17.1 0 -5.1
GTGAATTGTGTCAGGGTCAC
5648 SEQ ID N0:3839 -7.8 -23.6 71.4 -15.2 -0.3 -5.2
GGGATCAAACTTTTCCCAAA
5858 SEQ ID N0:3840 -7.8 -21.8 62.2 -11.9 -2.1 -7.7
TAGAGAACTCTATAAACTGG
5886 SEQ ID N0:3841 -7.8 -16.9 53.9 -8.6 0 -7.5
AAGCTGGACTTTGTTGGGTT
5954 SEQ ID N0:3842 -7.8 -24.1 71.2 -16.3 0 -5.1
ATCCATCTCTCCACTCTCAC
6056 SEQ ID N0:3843 -7.8 -26.5 77.4 -18.7 0 -0.5
GAGACTTTGGAGGGGTTTGA
6112 SEQ ID N0:3844 -7.8 -23.9 70.9 -16.1 0 -2.6
TTGCTTTAAAAGATAACATC
6206 SEQ ID N0:3845 -7.8 -15.5 50.7 -7.7 0 -4.3
GTAAGTCAATCCTCCCTTTA
6267 SEQ ID N0:3846 -7.8 -24.3 70.3 -16.5 0 -2.4
GTTTGTCTTTCTCAAACTTT
6408 SEQ ID N0:3847 -7.8 -20.4 63.7 -10.2 -2.4 -7.4
AGATAATTCTTTGTTTCTTT
6475 SEQ ID N0:3848 -7.8 -18.1 58.5 -10.3 0 -2.9
ACTATGAGTATTTGTTAAAA
6578 SEQ ID N0:3849 -7.8 -15.4 51 -7.6 0 -2.8
AGGTCACTTCACTGTCTTGT
6608 SEQ ID N0:3850 -7.8 -24.7 75.7 -16.9 0 -2.6
AATAGTGACATAGCATTATG
6885 SEQ ID N0:3851 -7.8 -17.7 56 -8.8 -1 -4.7
AGTGCAAAAGTAAAGGTGTT
7702 SEQ ID N0:3852 -7.8 -18.8 57.9 -11 0 -5.4
GATACTCATGTTGAATTAAA
7722 SEQ ID N0:3853 -7.8 -16.1 52.1 -8.3 0 -4.7
AGTTTTAGACATATTTTTAG
7816 SEQ ID N0:3854 -7.8 -16.5 54.7 -8 -0.4 -2.9
AAAACCCATTATCTAACTTT
8021 SEQ ID N0:3855 -7.8 -18.2 55.2 -10.4 0 -1.9
220
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal)
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TAATTATATATATTTTAAAC
8536 SEQ ID N0:3856 -7.8 -10.7 41.2 -2.9 0 -5
ACATGTGAACTTGATCCTTT
8693 SEQ ID N0:3857 -7.8 -21.3 63.5 -13.5 0 -6.1
TATTGTAGGTGGTTACTACT
8738 SEQ ID N0:3858 -7.8 -21.2 65.9 -11.8 -1.6 -5.2
TGAGTTTAGATGCTTATAGC
8784 SEQ ID N0:3859 -7.8 -20.3 63.5 -11.6 -0.8 -4.2
ACCTTATGTATACATAGGAG
8892 SEQ ID N0:3860 -7.8 -19.9 61.1 -9.9 -1.1 -12.6
TGCTCCTTTCCCAGTAAGCC
308 SEQ ID N0:3861 -7.7 -29.3 80.6 -20.7 -0.8 -4.5
GGAAGCTTTCAGGTCCTGGG
495 SEQ ID N0:3862 -7.7 -27.2 77.9 -18 -0.8 -10.8
TACCAAAATCTTGATAGCAA
830 SEQ ID N0:3863 -7.7 -18 55 -9.7 -0.3 -4.5
GTCAAAATAGTGCACATGAT
871 SEQ ID N0:3864 -7.7 -19.1 58.3 -10.4 0 -9.9
ACATATGCCATCACAATGAC
1060 SEQ ID N0:3865 -7.7 -21.2 62 -12.8 -0.5 -8.3
ACTCTGAATGTTCTCAACGC
1111 SEQ ID N0:3866 -7.7 -22.1 65.1 -13.5 -0.8 -4.6
GCCCCCACAATGGTCTTTAA
1168 SEQ ID N0:3867 -7.7 -27.6 73.9 -19 -0.7 -4.3
CCCATGAACAGCTGCAGCCC
1264 SEQ ID N0:3868 -7.7 -30.5 79.5 -20.3 0 -13.2
GCTTGGGGGCCACTGCAAAC
1301 SEQ ID N0:3869 -7.7 -28.5 76.9 -19.3 -l.4 -7.1
CATTTCCACAGAGTAAAGGG
1470 SEQ ID N0:3870 -7.7 -21.4 63.3 -13.7 0 -3.5
CCTTTGTTGTTTCCTTCAAG
2005 SEQ ID N0:3871 -7.7 -23.6 69.7 -15.9 0 -3.1
TGCTTCTTTTGACGCTGTCT
2058 SEQ ID N0:3872 -7.7 -25.2 73.6 -15.5 -2 -7.6
GCTCTCCATGTCTGTGCGGC
2310 SEQ ID N0:3873 -7.7 -30.4 85.5 -22.7 0 -5.1
TGGTGCCCTCTGGGGGAAGT
2478 SEQ ID N0:3874 -7.7 -30.3 83.3 -21 -1.5 -8
AGAGGGTATTTAAGACAATG
2778 5EQ TD N0:3875 -7.7 -17.9 56.3 -10.2 0 -2.6
TCTGCTGTGAAAATCCCAGT
2869 SEQ ID N0:3876 -7.7 -24 68.4 -15.8 -0.1 -3.6
GGCTGACAATAATTCCATCA
2952 SEQ ID N0:3877 -7.7 -22 63.9 -14.3 0 -3.7
CTCTAAGCAGTCTGAATGAT
3024 SEQ ID N0:3878 -7.7 -20.7 63 -13 0 -6.3
CGGGTTCAGTTTCAGCTTGT
3930 SEQ ID N0:3879 -7.7 -26.1 76.9 -18.4 0 -4.5
TCAGTAAAACAAGCTTCCGG
3964 SEQ ID N0:3880 -7.7 -21.3 61.5 -13.6 0 -6.4
GAAGCATTTCCAGAATGAAT
4221 SEQ ID N0:3881 -7.7 -19.5 58.4 -10.2 -1.6 -5.7
GAAATATGTTTGAAATCCAT
4256 SEQ ID N0:3882 -7.7 -16.6 52.3 -8.9 0 -4.1
TGAAATATGTTTGAAATCCA
4257 SEQ ID N0:3883 -7.7 -16.6 52.3 -8.9 0 -4.1
AGGTCTTAAAGCTCTTAATG
4385 SEQ ID N0:3884 -7.7 -19.2 59.8 -11.5 0 -5.7
221
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CAGCAAACAAATTCACACCC
4527 SEQ ID N0:3885 -7.7 -21.6 61 -13.9 0 -4.1
CCAGCAAACAAATTCACACC
4528 SEQ ID N0:3886 -7.7 -21.6 61 -13.9 0 -4.1
TAATGTCAAACATGTTACCC
4578 SEQ ID N0:3887 -7.7 -20 59.4 -11.1 -1.1 -9
GGCAGATGAGGATCATGATG
5064 SEQ ID N0:3888 -7.7 -22.4 66.3 -13.1 -l.6 -8.5
GTTGAGGCAGATGAGGATCA
5069 SEQ ID N0:3889 -7.7 -23.7 70.5 -14.8 -1.1 -6
GTCATCCGTTTCCACCATCA
5099 SEQ ID N0:3890 -7.7 -28 77.5 -20.3 0 -2.6
AAAACTAGGGTCATGTATTT
5125 SEQ ID N0:3891 -7.7 -18.5 57.6 -10.8 0 -4.7
CAAATTCTCCAGTGAACAGA
5172 SEQ ID N0:3892 -7.7 -20.4 60.7 -12.7 0 -3.9
TTCTATCATCTCAGCCAGAA
5285 SEQ ID N0:3893 -7.7 -23 68.6 -15.3 0 -3.6
TTCCCAAACCTCATAGAACA
5846 SEQ TD N0:3894 -7.7 -22.5 63.5 -14.8 0 -2.7
ACATCTGAAATTACGCTGAA
6191 SEQ ID N0:3895 -7.7 -18.8 56.4 -11.1 0 -3.3
AACATCTGAAATTACGCTGA
6192 SEQ ID N0:3896 -7.7 -18.8 56.4 -11.1 0 -3.3
GGGTGGTAGAGGAACTCCCA
6348 SEQ ID N0:3897 -7.7 -27.6 77.5 -17.2 -2.7 -8.2
GTAGCCATTGGGTTTCTCCT
6707 SEQ ID N0:3898 -7.7 -27.9 80.6 -19.3 -0.8 -6.3
TCACTTTGCACAACTATCCC
6737 SEQ ID N0:3899 -7.7 -24.3 69.2 -16.6 0 -5
TTATGAATAAACTATGAATT
6870 SEQ ID N0:3900 -7.7 -12.8 45.1 -5.1 0 -3.1
TCATTTACAAAAT1TAGTGAC
6896 SEQ ID N0:3901 -7.7 -14.8 49.3 -6.4 -0.5 -5
CCATCTAGAAAATGGAAGTA
7042 SEQ ID N0:3902 -7.7 -18.2 55.7 -9.5 -0.9 -7.2
AAAATTAAAGCCATCTAGAA
7052 SEQ ID N0:3903 -7.7 -15.7 50.2 -8 0 -6.2
TCTAGAATGGATTTATTAGA
7249 SEQ ID N0:3904 -7.7 -17 55 -9.3 0 -5.2
TGAAGAATGGATTGAGTAAA
7587 SEQ ID N0:3905 -7.7 -15.8 51 -8.l 0 -2.1
TATGATACTCATGTTGAATT
7725 SEQ ID N0:3906 -7.7 -17.5 55.7 -8.9 -0.8 -4.9
ATATGATACTCATGTTGAAT
7726 SEQ ID N0:3907 -7.7 -17.4 55.4 -8.8 -0.8 -5.1
AGACATATTTTTAGCAAAAT
7810 SEQ ID N0:3908 -7.7 -15.7 51.1 -6.8 -1.1 -5.3
GGAAATTATCCATTGAAAAA
7994 SEQ ID N0:3909 -7.7 -15.2 49 -6 -1.4 -6.8
GTAATAGCTTTAGTGCAGCA
8227 SEQ ID N0:3910 -7.7 -22.7 68.6 -13.4 -1.5 -6.5
AGTTCTTCAATACACTACAG
8381 SEQ ID N0:3911 -7.7 -19.4 60.7 -11.7 0 -3.1
AGCAATTCCCTGCATGCAGT
8398 SEQ ID N0:3912 -7.7 -27.4 76.3 -16.6 -1.9 -14.3
TATTCTTTTGGCTCAATAAT
8446 SEQ ID N0:3913 -7.7 -18.7 58.3 -11 0 -4.9
222
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATCAAACCTGAAAGTTGGAA
8712 SEQ TD N0:3914 -7.7 -18.4 55.6 -10 -0.4 -3.8
TTTGGTTTTGACCTCACATA
8970 SEQ ID N0:3915 -7.7 -22.3 66.5 -12.3 -2.3 -4.8
CCAAGATGGTTAGGGTATAA
158 SEQ ID N0:3916 -7.6 -21.1 62.7 -13 -0.2 -3.7
AGTTTTCTTGCTCCATAATC
226 SEQ ID N0:3917 -7.6 -22.1 67.2 -14.5 0 -4.4
CTTCTGTGAATTATCTCATT
359 SEQ ID N0:3918 -7.6 -19.7 61.6 -12.1 0.4 -3.2
TTGCATACGAATTACCTTAG
417 SEQ ID N0:3919 -7.6 -19.9 59.2 -12.3 0 -5.1
TTCTTTCCAGCTTCCAAGTC
631 SEQ ID N0:3920 -7.6 -25.5 75.1 -17.9 0 -4.5
CCATGAACAGCTGCAGCCCA
1263 5EQ ID N0:3921 -7.6 -29.2 77.2 -19.1 0 -13.2
ACAAATGTCCCATTTGAATC
1369 SEQ ID N0:3922 -7.6 -20.3 59.9 -8.9 -3.8 -10.4
GTCAACTGGTAAAGATTTTC
1627 SEQ ID N0:3923 -7.6 -18.7 58.6 -11.1 0 -3.2
ACAAAAAATATCATGTATGT
1666 SEQ ID N0:3924 -7.6 -14.3 47.9 -6.7 0 -4.7
GGAGCAGAATTTTTTGTCAC
2114 SEQ ID N0:3925 -7.6 -21.2 64.6 -13.6 0 -4.l
TTCATCATCAGCAAAGTCAT
2243 SEQ ID N0:3926 -7.6 -20.8 63.4 -13.2 0 -4.1
ATACTGGCCTGACTAACGTT
2341 SEQ ID N0:3927 -7.6 -23.7 67.2 -15.6 0 -7.8
TTGTCCAGTAGGTGACGTTA
2459 SEQ ID N0:3928 -7.6 -24.3 71.8 -15.6 -1 -7
AAGCTCCATTAAACTGAGGC
2969 SEQ TD N0:3929 -7.6 -22.2 64.5 -14.1 -0.1 -5
ATTGCCAATGATCTTAATTA
3083 SEQ ID N0:3930 -7.6 -18.7 57.3 -11.1 0 -4.9
CACAGAATTGCCAATGATCT
3089 SEQ ID N0:3931 -7.6 -21.3 62 -13.7 0 -4.9
CAGGCATTAGTGAAATATGT
4267 SEQ ID N0:3932 -7.6 -19.5 59.6 -11.9 0 -4
TGCCAGCAAACAAATTCACA
4530 SEQ ID N0:3933 -7.6 -21.2 60.7 -13.6 0 -5.2
TTGCATTGTAATATTTTTTC
4938 SEQ ID N0:3934 -7.6 -17.5 56.4 -9.9 0 -5.1
ATGATGCTGATATCAAAGAC
5050 SEQ ID N0:3935 -7.6 -18.1 56.3 -9.6 -0.8 -7.7
AGATGTTCCAGCCTATAGTG
5226 SEQ ID N0:3936 -7.6 -24.3 71.7 -16.7 0 -5.1
AGGATTCGGCCAATCCTGGC
5347 SEQ ID N0:3937 -7.6 -28.4 76.7 -17.1 -3.3 -15.1
TCTCAAAGTTGAACATGTCA
5532 SEQ ID N0:3938 -7.6 -19.4 59.8 -11.3 -0.1 -7
CAGGGTGAATTGTGTCAGGG
5652 SEQ ID N0:3939 -7.6 -24.2 71.3 -16.6 0 -3.3
TCTTCAGTAGCAACACTGAA
5791 SEQ ID N0:3940 -7.6 -21.1 63.7 -10.6 -2.9 -9.6
CATCTCAAAGTCATCCTCAC
5828 SEQ ID N0:3941 -7.6 -22.6 67.2 -15 0 -1.9
TCCCAAACCTCATAGAACAT
5845 SEQ ID N0:3942 -7.6 -22.4 63.2 -14.8 0 -2.5
223
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GAACTCTATAAACTGGGTCG
5882 SEQ TD N0:3943 -7.6 -20.2 60.1 -12.6 0 -2.7
TGGGTTTTGCTATGAGAAGA
5940 SEQ ID N0:3944 -7.6 -21.4 64.5 -13.8 0 -3.6
AGAGGAACTCCCATCTGTTT
6341 SEQ ID N0:3945 -7.6 -24.6 71.2 -14.6 -2.4 -6.7
GTTTCTCCTCAGCAGTGTCA
6696 SEQ ID N0:3946 -7.6 -27.1 81.9 -19.5 0 -4.2
TTCACTTTGCACAACTATCC
6738 SEQ ID N0:3947 -7.6 -22.4 66 -14.8 0 -5
TGGGGACCATGGAAATGCAC
6851 SEQ ID N0:3948 -7.6 -24.2 67.2 -14.4 -2.2 -9.8
TATGAATAAACTATGAATTG
6869 SEQ ID N0:3949 -7.6 -12.7 44.8 -5.1 0 -3.1
ATTATGAATAAACTATGAAT
6871 SEQ ID N0:3950 -7.6 -12.7 44.8 -5.1 0 -3.5
GTTCAGATAGAAACAAACAT
7091 SEQ ID N0:3951 -7.6 -16.3 52.1 -8 -0.5 -3.7
TATATATATATTTGCCCAAA
7418 SEQ ID N0:3952 -7.6 -17.8 54.8 -10.2 0 -6.7
TTATATTTAAACAAGTTTTA
7829 SEQ ID N0:3953 -7.6 -13.4 46.8 -5.8 0 -5.5
CACAAAGCTGCTTTTAATTT
8658 5EQ TD N0:3954 -7.6 -19.1 58.1 -10 -0.3 -10.9
TTTATATAATGCATTTAAGT
8872 SEQ ID N0:3955 -7.6 -15.5 51.3 -7.2 0 -8.8
GAGTTTGGTTTTGACCTCAC
8973 SEQ TD N0:3956 -7.6 -23.7 70.9 -13.8 -2.3 -6.2
TAAGAGTTTGGTTTTGACCT
8976 SEQ TD N0:3957 -7.6 -21.4 64.8 -11.5 -2.3 -6.3
TTCTCTGTGGATAAGAAAAC
47 SEQ ID N0:3958 -7.5 -17.4 55 -9.9 0 -3.5
TCTAGTAAAAAGGCGGAAGC
509 SEQ TD N0:3959 -7.5 -19.8 58.7 -10.7 -1.6 -7.2
CGTTTTTCGATAGCAGCAAG
535 SEQ ID N0:3960 -7.5 -22.2 64.4 -14.7 0 -5.4
CAGCTTCCAAGTCACTATTT
624 SEQ TD N0:3961 -7.5 -23.2 68.7 -15.7 0 -4.5
AAATAAATGGAAGGTTCTTT
645 SEQ TD N0:3962 -7.5 -16 51.6 -8.5 0 -4.2
AAGGTCATAAATACACAGTT
892 SEQ ID N0:3963 -7.5 -17.9 56.1 -10.4 0 -2.8
TCCAGTCAGGAGGGTTGCTC
912 SEQ ID N0:3964 -7.5 -28 82.7 -19.5 -0.9 -6.2
GAAATCCAGCCAGTTCCATG
1037 SEQ ID N0:3965 -7.5 -25.2 70.3 -17.7 0 -3.9
GGGCCCCCACAATGGTCTTT
1170 SEQ ID N0:3966 -7.5 -31 81.6 -21.7 -0.7 -11.8
ACGGATACTCAAGAGAGACT
2141 SEQ ID N0:3967 -7.5 -20.9 62.2 -11.8 -1.5 -6.2
GACATACTGGCCTGACTAAC
2344 SEQ ID N0:3968 -7.5 -23.1 66.5 -15.6 0 -7.2
GCTGGAAGCCCTGGCACCAT
2371 SEQ ID N0:3969 -7.5 -31.1 81.6 -22 -1.5 -10.6
TCCACAGTGCTGTGCATCTT
2398 SEQ ID N0:3970 -7.5 -27 78.3 -17.3 -1.7 -12.4
TGTCCAGTAGGTGACGTTAG
2458 SEQ ID N0:3971 -7.5 -24.2 71.7 -15.6 -1 -7
224
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GAGGAATCCTCCAGCATCTC
2551 SEQ ID N0:3972 -7.5 -26.3 75.4 -16.9 -1.9 -10
ACAAGATGTTTTACTTTTAA
2710 5EQ ID N0:3973 -7.5 -16.4 53.3 -8.9 0 -2.9
TCCATCAAAGATATTCCAGC
2939 SEQ ID N0:3974 -7.5 -22.1 64.6 -13.9 -0.4 -3.5
AACAATAAGGCACATGGTTT
3341 SEQ TD N0:3975 -7.5 -19.7 59 -12.2 0 -5.2
AATCAATTCCCTTTTGCATT
3501 SEQ ID N0:3976 -7.5 -22 64 -14.5 0 -5.1
TCATTTTCATCGATTACGTA
3718 SEQ ID N0:3977 -7.5 -20 60.5 -11.6 -0.7 -6.3
TATAATCATTTTCATCGATT
3723 SEQ TD N0:3978 -7.5 -17.1 54.5 -9.6 0 -6.3
CTGTGCTTCCTTCAGATGAG
3882 SEQ ID N0:3979 -7.5 -24.6 72.7 -17.1 0 -3.7
GTTCAGTTTCAGCTTGTTCA
3927 SEQ ID N0:3980 -7.5 -24.1 74.9 -16.6 0 -4.5
GTAGCAGGTTTTTCGAAGAT
4052 SEQ ID N0:3981 -7.5 -21.9 65.8 -13.7 -0.4 -6.8
CCACTACTGAGAAGGATCAT
4114 SEQ ID N0:3982 -7.5 -22 64.5 -13.6 -0.8 -6.3
ATCTTCAAAGGCCAATGCAC
4133 SEQ ID N0:3983 -7.5 -22.8 65.4 -13.8 -1.4 -7.7
AATGATTTGATGGCACCGAG
4360 SEQ ID NO:3984 -7.5 -22 62.8 -14.5 0 -4
TAGAGGTCTTAAAGCTCTTA
4388 SEQ ID N0:3985 -7.5 -20.2 63 -11.5 -1.1 -5.2
TTGCTCCAACAAGAGCATTC
4446 SEQ ID N0:3986 -7.5 -23 66.9 -12.1 -3.4 -9.5
TTGCCAGCAAACAAATTCAC
4531 SEQ ID N0:3987 -7.5 -20.6 59.9 -13.1 0 -7.1
TGCTGGTTGAAGTTATCTAT
4873 SEQ ID N0:3988 -7.5 -21.1 64.8 -13.6 0 -3.6
ATATTTTTTCTGTTCCTCTG
4928 SEQ ID N0:3989 -7.5 -21.4 66.3 -13.9 0 -1.8
CATTGTAATATTTTTTCTGT
4935 SEQ TD N0:3990 -7.5 -17.7 56.9 -10.2 0 -4.2
TGCATTGTAATATTTTTTCT
4937 SEQ ID NO:3991 -7.5 -18.3 58 -10.8 0 -4.7
TCATTGCATTGTAATATTTT
4941 SEQ ID N0:3992 -7.5 -18 57 -10.5 0 -6.2
TTCATTGCATTGTAATATTT
4942 SEQ ID N0:3993 -7.5 -18 57 -10.5 0 -6.2
TTCTTCATTGCATTGTAATA
4945 SEQ TD N0:3994 -7.5 -19.2 60 -11.7 0 -5.6
TTGGATCCAAGTTTCTTCAT
4957 SEQ ID N0:3995 -7.5 -22.2 66.7 -13 0 -11.5
CATGATGCTGATATCAAAGA
5051 SEQ ID N0:3996 -7.5 -18.6 57 -10.2 -0.8 -7.7
TTGAGGCAGATGAGGATCAT
5068 SEQ ID N0:3997 -7.5 -22.5 67 -13.1 -1.9 -7.8
GCCCTGGTCATCCGTTTCCA
5105 SEQ ID N0:3998 -7.5 -31.9 85.1 -23.7 -0.4 -4.2
CACAAATTCTCCAGTGAACA
5174 SEQ ID N0:3999 -7.5 -20.7 61 -13.2 0 -4.2
TTTGCTTTAAAAGATAACAT
6207 SEQ ID N0:4000 -7.5 -15.2 4g,g -7.7 0 -4.1
225
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATAGTTACTTGATATATTTT
6233 SEQ ID N0:4001 -7.5 -16.2 53.7 -8.7 0 -4.3
TCTTTTCCTTTGCTTTCTTT
6433 5EQ ID N0:4002 -7.5 -23.5 71.5 -16 0 -3.6
GGGTTTCTCCTCAGCAGTGT
6698 SEQ ID N0:4003 -7.5 -28.4 84.6 -20 -0.8 -5.7
GTACTAAAGGTGTTTGGTGT
6768 SEQ ID N0:4004 -7.5 -21.7 66.5 -13.3 -0.8 -4.6
CTTTTTCTGGTTTTGAGCAA
6998 SEQ ID N0:4005 -7.5 -21.7 65.9 -14.2 0 -4.1
GTGAAGAATGGATTGAGTAA
7588 SEQ ID N0:4006 -7.5 -17.7 55.6 -10.2 0 -2.1
TGAATTCATTCTATCACCAA
7634 SEQ ID N0:4007 -7.5 -19.5 59.2 -11.3 -0.4 -8
CAAAATATGAAGAATAGGTT
7796 SEQ ID N0:4008 -7.5 -14.3 47.8 -6.8 0 -2.7
TTCATGGCTAAAAAGAACAA
8263 SEQ ID N0:4009 -7.5 -16.1 51 -8.6 0 -4.7
ATTAACATTAAACTTTTGGT
8341 SEQ TD N0:4010 -7.5 -16.2 52.3 -8.7 0 -3.5
TGCAATAAAAAATGAAATTT
8465 SEQ ID N0:4011 -7.5 -11.4 41.9 -2.8 -1 -6.7
AAATATGCATTACAACTGGA
9011 SEQ ID N0:4012 -7.5 -17.7 54.6 -10.2 0 -6.8
AGCATAACAAAGCCCAGCAT
178 SEQ ID N0:4013 -7.4 -24 66.5 -15.7 -0.7 -5
GAGATTCTTTGCTCCTTTCC
317 5EQ ID N0:4014 -7.4 -25.4 74.8 -18 0 -4.2
CCTTCTGTGAATTATCTCAT
360 SEQ ID N0:4015 -7.4 -21.6 65.1 -14.2 0.4 -3.2
CCGGAAAAGCTCCAGGTCCC
378 SEQ ID N0:4016 -7.4 -29.1 75.6 -20.1 -1.5 -5.6
TGGGCTTCTTGGCTTTCTCT
564 SEQ ID N0:4017 -7.4 -27.3 80.6 -18.9 -0.9 -3.7
CAAGTCACTATTTGGCTTTG
617 SEQ ID N0:4018 -7.4 -21.4 64.6 -12.4 -1.5 -5
CCATCTCTGGAGGAATGTCT
669 SEQ ID N0:4019 -7.4 -24.7 71.9 -16.5 -0.6 -6.l
AGTTTTCTTATTGATATAGT
719 SEQ ID N0:4020 -7.4 -17.9 58.6 -10.5 0 -2.7
TGAATCGGAAAATTGCCTTT
759 SEQ ID N0:4021 -7.4 -19.8 57.7 -12.4 0 -4.4
AAAATATACAAGGCAGAGGT
784 SEQ ID N0:4022 -7.4 -18.2 55.9 -10.8 0 -4
AAAATCTTGATAGCAATTTT
826 SEQ ID N0:4023 -7.4 -15.7 51 -7.5 -0.6 -1.2
AGGGCCCCCACAATGGTCTT
1171 SEQ ID N0:4024 -7.4 -30.9 81.6 -21.7 -0.7 -11.8
TCTCCAATGTAATCCTTCCA
1414 SEQ ID N0:4025 -7.4 -24.4 69.5 -17 0 -2.2
ACCAGCCTTCACACAGATGT
1520 SEQ ID N0:4026 -7.4 -26.4 74.5 -18.4 -0.3 -3.8
TAGTTGGGGTTTCGACCAGC
1534 SEQ TD N0:4027 -7.4 -26.5 75.8 -16.4 -2.7 -7.1
CAACTTTGATGCTTCTGAAG
1925 SEQ ID N0:4028 -7.4 -19.9 60.3 -12 0 -7.8
AGCATCTCCATTGAAATCTG
2539 SEQ ID N0:4029 -7.4 -21.5 63.7 -14.1 0 -4.1
226
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAAATGAAGACGATGATGGC
3139 SEQ ID N0:4030 -7.4 -17.6 53.5 -10.2 0 -3.5
AGAGCTGCATGCCGACCACA
3162 SEQ ID N0:4031 -7.4 -28.8 76.8 -20.4 -0.8 -9.l
TGCAGATTATTCATTTCATT
3466 SEQ ID N0:4032 -7.4 -19.5 60.8 -11.6 -0.2 -4.9
TTTCATCGATTACGTATTTT
3714 SEQ ID N0:4033 -7.4 -19.1 58.6 -10.8 -0.7 -6.3
ACATATAATCATTTTCATCG
3726 SEQ ID N0:4034 -7.4 -17.3 54.6 -9.9 0 -2.5
GGTTCAGTTTCAGCTTGTTC
3928 SEQ ID N0:4035 -7.4 -24.6 76.7 -17.2 0 -4.5
TATCTTCAAAGGCCAATGCA
4134 SEQ ID N0:4036 -7.4 -22.3 64.3 -13.4 -1.4 -7.7
GTATATATCTTCAAAGGCCA
4139 SEQ ID N0:4037 -7.4 -21.1 63.2 -13.2 0 -7.7
TCTAGCCAGCACCAGGCATT
4279 SEQ ID N0:4038 -7.4 -28.7 79.8 -18.6 -2.7 -7.4
CAACAGCACATTCATGATAG
4472 SEQ ID N0:4039 -7.4 -19.8 59.8 -12.4 0 -6.4
TGGTTGAAGTTATCTATGAT
4870 SEQ ID N0:4040 -7.4 -19 59.8 -11.6 0 -2.6
CTATAGTGAAGTAGTAGTGT
5214 SEQ ID N0:4041 -7.4 -19.6 62.9 -12.2 0 -4.3
AGCCTATAGTGAAGTAGTAG
5217 SEQ ID N0:4042 -7.4 -21 65 -13.6 0 -5.1
TGTCATCAATTCCAGCTTCC
5517 SEQ ID N0:4043 -7.4 -25.1 72.9 -17.7 0 -4.5
TACATGTTCACCACAACCAG
5749 SEQ ID N0:4044 -7.4 -23 65.8 -14.9 -0.4 -6.5
TGACCGCGATGTACATGTTC
5760 SEQ ID N0:4045 -7.4 -24.3 68.3 -16.2 0 -8.9
GCAACACTGAAGTTCTCCAG
5782 SEQ ID N0:4046 -7.4 -23.4 68.1 -15.5 -0.2 -6.3
GGCAGATCCATGGCAATAAG
5971 SEQ ID N0:4047 -7.4 -23.4 66.7 -15.1 -0.7 -8
TGACCATGGGCAGATCCATG
5979 SEQ ID N0:4048 -7.4 -26.1 72.4 -15.8 -2.9 -8.8
TGGATCCGGTCACCACTGAC
5995 SEQ ID N0:4049 -7.4 -27.3 74.9 -16.5 -l.8 -14.9
TGAATGATAGCGGCAGACAC
6175 SEQ ID N0:4050 -7.4 -22.2 64 -14.8 0 -6.6
TAGTTACTTGATATATTTTT
6232 SEQ ID N0:4051 -7.4 -16.3 54.1 -8.9 0 -4.3
CATAGGAAGGAGGAGGGGTG
6363 SEQ ID N0:4052 -7.4 -23.9 69.7 -16.5 0 -1.2
CTTGTATAGGCACTGACTAT
6593 SEQ ID N0:4053 -7.4 -21.8 65.8 -13.7 -0.4 -4.8
GGTTTCTCCTCAGCAGTGTC
6697 SEQ ID N0:4054 -7.4 -27.6 83.8 -20.2 0 -4.2
CAATGTTCACTTTGCACAAC
6743 SEQ ID N0:4055 -7.4 -20.6 61.5 -13.2 0 -5
AAATAGTGACATAGCATTAT
6886 SEQ ID N0:4056 -7.4 -17 54.2 -9.6 0 -4.1
CTCATTTACAAAAATAGTGA
6897 SEQ ID N0:4057 -7.4 -15.5 50.6 -7.4 -0.5 -5
ATTTGATTTAATAGAAGTTG
7448 SEQ ID N0:4058 -7.4 -14.9 50.1 -7.5 0 -2.5
227
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AACTATGTTTAATGAATGAT
7521 SEQ ID N0:4059 -7.4 -15 49.7 -7.6 0 -3.1
TTTTTAGCAAAATATGAAGA
7803 SEQ ID N0:4060 -7.4 -14.7 48.9 -6.8 -0.1 -5.3
TTTTCTTATGTACAAAATGC
7882 SEQ ID N0:4061 -7.4 -16.9 54.1 -9.5 0 -6.8
TATCATGTTAGGTAATTGCA
8299 SEQ ID NO:4062 -7.4 -19.8 61.3 -12.4 0 -5.1
TAGCTCACCATTCTTTTTAG
8422 5EQ ID N0:4063 -7.4 -21.9 66.6 -14.5 0 -4.8
TCTTTTGGCTCAATAATGAC
8443 SEQ ID N0:4064 -7.4 -19.7 60.3 -11.6 -0.5 -5.3
ACAAAAAACCCCAGAGCCCA
8495 SEQ ID N0:4065 -7.4 -25.4 66 -18 0 -3.2
TTTTAAACTGCCAACAGCAA
8524 SEQ ID NO:4066 -7.4 -20.2 59 -11.2 -1.5 -8.9
CCTTTCCAGAATCCTCTCTG
20 SEQ ID N0:4067 -7.3 -26 73.8 -17.8 -0.7 -4.2
GTAAAAAGGCGGAAGCTTTC
505 SEQ ID N0:4068 -7.3 -20.3 59.7 -10.6 -2.4 -7.2
CTTTCCAGCTTCCAAGTCAC
629 SEQ TD NO:4069 -7.3 -25.9 74.7 -18.6 0 -4.5
CTTTATTCATTACTATAAAA
738 SEQ ID NO:4070 -7.3 -14.2 48.3 -6.9 0 -3.3
GTACCAAAATCTTGATAGCA
831 SEQ ID N0:4071 -7.3 -19.9 59.6 -12 -0.3 -4.4
GATCACGAAGAAACGTAAAA
1017 SEQ ID N0:4072 -7.3 -15.6 49.2 -7.4 -0.8 -6.1
CCCAATGAGAGCAAACACGC
1247 SEQ ID N0:4073 -7.3 -24 65 -16.7 0 -4.1
CATGAACAGCTGCAGCCCAA
1262 SEQ ID N0:4074 -7.3 -26.5 71.7 -16.7 0 -13.2
AAGCAGAATCGCTTGGGGGC
1311 SEQ ID N0:4075 -7.3 -26.3 72.8 -17.6 -1.3 -8.4
TAAAAGTGACTGTCATCTCC
1429 5EQ ID N0:4076 -7.3 -20.5 62.1 -12.5 -0.1 -8.8
CACACAGATGTATCCTTCTG
1511 SEQ ID N0:4077 -7.3 -22.7 67.3 -14.1 -1.2 -5
TCACACAGATGTATCCTTCT
1512 SEQ ID N0:4078 -7.3 -23.1 69.1 -15.1 -0.5 -3.7
TGCTTTTTAAGCTGTTCGAG
1816 SEQ ID N0:4079 -7.3 -21.9 65.5 -12 -2.6 -9.4
TTTGGAACTCAACTTTGATG
1934 SEQ ID N0:4080 -7.3 -18.7 57.6 -10.8 -0.3 -5
GAGCAGAATTTTTTGTCACT
2113 SEQ ID N0:4081 -7.3 -20.9 64 -13.6 0 -4.1
CGGATACTCAAGAGAGACTG
2140 SEQ ID N0:4082 -7.3 -20.7 61.5 -11.8 -1.5 -5.4
TATTGCGTCTTGGGGAAAAC
2169 SEQ ID N0:4083 -7.3 -21.3 62 -14 0 -5.2
AAAATGCTTGTTTTGCTATT
2185 SEQ ID N0:4084 -7.3 -18.7 57.7 -10.9 -0.2 -4.7
CACTGTGACGGTGAGGCTGG
3761 SEQ ID N0:4085 -7.3 -26.7 74.9 -18.2 -1.1 -6.5
CTCCAACAGCAATTGGCACT
3777 SEQ ID N0:4086 -7.3 -24.9 69.5 -16 -l.5 -8.1
TCTTCTTCGGGTTCAGTTTC
3937 SEQ ID N0:4087 -7.3 -24.6 75.2 -17.3 0 -3
228
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Tntra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligO
TCAACAATACTGTAGCAGGT
4063 SEQ ID N0:4088 -7.3 -21.2 63.8 -13 -0.7 -5.3
ATATATAGGTAAAGACTTTG
4203 5EQ ID N0:4089 -7.3 -15.7 51.8 -7.9 -0.1 -4.9
ACCAAAGAAACATCAACGAT
4306 SEQ ID N0:4090 -7.3 -17.6 52.8 -10.3 0 -3.5
GTTCTGAGTAGCCAAGAGCA
4341 SEQ ID N0:4091 -7.3 -25 73.6 -16.2 -1.4 -4.7
AGAGGTCTTAAAGCTCTTAA
4387 SEQ TD N0:4092 -7.3 -19.8 61.4 -11.5 -0.9 -5.6
ACCACCCTCATGCCTTCAAA
4423 SEQ ID N0:4093 -7.3 -27.6 73.5 -20.3 0 -4.4
AAGTTTAACATCTCGTGAAT
4754 SEQ ID N0:4094 -7.3 -18.2 56.4 -10.9 0 -3.9
GGACATCATCAAAGCAAAGA
5405 SEQ ID N0:4095 -7.3 -19.2 57.7 -11.3 -0.3 -4.4
CAACACTGAAGTTCTCCAGG
5781 SEQ ID N0:4096 -7.3 -22.8 66.4 -15.5 0.3 -6.3
CAGAGAGTTTAGAGAACTCT
5895 SEQ ID N0:4097 -7.3 -19.9 62.3 -8.6 -4 -9.5
CGGTCACCACTGACCATGGG
5989 5EQ ID N0:4098 -7.3 -28.2 75.5 -16.5 -4.4 -9.6
TGCTTTAAAAGATAACATCT
6205 SEQ ID N0:4099 -7.3 -16.3 52.2 -8.2 -0.6 -6.5
TAATTGCCTCTTTGTTATAG
6249 SEQ ID N0:4100 -7.3 -20 61.6 -12.7 0 -2.9
TAAAAATAGAATGGATGCAA
6793 SEQ ID N0:4101 -7.3 -14.1 47 -6.8 0 -5.6
TCTTTTTCTGGTTTTGAGCA
6999 SEQ ID N0:4102 -7.3 -22.8 69.9 -15.5 0 -4.1
TAAAGCCATCTAGAAAATGG
7047 SEQ ID N0:4103 -7.3 -17.5 53.8 -9.5 -0.5 -7.1
TGGATTGAGTAAAATAGAGC
7580 SEQ ID N0:4104 -7.3 -17.4 55 -10.1 0 -2.8
TATGAATAAAAGGTTATATT
8141 SEQ ID N0:4105 -7.3 -13.2 46 -5.9 0.2 -3
ACACTACAGTAAATAGTTTT
8370 SEQ TD N0:4106 -7.3 -17.3 55.5 -9.5 -0.1 -3.3
AAAAACCCCAGAGCCCAATA
8492 SEQ ID N0:4107 -7.3 -24.2 64.1 -16.9 0 -3.2
TTACAGCATAACAAAGCCCA
182 SEQ ID N0:4108 -7.2 -22.2 62.8 -15 0.6 -3.9
CTTGACAGGTATCTCATCCC
273 SEQ ID N0:4109 -7.2 -25.4 73.8 -18.2 0 -2.9
AAGTTTTCTTATTGATATAG
720 SEQ ID N0:4110 -7.2 -16 53.3 -8.1 -0.5 -3.7
GGCAGAGGTGGCACTGAATC
773 SEQ ID N0:4111 -7.2 -25.8 74.4 -17.7 -0.8 -4.7
GACTCAAAGGTATAGATTCC
958 SEQ ID N0:4112 -7.2 -20.3 61.8 -13.1 0 -2.5
AAAGTGACTGTCATCTCCAA
1427 SEQ ID N0:4113 -7.2 -21.5 63.9 -13.6 -0.1 -8.8
CAAAAAATATCATGTATGTT
1665 SEQ ID N0:4114 -7.2 -14.2 47.7 -7 0 -4.7
CTTCTTTTGACGCTGTCTTC
2056 SEQ ID N0:4115 -7.2 -23.9 71.4 -15.8 -0.8 -7.6
AGGAAGCTGCTTCTTTTGAC
2065 SEQ ID N0:4116 -7.2 -23 68.8 -13.2 -1.8 -13.3
229
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTCCAGTAGGTGACGTTAGA
2457 5EQ ID N0:4117 -7.2 -24.8 73.3 -17 -0.3 -7
TGGCAAATCTATACCAGCAT
2655 SEQ ID N0:4118 -7.2 -22.4 64.6 -14.5 -0.5 -4.5
AACACATTGGCAAATCTATA
2662 SEQ ID N0:4119 -7.2 -18.2 55.8 -11 0 -4.4
TTCACAAGATGTTTTACTTT
2713 SEQ ID N0:4120 -7.2 -18.5 58.5 -11.3 0 -3
GAGGCTGACAATAATTCCAT
2954 SEQ ID N0:4121 -7.2 -21.5 62.8 -14.3 0 -3.7
TGAGGCTGACAATAATTCCA
2955 SEQ ID N0:4122 -7.2 -21.5 62.8 -14.3 0 -3.7
AGCTCCATTAAACTGAGGCT
2968 SEQ ID N0:4123 -7.2 -23.8 68.5 -16.1 -O.l -4.6
ACAGAATTGCCAATGATCTT
3088 SEQ ID N0:4124 -7.2 -20.7 61.2 -13.5 0 -4.9
AGAAGTCGTTCATGTGCCAC
3240 SEQ ID N0:4125 -7.2 -24.6 71.3 -16.1 -1.2 -4.8
GAACCACAAGGTTTCCAATG
3378 SEQ ID N0:4126 -7.2 -22 62.9 -12.2 -2.6 -7.6
TGTCTATCTTATTGCCTTCA
3591 SEQ ID N0:4127 -7.2 -23.3 70.3 -16.1 0 -3
GATAATTAAGCTCTTTGCTT
3642 SEQ ID N0:4128 -7.2 -19.7 60.7 -10.3 -2.2 -8
AGATAATTAAGCTCTTTGCT
3643 SEQ ID N0:4129 -7.2 -19.6 60.5 -10.9 -1.4 -8
ATCGATTACGTATTTTTCAA
3710 SEQ ID N0:4130 -7.2 -18.3 56.4 -10.2 -0.7 -6.l
GACATATAATCATTTTCATC
3727 SEQ ID N0:4131 -7.2 -17.1 55.1 -9.9 0 -2.5
AATTGGCACTGTGACGGTGA
3767 SEQ ID N0:4132 -7.2 -24 68.2 -15 -l.8 -7.6
GCTTTCTTCTAGTTCTGACT
3839 SEQ ID N0:4133 -7.2 -23.6 73.1 -15.9 -0.2 -4
TCAGATGAGCTGGTTGCATT
3871 SEQ ID N0:4134 -7.2 -24.1 71.5 -15.3 -1.5 -8
TTCAGATGAGCTGGTTGCAT
3872 SEQ ID N0:4135 -7.2 -24.1 71.5 -15.3 -1.5 -8
GTAAAACAAGCTTCCGGTTT
3961 SEQ ID N0:4136 -7.2 -21.6 62.3 -13.6 -0.5 -8.6
TGTATATATCTTCAAAGGCC
4140 SEQ ID N0:4137 -7.2 -20.4 61.9 -13.2 0 -6.4
TCAAGAAATCTAGCCAGCAC
4287 SEQ ID N0:4138 -7.2 -21.8 63.8 -14.6 0 -4.6
TAATGATTTGATGGCACCGA
4361 SEQ ID N0:4139 -7.2 -21.7 62.1 -14.5 0 -4
CAGTCACTCAAATTGTTAAC
4603 SEQ ID N0:4140 -7.2 -18.4 57,5 -11.2 0 -5.8
CATTGCATTGTAATATTTTT
4940 SEQ ID N0:4141 -7.2 -17.7 56 -10.5 0 -5.6
AGGCAGATGAGGATCATGAT
5065 SEQ ID N0:4142 -7.2 -22.4 66.7 -13.1 -2.1 -8.5
TGAGGCAGATGAGGATCATG
5067 SEQ ID N0:4143 -7.2 -22.4 66.6 -13.1 -2.1 -7.8
GAGCTTCAGCACAAATTCTC
5183 SEQ ID N0:4144 -7.2 -22.3 66.7 -14.2 -0.7 -6.6
GGATTCGGCCAATCCTGGCA
5346 SEQ ID N0:4145 -7.2 -29.1 77.4 -17.6 -4.3 -13.6
230
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CTCCTTTGATCAGACGTAGG
5364 SEQ ID N0:4146 -7.2 -23.8 69.3 -16.6 0 -6.5
TTCCTTTTTAACATAGGCAA
5501 SEQ TD N0:4147 -7.2 -20.4 61.2 -13.2 0 -4
CATGTTCACCACAACCAGGA
5747 SEQ ID N0:4148 -7.2 -24.9 69.5 -17 -0.4 -5.7
ACGCTTTGTAAAGGCAAATA
6029 SEQ ID N0:4149 -7.2 -19.4 57.6 -10.2 -2 -7.2
AGAGACTTTGGAGGGGTTTG
6113 SEQ ID N0:4150 -7.2 -23.3 69.8 -16.1 0 -2.6
TAGAGGAACTCCCATCTGTT
6342 SEQ ID N0:4151 -7.2 -24.2 70.2 -14.6 -2.4 -6.7
TTGATCACAAAGATAATTCT
6485 SEQ ID N0:4152 -7.2 -16.3 52.5 -8.4 -0.5 -6.5
TGTCAACGTTGATACCCTGC
6651 SEQ ID N0:4153 -7.2 -25.1 70.1 -15.6 -0.1 -12.8
CTCCTCAGCAGTGTCAGCTG
6692 SEQ ID N0:4154 -7.2 -28 82.2 -19 -l.8 -8
GTAACTGAAACTGTAGCCAT
7025 SEQ ID N0:4155 -7.2 -21 62 -13.8 0 -3.3
ATCTAGAAAATGGAAGTAAC
7040 SEQ ID N0:4156 -7.2 -15 49.6 -7.8 0 -6.2
ACATAACTGTTCAGATAGAA
7099 SEQ ID N0:4157 -7.2 -17.6 55.7 -9.8 -0.3 -5.6
ATTTGACCTAAATTAAATAT
7213 SEQ TD N0:4158 -7.2 -14.3 47.8 -6.6 -O.l -3.2
ACTATTTACATAACATAGGG
7377 SEQ ID N0:4159 -7.2 -17.6 55.5 -9.9 -0.1 -4.2
GTGCAAAAGTAAAGGTGTTT
7701 SEQ ID N0:4160 -7.2 -18.9 58.1 -11.7 0 -5.4
TAATTTTCTTATGTACAAAA
7885 SEQ ID N0:4161 -7.2 -14.1 48 -6.9 0 -6.8
AGTGTTTGACCAATGTATCT
8084 SEQ ID N0:4162 -7.2 -21.6 65.3 -14.4 0 -3.1
TTAGGTAATTGCACAACTTT
8292 SEQ ID N0:4163 -7.2 -19.3 59.2 -12.1 0 -5.1
GCTATTGTAGGTGGTTACTA
8740 5EQ ID N0:4164 -7.2 -22.8 69.9 -15.1 -0.1 -4
TTGAAAGCTATTGTAGGTGG
8746 SEQ ID N0:4165 -7.2 -20.3 62 -13.1 0 -4.6
TTATATAATTTATTATGGGA
9070 SEQ ID N0:4166 -7.2 -15.2 50.7 -7.2 -0.6 -5
TTTTTTTTTGACCACAGAGG
99 SEQ ID N0:4167 -7.1 -21 63.4 -13.4 -0.2 -3.6
TTTTTCCGGAAAAGCTCCAG
383 SEQ ID N0:4168 -7.1 -23.1 65 -12.9 -1.5 -14.4
GCAAACACGCTCAGACAGAA
1237 SEQ ID N0:4169 -7.1 -22.2 63 -15.1 0 -3.6
CTCCTCATAGGCCATGGCCA
1739 SEQ ID N0:4170 -7.1 -30.4 82.2 -18.7 -2.5 -17.4
TTCTGCTCCTCATAGGCCAT
1744 SEQ ID N0:4171 -7.1 -27.9 79.2 -20.1 -0.5 -7.7
CTTCTGAAGAACTTTCCAAC
1914 SEQ ID N0:4172 -7.1 -20 60.1 -12.9 0.3 -7.2
CATCCATGGAGAAAAGGAAG
2079 SEQ ID N0:4173 -7.1 -19.2 57.1 -10.8 -0.4 -10.4
GGGAGCAGAATTTTTTGTCA
2115 5EQ ID N0:4174 -7.1 -22.2 66.7 -15.1 0 -4.1
231
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTTTACTTTTAACCATGCAT
2702 SEQ ID N0:4175 -7.1 -19.8 59.9 -12.7 0 -6.4
CCCCACAGAATTGCCAATGA
3092 SEQ ID N0:4176 -7.1 -26 69.1 -18.9 0 -4.3
CACATAATCAATTCCCTTTT
3506 SEQ ID N0:4177 -7.1 -20.7 61 -13.6 0 -2.5
TTCATCGATTACGTATTTTT
3713 SEQ ID N0:4178 -7.1 -19.1 58.6 -11.5 -0.1 -6.3
TTGTTTATGAATGACATATA
3739 SEQ ID N0:4179 -7.1 -16 52.3 -8 -0.7 -6
TCGGGGTAGAACAACATCAA
3902 SEQ ID N0:4180 -7.1 -21.1 61.3 -14 0 -3
AAAGTCTTCTTCGGGTTCAG
3941 SEQ ID N0:4181 -7.1 -22.6 67.9 -14.8 -0.5 -3.8
AGGCTAACCAAAGAAACATC
4312 SEQ ID N0:4182 -7.1 -18.9 56.5 -10.4 -1.3 -3.7
AGGCTCTTAGAGGTCTTAAA
4395 SEQ ID N0:4183 -7.1 -21.7 66.3 -14 -0.3 -5.3
GAGCATTCACAACCACCCTC
4434 SEQ ID N0:4184 -7.1 -26.9 73.8 -19.8 0 -4.1
GAATTGCTCCAACAAGAGCA
4449 SEQ ID N0:4185 -7.1 -22.4 64.3 -12.1 -3.2 -9.2
ATGATAGAGGGAATTGCTCC
4459 SEQ ID N0:4186 -7.1 -22.4 66 -14.4 -0.7 -6.1
AGAACTTGCCAGCAAACAAA
4536 SEQ ID N0:4187 -7.1 -20.2 58.5 -13.1 0 -7.2
TTTCCACCGAGCTTGCTTGC
4634 SEQ ID N0:4188 -7.1 -28.3 77.7 -20.6 -0.3 -6.4
CCATCCAGCCTTTAAATGTG
4713 SEQ ID N0:4189 -7.1 -24.2 67.7 -17.1 0 -4.3
AACATCTCGTGAATCAACAG
4748 SEQ ID N0:4190 -7.1 -19.1 57.7 -12 0 -4.6
TTGTAATATTTTTTCTGTTC
4933 SEQ ID N0:4191 -7.1 -17.5 57.3 -10.4 0 -4.2
GCCTATAGTGAAGTAGTAGT
5216 SEQ ID N0:4192 -7.1 -22.2 68.3 -15.1 0 -5.1
GTAGGATTCGGCCAATCCTG
5349 SEQ ID N0:4193 -7.1 -26.3 72.8 -15.3 -3.5 -15.6
CTGCCAGGGTGAATTGTGTC
5656 SEQ ID N0:4194 -7.1 -25.8 74.6 -18.7 0 -3.8
ACACTGAAGTTCTCCAGGAT
5779 SEQ ID N0:4195 -7.1 -23.4 68.8 -15.5 -0.6 -5.6
TTTCCCAAACCTCATAGAAC
5847 SEQ TD N0:4196 -7.1 -21.9 62.7 -14.8 0 -2.8
GACTTTGTTGGGTTTTGCTA
5948 SEQ ID N0:4197 -7.1 -23.5 70.8 -16.4 0 -3.6
CATCCATCTCTCCACTCTCA
6057 SEQ ID N0:4198 -7.1 -27 77.8 -19.9 0 -0.5
TTGCTTTCTTTTTCTGGTTT
6424 SEQ ID N0:4199 -7.1 -22.6 69.9 -15.5 0 -3.6
CACAGAGTTGCAGTGACAGA
6629 SEQ ID N0:4200 -7.1 -23.3 69.4 -16.2 0 -5.5
TTACAATGTTCACTTTGCAC
6746 SEQ ID N0:4201 -7.1 -20.4 62.2 -13.3 0 -5.4
AAAAATATGGCAGATATGGA
6816 SEQ ID N0:4202 -7.1 -16.7 52.4 -8.2 -1.3 -5.2
TGAATTGGGGACCATGGAAA
6856 SEQ ID N0:4203 -7.1 -21.5 61.4 -12.3 -2.1 -8.8
232
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGTAGCCATTACAATTCTTT
7014 SEQ ID N0:4204 -7.l -21 63.4 -13 -0.8 -3.7
ATAGAGCTCTGAAACTTAGA
7195 SEQ ID N0:4205 -7.1 -19 59.1 -10.9 0 -10
AGCCTTTAAACTATGTTTAA
7529 SEQ ID N0:4206 -7.1 -18.4 56.9 -9.7 -1.6 -7.4
AGAGCAGGTTGAATTCATTC
7643 SEQ ID N0:4207 -7.1 -21.2 65.1 -13.5 0 -8.4
CAAATTATTCTGCTTGACAT
7670 SEQ ID N0:4208 -7.1 -18.8 57.7 -11.7 0 -3.6
TTTTAGCAAAATATGAAGAA
7802 SEQ ID N0:4209 -7.1 -13.9 47.1 -6.8 0 -4.8
TTTATATTTAAACAAGTTTT
7830 SEQ ID N0:4210 -7.1 -13.8 47.7 -6.7 0 -5.5
ACCATAGTTGGTAGAAAATG
8115 SEQ ID N0:4211 -7.1 -18.5 56.8 -9.5 -1.9 -5.4
TTTAGTGCAGCAGGAATTAA
8219 SEQ ID N0:4212 -7.1 -20.3 61.7 -13.2 0 -6.1
CAATACACTACAGTAAATAG
8374 SEQ ID N0:4213 -7.1 -15.5 50.6 -8.4 0 -3.6
TATCAAACCTGAAAGTTGGA
8713 SEQ ID N0:4214 -7.l -18.8 56.8 -11 -0.4 -4.3
ATCCAAGGGTTCTTGAAAAA
8949 SEQ TD N0:4215 -7.1 -19.3 57.8 -10.1 -2.1 -5.7
TGGTTTTGACCTCACATAAA
8968 SEQ ID N0:4216 -7.1 -20.7 61.5 -11.3 -2.3 -5
TGCATACGAATTACCTTAGA
416 SEQ ID N0:4217 -7 -20.4 60.1 -13.4 0 -4.7
TCTCCATAAATAAATGGAAG
652 SEQ ID N0:4218 -7 -16.1 51.2 -6.8 -2.3 -7.8
AGTAGGGATCCAGGTCCTCC
702 SEQ ID N0:4219 -7 -29.1 83.4 -20.8 -1.2 -8.2
TTGCCCAGGTCCACAAACTC
1084 SEQ ID N0:4220 -7 -27.1 74.2 -20.1 0 -3.6
TGTTCTCAACGCTGAGACAT
1103 SEQ ID N0:4221 -7 -22.8 66.5 -13 -2.8 -8.2
ATGTTCTCAACGCTGAGACA
1104 SEQ ID N0:4222 -7 -22.8 66.5 -13 -2.8 -8.4
TTACCGACTGGATCAGGGCC
1185 SEQ ID N0:4223 -7 -27.6 75.2 -19.7 -0.8 -7.5
CTCCAATGTAATCCTTCCAG
1413 SEQ ID N0:4224 -7 -24 68.3 -17 0 -2.2
AGCCTTCACACAGATGTATC
1517 SEQ ID N0:4225 -7 -23.6 70.1 -15.9 -0.5 -4.2
TGGTAAAGATTTTCCCAATA
1621 SEQ ID N0:4226 -7 -19.7 58.9 -12.7 0 -4.6
GACAAAAAATATCATGTATG
1667 SEQ ID N0:4227 -7 -13.7 46.6 -6.7 0 -4.7
GGCCACCACAGCCAGGATCA
1724 SEQ ID N0:4228 -7 -30.9 82.2 -22.2 -1.7 -8.7
CCTCATAGGCCATGGCCACC
1737 SEQ ID N0:4229 -7 -31.3 82.4 -19.7 -2.5 -17.4
TTCCTTCAAGGTGCTCTCTC
1995 SEQ ID N0:4230 -7 -26 77.6 -18.2 -0.6 -5.3
TCTCCTTTGTTGTTTCCTTC
2008 SEQ ID N0:4231 -7 -25.3 76.4 -18.3 0 0
CATTGGCAAATCTATACCAG
2658 SEQ ID N0:4232 -7 -20.7 61 -13 -0.4 -3.9
233
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAGAGGGTATTTAAGACAAT
2779 SEQ ID N0:4233 -7 -17.2 54.5 -10.2 0 -2.9
CTGCTGTGAAAATCCCAGTA
2868 SEQ ID NO:4234 -7 -23.3 66.3 -15.8 -0.1 -3.7
AGTAATAAGGATCCATGGCA
2907 SEQ ID N0:4235 -7 -21.8 64 -14.1 0 -9
AGGCTGACAATAATTCCATC
2953 SEQ ID NO:4236 -7 -21.3 63 -14.3 0 -3.7
CAGCAAAAATGAAGACGATG
3144 SEQ ID N0:4237 -7 -16.5 5l -9.5 0 -4.1
GTGGGAGCGTACAGTCATCA
3219 SEQ ID N0:4238 -7 -26 75.7 -19 0 -4.8
ACAGCACGCGGAACACAATC
3273 SEQ ID NO:4239 -7 -23.6 65 -16.1 0 -7.9
TTTCTAAAAAAGGCTTTTTG
3550 SEQ ID N0:4240 -7 -l6 51.7 -7.6 -1.3 -7.7
TAATCATTTTCATCGATTAC
3721 SEQ ID N0:4241 -7 -17.3 55 -9.6 -0.5 -6.3
CACAATGAAAGTCTCAAACC
4091 SEQ ID N0:4242 -7 -18.5 55.8 -11.5 0.2 -3.1
TAGAACTTGCCAGCAAACAA
4537 SEQ ID N0:4243 -7 -20.6 59.8 -13.6 0 -7.4
TCTGTCATAAAGATGTCTTG
4912 SEQ ID N0:4244 -7 -19.1 60 -12.1 0.2 -6.8
GTAATATTTTTTCTGTTCCT
4931 SEQ ID N0:4245 -7 -20.3 63.2 -13.3 0 -4.2
CTTCCTTTTTAACATAGGCA
5502 SEQ ID N0:4246 -7 -22 65.2 -15 0 -4
AGGTCTCAAAGTTGAACATG
5535 SEQ ID N0:4247 -7 -19.5 59.9 -11.6 -0.8 -6.5
AGGGTGAATTGTGTCAGGGT
5651 SEQ ID NO:4248 -7 -24.7 73.7 -17.7 0 -3.3
TTAACCTTTGCTTTAAAAGA
6213 SEQ TD N0:4249 -7 -17.5 54.4 -10 -0.1 -4.8
GGAGTTCCCATTTAGTTTGT
6311 SEQ ID N0:4250 -7 -24.7 73.5 -17.2 -0.1 -3.4
ACTATCATAGGAAGGAGGAG
6368 SEQ ID N0:4251 -7 -20.3 62.1 -13.3 0 -3.4
AAGATAATTCTTTGTTTCTT
6476 SEQ ID NO:4252 -7 -17.3 56.1 -9.4 -0.8 -3.9
GAAGTCCAGTTGACACATAT
6531 SEQ ID N0:4253 -7 -21.6 64.6 -12.8 -1.8 -4.5
TGAAGTCCAGTTGACACATA
6532 SEQ ID N0:4254 -7 -21.6 64.5 -12.8 -1.8 -5.6
TGTTAAAACAGTCAGTTTGG
6566 SEQ ID N0:4255 -7 -18.7 58.4 -10.5 -1.1 -6.7
GAGAGGTCACTTCACTGTCT
6611 SEQ ID N0:4256 -7 -24.6 74.9 -17.6 0 -3.4
AATTCTTTTTCTGGTTTTGA
7002 SEQ ID N0:4257 -7 -19.7 61.9 -12.7 0 -2.3
ACTGTAGCCATTACAATTCT
7016 SEQ ID NO:4258 -7 -21.9 65.2 -13.9 -0.9 -3.9
ATAACATAGGGTATTTAATT
7368 SEQ ID N0:4259 -7 -16.2 52.6 -9.2 0 -2.9
ATATATATATTTGCCCAAAC
7417 SEQ ID N0:4260 -7 -18.3 55.8 -11.3 0 -6.3
TTAACATGCATTAGTGATAG
7547 SEQ ID N0:4261 -7 -17.8 56.3 -10.8 0 -6.6
234
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Tntra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GAAGAATGGATTGAGTAAAA
7586 SEQ ID N0:4262 -7 -15.1 49.4 -8.1 0 -2.1
AGTATCCAGTGTGTTTCCTT
7764 SEQ ID N0:4263 -7 -25.2 75.9 -18.2 0 -3.7
TTTAGCAAAATATGAAGAAT
7801 SEQ ID N0:4264 -7 -13.8 46.8 -6.8 0 -4.2
AACCTGAAAGTTGGAACATG
8708 SEQ ID N0:4265 -7 -18.9 56.6 -11.1 -0.6 -4.8
TTACTACTATTATTATCAAA
8726 SEQ ID N0:4266 -7 -14.7 49.6 -7.7 0 -1.2
ATAAGAGTTTGGTTTTGACC
8977 SEQ ID N0:4267 -7 -20.5 62.8 -11.9 -1.5 -6.3
CCTCTGGCAGCTGTTCAGCT
130 SEQ ID N0:4268 -6.9 -29.7 85 -21 -1.7 -10.8
TTCAGTTTTCTTGCTCCATA
229 SEQ ID N0:4269 -6.9 -23.6 71.3 -16.7 0 -4.4
TCCAAGTCACTATTTGGCTT
619 SEQ ID N0:4270 -6.9 -23.7 69.8 -15.3 -1.4 -5.1
CATATGCCATCACAATGACA
1059 SEQ ID N0:4271 -6.9 -21.7 62.7 -14.1 -0.4 -7.5
TCAGAAAGCTTCTTTACCGA
1198 SEQ ID N0:4272 -6.9 -21.9 63.9 -14.1 -0.7 -6.5
CAATGAGAGCAAACACGCTC
1245 SEQ ID N0:4273 -6.9 -21.3 61.3 -12.2 -2.2 -7.2
GATTGCCCATGAACAGCTGC
1269 SEQ ID N0:4274 -6.9 -26.5 73 -18.9 -0.2 -8.9
TCAGATTGCCCATGAACAGC
1272 SEQ ID N0:4275 -6.9 -24.9 70.1 -18 0 -4.5
AGAATCGCTTGGGGGCCACT
1307 SEQ ID N0:4276 -6.9 -28.3 76.6 -20.7 -0.5 -7
TGGCCACCACAGCCAGGATC
1725 SEQ ID N0:4277 -6.9 -30.2 81.1 -20.9 -2.4 -8.3
CCTGATTCTGCTCCTCATAG
1749 SEQ ID N0:4278 -6.9 -25.7 74.2 -18.8 0 -3.6
TCTGCTTCTTCCAAGGTGGC
1768 SEQ ID N0:4279 -6.9 -27.3 79 -19.5 -0.7 -4.9
CCACTGAAATCTCTTGAAGC
1873 SEQ TD N0:4280 -6.9 -21.4 62.8 -14.5 0 -2.8
GACTGATGAGGGGAGCAGAA
2125 SEQ TD N0:4281 -6.9 -23.5 68.2 -15.9 -0.5 -4.1
CAGATCAAGAACACATTGGC
2671 SEQ ID N0:4282 -6.9 -20.5 61 -13.6 0 -5.4
TTGCCAACTTGAAAACTCTA '
3039 SEQ ID N0:4283 -6.9 -19.7 58.5 -12.8 0 -3
CAATGATCTTAATTAGCATA
3078 SEQ ID N0:4284 -6.9 -17 54.1 -10.1 0 -4.9
ATTCCCTTTTGCATTCTTCC
3496 SEQ ID N0:4285 -6.9 -26.1 74.9 -19.2 0 -5.1
AGGCTTTTTGGAAACACTCC
3540 SEQ ID N0:4286 -6.9 -23.1 66.9 -15.4 -0.6 -5.4
TCAAACCAGTTGTGCTCAAC
4078 SEQ TD N0:4287 -6.9 -22.4 65.5 -13.3 -2.2 -5.3
ATATATCTTCAAAGGCCAAT
4137 SEQ ID N0:4288 -6.9 -19.5 58.7 -12.1 0 -7.7
CAAGAGCATTGGCTACCAGG
4329 SEQ ID N0:4289 -6.9 -24.9 70.4 -16.2 -1.8 -7
TGATAGAGGGAATTGCTCCA
4458 SEQ ID N0:4290 -6.9 -23.1 67.2 -14.4 -1.8 -5.3
235
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CACATTCATGATAGAGGGAA
4466 SEQ ID N0:4291 -6.9 -20 60.5 -13.1 0 -6.l
GCAGATGAGGATCATGATGC
5063 SEQ ID N0:4292 -6.9 -23 67.9 -13 -3.1 -8.6
TCATGGTGACCATGTTGAGG
5082 SEQ ID N0:4293 -6.9 -24.1 70.3 -14 -3.2 -11.5
TTGCCCTGGTCATCCGTTTC
5107 SEQ ID N0:4294 -6.9 -29.3 80.9 -21.2 -1.1 -4.4
ACTAGGTTGATCCGGGACAA
5143 SEQ ID N0:4295 -6.9 -24.3 68.6 -16.2 -1.1 -8.5
GGCCGATGTTAAACAACGCA
5430 SEQ ID N0:4296 -6.9 -23.7 64.3 -16.8 2.1 -7.4
TAGCAACACTGAAGTTCTCC
5784 SEQ ID N0:4297 -6.9 -22.4 66.3 -15.5 0 -6.3
GTTGGGTTTTGCTATGAGAA
5942 SEQ ID N0:4298 -6.9 -22.1 66.6 -15.2 0 -3.6
ATAAGCTGGACTTTGTTGGG
5956 SEQ ID N0:4299 -6.9 -22.5 66.8 -15 -0.3 -5.1
TCAAGACAGTGGATCCGGTC
6004 5EQ ID N0:4300 -6.9 -24.9 71.6 -17.1 0 -9.6
GAACTCCCATCTGTTTTTTC
6337 SEQ ID N0:4301 -6.9 -23.5 69.4 -16.6 0 -3.5
GAGGGGTGGTAGAGGAACTC
6351 SEQ ID N0:4302 -6.9 -24.7 73.3 -15.8 -2 -5.5
CTCAAACTTTTCCTTGTCTG
6398 SEQ ID N0:4303 -6.9 -21.9 65.5 -15 0 -2.8
GATAATTCTTTGTTTCTTTT
6474 SEQ ID N0:4304 -6.9 -18.2 58.6 -11.3 0 -2.9
TGGATGCAAGGACTGTACTA
6782 SEQ ID N0:4305 -6.9 -22.2 65.6 -15.3 0 -5.6
GAATGGATGCAAGGACTGTA
6785 SEQ ID N0:4306 -6.9 -21.3 62.9 -14.4 0 -5.6
GACCATGGAAATGCACTAGA
6847 SEQ ID N0:4307 -6.9 -21.8 62.9 -13.5 -1.3 -8.8
GGGGACCATGGAAATGCACT
6850 SEQ ID N0:4308 -6.9 -25.1 69.1 -16.6 -1.5 -8.5
CCTCATTTACAAAAATAGTG
6898 SEQ ID N0:4309 -6.9 -16.9 53.1 -9.3 -0.5 -4.1
GTTTCTTCAACGTAAACCTC
6914 5EQ ID N0:4310 -6.9 -21.2 62.8 -13.7 -0.3 -5.6
GGCAAAACACCTTTGTCTGA
6963 SEQ ID N0:4311 -6.9 -22.9 65.5 -14.4 -1.6 -6.5
TTGCACAACTTTGCCACTTT
8284 SEQ ID N0:4312 -6.9 -23.9 68.2 -16 -0.9 -5
TAACATTAAACTTTTGGTTT
8339 SEQ ID N0:4313 -6.9 -16.3 52.6 -8.2 -1.1 -4.7
GCAATTCCCTGCATGCAGTT
8397 SEQ ID N0:4314 -6.9 -27.5 76.3 -17.5 -1.1 -14.3
TTATTAATTATATATATTTT
8540 SEQ ID N0:4315 -6.9 -12.1 44.3 -5.2 0 -5.2
GTTTGTTGTAAAATTCATGT
8599 SEQ ID N0:4316 -6.9 -17.9 56.9 -11 0.1 -6.6
TCAATTATATTGAAAGAAGA
8804 SEQ ID N0:4317 -6.9 -13.7 47 -5.2 -1.5 -5.6
AAGAGTTTGGTTTTGACCTC
8975 SEQ ID N0:4318 -6.9 -22.1 67 -12,g -2.3 -6.3
ATTATGGGAGAATTATGAAA
9059 SEQ ID N0:4319 -6.9 -15.7 50.9 -g,g 0 -3.2
236
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGATGGTTAGGGTATAACGT
155 SEQ ID N0:4320 -6.8 -21.3 63.9 -13.2 -1.2 -5
GATGTGGCTTGGCTTCAGTT
242 SEQ ID N0:4321 -6.8 -26.2 77.5 -18.7 -0.4 -6
GGCTTCTTGGCTTTCTCTTC
562 SEQ ID N0:4322 -6.8 -26.6 80.4 -18.8 -0.9 -3.7
AGGCAGAGGTGGCACTGAAT
774 SEQ ID N0:4323 -6.8 -25.4 73 -17.7 -0.8 -4.7
CAAGGTCATAAATACACAGT
893 SEQ ID N0:4324 -6.8 -18.5 57.1 -11.7 0 -2.8
GCCAAGATTTTTATAAGTGA
976 SEQ ID N0:4325 -6.8 -19.3 59 -12.5 0 -4.1
ATCTTCTAAGCAAAACCCTC
998 SEQ ID N0:4326 -6.8 -21.6 62.9 -14.8 0 -4.l
GCCCATGAACAGCTGCAGCC
1265 SEQ ID N0:4327 -6.8 -30.3 80.4 -21 0 -13.2
CACAGAGTAAAGGGTCTTTT
1464 SEQ ID N0:4328 -6.8 -20.9 63.7 -13.4 -0.4 -4.1
ATTCTGCTCCTCATAGGCCA
1745 SEQ ID N0:4329 -6.8 -27.9 79.2 -20.4 -0.5 -7.7
ATGCTGCCGCAACTGCCTGA
1848 SEQ ID N0:4330 -6.8 -29.5 77.4 -21.1 -1.6 -8
GGAGAAAAGGAAGCTGCTTC
2072 SEQ ID N0:4331 -6.8 -21.3 62.9 -12.4 -1 -12.4
GGGGAGCAGAATTTTTTGTC
2116 SEQ ID N0:4332 -6.8 -22.7 68.2 -15.9 0 -3.3
GAGAACCATTTCTGCTGTGA
2879 SEQ ID N0:4333 -6.8 -23.4 68.3 -15.2 -1.3 -5.8
AAAACTCTAAGCAGTCTGAA
3028 SEQ ID N0:4334 -6.8 -18.2 56.3 -11.4 0 -4.1
TGACATATAATCATTTTCAT
3728 SEQ ID N0:4335 -6.8 -16.7 53.8 -9.9 0 -3.4
GTCTCAAACCAGTTGTGCTC
4081 SEQ ID N0:4336 -6.8 -24.7 72.9 -17.2 -0.4 -4.9
AGAAGCATTTCCAGAATGAA
4222 SEQ ID N0:4337 -6.8 -19.5 58.6 -11.7 -0.9 -6
CCATTTGAGAAGCATTTCCA
4229 SEQ ID N0:4338 -6.8 -23.2 66.6 -15.6 -0.6 -4.1
AAATATGTTTGAAATCCATA
4255 SEQ ID N0:4339 -6.8 -15.7 50.6 -8.9 0 -3.3
AAATCTAGCCAGCACCAGGC
4282 SEQ ID N0:4340 -6.8 -26.5 73.4 -18.1 -1.6 -6.1
CCAGGCTAACCAAAGAAACA '
4314 SEQ ID N0:4341 -6.8 -21.2 59.8 -13 -1.3 -4.2
ACCGGGATAAGGCTCTTAGA
4404 SEQ ID N0:4342 -6.8 -24.6 69.6 -17.3 -0.2 -7.4
GTTGTCATGTTAACACAGTG
4558 SEQ ID N0:4343 -6.8 -20.9 64.4 -13.3 -0.5 -8.7
TACATGTACAGATTTTCTTC
4786 SEQ ID N0:4344 -6.8 -19.1 60.7 -11.6 0 -8.7
ATGATAAAGATGACAAAGTA
4810 SEQ ID N0:4345 -6.8 -14.5 48.4 -7.7 0 -2.8
CCCAAAGATGATAAAGATGA
4817 SEQ ID N0:4346 -6.8 -18 54.2 -11.2 0 -2.1
AATATTTTTTCTGTTCCTCT
4929 SEQ ID N0:4347 -6.8 -20.7 64.1 -13.9 0 -3.8
AAGTTTCTTCATTGCATTGT
4949 SEQ ID N0:4348 -6.8 -21.1 65.1 -14.3 0 -6.2
237
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CAAAGACCATTCCTTGGAAT
5013 SEQ ID N0:4349 -6.8 -21.4 61.4 -13 -1.5 -8.1
CCTGGTCATCCGTTTCCACC
5103 SEQ ID N0:4350 -6.8 -30.3 81.4 -22.3 -1.1 -4.5
GGACACAGAATACTTTTCTA
5300 SEQ ID N0:4351 -6.8 -19.6 60.3 -11.8 -0.9 -4.4
GAGGCCGATGTTAAACAACG
5432 SEQ ID N0:4352 -6.8 -21.8 61 -15 3.3 -8.1
CCAACAGATGGGTCCCCACG
5692 SEQ ID N0:4353 -6.8 -29.2 75.5 -21.4 -0.9 -8.8
AAATCCCAACAGATGGGTCC
5697 SEQ ID N0:4354 -6.8 -24.5 67.9 -14.5 -3.2 -7.9
CAATAAGCTGGACTTTGTTG
5958 SEQ ID N0:4355 -6.8 -20.1 60.7 -12.7 -0.3 -4.6
ATATATTTTTTAACCTTTGC
6222 SEQ ID N0:4356 -6.8 -18 56.7 -11.2 0 -3.3
TACTTTACCTTCATAGGCTG
6512 SEQ ID N0:4357 -6.8 -22.6 67.4 -14.6 -1.1 -3.7
ACAAAAATAGTGACATAGCA
6890 SEQ ID N0:4358 -6.8 -16.7 52.6 -9.9 0 -4.1
TAGAGGAGACTTTACAGGCA
7118 SEQ ID N0:4359 -6.8 -22.3 67.1 -14.6 -0.7 -5.2
TCATTCTATCACCAATATGT
7629 SEQ ID N0:4360 -6.8 -20.4 62 -13.6 0 -2.8
TAGCTTCAAATTATTCTGCT
7676 SEQ ID N0:4361 -6.8 -20.1 61.7 -13.3 0 -4.6
AGTCCATGTTATATTTGTAA
8243 SEQ ID N0:4362 -6.8 -19.4 60.6 -12.6 0 -4.3
ATTGCACAACTTTGCCACTT
8285 SEQ ID N0:4363 -6.8 -23.8 67.9 -16 -0.9 -5
TTATTCTTTTGGCTCAATAA
8447 SEQ ID N0:4364 -6.8 -18.8 58.6 -12 0 -4.9
ATATATTTTAAACTGCCAAC
8529 SEQ ID N0:4365 -6.8 -17.1 53.5 -10.3 0 -4.4
GAAAGCTATTGTAGGTGGTT
8744 SEQ ID N0:4366 -6.8 -21.5 65.3 -14.7 0 -5.1
TTTAGATGCTTATAGCCAAG
8780 SEQ TD N0:4367 -6.8 -20.5 62 -12.4 -1.2 -4.6
AGCATCAATTATATTGAAAG
8808 SEQ ID N0:4368 -6.8 -15.7 51.2 -6.9 -2 -8.1
ATAGGAGTTTATATAATGCA
8879 SEQ ID N0:4369 -6.8 -17.8 56.6 -11 0 -5.5
TTCCAGAATCCTCTCTGCTT
17 SEQ ID N0:4370 -6.7 -25.8 74.6 -18.1 -0.9 -4.5
GTTTTCTTGCTCCATAATCT
225 SEQ ID N0:4371 -6.7 -23 69 -16.3 0 -3.6
GGGCCACTGCAAACATTTAT
1295 SEQ ID N0:4372 -6.7 -23.9 67.1 -15.7 -1.4 -7.6
TTCCAGTTAAATGTGCTCAT
1399 SEQ ID N0:4373 -6.7 -21.8 65.1 -14.4 -0.4 -5.6
ATCTCCAATGTAATCCTTCC
1415 SEQ ID N0:4374 -6.7 -23.7 68.4 -17 0 -1.7
CCACAGAGTAAAGGGTCTTT
1465 SEQ ID N0:4375 -6.7 -22.8 67.2 -15.6 -0.2 -3.9
AATGACCAGGACAAAAAATA
1676 SEQ ID N0:4376 -6.7 -15.7 49.6 -9 0 -3.1
CACCAAATAAAATGAGCCCA
1700 SEQ ID N0:4377 -6.7 -20.9 58.5 -14.2 0 -3.2
238
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTTCCTTCAAGGTGCTCTCT
1996 SEQ ID N0:4378 -6.7 -25.7 76.2 -18.2 -0.6 -5.3
GTCTTGGGGAAAACAGGGAG
2163 SEQ TD N0:4379 -6.7 -22.6 65.8 -15,9 0 -2.7
TCAGATCCAACATCCTTTGC
2221 SEQ ID N0:4380 -6.7 -24.3 69.8 -17.1 -0.1 -4.5
CAGTGGTGGTGCCCTCTGGG
2484 SEQ ID N0:4381 -6.7 -31.1 86.6 -23.4 -0.9 -5.7
GGCTATGCTCACGGCTCTTT
2579 SEQ ID N0:4382 -6.7 -27.8 78.6 -19.9 -1.1 -5.3
CTATACCAGCATGGCGGACA
2647 SEQ ID N0:4383 -6.7 -26.2 71.8 -18.3 -1.1 -7.4
TCTAAGCAGTCTGAATGATC
3023 SEQ ID N0:4384 -6.7 -20.2 62.4 -13.5 0 -6.3
CTGCATGCCGACCACAGCAA
3158 SEQ ID N0:4385 -6.7 -28.2 74 -20.3 -1.1 -9.1
CTCCCGCATCTTATTTTTCA
3524 5EQ ID N0:4386 -6.7 -25.2 71.5 -18.5 0 -3.1
ATATAATCATTTTCATCGAT
3724 SEQ ID N0:4387 -6.7 -17 54.1 -10.3 0 -6
CCTTCAGATGAGCTGGTTGC
3874 SEQ ID N0:4388 -6.7 -26.3 76.2 -18.4 -1.1 -5
TCGGGTTCAGTTTCAGCTTG
3931 SEQ ID N0:4389 -6.7 -25.3 75 -18.6 0 -4.5
CTTCAGTAAAACAAGCTTCC
3966 SEQ ID N0:4390 -6.7 -20.3 60.7 -13.6 0 -6.4
AGCATTTCCAGAATGAATAT
4219 SEQ ID N0:4391 -6.7 -19.3 58.5 -11 -1.6 -5.2
GAGCATTGGCTACCAGGCTA
4326 SEQ ID N0:4392 -6.7 -27.3 77.1 -18.6 -2 -8.4
GCCTTTAAATGTGGCCACTT
4706 SEQ ID N0:4393 -6.7 -25.3 70.6 -16.2 -1 -13
CAAAACTAGGGTCATGTATT
5126 SEQ TD N0:4394 -6.7 -19.1 58.5 -12.4 0 -4.7
CACTAGGTTGATCCGGGACA
5144 SEQ ID N0:4395 -6.7 -25.7 72 -18.4 -0.3 -6.8
TTGCTCCTTTGATCAGACGT
5367 SEQ ID N0:4396 -6.7 -24.8 71.5 -18.1 0 -6.5
GACATCATCAAAGCAAAGAG
5404 SEQ ID N0:4397 -6.7 -18 55.5 -11.3 0 -4.1
TTGTGTCAGGGTCACAGTCG
5643 SEQ ID N0:4398 -6.7 -25.6 76.1 -17.3 -1.6 -5.8
AAATCAGAGAGTTTAGAGAA '
5899 SEQ TD N0:4399 -6.7 -16.5 53.6 -9.8 0 -3.2
TGTTGGGTTTTGCTATGAGA
5943 SEQ ID N0:4400 -6.7 -22.8 68.8 -16.1 0 -3.6
GGGCAGATCCATGGCAATAA
5972 SEQ ID N0:4401 -6.7 -24.6 68.9 -16.9 -0.9 -8
ATCAAGACAGTGGATCCGGT
6005 SEQ ID N0:4402 -6.7 -24.5 69.9 -17.1 0 -8.9
CCACTCTCACACAAAACACG
6046 SEQ ID N0:4403 -6.7 -21.8 61.4 -15.1 0 -3
GCTCATAAGAGACTTTGGAG
6120 SEQ ID N0:4404 -6.7 -21.1 64.1 -13 -1.3 -6.3
ATAGCGGCAGACACCTCCTC
6169 SEQ ID N0:4405 -6.7 -28.3 77.8 -21.6 0.4 -6.6
GATAGCGGCAGACACCTCCT
6170 SEQ ID N0:4406 -6.7 -28.5 77.4 -21.3 -0.1 -6.6
239
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal)
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGATCACAAAGATAATTCTT
6484 SEQ ID N0:4407 -6.7 -16.3 52.5 -8.4 -1.l -8.2
TATTTGTTAAAACAGTCAGT
6570 SEQ ID N0:4408 -6.7 -17.2 55.3 -10.5 0 -5.9
ATATTAGAGGAGACTTTACA
7122 SEQ ID N0:4409 -6.7 -18.4 58.3 -10.8 -0.7 -5.5
GACATATTTTTAGCAAAATA
7809 SEQ ID N0:4410 -6.7 -15.4 50.5 -6.8 -1.9 -6.6
ATAATTTTCTTATGTACAAA
7886 SEQ ID N0:4411 -6.7 -14.8 49.7 -8.1 0 -6.8
AAATAAATTGTGATGTCATC
7915 SEQ ID N0:4412 -6.7 -15.5 50.9 -8.8 0 -5.1
ACAGTAAATAGTTTTGTAAA
8365 SEQ ID N0:4413 -6.7 -15.1 50.4 -8.4 0 -3.5
CGTAGCTCACCATTCTTTTT
8424 SEQ ID N0:4414 -6.7 -24.2 70.4 -17.5 0 -4.8
TTCTCAATAACTATATCATT
8915 SEQ ID N0:4415 -6.7 -16.5 53.6 -9.8 0 -2.4
CAGCTGTTCAGCTTTTTTTT
123 SEQ ID N0:4416 -6.6 -23.2 70.7 -14.7 -1.8 -11
TTGGCTTCAGTTTTCTTGCT
234 SEQ ID N0:4417 -6.6 -24.8 74.9 -17.5 -0.4 -3.7
TCAAACCTTGATGTGGCTTG
251 SEQ ID N0:4418 -6.6 -22.7 65.7 -15.3 -0.6 -4.9
CATAAATACACAGTTGGTCA
887 SEQ ID N0:4419 -6.6 -19.3 59.1 -12.7 0 -2.8
TCACATATGCCATCACAATG
1062 SEQ ID N0:4420 -6.6 -21.5 62.8 -14.4 -0.1 -6.5
AAAAGCAGAATCGCTTGGGG
1313 SEQ ID N0:4421 -6.6 -21.9 62.3 -13.5 -1.8 -9.3
GGACAAAAAATATCATGTAT
1668 SEQ ID N0:4422 -6.6 -14.9 48.9 -8.3 0 -4.7
GCTCCTCATAGGCCATGGCC
1740 SEQ ID N0:4423 -6.6 -31.5 85.6 -20.9 -1.4 -16.1
TTCTGCTTCTTCCAAGGTGG
1769 SEQ ID N0:4424 -6.6 -25.6 74.9 -18.3 -0.5 -4.6
AATTCGGCCTCTTTTTGTTC
1786 SEQ ID N0:4425 -6.6 -23.9 69.9 -17.3 0 -6.2
CTGCCGCAACTGCCTGAGCT
1845 SEQ ID N0:4426 -6.6 -30.4 79.7 -22.6 -1.1 -7.3
TCATCATCAGCAAAGTCATT
2242 SEQ ID N0:4427 -6.6 -20.8 63.4 -14.2 0 -4.1
AAAATCCCAGTAAAGACCAG
2860 SEQ ID N0:4428 -6.6 -20 58.1 -13.4 0 -2.1
CGTGGGAGCGTACAGTCATC
3220 SEQ ID N0:4429 -6.6 -26.1 74.4 -19 -0.2 -4.8
TCCCACATGGTCTCTATCCA
3301 SEQ ID N0:4430 -6.6 -27.8 78.2 -20.5 -0.5 -4.9
ATAATCATTTTCATCGATTA
3722 SEQ ID N0:4431 -6.6 -17.1 54.5 -9.6 -0.8 -6.3
GCTGGTTGCATTTAATTTCT
3863 SEQ ID N0:4432 -6.6 -22.4 67.2 -14.9 -0.7 -5.1
TTCAGTAAAACAAGCTTCCG
3965 SEQ TD N0:4433 -6.6 -20.2 59.4 -13.6 0 -6.4
AAAGGCCAATGCACCACTAC
4127 SEQ ID N0:4434 -6.6 -24 66.2 -15.9 -1.4 -7.7
AATATATAGGTAAAGACTTT
4204 SEQ ID N0:4435 -6.6 -15 50.1 -7.9 -0.1 -4.3
240
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGTTCTGAGTAGCCAAGAGC
4342 SEQ ID N0:4436 -6.6 -24.3 72.7 -17.1 -0.3 -3.4
GTCATGTTAACACAGTGGTA
4555 SEQ TD N0:4437 -6.6 -21.7 66.3 -14.3 -0.5 -8.7
CTAGGTTGATCCGGGACAAA
5142 SEQ ID N0:4438 -6.6 -23.4 66 -15.6 -1.1 -8.2
TTCCAGCCTATAGTGAAGTA
5221 SEQ ID N0:4439 -6.6 -23.3 68.8 -16.7 0 -5.1
GAGAGTTTAGAGAACTCTAT
5893 SEQ ID N0:4440 -6.6 -18.9 60.1 -8.1 -4.2 -9.6
CAGATCCATGGCAATAAGCT
5969 SEQ ID N0:4441 -6.6 -23.1 66.1 -15.1 -1.3 -7.4
CACTGACCATGGGCAGATCC
5982 SEQ ID N0:4442 -6.6 -27.2 75 -18.8 -1.8 -8.8
ATATACTTTACCTTCATAGG
6515 SEQ ID N0:4443 -6.6 -19.6 60.6 -12 -0.9 -4.2
ATACTGTTTCTTCAACGTAA
6919 SEQ ID N0:4444 -6.6 -19.2 59.1 -11:3 -1.2 -5.3
AATGGAAGTAACTGAAACTG
7032 SEQ ID N0:4445 -6.6 -16 51.1 -9.4 0 -3
TCCTTTAAATATTAGAGGAG
7130 SEQ ID N0:4446 -6.6 -17.7 55.9 -9.3 -1.8 -7.4
TAAATTAAATATAGAGCTCT
7205 SEQ ID N0:4447 -6.6 -14.7 49.3 -7.2 0 -9.6
AGCATTTGACCTAAATTAAA
7216 SEQ ID N0:4448 -6.6 -17.1 53.2 -9.9 -0.3 -4
GAGCAGAAGATGGCAAAGCA
7324 SEQ ID N0:4449 -6.6 -22.4 64.7 -14.9 -0.8 -5.6
GAATGATACAGGATACATCC
7508 SEQ ID N0:4450 -6.6 -19.9 59.9 -12.6 -0.5 -6.5
GTGACATTCTTTAACCAAGA
7611 SEQ ID N0:4451 -6.6 -20.1 60.6 -12.6 -0.7 -5.9
TTAGCAAAATATGAAGAATA
7800 SEQ ID N0:4452 -6.6 -13.4 46 -6.8 0 -4.1
AAATGAAATTTATTCTTTTG
8456 SEQ ID N0:4453 -6.6 -13.4 46.5 -5.6 -1.1 -4.7
TTTAAACTGCCAACAGCAAA
8523 SEQ ID N0:4454 -6.6 -19.4 57 -11.2 -1.5 -8.9
TATTAGCCACCAAGTAATTA
8834 SEQ ID N0:4455 -6.6 -20.2 60.2 -13.1 -0.1 -4.1
AATCCTCTCTGCTTATGCCT
11 5EQ ID N0:4456 -6.5 -26.4 75.3 -19 -0.8 -4.6
TCTCTGATAAAACAGAGCCT
208 SEQ TD N0:4457 -6.5 -2l 62.2 -11.5 -3 -8.7
GTGGCTTGGCTTCAGTTTTC
239 SEQ ID N0:4458 -6.5 -26.2 79.1 -19 -0.4 -6
GGTCCCTTCTGTGAATTATC
364 SEQ ID N0:4459 -6.5 -24.4 71.8 -17.9 0 -3.2
GCTTCTTGGCTTTCTCTTCT
561 SEQ ID N0:4460 -6.5 -26.3 79,7 -19.3 -0.1 -3.7
GTAGGGATCCAGGTCCTCCA
701 SEQ ID N0:4461 -6.5 -29.8 84 -21.3 -2 -10.3
ATACAAGGCAGAGGTGGCAC
779 SEQ ID N0:4462 -6.5 -24.5 71 -17.1 -0.8 -4.l
TACACAGTTGGTCAAAATAG
881 SEQ ID N0:4463 -6.5 -17.9 56.1 -11.4 0 -3.8
TGACTCAAAGGTATAGATTC
959 SEQ ID N0:4464 -6.5 -18.3 57,g -11.8 0 -2.8
241
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TCTTGCCAAGATTTTTATAA
980 SEQ ID N0:4465 -6.5 -18.9 58.1 -11.7 -0.4 -6
GTCACATATGCCATCACAAT
1063 SEQ ID N0:4466 -6.5 -22.7 65.9 -16.2 0 -6.5
GGCCCCCACAATGGTCTTTA
1169 SEQ ID N0:4467 -6.5 -29.5 78.6 -22.3 -0.2 -8.5
CAGAAAGCTTCTTTACCGAC
1197 SEQ ID NO:4468 -6.5 -21.7 63 -14.3 -0.7 -7
GCAGCCCAATGAGAGCAAAC
1251 SEQ ID N0:4469 -6.5 -24.8 68.3 -17.5 -0.6 -4.8
AGCCATTTCCACAGAGTAAA
1473 SEQ ID N0:4470 -6.5 -22.8 66 -16.3 0 -3.2
CCACCACAGCCAGGATCAAA
1722 5EQ ID N0:4471 -6.5 -26.5 71.1 -20 0 -5.3
GAAATTCGGCCTCTTTTTGT
1788 SEQ ID N0:4472 -6.5 -23.3 67.1 -16.8 0 -6.7
TTTTGTCACTGGTCAGTCTG
2103 SEQ ID N0:4473 -6.5 -23.7 73 -17.2 0 -6.6
AAAACAGGGAGCCACGGATA
2154 SEQ ID N0:4474 -6.5 -22.8 63.4 -15.7 -0.3 -4.3
GCAATCCACAGTGCTGTGCA
2402 5EQ ID N0:4475 -6.5 -27.4 77 -18.7 -1.7 -12.4
ATGCTGGCTATGCTCACGGC
2584 SEQ ID N0:4476 -6.5 -28.1 78 -20.9 -0.4 -6.5
TGAAAATCCCAGTAAAGACC
2862 SEQ ID N0:4477 -6.5 -19.9 57.9 -13.4 0 -2.1
CTGACAATAATTCCATCAAA
2950 SEQ ID N0:4478 -6.5 -17.6 54 -11.1 0 -2.9
TTAAACTGAGGCTGACAATA
2961 SEQ ID N0:4479 -6.5 -18.5 56.6 -12 0 -3.7
TTCCTAGAGCCCCCACAGAA
3102 SEQ ID N0:4480 -6.5 -29 77.1 -22.5 0 -3.8
AGCTGCATGCCGACCACAGC
3160 SEQ ID N0:4481 -6.5 -30 79.7 -21.2 -2.3 -9.3
ACAGTCATCATTGATCTTGC
3209 SEQ ID N0:4482 -6.5 -22.2 67.8 -15 -0.5 -5.6
AGTTTCAGCTTGTTCACCTT
3923 SEQ ID N0:4483 -6.5 -24.9 74.8 -18.4 0 -4.5
CTTTCGCTGTTCAATGTATA
4154 SEQ ID N0:4484 -6.5 -21.3 64.1 -14.8 0 -2.7
GTAGAACTTGCCAGCAAACA
4538 SEQ ID N0:4485 -6.5 -22.5 64.6 -16 0 -7.4
TTTCTTCATTGCATTGTAAT
4946 SEQ ID N0:4486 -6.5 -19.6 61 -13.1 0 -6.2
GATCATGATGCTGATATCAA
5054 SEQ ID NO:4487 -6.5 -19.7 60 -12.3 -0.6 -8.5
ACCATGTTGAGGCAGATGAG
5074 SEQ ID N0:4488 -6.5 -23.7 69.1 -17.2 0 -4.3
CATCATCAAAGCAAAGAGCA
5402 SEQ ID NO:4489 -6.5 -19.7 58.7 -11.6 -1.6 -4.4
TTCAGTAGCAACACTGAAGT
5789 SEQ ID N0:4490 -6.5 -21 63.7 -11.6 -2.9 -9.6
TTAGAGAACTCTATAAACTG
5887 SEQ ID NO:4491 -6.5 -15.8 51.8 -8.6 -0.3 -8
GTTTAGAGAACTCTATAAAC
5889 SEQ ID N0:4492 -6.5 -16.2 53 -8.1 -1.5 -8.1
GGAGGATCCAGGGCAGCTGC
5920 SEQ ID N0:4493 -6.5 -30.1 84.2 -19.5 -1.8 -16.4
242
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CACTCTCACACAAAACACGC
6045 SEQ ID N0:4494 -6.5 -21.6 61.7 -15.1 0 -3.3
AAGAGACTTTGGAGGGGTTT
6114 SEQ TD N0:4495 -6.5 -22.6 67.6 -16.1 0 -2.8
GAGTTCCCATTTAGTTTGTC
6310 SEQ ID N0:4496 -6.5 -23.9 72.5 -17.4 0 -1.7
AGGGGTGGTAGAGGAACTCC
6350 SEQ ID N0:4497 -6.5 -26.1 75.7 -17.2 -2.4 -6.3
TGTTTCTTTTTACTTTTGAT
6464 SEQ TD N0:4498 -6.5 -18.8 60.2 -12.3 0 -2.2
AGAGGTCACTTCACTGTCTT
6610 SEQ ID N0:4499 -6.5 -24.1 73.9 -17.6 0 -3.4
AGAAAATGGAAGTAACTGAA
7036 SEQ ID N0:4500 -6.5 -14.8 48.6 -8.3 0 -3
AGCAATACTTTAGATATATT
7271 SEQ ID N0:4501 -6.5 -16.6 53.9 -10.1 0 -4.3
TATATATATTTGCCCAAACA
7416 SEQ ID N0:4502 -6.5 -19 57 -12.5 0 -5.4
GAAGCTTGCAAAAGACACAT
7482 SEQ ID N0:4503 -6.5 -19.5 58 -10.9 -2.1 -7
TAACATGCATTAGTGATAGC
7546 SEQ ID N0:4504 -6.5 -19.5 60.1 -13 0 -6.8
ATACTCATGTTGAATTAAAA
7721 SEQ ID N0:4505 -6.5 -14.8 49.2 -8.3 0 -4.1
ATACCATATGATACTCATGT
7731 SEQ ID N0:4506 -6.5 -20 60.9 -12.6 -0.8 -6
TAGCAAAATATGAAGAATAG
7799 SEQ ID N0:4507 -6.5 -13.3 45.9 -6.8 0 -4.1
AAGTTTTAGACATATTTTTA
7817 SEQ ID N0:4508 -6.5 -15.8 52.6 -8.6 -0.4 -2.9
CAAAAAACCCCAGAGCCCAA
8494 SEQ ID N0:4509 -6.5 -24.5 63.8 -l8 0 -3.2
TCACAAAGCTGCTTTTAATT
8659 SEQ ID N0:4510 -6.5 -19.4 59 -11.4 -0.3 -10.9
TTGGAACATGTGAACTTGAT
8698 SEQ ID N0:4511 -6.5 -19 57.9 -11.7 -0.6 -6.5
ACCTTATATAATTTATTATG
9073 SEQ ID N0:4512 -6.5 -15.3 50.7 -8 -0.6 -5.3
AATGTCTCCATAAATAAATG
656 SEQ ID N0:4513 -6.4 -15.5 50.1 -8.5 -0.3 -2.9
ATAGTAGGGATCCAGGTCCT
704 SEQ ID N0:4514 -6.4 -26.4 77.1 -18 -2 -8.9
CTACATTCTTTGTCCAGTCA
924 SEQ ID N0:4515 -6.4 -23.7 71.4 -16.7 -0.3 -3.1
AAAACCCTCTTGCCAAGATT
987 SEQ ID N0:4516 -6.4 -22.9 63.8 -15.7 -0.6 -6.3
ACGAAGAAACGTAAAATCTT
1013 SEQ ID N0:4517 -6.4 -15.3 48.8 -8.1 -0.6 -5.6
TGCCCAGGTCCACAAACTCT
1083 5EQ ID N0:4518 -6.4 -27.9 75.7 -21.5 0 -3.6
AACTCTGAATGTTCTCAACG
1112 SEQ ID N0:4519 -6.4 -19.6 59.1 -12.3 -0.8 -5.3
GGAGAACTCTGAATGTTCTC
1116 SEQ ID N0:4520 -6.4 -21 64.3 -10.8 -3.8 -11.4
CCCCACAATGGTCTTTAAAC
1166 SEQ ID N0:4521 -6.4 -23.3 65.1 -16 -0.7 -5.4
AGTTGGGGTTTCGACCAGCC
1533 SEQ ID N0:4522 -6.4 -28.8 79.9 -19.7 -2.7 -7.6
243
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TCCTCATAGGCCATGGCCAC
1738 SEQ ID N0:4523 -6.4 -29.7 80.9 -18.7 -2.5 -17.4
TTCTTCCAAGGTGGCCTGAT
1763 SEQ ID N0:4524 -6.4 -26.8 75.7 -19.7 -0.4 -7.2
ATTCGGCCTCTTTTTGTTCT
1785 SEQ ID N0:4525 -6.4 -25.5 74.4 -19.1 0 -6.7
GCTCTCCTAACCCACCTACT
1893 SEQ ID N0:4526 -6.4 -29.1 78.6 -22.7 0 -2.8
GCAGAATTTTTTGTCACTGG
2111 SEQ ID N0:4527 -6.4 -21.5 64.9 -14.5 -0.3 -4.1
ATAAAGAGGGTATTTAAGAC
2782 SEQ ID N0:4528 -6.4 -16.2 52.7 -9.8 0 -3
TTGAGAACCATTTCTGCTGT
2881 SEQ ID N0:4529 -6.4 -22.9 67.4 -15.1 -1.3 -5.8
ATCCCTCCACATTTGACAGA
2991 SEQ ID N0:4530 -6.4 -25.6 71.8 -19.2 0 -2.4
TGGAAGAAGTCGTTCATGTG
3244 SEQ ID N0:4531 -6.4 -21 63.1 -13.9 -0.4 -4.9
TATGAATGACATATAATCAT
3734 SEQ ID N0:4532 -6.4 -14.9 49.4 -7.6 -0.7 -5.2
AAACTTTTTAATACACCCTT
3983 SEQ ID N0:4533 -6.4 -18.9 56.9 -12.5 0 -2.5
AAGGCCAATGCACCACTACT
4126 SEQ ID N0:4534 -6.4 -25.6 70.1 -17.7 -1.4 -7.7
TAGTCTTTCGCTGTTCAATG
4158 SEQ ID N0:4535 -6.4 -22 66.5 -15.6 0 -3.1
GTGAAATATGTTTGAAATCC
4258 SEQ ID N0:4536 -6.4 -17.1 53.8 -10.7 0 -4.1
CTTAGAGGTCTTAAAGCTCT
4390 SEQ ID N0:4537 -6.4 -21.4 65.7 -14 -0.9 -5
ACAGTCACTCAAATTGTTAA
4604 SEQ ID N0:4538 -6.4 -18.4 57.5 -12 0 -4.6
ATCCATCCAGCCTTTAAATG
4715 SEQ ID N0:4539 -6.4 -23.4 66.2 -17 0 -4.3
AGCTTCAGCACAAATTCTCC
5182 SEQ ID N0:4540 -6.4 -23.7 69.2 -16.4 -0.7 -6.6
TCCTTTTTAACATAGGCAAA
5500 SEQ ID N0:4541 -6.4 -19.6 58.9 -13.2 0 -4
AAAGTTGAACATGTCATCAA
5528 SEQ ID N0:4542 -6.4 -17.4 54.6 -9.9 -0.8 -9.7
GAGGTTGTAATTTGGAACAA
5575 SEQ ID N0:4543 -6.4 -18.8 57.8 -10.9 -1.4 -7.3
TCCATCCCAGCCAGCAGAGG
5591 SEQ ID N0:4544 -6.4 -31 83.4 -24.6 0 -4.6
AACACTGAAGTTCTCCAGGA
5780 SEQ ID N0:4545 -6.4 -22.7 66.6 -15.5 -0.6 -6.3
CTTTGCTTTAAAAGATAACA
6208 SEQ ID N0:4546 -6.4 -16.1 51.7 -9.2 -0.1 -4.3
AGTTCCCATTTAGTTTGTCA
6309 SEQ ID N0:4547 -6.4 -24 72.2 -17.6 0 -1.7
TCATAGGAAGGAGGAGGGGT
6364 SEQ ID N0:4548 -6.4 -24.3 71.5 -17.9 0 -2.4
TTTGCTTTCTTTTTCTGGTT
6425 SEQ ID N0:4549 -6.4 -22.6 69.9 -16.2 0 -3.6
TCTTTGTTTCTTTTTACTTT
6468 SEQ ID N0:4550 -6.4 -19.6 62.9 -13.2 0 -1.8
ATTTGTTAAAACAGTCAGTT
6569 SEQ ID N0:4551 -6.4 -17.6 56.2 -10.5 -0.4 -5.9
244
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GAGTATTTGTTAAAACAGTC
6573 SEQ ID NO:4552 -6.4 -17.1 55.3 -10.7 0 -6.l
TGTACTAAAGGTGTTTGGTG
6769 SEQ ID N0:4553 -6.4 -20.5 63 -13.2 -0.8 -5.1
AATGGATGCAAGGACTGTAC
6784 SEQ ID N0:4554 -6.4 -20.9 62.2 -14.5 0 -5.6
AGATTACTTTTTGGAAAGCA
7232 SEQ ID N0:4555 -6.4 -18.8 58.1 -10.8 -1.6 -5.5
AATGGATTTATTAGATTACT
7244 SEQ ID N0:4556 -6.4 -16.3 53.1 -9.9 0 -2.4
AAGAATGGATTGAGTAAAAT
7585 SEQ ID N0:4557 -6.4 -14.5 48.3 -8.1 0 -2.2
ATATTTTTACATTATTTATA
7844 SEQ ID N0:4558 -6.4 -14.1 48.8 -7.7 0 -1.8
TATATTTTTACATTATTTAT
7845 SEQ ID N0:4559 -6.4 -14.1 48.8 -7.7 0 -2.2
CTCAATAATGACGTAGCTCA
8435 SEQ ID NO:4560 -6.4 -20.6 61.3 -13.5 -0.5 -5.6
GGCTCAATAATGACGTAGCT
8437 SEQ ID N0:4561 -6.4 -22.5 65.2 -14.8 -1.2 -6.5
TACCTTATGTATACATAGGA
8893 SEQ ID N0:4562 -6.4 -19.6 60.3 -11 -1.1 -12.6
AATCCAAGGGTTCTTGAAAA
8950 SEQ TD N0:4563 -6.4 -19.3 57.8 -10.8 -2.1 -6.7
TCACATAAATCCAAGGGTTC
8957 SEQ ID N0:4564 -6.4 -20.8 61.9 -14.4 0 -4.3
TTTGACCTCACATAAATCCA
8964 SEQ ID N0:4565 -6.4 -21.3 62 -14.9 0 -2.9
GGAGAATTATGAAATACATA
9053 SEQ TD N0:4566 -6.4 -15 49.4 -7.7 -0.8 -4.5
TCCAGAATCCTCTCTGCTTA
16 SEQ ID N0:4567 -6.3 -25.4 73.6 -18.1 -0.9 -4.5
CTTGGCTTCAGTTTTCTTGC
235 SEQ ID N0:4568 -6.3 -24.8 74.9 -18.5 0 -3.7
CGGAAAAGCTCCAGGTCCCT
377 SEQ ID N0:4569 -6.3 -28 74.2 -20.1 -1.5 -6.7
CGGAAGCTTTCAGGTCCTGG
496 SEQ ID N0:4570 -6.3 -26.8 75 -19 -0.8 -10.8
CTCTGGAGGAATGTCTCCAT
665 SEQ ID N0:4571 -6.3 -24.7 71.9 -15.1 -3.3 -8.5
AATTTTCCTAACAGGGTTTA
812 SEQ ID N0:4572 -6.3 -20.3 61.5 -13.1 -0.7 -4.1
TTCCAGTGAATGTGTACTCT '
942 SEQ TD N0:4573 -6.3 -22.8 68.6 -16.5 0 -4.9
CTCTGAATGTTCTCAACGCT
1110 SEQ ID N0:4574 -6.3 -22.8 66.4 -15.6 -0.8 -5.3
TTTCAGTGCTCGGAGAACTC
1127 SEQ ID N0:4575 -6.3 -23.6 69.8 -16.4 -0.7 -6.4
AGCCATAGTTGGGGTTTCGA
1539 SEQ ID N0:4576 -6.3 -26.3 75.1 -18.5 -1.4 -7.6
AATTTTTTGTCACTGGTCAG
2107 SEQ ID N0:4577 -6.3 -20.7 64 -14.4 0 -5
GCCACGGATACTCAAGAGAG
2144 SEQ ID N0:4578 -6.3 -23.7 67.3 -16.2 -1.1 -5.7
GTAATAAGGATCCATGGCAA
2906 SEQ ID N0:4579 -6.3 -21.1 61.8 -14.1 0 -9
GTGGGCCAGGATTTTGCCAA
3052 SEQ ID N0:4580 -6.3 -28 76.8 -19.4 -2.3 -7.9
245
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGCAAAAATGAAGACGATGA
3143 SEQ ID N0:4581 -6.3 -16.4 5l -10.1 0 -4.1
TCTGCAGATTATTCATTTCA
3468 SEQ ID N0:4582 -6.3 -20.7 64.1 -13.4 -0.2 -9.8
GGCACTGTGACGGTGAGGCT
3763 SEQ ID N0:4583 -6.3 -28.5 79.4 -20.4 -1.8 -7.6
TGCATTTAATTTCTCTTTGC
3857 SEQ ID N0:4584 -6.3 -20.5 63.2 -13.7 -O.l -4.7
TTCAATGTATATATCTTCAA
4145 SEQ ID N0:4585 -6.3 -16.6 54 -10.3 0 -3.9
CCAAAGAAACATCAACGATC
4305 SEQ ID N0:4586 -6.3 -17.8 53.5 -11.5 0 -3.5
TGGCACCGAGTTCTGAGTAG
4350 SEQ TD N0:4587 -6.3 -25.4 73.2 -19.1 0 -4
TCTTAATGTCCGTAATGATT
4373 SEQ ID N0:4588 -6.3 -19.7 59.5 -13.4 0 -2.6
CTAATGTCAAACATGTTACC
4579 SEQ ID N0:4589 -6.3 -18.9 57.6 -11.4 -1.1 -9
CTGGTTGAAGTTATCTATGA~
4871 SEQ ID N0:4590 -6.3 -19.9 61.8 -13.6 0 -2.6
ATTGTAATATTTTTTCTGTT
4934 SEQ TD N0:4591 -6.3 -17.1 55.9 -10.8 0 -3.9
GATCCAAGTTTCTTCATTGC
4954 SEQ ID N0:4592 -6.3 -22.8 68.4 -16.5 0 -4.3
CCTATAGTGAAGTAGTAGTG
5215 SEQ ID N0:4593 -6.3 -20.4 63.6 -14.1 0 -5.1
CAAAGATGGCATAGATAAAC
5469 SEQ ID N0:4594 -6.3 -16.4 51.9 -10.1 0 -4
GCTTCCTTTTTAACATAGGC
5503 SEQ ID N0:4595 -6.3 -23.1 68.3 -16.8 0 -3.6
CAAAGTTGAACATGTCATCA
5529 SEQ ID N0:4596 -6.3 -18.8 57.7 -11.9 -0.3 -7.3
AATAAGCTGGACTTTGTTGG
5957 SEQ ID N0:4597 -6.3 -20.6 62.1 -13.7 -0.3 -5.1
CGCTTTGTAAAGGCAAATAA
6028 SEQ ID N0:4598 -6.3 -18.5 55.4 -10.2 -2 -6.4
CAGACACCTCCTCTTGTTTA
6162 SEQ ID N0:4599 -6.3 -25.1 72.9 -18.8 0 -3
GCAGACACCTCCTCTTGTTT
6163 SEQ ID N0:4600 -6.3 -27.2 77.9 -20.9 0 -3.5
CTTTTCCTTTGCTTTCTTTT
6432 SEQ ID N0:4601 -6.3 -23.2 70.1 -16.9 0 -3.6
AAAGATAATTCTTTGTTTCT
6477 SEQ ID N0:4602 -6.3 -16.5 53.8 -8.4 -1.8 -5.2
TAAAACAGTCAGTTTGGCAT
6563 SEQ ID N0:4603 -6.3 -19.9 60.5 -12 -1.6 -7.7
TCACAGAGTTGCAGTGACAG
6630 SEQ ID N0:4604 -6.3 -23.1 69.7 -15.6 -1.1 -7
GTCAACGTTGATACCCTGCT
6650 SEQ ID N0:4605 -6.3 -26 72.1 -17.4 -0.1 -12.8
CTGGCAAAACACCTTTGTCT
6965 SEQ ID N0:4606 -6.3 -23.2 66.1 -14.6 -2.3 -5.8
ATGGATTTATTAGATTACTT
7243 SEQ ID N0:4607 -6.3 -17.1 55.3 -10.8 0 -2.4
CAGAGCAGGTTGAATTCATT
7644 SEQ ID N0:4608 -6.3 -21.5 64.8 -14.6 0 -8.4
GTTGATTATATTTTTACATT
7851 SEQ ID N0:4609 -6.3 -16.5 54.2 -10.2 0 -2.2
246
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAAATAAATTGTGATGTCAT
7916 SEQ ID N0:4610 -6.3 -14.4 48.2 -8.1 0 -5.1
TTAGTGCAGCAGGAATTAAA
8218 SEQ ID N0:4611 -6.3 -19.5 59.3 -13.2 0 -6.6
TAGGTAATTGCACAACTTTG
8291 SEQ ID N0:4612 -6.3 -19.2 58.8 -12.9 0 -5.1
TCAATACACTACAGTAAATA
8375 SEQ TD N0:4613 -6.3 -15.9 51.6 -9.6 0 -3.6
TATTATCAAACCTGAAAGTT
8716 SEQ ID N0:4614 -6.3 -16.8 53.1 -10.5 0.1 -3.1
AGAAGATGAGTTTAGATGCT
8790 SEQ ID N0:4615 -6.3 -19.5 60.8 -13.2 0 -3.6
ACATTTATTAGCCACCAAGT
8839 SEQ ID N0:4616 -6.3 -22.5 65.4 -16.2 0 -3.2
TCTCAATAACTATATCATTA
8914 SEQ TD N0:4617 -6.3 -16.1 52.8 -9.8 0 -2.4
AAATTCTCAATAACTATATC
8918 SEQ ID N0:4618 -6.3 -14.3 48.5 -8 0 -3.1
GAATCCTCTCTGCTTATGCC
12 SEQ ID N0:4619 -6.2 -26.1 74.6 -19 -0.8 -4.6
GCCTTATGAATTACAGCATA
192 SEQ ID N0:4620 -6.2 -21.3 63 -15.1 0 -4.1
ATCCCTGTCAAACCTTGATG
258 SEQ ID N0:4621 -6.2 -24 67.5 -16.6 -1.1 -4.5
TGAATCCTTGACAGGTATCT
279 SEQ ID N0:4622 -6.2 -22.2 66.1 -14.6 -1.3 -3.8
CTTTGGTTTGTTCTCATCAT
602 SEQ ID N0:4623 -6.2 -22.5 69.3 -16.3 0 -1.9
CCTTTATTCATTACTATAAA
739 SEQ TD N0:4624 -6.2 -16.9 53.8 -10.7 0 -3.2
AAACCCTCTTGCCAAGATTT
986 SEQ ID N0:4625 -6.2 -23.7 66.1 -16.7 -0.6 -6.3
GTCCACAAACTCTGTCACAT
1076 SEQ ID N0:4626 -6.2 -23.4 68.2 -16.7 -0.1 -4.2
TTGCCCATGAACAGCTGCAG
1267 SEQ ID N0:4627 -6.2 -26.6 73.1 -19.5 -0.3 -9.4
ACAGAGTAAAGGGTCTTTTT
1463 SEQ ID N0:4628 -6.2 -20.3 62.8 -13.4 -0.4 -4.1
TTGAGTCATGAGTCGAAATA
1598 SEQ ID N0:4629 -6.2 -18.9 58.3 -11 0 -11.6
CAACTGGTAAAGATTTTCCC
1625 SEQ ID N0:4630 -6.2 -21.1 61.8 -14.9 0 -3.3
GAGCATCTGCTGAAATTCGG
1799 SEQ ID N0:4631 -6.2 -22.8 65.6 -15.6 -0.9 -7.9
ACTGGTCAGTCTGTTTCCAT
2096 SEQ ID N0:4632 -6.2 -25.6 76.8 -18.9 -0.1 -7.3
GGGAAAACAGGGAGCCACGG
2157 SEQ ID N0:4633 -6.2 -25.5 68.5 -18.7 -0.3 -4.3
AGTTGTCCAGTAGGTGACGT
2461 SEQ ID N0:4634 -6.2 -25.7 76 -18.4 -l -5.8
AAATTCACAAGATGTTTTAC
2716 SEQ ID N0:4635 -6.2 -16 52.1 -9.8 0 -4.3
TAAAGAGGGTATTTAAGACA
2781 SEQ TD N0:4636 -6.2 -16.9 53.9 -10.7 0 -2.9
CTGAATTGCTCAGTCATGGG
2818 SEQ ID N0:4637 -6.2 -23.4 68.9 -15.9 -1.2 -8.7
GCTGACAATAATTCCATCAA
2951 SEQ ID N0:4638 -6.2 -20.1 59.5 -13.9 0 -2.9
247
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CTCCATTAAACTGAGGCTGA
2966 SEQ ID N0:4639 -6.2 -22.6 65.3 -16.4 0 -3.7
TTTTTCACATAATCAATTCC
3511 SEQ ID N0:4640 -6.2 -18.3 57 -12.1 0 -2.5
CTGGTGGTTCCATTCCCATC
3667 SEQ ID N0:4641 -6.2 -28.5 80.1 -21.1 -1.1 -6.6
GGTTGCATTTAATTTCTCTT
3860 SEQ ID N0:4642 -6.2 -21.1 64.9 -14.9 0 -5.1
AACCAGTTGTGCTCAACAAT
4075 SEQ ID N0:4643 -6.2 -22 64 -13.3 -2.5 -5.8
ATATAGGTAAAGACTTTGTC
4201 SEQ ID N0:4644 -6.2 -17.6 56.6 -10.9 -0.1 -4.1
TAAAGCTCTTAATGTCCGTA
4379 SEQ ID N0:4645 -6.2 -20.7 61.5 -14.5 0 -5
GATAGAGGGAATTGCTCCAA
4457 SEQ ID N0:4646 -6.2 -22.4 65.1 -14.4 -1.8 -6.l
GTATAAATACATGTACAGAT
4793 SEQ ID N0:4647 -6.2 -16.2 52.6 -9.5 0 -8.2
ATCATGATGCTGATATCAAA
5053 SEQ ID N0:4648 -6.2 -18.4 56.8 -11.3 -0.8 -7.7
AGGCCGATGTTAAACAACGC
5431 5EQ ID N0:4649 -6.2 -23 63.4 -16.8 2.6 -8.1
AGCAATCCATCCCAGCCAGC
5596 SEQ ID N0:4650 -6.2 -30.3 80.9 -24.1 0 -4.1
GTGGAGTTCCCATTTAGTTT
6313 SEQ ID NO:4651 -6.2 -24.7 73.5 -17.2 -l.2 -4.4
GATCACAAAGATAATTCTTT
6483 SEQ ID N0:4652 -6.2 -16.4 52.8 -8.4 -l.8 -8.3
GACTGTACTAAAGGTGTTTG
6772 SEQ ID N0:4653 -6.2 -19.8 61.2 -13.6 0 -5.l
TAGCATTATGAATAAACTAT
6875 SEQ ID N0:4654 -6.2 -15 49.6 -8.8 0 -4.1
ATAGCATTATGAATAAACTA
6876 SEQ ID N0:4655 -6.2 -15 49.6 -8.8 0 -4.1
CAGATAGAAACAAACATAAC
7088 SEQ ID N0:4656 -6.2 -13.8 46.6 -7.6 0 -1.2
AATTGACATAGACTATCAGC
7352 SEQ ID N0:4657 -6.2 -18.9 58.8 -12.7 0 -3.3
AAACTATGTTTAATGAATGA
7522 SEQ ID N0:4658 -6.2 -14.3 48.1 -7.6 -0.2 -4.3
ATTTTTAGCAAAATATGAAG
7804 SEQ ID N0:4659 -6.2 -14.1 47.7 -6.8 -1 -5.3
TTAAACAAGTTTTAGACATA
7823 SEQ ID N0:4660 -6.2 -15 50 -8.1 -0.4 -5.5
AGTTGATTATATTTTTACAT
7852 SEQ ID N0:4661 -6.2 -16.4 54 -10.2 0 -2.6
TTTCTTATGTACAAAATGCT
7881 SEQ ID N0:4662 -6.2 -17.7 55.6 -11.5 0 -6.8
TAAATTGTGATGTCATCAAC
7912 SEQ ID N0:4663 -6.2 -17.1 54.5 -9.8 -1 -7.2
AAAAGTTTGGAATTGTGATT
7962 SEQ ID N0:4664 -6.2 -16.4 52.6 -10.2 0 -4.6
TTAGCAATAGCAATTCCCTG
8406 SEQ ID N0:4665 -6.2 -22.5 64.9 -14.6 -1.7 -4.9
TATATATTTTAAACTGCCAA
8530 SEQ ID N0:4666 -6.2 -16.6 52.5 -10.4 0 -4.4
TATATCATTAATACCTTATG
8904 SEQ ID N0:4667 -6.2 -16.2 52.5 -10 0 -4.2
248
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAAATATGCATTACAACTGG
9012 SEQ ID N0:4668 -6.2 -16.4 51.7 -10.2 0 -6.5
ATTACAGCATAACAAAGCCC
183 SEQ ID N0:4669 -6.1 -21.5 61.7 -14.9 -0.2 -4.1
GCTCCTTTCCCAGTAAGCCA
307 SEQ ID N0:4670 -6.l -30 81.8 -23.4 -0.1 -3.6
GCACATTTAATTACGTGTAG
441 SEQ ID N0:4671 -6.1 -19.5 59.4 -12.8 -0.3 -5.4
AACAGTGCCTGTGCCATCTT
469 SEQ ID N0:4672 -6.1 -27.2 76.4 -19.5 -1.5 -8.7
TCCTAACAGGGTTTAGTGGA
807 SEQ ID N0:4673 -6.1 -23.7 70 -16.7 -0.7 -4.3
AAGAAACGTAAAATCTTCTA
1010 SEQ ID N0:4674 -6.1 -14.7 48.5 -8.1 -0.2 -6.1
TGAAATCCAGCCAGTTCCAT
1038 SEQ ID N0:4675 -6.1 -25.2 70.3 -19.1 0 -3.2
AAATAAAATGAGCCCAAGAA
1696 SEQ ID N0:4676 -6.1 -16.5 50.8 -10.4 0 -3.2
AAATTCGGCCTCTTTTTGTT
1787 SEQ ID N0:4677 -6.l -22.8 66.2 -16.7 0 -6.7
TGTCTCTCTCTCCTTTGTTG
2016 SEQ ID N0:4678 -6.1 -25.2 77.2 -19.1 0 0
CAAGAGAGACTGATGAGGGG
2132 SEQ TD N0:4679 -6.1 -21.7 64.3 -15.6 0 -2.2
CCTGGATGACATACTGGCCT
2351 SEQ ID N0:4680 -6.1 -26.9 74 -20.8 0 -7.2
TTGCAATCCACAGTGCTGTG
2404 SEQ ID N0:4681 -6.1 -25 71.8 -16.8 -1.5 -12.1
GTAAAGACCAGGTTTCCTAC
2851 SEQ ID N0:4682 -6.1 -22.8 66.9 -16.2 -0.1 -5.9
GCCAACTTGAAAACTCTAAG
3037 SEQ ID N0:4683 -6.1 -18.9 56.6 -12.8 0 -2.9
TGCCAACTTGAAAACTCTAA
3038 SEQ ID N0:4684 -6.1 -18.9 56.4 -12.8 0 -3
AAGTCGTTCATGTGCCACCG
3238 SEQ ID N0:4685 -6.1 -26.8 73.2 -20.7 0 -4.7
GCGACCTCCATACAGTCCCA
3316 SEQ ID N0:4686 -6.1 -30.3 80.1 -23.7 -0.1 -3.4
CATATAATCATTTTCATCGA
3725 SEQ ID N0:4687 -6.1 -17.7 55.4 -11.6 0 -4.8
TGGTTGCATTTAATTTCTCT
3861 SEQ ID N0:4688 -6.1 -21 64.4 -14.9 0 -5.1
CTGGTTGCATTTAATTTCTC '
3862 SEQ ID N0:4689 -6.1 -21 64.4 -14.9 0 -4.8
GGAAACTTTTTAATACACCC
3985 SEQ ID N0:4690 -6.1 -19.7 58.3 -13.6 0 -2.5
CAAACCAGTTGTGCTCAACA
4077 SEQ ID N0:4691 -6.1 -22.7 65.2 -13.3 -3.3 -6.6
TTCGCTGTTCAATGTATATA
4152 SEQ ID N0:4692 -6.1 -20 61.2 -13.9 0 -3.6
TCTGAGTAGCCAAGAGCATT
4339 5EQ ID N0:4693 -6.1 -23.8 70.1 -16.2 -1.4 -4.1
TTCTGAGTAGCCAAGAGCAT
4340 SEQ ID N0:4694 -6.1 -23.8 70.1 -16.2 -1.4 -4.8
CCACCCTCATGCCTTCAAAC
4422 SEQ ID N0:4695 -6.1 -27.6 73.5 -21.5 0 -4.4
ATTGCTCCAACAAGAGCATT
4447 SEQ ID N0:4696 -6.1 -22.6 65.4 -13.1 -3.4 -9.5
249
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TATACAGGCTGAAGTTTAAC
4765 SEQ ID N0:4697 -6.1 -18.7 58.2 -12.6 0 -4.1
CTGTCATAAAGATGTCTTGA
4911 SEQ ID N0:4698 -6.l -19.3 60 -12.5 -0.4 -6.8
CTCTGTCATAAAGATGTCTT
4913 SEQ ID N0:4699 -6.1 -20 62.2 -13.2 -0.4 -6.5
TGTAATATTTTTTCTGTTCC
4932 SEQ ID N0:4700 -6.l -19.4 61.1 -13.3 0 -4.2
TCTTGGATCCAAGTTTCTTC
4959 SEQ ID N0:4701 -6.1 -22.8 69.2 -13 -1.3 -15.5
TGTTGAGGCAGATGAGGATC
5070 SEQ ID N0:4702 -6.l -23 69.1 -16.9 0 -4.1
AGGTTGATCCGGGACAAAAC
5140 SEQ ID N0:4703 -6.l -22.3 63.2 -15 -1.1 -8.7
GGAAGGGACATCATCAAAGC
5410 SEQ ID N0:4704 -6.1 -21.6 63.4 -14.9 -0.3 -3.1
AATTCCAGCTTCCTTTTTAA
5510 SEQ ID N0:4705 -6.1 -22 64.9 -15.9 0 -4.5
CTTCAGTAGCAACACTGAAG
5790 SEQ ID N0:4706 -6.1 -20.7 62.5 -10.6 -4 -11.8
ACTTTCTTCAGTAGCAACAC
5795 SEQ ID N0:4707 -6.1 -21.6 66.1 -14.8 -0.5 -0.8
CTCAAAGTCATCCTCACTCA
5825 SEQ ID N0:4708 -6.l -23.5 69.2 -17.4 0 -2.6
TAAGAGACTTTGGAGGGGTT
6115 SEQ ID N0:4709 -6.1 -22.2 66.6 -16.1 0 -2.9
CTCATAAGAGACTTTGGAGG
6119 SEQ ID N0:4710 -6.1 -20.5 62.5 -12.6 -1.8 -5.4
GAATGATAGCGGCAGACACC
6174 SEQ ID N0:4711 -6.l -24.2 67.6 -18.1 0 -6.6
ATTGCCTCTTTGTTATAGTT
6247 SEQ ID N0:4712 -6.1 -22.3 68.2 -16.2 0 -3
ATTGATCACAAAGATAATTC
6486 SEQ ID N0:4713 -6.1 -15.4 50.7 -8.4 -0.8 -6.3
TTCACAGAGTTGCAGTGACA
6631 SEQ ID N0:4714 -6.l -23.2 69.8 -15.6 -1.4 -7.4
ACCTCATTTACAAAAATAGT
6899 SEQ TD N0:4715 -6.1 -17.1 53.6 -10.4 -0.3 -3.9
CAAAATTAAAGCCATCTAGA
7053 SEQ ID N0:4716 -6.1 -17.1 53 -11 0 -5.8
TTTACAGGCACATAACTGTT
7108 SEQ ID N0:4717 -6.1 -20.8 62.7 -13.1 -1.5 -5.2
TTTAAATATTAGAGGAGACT
7127 SEQ ID N0:4718 -6.1 -16.1 52.6 -9.3 -0.5 -5.7
AAAAGTGCAAAAGTAAAGGT
7705 SEQ ID N0:4719 -6.1 -15.4 49.7 -9.3 0 -4.9
AATAATTTTCTTATGTACAA
7887 SEQ ID N0:4720 -6.1 -14.8 49.7 -8.7 0 -6.8
TTGTGATGTCATCAACCTGA
7908 SEQ ID N0:4721 -6.1 -22.3 66 -15.1 -1 -6.9
ATAAATTGTGATGTCATCAA
7913 SEQ ID N0:4722 -6.1 -16.9 53.9 -9.7 -1 -6.9
ATTATGAAATACATATTTAG
9048 SEQ ID N0:4723 -6.1 -13.2 46.2 -6 -1 -5.2
TTCCAAGTCACTATTTGGCT
620 SEQ ID N0:4724 -6 -23.7 69.8 -16.2 -1.4 -5.1
AATAAATGGAAGGTTCTTTC
644 SEQ ID N0:4725 -6 -17.1 54.5 -11.1 0 -4.2
250
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TAGTAGGGATCCAGGTCCTC
703 SEQ ID N0:4726 -6 -26.8 79 -18.8 -2 -8.9
CTGAATCGGAAAATTGCCTT
760 SEQ ID N0:4727 -6 -20.6 59.1 -14.6 0 -4.4
TGGTCAAAATAGTGCACATG
873 SEQ ID N0:4728 -6 -19.7 59.4 -12.7 0 -9.9
TTCTCAACGCTGAGACATTG
1101 SEQ ID N0:4729 -6 -21.7 63.8 -12.9 -2.8 -8.2
TCTTTACCGACTGGATCAGG
1188 SEQ ID N0:4730 -6 -24 68.9 -17.1 -0.7 -5.3
AAAGCAGAATCGCTTGGGGG
1312 SEQ ID N0:4731 -6 -23.8 66.7 -16 -1.8 -9.3
GCCATTTCCACAGAGTAAAG
1472 SEQ ID N0:4732 -6 -22.8 66 -16.8 0 -2.7
CCTTCAAGGTGCTCTCTCTG
1993 SEQ ID N0:4733 -6 -26.4 77.2 -20.4 0 -4.8
GAGAAAAGGAAGCTGCTTCT
2071 SEQ ID N0:4734 -6 -21 62.3 -12.4 -1.8 -13.3
CACTGGTCAGTCTGTTTCCA
2097 SEQ ID N0:4735 -6 -26.3 78 -20.3 0 -6.6
ATCTTCCCATTTGCTGGAAG
2383 SEQ ID N0:4736 -6 -24.5 70.1 -l6 -2.5 -7.5
AGAGCTTAACCTTCTCTTTC
2516 SEQ ID NO:4737 -6 -22.8 69.2 -16 -0.6 -5.2
AGGAATCCTCCAGCATCTCC
2550 SEQ ID N0:4738 -6 -27.7 77.6 -19.8 -1.9 -7.1
TGCTGGCTATGCTCACGGCT
2583 SEQ ID N0:4739 -6 -29 80 -21.8 -1.1 -7.5
GCAAATCTATACCAGCATGG
2653 SEQ ID N0:4740 -6 -22.4 64.6 -14.6 -1.8 -7
AAGACCAGGTTTCCTACAGT
2848 SEQ ID N0:4741 -6 -24.5 71.2 -18 -0.1 -5.9
AAACTGAGGCTGACAATAAT
2959 SEQ ID N0:4742 -6 -18 55 -12 0 -3.7
AACTTGAAAACTCTAAGCAG
3034 SEQ ID N0:4743 -6 -16.9 53.2 -10.9 0 -4.1
ACCGTGGGAGCGTACAGTCA
3222 SEQ ID N0:4744 -6 -27.9 76.9 -21 -0.7 -4.8
CACCGTGGGAGCGTACAGTC
3223 SEQ ID N0:4745 -6 -27.9 76.9 -21 -0.7 -4.8
CCACCGTGGGAGCGTACAGT
3224 SEQ ID N0:4746 -6 -29.5 78.6 -22.6 -0.7 -7.8
CTACTGCAATCTGCAGATTA
3477 SEQ ID N0:4747 -6 -21.7 64.7 -11.3 -4.4 -14
AATTCCCTTTTGCATTCTTC
3497 SEQ ID N0:4748 -6 -23.4 68.8 -17.4 0 -5.1
ATGAATGACATATAATCATT
3733 SEQ TD N0:4749 -6 -15.3 50.2 -7.6 -1.7 -7.9
CAGCAATTGGCACTGTGACG
3771 SEQ ID N0:4750 -6 -24.2 68 -16.6 -1.5 -7.1
CGCTGTTCAATGTATATATC
4150 SEQ ID N0:4751 -6 -19.9 60.8 -13.9 0 -3.9
TCGCTGTTCAATGTATATAT
4151 SEQ ID N0:4752 -6 -19.9 60.8 -13.9 0 -3.8
AGAATGAATATATAGGTAAA
4210 SEQ ID N0:4753 -6 -13.6 46.8 -7.6 0 -4.2
TTGAGAAGCATTTCCAGAAT
4225 SEQ ID N0:4754 -6 -20.3 60.9 -13.5 -0.6 -4.1
251
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAGGCTCTTAGAGGTCTTAA
4396 SEQ ID N0:4755 -6 -21.7 66.3 -15.1 -0.3 -5.3
AAGAGCATTCACAACCACCC
4436 SEQ ID N0:4756 -6 -24.9 68.6 -18.3 -0.3 -4.1
CAGCGCCAACATTATCAAAG
4668 SEQ ID N0:4757 -6 -21.5 61.1 -l5 0 -7.6
TAGGTTGATCCGGGACAAAA
5141 SEQ ID N0:4758 -6 -21.8 62.2 -14.6 -1.1 -8.7
GAAGTAGTAGTGTCTGAGGG
5207 SEQ ID NO:4759 -6 -22.4 69.6 -16.4 0 -2.9
GATCCCCTTTGCTCCTTTGA
5375 SEQ TD N0:4760 -6 -28.9 79.3 -22.9 0 -3.6
CCTTTTTAACATAGGCAAAG
5499 SEQ ID N0:4761 -6 -19.2 57.8 -13.2 0 -4
AAGTTGAACATGTCATCAAT
5527 SEQ TD N0:4762 -6 -18.1 56.5 -10.8 -1 -9.9
GGGTGGTGCACTATTAAGAA
5624 SEQ ID N0:4763 -6 -22.3 65.9 -15.1 -1.1 -8.7
TCCCTTAACTGAGCTGCCAG
5669 SEQ ID N0:4764 -6 -27.3 75.2 -20.6 -0.2 -8.8
GACCGCGATGTACATGTTCA
5759 SEQ ID N0:4765 -6 -25 69.5 -18.4 0 -8.4
AAAATCAGAGAGTTTAGAGA
5900 5EQ ID N0:4766 -6 -16.5 53.6 -10.5 0 -4.2
GTTTTGCTATGAGAAGAGGA
5937 SEQ ID N0:4767 -6 -20.8 63.6 -14.8 0 -2.9
ATAAGAGACTTTGGAGGGGT
6116 SEQ TD N0:4768 -6 -22.1 66.2 -16.1 0 -2.9
AGTCCAGTTGACACATATAC
6529 SEQ TD NO:4769 -6 -21.6 65.5 -13.8 -1.8 -5.1
CAGTTTGGCATGGACCTCCT
6554 SEQ ID N0:4770 -6 -28 78.2 -21.5 -0.1 -5.1
GCCATTGGGTTTCTCCTCAG
6704 SEQ ID N0:4771 -6 -28.1 80.5 -21.2 -0.8 -6.3
AACCTCATTTACAAAAATAG
6900 SEQ ID N0:4772 -6 -15.2 49.4 -8.5 -0.5 -3
ATTCTTTTTCTGGTTTTGAG
7001 SEQ ID N0:4773 -6 -20.4 64.4 -14.4 0 -2.3
TAAAGCAATACTTTAGATAT
7274 SEQ ID N0:4774 -6 -15.1 50 -7.5 -1.6 -5.7
TGTGAAGAATGGATTGAGTA
7589 SEQ ID N0:4775 -6 -18.4 57.4 -12.4 0 -2.1
AATAAAGTTGATTATATTTT
7857 SEQ ID N0:4776 -6 -13.3 46.5 -7.3 0 -2.9
TAAAACCCATTATCTAACTT
8022 SEQ ID N0:4777 -6 -17.8 54.4 -11.8 0 -1.6
AATTGCACAACTTTGCCACT
8286 SEQ ID N0:4778 -6 -23 65.4 -16 -0.9 -5
GTTAGGTAATTGCACAACTT
8293 SEQ ID N0:4779 -6 -20.4 61.9 -14.4 0 -5.3
AAAAACAAAAATTTATATCA
8314 SEQ ID N0:4780 -6 -10 39.6 -4 0 -5.2
AAAAAACCCCAGAGCCCAAT
8493 SEQ ID N0:4781 -6 -23.8 62.8 -17.8 0 -3.2
AACAAAAAACCCCAGAGCCC
8496 SEQ ID N0:4782 -6 -24 63.3 -18 0 -3.2
AATTATATATATTTTAAACT
8535 SEQ ID N0:4783 -6 -11.9 43.6 -5.9 0 -5.2
252
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGTTTGTTGTAAAATTCATG
8600 SEQ ID N0:4784 -6 -16.7 54.1 -10 -0.4 -5.2
ATTGAAAGCTATTGTAGGTG
8747 SEQ ID N0:4785 -6 -19.1 59.3 -13.1 0 -5.1
TTATATAATGCATTTAAGTA
8871 SEQ ID N0:4786 -6 -15.1 50.4 -8.4 0 -8.8
CTCTGCTTATGCCTCCGCTT
SEQ ID N0:4787 -5.9 -29.4 80.5 -22.6 -0.8 -5
CCAGAATCCTCTCTGCTTAT
SEQ ID N0:4788 -5.9 -25 71.9 -18.1 -0.9 -4.5
CTTACAATATCCCTAGAAGA
335 SEQ ID N0:4789 -5.9 -20.1 60 -14.2 0 -3.8
CCCTTCTGTGAATTATCTCA
36l SEQ ID N0:4790 -5.9 -23.6 68.9 -17.2 -0.1 -3.2
GCATACGAATTACCTTAGAT
415 SEQ ID N0:4791 -5.9 -20.4 60.2 -14.5 0 -3.4
TAGGGATCCAGGTCCTCCAG
700 SEQ ID N0:4792 -5.9 -28.6 80.7 -20.7 -2 -10.3
CTTTCCTTTATTCATTACTA
743 SEQ ID N0:4793 -5.9 -20.1 62.3 -14.2 0 -0.7
TACAAGGCAGAGGTGGCACT
778 SEQ ID N0:4794 -5.9 -25.4 73 -18.6 -0.8 -4.5
ATTTTCCTAACAGGGTTTAG
811 SEQ ID N0:4795 -5.9 -21 63.8 -14.6 -0.1 -3.6
TTCTTTGTCCAGTCAGGAGG
919 SEQ ID N0:4796 -5.9 -25.2 75.8 -17.9 -1.3 -4.7
AATGTTCTCAACGCTGAGAC
1105 SEQ ID N0:4797 -5.9 -21.4 63.2 -13 -2.5 -7.9
ATGAACAGCTGCAGCCCAAT
1261 SEQ ID N0:4798 -5.9 -25.8 70.6 -17.4 0 -13.2
GGCCACTGCAAACATTTATT
1294 SEQ ID N0:4799 -5.9 -22.8 65 -15.4 -l.4 -7
AAAACATAAAAGTGACTGTC
1435 SEQ ID N0:4800 -5.9 -14.9 49.1 -9 0 -6
GTTGGGGTTTCGACCAGCCT
1532 SEQ ID N0:4801 -5.9 -29.7 81.5 -21.9 -1.9 -7
CAGGACAAAAAATATCATGT
1670 SEQ ID N0:4802 -5.9 -15.9 50.7 -10 0 -4.7
GCTGCCGCAACTGCCTGAGC
1846 SEQ ID N0:4803 -5.9 -31.3 82 -24.5 -0.8 -6.4
TACTCAAGAGAGACTGATGA
2136 SEQ TD N0:4804 -5.9 -19.3 59.7 -11.8 -1.5 -5.4
GATACTCAAGAGAGACTGAT
2138 SEQ ID N0:4805 -5.9 -19.3 59.8 -11.8 -1.5 -5.4
TCTGACTTCCGTTTCAGTGG
2498 SEQ ID N0:4806 -5.9 -25.2 73.6 -18.1 -1.1 -5.7
ACAGCAAAAATGAAGACGAT
3145 SEQ ID N0:4807 -5.9 -16.7 51.5 -10.8 0 -4.1
AGAACCACAAGGTTTCCAAT
3379 SEQ ID N0:4808 -5.9 -22 63.2 -13.5 -2.6 -7.6
AGAGGTTCAGAACCACAAGG
3387 SEQ ID N0:4809 -5.9 -22.4 65.6 -13.8 -2.7 -12
GCAGATTATTCATTTCATTG
3465 SEQ ID N0:4810 -5.9 -19.5 60.8 -13.1 -0.2 -3.7
TTTTGGCTTTCTAAAAAAGG
3557 SEQ ID N0:4811 -5.9 -17.1 53.8 -9.7 -1.4 -5.5
CCACTGGTGGTTCCATTCCC
3670 SEQ ID N0:4812 -5.9 -30.3 82.5 -23.2 -1,1 -9.1
253
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGAATGACATATAATCATTT
3732 SEQ ID N0:4813 -5.9 -15.4 50.5 -7.6 -1.9 -8.1
TTCAGTTTCAGCTTGTTCAC
3926 SEQ ID N0:4814 -5.9 -23,1 71.7 -17.2 0 -4.5
GTCTTCTTCGGGTTCAGTTT
3938 SEQ ID N0:4815 -5.9 -25.4 77.2 -19.5 0 -3
GATCAAGAAATCTAGCCAGC
4289 SEQ ID N0:4816 -5.9 -21.5 63.4 -15.6 0 -4.7
GAGGGAATTGCTCCAACAAG
4453 SEQ ID N0:4817 -5.9 -22.3 64 -14.6 -1.8 -5.2
TAGAGGGAATTGCTCCAACA
4455 SEQ ID N0:4818 -5.9 -22.7 65.6 -15.7 -1 -6.1
ACAGGCTGAAGTTTAACATC
4762 SEQ ID N0:4819 -5.9 -20.4 62 -14.5 0 -4.5
ATATACAGGCTGAAGTTTAA
4766 SEQ ID N0:4820 -5.9 -18.5 57.7 -12.6 0 -3.9
GTTCCTCTGTCATAAAGATG
4917 SEQ ID N0:4821 -5.9 -21.1 64.1 -14.7 -O.l -3.5
TCATCCGTTTCCACCATCAT
5098 SEQ ID N0:4822 -5.9 -26.8 74.1 -20.9 0 -2.1
ACAAATTCTCCAGTGAACAG
5173 SEQ ID N0:4823 -5.9 -20 60 -14.1 0 -3.9
ACAACGCAGGAAGGGACATC
5418 SEQ ID N0:4824 -5.9 -23.1 65.4 -17.2 0 -3.3
GGTCTCAAAGTTGAACATGT
5534 SEQ ID N0:4825 -5.9 -20.7 62.8 -13.9 -0.8 -6.8
ATTGTGTCAGGGTCACAGTC
5644 SEQ ID N0:4826 -5.9 -24.8 76.3 -17.3 -1.6 -5.8
GCCAGGGTGAATTGTGTCAG
5654 SEQ ID N0:4827 -5.9 -25.6 74.2 -19.7 0 -3.8
GGGCTCTGCACTTTCTTCAG
5804 SEQ ID N0:4828 -5.9 -26.7 78.8 -19.9 -0.7 -6.4
TCTATAAACTGGGTCGCATC
5878 SEQ ID N0:4829 -5.9 -22.1 65 -16.2 0 -3.6
AGATCCATGGCAATAAGCTG
5968 SEQ ID N0:4830 -5.9 -22.4 64.8 -15.1 -1.3 -8
CCGGTCACCACTGACCATGG
5990 SEQ ID N0:4831 -5.9 -29 76.4 -18.7 -4.4 -10.3
GGGTTTGATGCCATAAACCT
6100 SEQ TD N0:4832 -5.9 -24.3 68.1 -15.3 -3.1 -9.5
GCTTTAAAAGATAACATCTG
6204 SEQ ID N0:4833 -5.9 -16.3 52.2 -9.5 -0.8 -6.5
TCTTTCTCAAACTTTTCCTT
6403 SEQ ID N0:4834 -5.9 -21.3 64.7 -15.4 0 -1.7
TATACTTTACCTTCATAGGC
6514 SEQ ID N0:4835 -5.9 -21.4 64.9 -14.3 -1.1 -3.7
TTTCTCCTCAGCAGTGTCAG
6695 SEQ ID N0:4836 -5.9 -25.9 78.3 -20 0 -4.2
AAAAATAGAATGGATGCAAG
6792 SEQ TD N0:4837 -5.9 -14.4 47.6 -8.5 0 -5.6
TTTTTCTGGTTTTGAGCAAA
6997 SEQ ID N0:4838 -5.9 -20.1 61.7 -14.2 0 -5.5
TAGCCATTACAATTCTTTTT
7012 SEQ ID N0:4839 -5.9 -20 61 -14.1 0 -3.2
AAATGGAAGTAACTGAAACT
7033 SEQ ID N0:4840 -5.9 -15.3 49.6 -9.4 0 -3
TATTTGATTTAATAGAAGTT
7449 SEQ ID N0:4841 -5.9 -14.6 49.6 -8.7 0 -2.5
254
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GCCTTTAAACTATGTTTAAT
7528 SEQ ID N0:4842 -5.9 -18.4 56.7 -10.4 -2.1 -8
ATTATTTATATTTAAACAAG
7834 SEQ ID N0:4843 -5.9 -12.1 44 -5.6 -0.3 -4.9
ATAAAGTTGATTATATTTTT
7856 SEQ ID N0:4844 -5.9 -14.1 48.5 -8.2 0 -2.6
AATAAATTGTGATGTCATCA
7914 SEQ ID N0:4845 -5.9 -16.9 53.9 -10.1 -0.8 -6.7
AAGTCCATGTTATATTTGTA
8244 SEQ ID N0:4846 -5.9 -19.4 60.6 -13.5 0 -3.8
TGTTAGGTAATTGCACAACT
8294 SEQ ID N0:4847 -5.9 -20.3 61.5 -14.4 0 -6.1
TTCAATACACTACAGTAAAT
8376 SEQ ID N0:4848 -5.9 -16.3 52.5 -10.4 0 -3.6
ATAAAAAATGAAATTTATTC
8461 SEQ ID N0:4849 -5.9 -9.8 39.3 -3 -0.7 -5.2
TTAAACTGCCAACAGCAAAA
8522 SEQ ID N0:4850 -5.9 -18.6 55 -11.2 -1.4 -6.6
TTAATTATATATATTTTAAA
8537 SEQ ID N0:4851 -5.9 -10.6 41 -4.7 0 -6.2
TTTATTAATTATATATATTT
8541 SEQ ID N0:4852 -5.9 -12.1 44.3 -6.2 0 -5.2
ATTATCAAACCTGAAAGTTG
8715 SEQ ID N0:4853 -5.9 -17.1 53.5 -10.5 -0.4 -3.6
TAGGAGTTTATATAATGCAT
8878 SEQ ID N0:4854 -5.9 -17.8 56.6 -11.9 0 -7
ACATAAATCCAAGGGTTCTT
8955 SEQ ID N0:4855 -5.9 -20.7 61.6 -14.8 0 -3.8
ATCCTCTCTGCTTATGCCTC
SEQ ID N0:4856 -5.8 -27.5 79.7 -20.8 -0.8 -4.6
TCTCTGTGGATAAGAAAACA
46 SEQ ID N0:4857 -5.8 -18 55.9 -12.2 0 -2.8
AGCATCCAAGATGGTTAGGG
163 SEQ ID N0:4858 -5.8 -24.1 70 -16.8 -1.4 -6.2
CCTTTCCCAGTAAGCCACTC
304 SEQ ID N0:4859 -5.8 -28.4 78.1 -22.6 0 -3.4
TCCTTTCCCAGTAAGCCACT
305 SEQ ID N0:4860 -5.8 -28.4 78.1 -22.6 0 -3.4
CTCCTTTCCCAGTAAGCCAC
306 SEQ ID N0:4861 -5.8 -28.4 78.1 -22.6 0 -3.2
TACAATATCCCTAGAAGAGA
333 SEQ ID N0:4862 -5.8 -19.7 59.2 -13.9 0 -3.8
AGGTCCCTTCTGTGAATTAT
365 SEQ ID N0:4863 -5.8 -24 70.4 -18.2 0 -4
AAAAGCTCCAGGTCCCTTCT
374 SEQ ID N0:4864 -5.8 -26.8 74.4 -21 0 -5
GAACTCTGAATGTTCTCAAC
1113 SEQ ID N0:4865 -5.8 -19.4 59.8 -12.3 -1.2 -6.2
TACCGACTGGATCAGGGCCC
1184 SEQ ID N0:4866 -5.8 -29.5 78.2 -22.1 -0.8 -11.1
TTTACCGACTGGATCAGGGC
1186 SEQ ID N0:4867 -5.8 -25.7 72.1 -19 -0.8 -5.3
TGTCATCTCCAATGTAATCC
1419 SEQ ID N0:4868 -5.8 -22.6 66.7 -16.2 -0.3 -3
TCTCTCCTGCTTTCGCCGTC
2278 SEQ ID N0:4869 -5.8 -30.2 83.5 -23.7 -0.5 -3.6
CATACTGGCCTGACTAACGT
2342 SEQ ID N0:4870 -5.8 -24.3 68 -18.5 0 -7.2
255
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CAAATCTATACCAGCATGGC
2652 SEQ ID N0:4871 -5.8 -22.4 64.6 -14.6 -2 -7.3
TACAGTCATCATTGATCTTG
3210 SEQ ID N0:4872 -5.8 -20.1 62.7 -14.3 0 -5.6
CCGTGGGAGCGTACAGTCAT
3221 SEQ ID N0:4873 -5.8 -27.7 76.3 -2l -0.7 -4.8
CTCCATACAGTCCCACATGG
3311 SEQ ID N0:4874 -5.8 -27 74.8 -20.3 -0.8 -5.2
AAAAAAGGCTTTTTGGAAAC
3545 SEQ ID N0:4875 -5.8 -15.4 49.6 -8.2 -1.3 -7.7
AGCAGGTTTTTCGAAGATTC
4050 SEQ ID N0:4876 -5.8 -21.5 65 -15 -0.4 -6.8
TGTTCAATGTATATATCTTC
4147 SEQ ID N0:4877 -5.8 -17.8 57.7 -12 0 -3.9
AAAGCTCTTAATGTCCGTAA
4378 SEQ ID N0:4878 -5.8 -20.3 60.1 -14.5 0 -5
ATACATAATATCCATCCAGC
4724 SEQ ID N0:4879 -5.8 -21.3 62.8 -15.5 0 -2.8
GCTGGTTGAAGTTATCTATG
4872 SEQ ID N0:4880 -5.8 -21.1 64.8 -15.3 0 -2.8
CCACCATCATGGTGACCATG
5088 SEQ ID NO:4881 -5.8 -26.6 72.6 -17.1 -3.7 -11.1
TCATCTCAGCCAGAAACATA
5280 SEQ ID N0:4882 -5.8 -21.8 64.2 -16 0 -3.6
GCAATAAGCTGGACTTTGTT
5959 SEQ ID N0:4883 -5.8 -21.9 64.9 -15.4 -0.5 -5.l
TATAGTTACTTGATATATTT
6234 SEQ ID N0:4884 -5.8 -15.8 52.8 -10 0 -4.3
CTTTGCTTTCTTTTTCTGGT
6426 SEQ ID N0:4885 -5.8 -23.4 71.6 -17.6 0 -3.6
ATACTTTACCTTCATAGGCT
6513 SEQ ID N0:4886 -5.8 -22.6 67.5 -15.6 -1.1 -3.7
TACAAAAATAGTGACATAGC
6891 SEQ ID N0:4887 -5.8 -15.7 50.9 -9.9 0 -3.5
CATTTACAAAAATAGTGACA
6895 SEQ ID N0:4888 -5.8 -15.1 49.4 -8.6 -0.5 -4.8
ACCTAAATTAAATATAGAGC
7208 SEQ ID N0:4889 -5.8 -15.6 50.6 -9.8 0 -3
TGTGACATTCTTTAACCAAG
7612 SEQ ID N0:4890 -5.8 -19.5 59.2 -13.7 0 -2.9
CATAAAGTAAAATAAATTGT
7924 SEQ TD N0:4891 -5.8 -11.4 42.2 -5.6 0 -3.2
CACAACTTTGCCACTTTGTT
8281 SEQ ID N0:4892 -5.8 -23.3 67.3 -17 -0.2 -3.8
CTTTTGGCTCAATAATGACG
8442 SEQ ID N0:4893 -5.8 -20.1 59.5 -13.6 -0.5 -5.3
TTATGGGAGAATTATGAAAT
9058 SEQ ID N0:4894 -5.8 -15.7 50.9 -9.9 0 -3.2
CTATAAAAGTTTTCTTATTG
726 SEQ ID N0:4895 -5.7 -14.9 50.2 -8.1 -l -6.3
TGTACTCTACATTCTTTGTC
930 SEQ ID N0:4896 -5.7 -21.1 66.5 -14.7 -0.4 -5.4
GGTCTTTTTGCCCATCCAAA
1452 SEQ ID N0:4897 -5.7 -26.3 72.8 -20.1 -0.2 -3.5
AATAAAATGAGCCCAAGAAA
1695 SEQ ID N0:4898 -5.7 -16.5 50.8 -10.8 0 -3.2
ATTGCGTCTTGGGGAAAACA
2168 SEQ ID N0:4899 -5.7 -22.3 63.7 -16.6 0 -5.2
256
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAGTTGTCCAGTAGGTGACG
2462 SEQ ID N0:4900 -5.7 -23.8 69.9 -17.4 -0.4 -5.2
GGTATTTAAGACAATGCAAA
2774 SEQ ID N0:4901 -5.7 -17.2 53.8 -11 -0.1 -5.6
TAAACTGAGGCTGACAATAA
2960 SEQ ID N0:4902 -5.7 -17.7 54.5 -12 0 -3.7
GTCGTTCATGTGCCACCGTG
3236 SEQ ID N0:4903 -5.7 -28.7 78.4 -23 0 -4.7
ATCAATTCCCTTTTGCATTC
3500 SEQ ID N0:4904 -5.7 -23.1 67.6 -17.4 0 -5.1
TTCAAAGGCCAATGCACCAC
4130 SEQ TD NO:4905 -5.7 -24.4 67.2 -17.2 -1.4 -7.7
CTTTGTCAGCATATTCTAGC
4188 SEQ ID N0:4906 -5.7 -22.5 69.1 -16.8 0 -4.1
CTGAGTAGCCAAGAGCATTG
4338 SEQ ID N0:4907 -5.7 -23.4 68.3 -16.2 -1.4 -4.6
CCAACAAGAGCATTCACAAC
4441 SEQ ID N0:4908 -5.7 -20.9 60.8 -14.6 -0.3 -4.1
GACAGTCACTCAAATTGTTA
4605 SEQ TD N0:4909 -5.7 -19.7 60.8 -14 0 -5.7
ACATCTCGTGAATCAACAGC
4747 SEQ ID N0:4910 -5.7 -21.6 63.6 -15.9 0 -4.6
GGTTGAAGTTATCTATGATG
4869 SEQ ID N0:4911 -5.7 -19 59.8 -13.3 0 -3.2
ACAACCAGGAAGGATATGAT
5737 SEQ ID N0:4912 -5.7 -20.3 59.9 -13.8 -0.6 -4.5
CTCCAGGATGACCGCGATGT
5768 SEQ ID N0:4913 -5.7 -27.8 74.1 -21.4 -0.5 -7.2
TCAGTAGCAACACTGAAGTT
5788 SEQ ID N0:4914 -5.7 -21 63.7 -13.4 -1.9 -7.6
CAAGACAGTGGATCCGGTCA
6003 SEQ ID N0:4915 -5.7 -25.2 71.1 -17.9 -1.1 -10.8
CGCTGAATGATAGCGGCAGA
6178 SEQ ID N0:4916 -5.7 -24.6 67.7 -16.2 -2.7 -9.5
TTTTAACCTTTGCTTTAAAA
6215 SEQ ID N0:4917 -5.7 -17.1 53.6 -10.5 -0.7 -4.3
TTTTTTCTGGAGTGGAGTTC
6324 SEQ ID N0:4918 -5.7 -22.3 69.7 -16.6 0 -2.4
TTGTTTCTTTTTACTTTTGA
6465 SEQ ID NO:4919 -5.7 -18.9 60.6 -13.2 0 -2.2
TAGGCTGTAAACAATTGATC
6499 SEQ ID N0:4920 -5.7 -18.4 57.1 -12.7 0 -7.2
TTTACCTTCATAGGCTGTAA
6509 SEQ ID N0:4921 -5.7 -22 65.8 -15.1 -1.1 -4.5
TTTGTTAAAACAGTCAGTTT
6568 SEQ ID N0:4922 -5.7 -17.7 56.6 -10.5 -1.4 -5.9
TCCTCAGCAGTGTCAGCTGG
6691 SEQ ID N0:4923 -5.7 -28.3 82.9 -19.8 -2.8 -9.2
TTGTAAAAATATGGCAGATA
6820 SEQ ID N0:4924 -5.7 -15.9 51.2 -10.2 0 -4
AAAATAGTGACATAGCATTA
6887 SEQ ID N0:4925 -5.7 -16.3 52.4 -10.6 0 -4.1
AAGCATTTGACCTAAATTAA
7217 SEQ ID N0:4926 -5.7 -17.1 53.2 -10.8 -0.3 -4
ATATGTGACATTCTTTAACC
7615 SEQ ID N0:4927 -5.7 -19.2 59.2 -13.5 0 -3.9
TTGAATTAAAAGTGCAAAAG
7712 SEQ ID N0:4928 -5.7 -13.3 45.7 -7.6 0 -5.4
257
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAAATATGAAGAATAGGTTT
7795 SEQ ID N0:4929 -5.7 -13.7 46.8 -8 0 -2.7
TAAAGTAAAATAAATTGTGA
7922 SEQ ID N0:4930 -5.7 -11.3 42.1 -5.6 0 -3.2
TCAAAAGTTTGGAATTGTGA
7964 SEQ ID N0:4931 -5.7 -17.4 54.7 -11.2 -0.1 -6.9
GAAATTATCCATTGAAAAAT
7993 SEQ ID N0:4932 -5.7 -14 46.8 -7.7 -0.3 -3.8
GTGTTTGACCAATGTATCTC
8083 SEQ ID N0:4933 -5.7 -22 66.7 -16.3 0 -3.4
AAAAACATCTATGAATAAAA
8150 SEQ ID N0:4934 -5.7 -10.6 40.6 -4.9 0 -2.9
AAAAAACATCTATGAATAAA
8151 SEQ ID N0:4935 -5.7 -10.6 40.6 -4.9 0 -3.8
GCAATAAAAAATGAAATTTA
8464 SEQ ID N0:4936 -5.7 -ll.l 41.5 -4.1 -1.2 -5.7
ATTTTAAACTGCCAACAGCA
8525 SEQ ID N0:4937 -5.7 -20.9 60.9 -13.6 -1.5 -7.3
TGAAAGCTATTGTAGGTGGT
8745 SEQ ID N0:4938 -5.7 -21.4 64.8 -15.7 0 -5.l
CTCTGATAAAACAGAGCCTT
207 SEQ ID N0:4939 -5.6 -20.7 61.2 -12.7 -2.4 -7.6
ATCTCTGATAAAACAGAGCC
209 SEQ ID N0:4940 -5.6 -20.1 60.3 -11.5 -3 -8.7
TCTTGCTCCATAATCTCTGA
221 SEQ ID N0:4941 -5.6 -23.4 69.4 -17.8 0 -3.6
CTTCAGTTTTCTTGCTCCAT
230 SEQ ID N0:4942 -5.6 -24.8 74.1 -19.2 0 -4.4
TCCCTTCTGTGAATTATCTC
362 SEQ ID N0:4943 -5.6 -23.3 69.4 -17.2 -0.1 -3.2
GTTTTTCGATAGCAGCAAGA
534 SEQ ID N0:4944 -5.6 -22 65.4 -16.4 0 -5.4
TGTTCTCATCATCATTATCT
594 SEQ ID N0:4945 -5.6 -21 65.8 -15.4 0 -1.7
ATGGAAGGTTCTTTCCAGCT
639 SEQ ID N0:4946 -5.6 -24.9 72.9 -16.2 -3.1 -9.4
TTCCTAACAGGGTTTAGTGG
808 SEQ ID N0:4947 -5.6 -23.2 69 -16.7 -0.7 -4.1
GTACTCTACATTCTTTGTCC
929 SEQ ID N0:4948 '5.6 -23.1 70.8 -16.9 -0.3 -4.6
CGAAGAAACGTAAAATCTTC
1012 SEQ ID N0:4949 -5.6 -15.5 49.4 -8.1 -1.8 -8
AAGCTTCTTTACCGACTGGA
1193 SEQ ID N0:4950 -5.6 -23.8 67.9 -17.3 -0.7 -7.3
TCCTTCCAGTTAAATGTGCT
1402 SEQ ID NO:4951 -5.6 -24 69.6 -18.4 0 -5.6
TCGGCCTCTTTTTGTTCTGC
1783 SEQ ID N0:4952 -5.6 -27.2 78.4 -21.6 0 -6.7
CTGAAATCTCTTGAAGCAGC
1870 SEQ ID N0:4953 -5.6 -21 62.8 -15.4 0 -4.1
AAGAGAGACTGATGAGGGGA
2131 SEQ ID N0:4954 -5.6 -21.6 64.4 -16 0 -2.2
TGCGGCACAAACAGTGAGTC
2296 SEQ ID N0:4955 -5.6 -24.1 68.6 -17.6 -0.8 -7.2
CACCATTGCAATCCACAGTG
2409 SEQ ID N0:4956 -5.6 -24.7 69.1 -18.5 0 -8.6
TCTATACCAGCATGGCGGAC
2648 SEQ ID N0:4957 -5.6 -25.9 72.3 -18.3 -2 -7.4
258
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CCGGTTTAAAGTCTTCTTCG
3948 SEQ ID N0:4958 -5.6 -22.9 66 -16.6 -0.5 -6.2
TTTGAGAAGCATTTCCAGAA
4226 SEQ ID N0:4959 -5.6 -20.4 61.2 -14.2 -0.3 -4.1
TCAAACCGGGATAAGGCTCT
4408 SEQ TD N0:4960 -5.6 -23.9 66.6 -18.3 0 -6.2
TCCAGCCTTTAAATGTGGCC
4710 SEQ ID N0:4961 -5.6 -26.5 73.1 -19.1 -l.8 -8.6
TTTGCTCCTTTGATCAGACG
5368 SEQ ID N0:4962 -5.6 -23.7 68.6 -18.1 0 -6.5
CACCACAACCAGGAAGGATA
5741 SEQ ID N0:4963 -5.6 -23.3 65 -16.9 -0.6 -4.3
GCATCGGGATCAAACTTTTC
5863 SEQ ID N0:4964 -5.6 -22.2 64.7 -16.6 0 -5.3
AGGCTGTAAACAATTGATCA
6498 SEQ ID N0:4965 -5.6 -19.4 58.8 -13.8 0 -7.2
CTTTGCACAACTATCCCTAT
6734 SEQ ID N0:4966 -5.6 -23.6 67.4 -18 0 -5
TGTAAAAATATGGCAGATAT
6819 SEQ ID N0:4967 -5.6 -15.8 50.9 -10.2 0 -4.4
CAATATGTGACATTCTTTAA
7617 SEQ TD N0:4968 -5.6 -17 54.2 -11.4 0 -3.9
TCAAATTATTCTGCTTGACA
7671 SEQ ID N0:4969 -5.6 -19.2 59 -13.6 0 -3.6
TGGAATTGTGATTAAAAATC
7955 SEQ ID N0:4970 -5.6 -14.4 48.2 -8.1 -0.5 -4.l
AAAGTTTGGAATTGTGATTA
7961 SEQ ID N0:4971 -5.6 -16.8 53.8 -11.2 0 -3.7
AAGAAGATGAGTTTAGATGC
8791 SEQ ID N0:4972 -5.6 -17.9 56.7 -12.3 0 -2.6
CATCAATTATATTGAAAGAA
8806 SEQ ID N0:4973 -5.6 -13.8 47 -6.2 -2 -6.6
TAGCATCAATTATATTGAAA
8809 SEQ TD N0:4974 -5.6 -15.4 50.5 -8.2 -1.5 -8.1
TAAATTCTCAATAACTATAT
8919 SEQ ID N0:4975 -5.6 -13.6 46.9 -8 0 -3.1
ATAAATTCTCAATAACTATA
8920 SEQ ID N0:4976 -5.6 -13.6 46.9 -8 0 -3.1
TATAAATTCTCAATAACTAT
8921 SEQ ID N0:4977 -5.6 -13.6 46.9 -8 0 -3.l
ACAATTTTTTTTCTTTCTTT
65 SEQ ID N0:4978 -5.5 -17.9 57.7 -12.4 0 -2.6
CATCCCTGTCAAACCTTGAT
259 SEQ ID N0:4979 -5.5 -24.7 68.8 -18 -l.1 -4.5
TTGATAGCAATTTTCCTAAC
820 SEQ ID N0:4980 -5.5 -19 58.3 -13 -O.l -0.2
GTTGCTCAAGGTCATAAATA
899 SEQ ID N0:4981 -5.5 -19.9 60.9 -14.4 0 -3.6
TACATTCTTTGTCCAGTCAG
g23 SEQ ID N0:4982 -5.5 -22.8 69.6 -16.7 -0.3 -3.1
TCCAGTGAATGTGTACTCTA
941 SEQ ID N0:4983 -5.5 -22.4 67.6 -16.9 0 -4.9
CTCTGTCACATATGCCATCA
1067 SEQ ID N0:4984 -5.5 -24.7 71.9 -19.2 0 -6.5
GAAATTGTTTTCAGTGCTCG
1135 SEQ ID N0:4985 -5.5 -21 63 -14 -1.4 -6.4
AACAAATGTCCCATTTGAAT
1370 SEQ ID N0:4986 -5.5 -19.2 56.9 -9.9 -3.8 -10.4
259
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTATCCTTCTGGACACTGGC
1502 SEQ ID N0:4987 -5.5 -26.4 76.6 -19.5 -1.3 -5.3
GCTTGTGTAGCCATAGTTGG
1547 SEQ ID N0:4988 -5.5 -25.6 75.5 -19 -1 -4.8
GTCATGAGTCGAAATAGAGA
1594 SEQ ID N0:4989 -5.5 -19.4 59.5 -13.9 0 -6.6
AGTCATGAGTCGAAATAGAG
1595 SEQ ID N0:4990 -5.5 -18.8 58.4 -13.3 0 -6.6
CCAGGACAAAAAATATCATG
1671 SEQ ID N0:4991 -5.5 -16.7 51.7 -11.2 0 -4.1
GAAAAGGAAGCTGCTTCTTT
2069 SEQ ID N0:4992 -5.5 -20.6 61.5 -12.4 -1.8 -13.5
AGAAAAGGAAGCTGCTTCTT
2070 SEQ ID N0:4993 -5.5 -20.5 61.3 -12.4 -1.8 -13.3
AGACTGATGAGGGGAGCAGA
2126 SEQ ID N0:4994 -5.5 -24.2 70.8 -18 -0.5 -4.1
ATGTTTTACTTTTAACCATG
2705 SEQ ID N0:4995 -5.5 -18.5 57.6 -13 0 -3.9
GTATTTAAGACAATGCAAAT
2773 SEQ ID N0:4996 -5.5 -16 51.4 -10 -0.1 -5.6
CAGGTTTCCTACAGTCAACA
2843 SEQ TD N0:4997 -5.5 -23.7 69.8 -17.7 -0.2 -3.9
TGAGAACCATTTCTGCTGTG
2880 5EQ ID N0:4998 -5.5 -22.8 66.9 -15.9 -1.3 -5.8
GCAATGATCTTGAGAACCAT
2890 SEQ ID N0:4999 -5.5 -21.2 62.1 -15 -0.4 -6.2
TCCATTAAACTGAGGCTGAC
2965 SEQ ID N0:5000 -5.5 -21.9 64 -16.4 0 -3.7
GAGGTTCAGAACCACAAGGT
3386 SEQ ID N0:5001 -5.5 -23.6 68.5 -15.4 -2.7 -12
TGTCATCATCAGTAGCAGCA
3447 SEQ ID N0:5002 -5.5 -24.4 73.7 -18.9 0 -5.4
CACTACTGAGAAGGATCATG
4113 SEQ ID N0:5003 -5.5 -20 60.7 -13.8 -0.5 -5.9
CAGAATGAATATATAGGTAA
4211 SEQ ID N0:5004 -5.5 -15 49.7 -9.5 0 -4.2
GAGAAGCATTTCCAGAATGA
4223 SEQ ID N0:5005 -5.5 -20.8 61.8 -13.7 -1.6 -6
GTCCGTAATGATTTGATGGC
4366 SEQ ID N0:5006 -5.5 -23 66.5 -17.5 0 -3.3
GCAGTGCAAGATAGCCAGCG
4683 SEQ ID N0:5007 -5.5 -26.9 74.4 -20.7 -0.2 -8.9
CATATACAGGCTGAAGTTTA
4767 SEQ ID N0:5008 -5.5 -19.9 61 -14.4 0 -4.1
AAAGATGTTCCAGCCTATAG
5228 SEQ ID N0:5009 -5.5 -21.7 63.9 -16.2 0 -4.7
ACCAGGAAGGATATGATGAT
5734 SEQ ID NO:5010 -5.5 -20.7 61.3 -14.4 -0.6 -4
TTTAGAGAACTCTATAAACT
5888 SEQ ID N0:5011 -5.5 -15.9 52.1 -9.7 -0.3 -8
TTGGAGGGGTTTGATGCCAT
6106 SEQ ID N0:5012 -5.5 -26 74 -19.4 -1 -4.8
GGTGGTAGAGGAACTCCCAT
6347 SEQ ID N0:5013 -5.5 -26.4 74.8 -18 -2.9 -8.2
CACTATCATAGGAAGGAGGA
6369 SEQ ID N0:5014 -5.5 -21 63.1 -15.5 0 -3.4
TTGTTAAAACAGTCAGTTTG
6567 SEQ TD N0:5015 -5.5 -17.6 56.2 -10.5 -1.6 -7
260
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GACTATGAGTATTTGTTAAA
6579 SEQ ID N0:5016 -5.5 -16.7 54.1 -10.7 -0.1 -3
TTAAAGCCATCTAGAAAATG
7048 SEQ ID N0:5017 -5.5 -16.4 51.8 -10.9 0 -6.2
TTCAGATAGAAACAAACATA
7090 SEQ ID N0:5018 -5.5 -14.8 49 -9.3 0 -3.4
TAACATAGGGTATTTAATTG
7367 SEQ ID N0:5019 -5.5 -16.2 52.6 -10.7 0 -2.9
ACATATTTTTAGCAAAATAT
7808 SEQ TD N0:5020 -5.5 -14.8 49.2 -6.8 -2.5 -7.8
CATTATTTATATTTAAACAA
7835 SEQ ID N0:5021 -5.5 -12.8 45.2 -7.3 0.2 -4.9
AAGTTGATTATATTTTTACA
7853 SEQ ID N0:5022 -5.5 -15.7 52.1 -10.2 0 -2.6
TAGTGCAGCAGGAATTAAAA
8217 SEQ ID N0:5023 -5.5 -18.7 57.1 -13.2 0 -6.6
TAATAGCTTTAGTGCAGCAG
8226 SEQ ID N0:5024 -5.5 -21.5 65.4 -15.1 -0.7 -6.6
TCCCTGCATGCAGTTCTTCA
8392 SEQ ID N0:5025 -5.5 -28.1 80.1 -19.5 -0.2 -14.3
TTATCAAACCTGAAAGTTGG
8714 SEQ ID N0:5026 -5.5 -18.3 55.9 -12.1 -0.4 -3.6
ATTCTCAATAACTATATCAT
8916 SEQ ID N0:5027 -5.5 -16.4 53.3 -10.9 0 -2.4
TCCAAGGGTTCTTGAAAAAA
8948 SEQ ID N0:5028 -5.5 -18.6 56 -11 -2.1 -5.7
ATATGCATTACAACTGGAGT
9009 SEQ ID N0:5029 -5.5 -20.3 61.4 -14.8 0 -6.8
CACCTTATATAATTTATTAT
9074 SEQ ID N0:5030 -5.5 -16 52 -9.8 -0.4 -5.3
TCTTCCTCTGGCAGCTGTTC
134 SEQ ID NO:5031 -5.4 -28.1 83.2 -22 0 -8.9
GCCCAGCATCCAAGATGGTT
167 SEQ ID N0:5032 -5.4 -28.5 77.6 -21.6 -1.4 -6.2
GCTTCAGTTTTCTTGCTCCA
231 SEQ ID N0:5033 -5.4 -26.6 78.8 -21.2 0 -4.4
CTCTTCTGCAGCACGTTTTT
548 SEQ ID N0:5034 -5.4 -25.2 73.6 -19.3 0 -7.7
AAGGCAGAGGTGGCACTGAA
775 SEQ ID N0:5035 -5.4 -24.7 70.6 -18.4 -0.8 -4.7
GAAGAAACGTAAAATCTTCT
1011 SEQ ID N0:5036 -5.4 -15.6 50.2 -8.1 -2.1 -8.6
AGACAGAACACAGTCAGGAT
1225 SEQ ID N0:5037 -5.4 -21.3 64.1 -14.4 -1.4 -4.6
CAGATTGCCCATGAACAGCT
1271 SEQ ID N0:5038 -5.4 -25.4 70.4 -19.5 -0.2 -4.5
AAATGACCAGGACAAAAAAT
1677 SEQ ID N0:5039 -5.4 -15.3 48.6 -9.9 0 -4
GCCACCACAGCCAGGATCAA
1723 SEQ ID N0:5040 -5.4 -29 77.3 -23.6 0 -5.3
CTTCTTCCAAGGTGGCCTGA
1764 SEQ ID N0:5041 -5.4 -27.7 77.7 -21.4 -0.7 -7.2
TGCTGCCGCAACTGCCTGAG
1847 SEQ ID N0:5042 -5.4 -29.5 77.7 -22.8 -1.2 -7.1
CATCATCAGCAAAGTCATTT
2241 SEQ ID N0:5043 -5.4 -20.5 62.2 -15.1 0 -4.l
GAATGCTGGCTATGCTCACG
2586 SEQ ID N0:5044 -5.4 -25 70.2 -18.9 -0.4 -5.9
261
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GCATGGCGGACATTTCTGTC
2639 SEQ ID N0:5045 -5.4 -26.1 74.5 -18.8 -1.9 -8.8
ATACCAGCATGGCGGACATT
2645 SEQ ID N0:5046 -5.4 -25.7 70.8 -18.3 -2 -7.4
GATGTTTTACTTTTAACCAT
2706 SEQ ID N0:5047 -5.4 -19.1 58.9 -13.7 0 -2.8
CAATCTGCAGATTATTCATT
3471 SEQ ID N0:5048 -5.4 -19.5 60 -11.2 -0.2 -l4
TCCTACTGCAATCTGCAGAT
3479 SEQ ID N0:5049 -5.4 -24.3 70.1 -15.4 -3.5 -12.2
AAGATAATTAAGCTCTTTGC
3644 SEQ ID N0:5050 -5.4 -18 56.6 -11.9 -0.4 -5.7
TGAGAAGCATTTCCAGAATG
4224 SEQ ID N0:5051 -5.4 -20.2 60.5 -13.5 -1.2 -6
AACCAAAGAAACATCAACGA
4307 SEQ ID N0:5052 -5.4 -16.9 51.3 -11.5 0 -3.5
ATGGCACCGAGTTCTGAGTA
4351 SEQ ID N0:5053 -5.4 -25.4 72.8 -20 0 -4
TTGATGGCACCGAGTTCTGA
4354 SEQ ID N0:5054 -5.4 -25.2 71.3 -19.8 0 -4
CATTCATGATAGAGGGAATT
4464 SEQ ID N0:5055 -5.4 -19.2 59 -13.3 -0.1 -6.4
GCCAGCAAACAAATTCACAC
4529 SEQ ID N0:5056 -5.4 -21.4 61.2 -16 0 -4.1
TAATATTTTTTCTGTTCCTC
4930 SEQ ID N0:5057 -5.4 -19.5 61.4 -14.1 0 -4.2
CGTTTCCACCATCATGGTGA
5093 SEQ ID NO:5058 -5.4 -26.3 73.1 -17.2 -3.7 -ll.l
CTCCAGTGAACAGAACAATG
5166 SEQ ID N0:5059 -5.4 -20.1 59.5 -14.2 -0.1 -3.9
GGGTGAATTGTGTCAGGGTC
5650 SEQ ID N0:5060 -5.4 -25.1 75.2 -19.7 0 -3.3
AACCAGGAAGGATATGATGA
5735 SEQ ID N0:5061 -5.4 -20 59.3 -13.8 -0.6 -4
AACTCTATAAACTGGGTCGC
5881 SEQ ID N0:5062 -5.4 -21.4 62.8 -16 0 -2.7
GCTGCAAAATCAGAGAGTTT
5905 SEQ ID N0:5063 -5.4 -20.8 62.5 -14.7 -0.4 -4.9
TCTTTGTTATAGTTACTTGA
6241 SEQ ID N0:5064 -5.4 -19 61 -13.6 0 -2.5
TGGAGTTCCCATTTAGTTTG
6312 SEQ ID N0:5065 -5.4 -23.5 69.8 -17.2 -0.8 -4.4
AACTGTAGCCATTACAATTC
7017 SEQ ID N0:5066 -5.4 -20.3 61.1 -13.9 -0.9 -3.9
AAATACTTTCAAAATTAAAG
7062 SEQ ID N0:5067 -5.4 -ll 41.5 -5.6 0.4 -4.4
CAGAAGATGGCAAAGCAATA
7321 SEQ ID N0:5068 -5.4 -19 56.9 -12.7 -0.7 -4.3
ATATATATTTGCCCAAACAT
7415 SEQ ID N0:5069 -5.4 -19.3 57.5 -13.9 0 -5.4
CTTGCAAAAGACACATACAC
7478 SEQ ID N0:5070 -5.4 -18.6 56.3 -11.7 -l.4 -6.9
GAATGGATTGAGTAAAATAG
7583 SEQ ID N0:5071 -5.4 -14.9 49.3 -9.5 0 -2.3
TATTTTTAGCAAAATATGAA
7805 SEQ ID N0:5072 -5.4 -13.8 47.1 -6.8 -1.6 -6
CTATGAATAAAAGGTTATAT
8142 SEQ ID N0:5073 -5.4 -14 47.6 -8 -0.3 -3.2
262
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAAGAAGATGAGTTTAGATG
8792 SEQ ID N0:5074 -5.4 -15.4 50.9 -10 0 -1.9
ATGTAACATTTATTAGCCAC
8844 SEQ ID N0:5075 -5.4 -19.5 59.6 -14.1 0 -3.6
CTATATCATTAATACCTTAT
8905 SEQ ID N0:5076 -5.4 -17.1 54.5 -11.7 0 -4.2
CATAAATCCAAGGGTTCTTG
8954 SEQ ID N0:5077 -5.4 -20.5 61 -13.4 -1.7 -5.1
ATTGTCTTTAAAAATATGCA
9022 SEQ ID N0:5078 -5.4 -15.9 51.5 -10.5 0 -5.2
AGAATCCTCTCTGCTTATGC
13 SEQ ID N0:5079 -5.3 -24.1 71.2 -18.1 -0.4 -4.2
AAATTAGTTACAATTTTTTT
74 SEQ ID N0:5080 -5.3 -14.2 48.5 -8.3 -0.3 -3.7
CCCAGCATCCAAGATGGTTA
166 SEQ ID N0:5081 -5.3 -26.4 72.9 -20.2 -0.8 -5.7
CTTATGAATTACAGCATAAC
190 SEQ ID N0:5082 -5.3 -17 53.9 -10.6 -1 -5.1
TTTTCGATAGCAGCAAGAGA
532 SEQ ID N0:5083 -5.3 -21.3 63.5 -16 0 -5.4
AAATGGAAGGTTCTTTCCAG
641 SEQ ID N0:5084 -5.3 -20.8 62.2 -12.4 -3.1 -9.4
CAGCTGCAGCCCAATGAGAG
1256 SEQ ID N0:5085 -5.3 -26.9 74.1 -19.1 0 -13.2
TCATCTCCAATGTAATCCTT
1417 SEQ ID N0:508& -5.3 -22.4 65.9 -16.5 -0.3 -3
TCTGCTCCTCATAGGCCATG
1743 SEQ ID N0:5087 -5.3 -27.8 78.6 -21.8 -0.5 -8.3
TCTTCCAAGGTGGCCTGATT
1762 SEQ ID N0:5088 -5.3 -26.8 75.7 -20.6 -0.7 -7.2
AGCTGATGCTGCCGCAACTG
1853 SEQ TD N0:5089 -5.3 -27.5 74.4 -20.6 -1.6 -8
TCACTGGTCAGTCTGTTTCC
2098 SEQ ID N0:5090 -5.3 -26 78.8 -20.7 0 -6.6
ATACTCAAGAGAGACTGATG
2137 SEQ ID N0:5091 -5.3 -18.7 58.4 -11.8 -1.5 -5.4
TCAGTGGTGGTGCCCTCTGG
2485 SEQ ID N0:5092 -5.3 -30.3 85.9 -23.4 -1.5 -5.8
TTTCAGTGGTGGTGCCCTCT
2487 SEQ ID N0:5093 -5.3 -29.3 84.2 -23.4 -0.3 -5.l
ACATGGTCTCTATCCACTCT
3297 SEQ ID N0:5094 -5.3 -25.1 74.4 -18.9 -0.7 -5.2
GAAAGAGGTTCAGAACCACA
3390 SEQ ID N0:5095 -5.3 -21.1 62 -13.1 -2.7 -12
ATGACATATAATCATTTTCA
3729 SEQ ID N0:5096 -5.3 -16.7 53.8 -10.8 -0.3 -5.1
TCTCCAACAGCAATTGGCAC
3778 SEQ TD N0:5097 -5.3 -24.4 69.2 -17.5 -1.5 -8.1
GAAGGATCATGAACACAATG
4104 SEQ ID N0:5098 -5.3 -17.8 54.8 -12.5 0 -6.9
AATTGCTCCAACAAGAGCAT
4448 SEQ ID N0:5099 -5.3 -21.8 63 -13.1 -3.4 -9.5
CCAAAGATGATAAAGATGAC
4816 SEQ ID N0:5100 -5.3 -16.2 51.2 -10.9 0 -2.1
ATCCAAGTTTCTTCATTGCA
4953 SEQ ID N0:5101 -5.3 -22.9 68.2 -17.6 0 -4.8
ATGCTGATATCAAAGACTTG
5047 SEQ ID N0:5102 -5.3 -18.5 57.2 -12.7 0 -7.7
263
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ACAAAACTAGGGTCATGTAT
5127 SEQ ID N0:5103 -5.3 -19.2 58.7 -13.4 -0.1 -4.7
GCACAAATTCTCCAGTGAAC
5175 SEQ ID N0:5104 -5.3 -21.8 63.7 -15.7 -0.6 -4.6
GTTCCAGCCTATAGTGAAGT
5222 SEQ ID N0:5105 -5.3 -24.8 72.9 -19.5 0 -5.1
ATACTTTTCTATCATCTCAG
5291 SEQ ID N0:5106 -5.3 -19.6 62.3 -14.3 0 -1.6
GACACAGAATACTTTTCTAT
5299 SEQ ID N0:5107 -5.3 -18.4 57.7 -12.2 -0.7 -4.4
AACGCAGGAAGGGACATCAT
5416 SEQ ID N0:5108 -5.3 -22.9 64.9 -17.6 0 -3.6
ATCCAGGGCAGCTGCAAAAT
5915 SEQ ID N0:5109 -5.3 -25.1 69.7 -16.9 -1 -14
AGTGGAGTTCCCATTTAGTT
6314 SEQ TD N0:5110 -5.3 -24.6 73.4 -18 -1.2 -6.4
ATAGGCTGTAAACAATTGAT
6500 SEQ ID N0:5ll1 -5.3 -18 55.8 -12.7 0 -7.2
CAACTATCCCTATAGTCTAG
6727 SEQ ID N0:5112 -5.3 -21.7 64.9 -14.4 -2 -7.4
GGATGCAAGGACTGTACTAA
6781 SEQ TD N0:5113 -5.3 -21.5 63.6 -16.2 0 -5.6
CTATGAATTGGGGACCATGG
6859 SEQ ID N0:5114 -5.3 -22.9 65.3 -15.2 -2.4 -8.3
AAACCTCATTTACAAAAATA
6901 SEQ TD N0:5115 -5.3 -14.5 47.8 -8.5 -0.5 -3
TGGCAAAACACCTTTGTCTG
6964 SEQ ID N0:5116 -5.3 -22.3 64.2 -14.7 -2.3 -6.6
TTCTTTTTCTGGTTTTGAGC
7000 SEQ ID N0:5117 -5.3 -22.2 69.1 -16.9 0 -2.8
CTGAAACTGTAGCCATTACA
7021 SEQ ID N0:5118 -5.3 -21.3 62.5 -15.1 -0.8 -3.7
TTACAGGCACATAACTGTTC
7107 SEQ TD N0:5119 -5.3 -21.1 63.8 -14.2 -1.5 -5.2
AGCAGAAGATGGCAAAGCAA
7323 SEQ ID N0:5120 -5.3 -21.1 61.4 -14.9 -0.8 -5.6
CATAACATAGGGTATTTAAT
7369 SEQ ID N0:5121 -5.3 -16.8 53.6 -11.5 0 -2.9
TTGCAAAAGACACATACACT
7477 SEQ ID N0:5122 -5.3 -18.6 56.3 -13.3 0 -6.6
AAATAATTTTCTTATGTACA
7888 SEQ ID N0:5123 -5.3 -14.8 49.7 -9.5 0 -6.4
AAAGTAAAATAAATTGTGAT
7921 SEQ ID N0:5124 -5.3 -11.6 42.6 -6.3 0 -3.2
TAATTGCACAACTTTGCCAC
8287 SEQ ID N0:5125 -5.3 -21.8 63.1 -16 -0.2 -5
TTTGGCTCAATAATGACGTA
8440 SEQ ID N0:5126 -5.3 -20 59.7 -14 -0.5 -5.3
AATTGAAAGCTATTGTAGGT
8748 SEQ ID N0:5127 -5.3 -18.4 57.4 -13.1 0 -5.1
TCTCTGCTTATGCCTCCGCT
6 SEQ ID N0:5128 -5.2 -29.7 81.9 -23.6 -0.8 -4.3
AATTAGTTACAATTTTTTTT
73 SEQ ID N0:5129 -5.2 -15 50.6 -9.8 0 -2.6
'
CCTTATGAATTACAGCATAA
191 SEQ ID N0:5130 -5.2 -18.8 57.1 -12.7 -0.8 -4.9
CTTGCTCCATAATCTCTGAT
220 SEQ ID N0:5131 -5.2 -23 67.7 -17.8 0 -3.6
264
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGCACATTTAATTACGTGTA
442 SEQ ID N0:5132 -5.2 -19.5 59.2 -13.7 -0.3 -5.4
TTCGATAGCAGCAAGAGATT
530 SEQ ID N0:5133 -5.2 -21.2 63.1 -16 0 -5.4
TTTCGATAGCAGCAAGAGAT
531 SEQ ID N0:5134 -5.2 -21.2 63.1 -16 0 -5.4
GAGGAATGTCTCCATAAATA
660 SEQ ID N0:5135 -5.2 -19.3 58.6 -12.3 -1.8 -4.8
TTTTCCTAACAGGGTTTAGT
810 SEQ ID N0:5136 -5.2 -22.2 67.2 -16.1 -0.7 -4.1
ACCGACTGGATCAGGGCCCC
1183 SEQ ID N0:5137 -5.2 -31.8 82 -24.9 -0.8 -11.5
AGAAAGCTTCTTTACCGACT
1196 SEQ ID N0:5138 -5.2 -21.9 63.7 -15.8 -0.7 -7
GTTAAATGTGCTCATTGTTA
1394 SEQ ID N0:5139 -5.2 -19.7 61.1 -12.9 -1.6 -4
CATGAGTCGAAATAGAGACA
1592 SEQ ID N0:5140 -5.2 -18.7 57 -12.7 -0.6 -5.8
TCAACTGGTAAAGATTTTCC
1626 SEQ ID N0:5141 -5.2 -19.5 59.4 -14.3 0 -3.3
CTGCTTCTTTTGACGCTGTC
2059 SEQ ID N0:5142 -5.2 -25.2 73.6 -18 -2 -6.6
AGCAGAATTTTTTGTCACTG
2112 SEQ ID N0:5143 -5.2 -20.3 62.5 -15.1 0 -4.1
GAACACATTGGCAAATCTAT
2663 SEQ ID N0:5144 -5.2 -19.1 57.6 -13.9 0 -4.4
ATCAAAGATATTCCAGCCTT
2936 SEQ ID N0:5145 -5.2 -22 64.2 -16.1 -0.4 -3.8
AATGATCTTAATTAGCATAT
3077 SEQ ID N0:5146 -5.2 -16.3 52.8 -11.1 0 -4.9
TGCATGCCGACCACAGCAAA
3157 SEQ ID N0:5147 -5.2 -26.6 70.2 -20.3 -1 -9.1
CCTACTGCAATCTGCAGATT
3478 SEQ ID N0:5148 -5.2 -24 68.9 -14.4 -4.4 -13.6
TACACCACTGGTGGTTCCAT
3674 SEQ ID NO:5149 -5.2 -26.6 75 -18.8 -2.6 -12
CCTTCAGTAAAACAAGCTTC
3967 SEQ ID N0:5150 -5.2 -20.3 60.7 -15.1 0 -6.4
GAGAAGGATCATGAACACAA
4106 SEQ ID N0:5151 -5.2 -18.4 56.2 -12.5 -0.5 -6.9
GATGGCACCGAGTTCTGAGT
4352 5EQ ID N0:5152 -5.2 -26.3 74.8 -21.1 0 -4
AACAAGAGCATTCACAACCA
4439 SEQ ID N0:5153 -5.2 -20.9 60.8 -15.7 0.5 -4.1
AGCAAACAAATTCACACCCA
4526 SEQ ID N0:5154 -5.2 -21.6 61 -16.4 0 -4.1
GGATCCAAGTTTCTTCATTG
4955 SEQ ID N0:5155 -5.2 -22.2 66.7 -16.5 0 -8.3
TCATGATGCTGATATCAAAG
5052 SEQ ID N0:5156 -5.2 -18.4 57 -12.3 -0.8 -7.7
CATCCGTTTCCACCATCATG
5097 SEQ ID N0:5157 -5.2 -26.4 72.4 -21.2 0 -4.1
CCCTGGTCATCCGTTTCCAC
5104 SEQ ID N0:5158 -5.2 -30.3 81.4 -23.9 -1.1 -4.5
GAAGGGACATCATCAAAGCA
5409 SEQ ID N0:5159 -5.2 -21.1 62.1 -15.9 0.5 -3.6
CATAGGCAAAGTTGGACATC
5490 SEQ ID N0:5160 -5.2 -21.1 63 -15.9 0 -4.2
265
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TATCAAGACAGTGGATCCGG
6006 SEQ TD N0:5161 -5.2 -23 66.2 -17.1 0 -8.9
GCTTTGTAAAGGCAAATAAA
6027 SEQ ID N0:5162 -5.2 -17 53 -10.2 -1.6 -5.9
CATCTGAAATTACGCTGAAT
6190 SEQ ID N0:5163 -5.2 -18.6 56 -13.4 0 -3.3
TCATGTTGAATTAAAAGTGC
7717 SEQ ID N0:5164 -5.2 -17 54 -11.8 0 -4.7
ATATTTTTAGCAAAATATGA
7806 SEQ ID N0:5165 -5.2 -14.5 48.7 -6.8 -2.5 -7.8
CTAAAAAGAACAAAGTCCAT
8256 SEQ ID N0:5166 -5.2 -15.5 49.5 -10.3 0 -2.8
TCATGGCTAAAAAGAACAAA
8262 SEQ ID N0:5167 -5.2 -15.3 49.2 -10.1 0 -4.7
TGGCTCAATAATGACGTAGC
8438 5EQ ID NO:5168 -5.2 -21.6 63.2 -15.7 -0.5 -5.6
ATGCATTTAAGTAACAAAGA
8864 SEQ ID NO:5169 -5.2 -16 51.5 -10.8 0 -6.4
GGAGTTTTCCACTGAGAATA
8994 SEQ ID N0:5170 -5.2 -21.7 65 -15.1 -1.3 -4.8
TTTTTTTTGACCACAGAGGT
98 SEQ ID NO:5171 -5.1 -22.1 66.2 -15.6 -1.3 -4.7
TTCTTGCTCCATAATCTCTG
222 SEQ TD NO:5172 -5.1 -22.9 68.4 -17.8 0 -2.9
ATGAATCCTTGACAGGTATC
280 SEQ ID N0:5173 -5.1 -21.3 64.1 -15.2 -0.9 -3.5
GGAAAAGCTCCAGGTCCCTT
376 SEQ ID N0:5174 -5.1 -27.3 74.7 -21.1 -1 -6.6
TTTCCAGCTTCCAAGTCACT
628 SEQ ID N0:5175 -5.1 -25.9 74.7 -20.8 0 -4.3
TCTGGAGGAATGTCTCCATA
664 SEQ ID N0:5176 -5.1 -23.5 69.3 -15.1 -3.3 -8.5
ATCTCTGGAGGAATGTCTCC
667 SEQ ID N0:5177 -5.1 -24.4 72.5 -17.2 -2.1 -7.4
GCAGAGGTGGCACTGAATCG
772 SEQ ID N0:5178 -5.l -25.4 71.7 -19.4 -0.7 -4.5
CTGTCACATATGCCATCACA
1065 SEQ ID N0:5179 -5.1 -24.3 70 -19.2 0 -6.5
TCATTGTTACATTAACAAAT
1383 SEQ ID N0:5180 -5.l -15.7 51.1 -7.8 -2.8 -8.5
ATCCTTCCAGTTAAATGTGC
1403 SEQ ID NO:5181 -5.1 -23.1 67.6 -18 0 -5.6
TTCACACAGATGTATCCTTC
1513 SEQ ID N0:5182 -5.1 -22.3 67.4 -16.5 -0.5 -3.6
TCATGAGTCGAAATAGAGAC
1593 SEQ ID N0:5183 -5.1 -18.4 57 -12.7 -0.3 -6.9
TGCTCCTCATAGGCCATGGC
1741 SEQ ID N0:5184 -5.1 -29.5 81.9 -22.2 -0.5 -12.5
ATCTATACCAGCATGGCGGA
2649 SEQ ID N0:5185 -5.1 -25.7 71.7 -18.6 -2 -7.4
AGAACCATTTCTGCTGTGAA
2878 SEQ ID N0:5186 -5.l -22.1 64.8 -16.1 -0.8 -5.5
TGTTTATGAATGACATATAA
3738 SEQ ID N0:5187 -5.1 -15.2 50.2 -9 -1 -5.8
GTACTTACTTGACAGAATGG
4003 SEQ ID N0:5188 -5.1 -19.6 60.3 -13.8 -0.4 -4.5
TGTAGCAGGTTTTTCGAAGA
4053 SEQ ID N0:5189 -5.1 -21.9 65.7 -16.3 -0.2 -6.8
266
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GGTAAAGACTTTGTCAGCAT
4196 SEQ ID N0:5190 -5.1 -21.4 64.6 -15 -1.2 -5.3
AGGTAAAGACTTTGTCAGCA
4197 SEQ ID N0:5191 -5.1 -21.4 64.9 -15 -1.2 -5.3
CGATCAAGAAATCTAGCCAG
4290 SEQ ID N0:5192 -5.1 -20.5 59.9 -15.4 0 -4.9
TTAAAGCTCTTAATGTCCGT
4380 SEQ ID N0:5193 -5.1 -21.1 62.4 -16 0 -5.6
GTCTTAAAGCTCTTAATGTC
4383 SEQ ID N0:5194 -5.1 -19.6 61.5 -14.5 0 -5.9
TATAAATACATGTACAGATT
4792 SEQ ID N0:5195 -5.1 -15.1 50.1 -9.5 0 -8.2
CAGCACAAATTCTCCAGTGA
5177 SEQ ID N0:5196 -5.1 -23 66.7 -17.1 -0.6 -4.6
GGGACACAGAATACTTTTCT
5301 SEQ ID N0:5197 -5.1 -21.1 63.5 -15.1 -0.8 -4.2
CCCCTTTGCTCCTTTGATCA
5372 SEQ TD N0:5198 -5.1 -29 79 -23.9 0 -6.1
GGTTGTAATTTGGAACAAGC
5573 SEQ ID N0:5199 -5.1 -20 60.5 -13.3 -l.6 -7.3
AGAGGTTGTAATTTGGAACA
5576 SEQ ID N0:5200 -5.1 -19.5 60 -13.7 -0.4 -4.7
GGTCACAGTCGGGTGGTGCA
5634 SEQ ID N0:5201 -5.1 -29.3 83.7 -23 -0.7 -10.2
AAACTTTTCCCAAACCTCAT
5852 SEQ ID N0:5202 -5.1 -21.9 62 -16.8 0 -2.4
CATCGGGATCAAACTTTTCC
5862 SEQ ID N0:5203 -5.1 -22.4 64.3 -17.3 0 -5.3
CACAAAACACGCTTTGTAAA
6037 SEQ ID N0:5204 -5.1 -17.8 53.6 -11.2 -1.4 -6.6
TGGAGGGGTTTGATGCCATA
6105 SEQ ID N0:5205 -5.1 -25.6 73 -19.4 -1 -4.6
ATAATTCTTTGTTTCTTTTT
6473 SEQ ID N0:5206 -5.1 -17.7 57.6 -12.6 0 -2.9
TTTGTAAAAATATGGCAGAT
6821 SEQ ID N0:5207 -5.1 -16.3 52 -10.2 -0.9 -4.9
TGAAACTGTAGCCATTACAA
7020 SEQ ID N0:5208 -5.1 -19.7 58.7 -13.6 -0.9 -3.9
AATATGTGACATTCTTTAAC
7616 SEQ ID N0:5209 -5.1 -16.5 53.4 -11.4 0 -3.9
TAAAAGTGCAAAAGTAAAGG
7706 SEQ ID N0:5210 -5.1 -13.9 46.8 -8.8 0 -5.4
ATAAAGTAAAATAAATTGTG
7923 SEQ ID N0:5211 -5.1 -10.7 40.9 -5.6 0 -3.2
GCATAAAGTAAAATAAATTG
7925 SEQ ID N0:5212 -5.1 -12 43.2 -6.9 0 -3.4
AAAACATCTATGAATAAAAG
8149 SEQ ID N0:5213 -5.1 -11.3 42 -6.2 0 -3.8
AGTGCAGCAGGAATTAAAAA
8216 SEQ ID N0:5214 -5.1 -18.3 55.8 -13.2 0 -6.6
GCTAAAAAGAACAAAGTCCA
8257 SEQ ID N0:5215 -5.1 -17.3 53 -12.2 0 -2.8
CATGTTAGGTAATTGCACAA
8296 SEQ ID N0:5216 -5.1 -19.9 60.3 -14.8 0 -5.3
TTCACAAAGCTGCTTTTAAT
8660 SEQ ID N0:5217 -5.1 -19.4 59 -12.9 -0.1 -10.7
TAGATGCTTATAGCCAAGGG
8778 SEQ ID NO:5218 -5.1 -22.7 66.4 -16.9 -0.5 -4.2
267
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATACCTTATGTATACATAGG
8894 SEQ ID N0:5219 -5.1 -19 59 -11.9 -0.7 -12.1
ATCCAAGATGGTTAGGGTAT
160 SEQ ID N0:5220 -5 -22.5 66.9 -16.6 -0.8 -4.9
CATAACAAAGCCCAGCATCC
176 SEQ ID N0:5221 -5 -24.6 67.2 -18.7 -0.7 -4.1
AGCCTTATGAATTACAGCAT
193 SEQ ID N0:5222 -5 -21.6 63.7 -15.9 -0.4 -4.1
TCAAGGTCATAAATACACAG
894 SEQ ID N0:5223 -5 -17.7 55.5 -12.7 0 -2
TGTGTACTCTACATTCTTTG
932 SEQ ID N0:5224 -5 -20.7 64.7 -14.8 -0.8 -4.8
ATGTGTACTCTACATTCTTT
933 SEQ ID N0:5225 -5 -20.7 64.8 -14.8 -0.8 -5.4
ATCACGAAGAAACGTAAAAT
1016 SEQ ID N0:5226 -5 -15 48.1 -9.1 -0.8 -6.l
TTCAGTGCTCGGAGAACTCT
1126 SEQ ID N0:5227 -5 -24.4 71.4 -18.5 -0.7 -6.4
TGCCCATGAACAGCTGCAGC
1266 SEQ ID N0:5228 -5 -28.3 76.8 -21 -0.2 -12.8
ATTGTTACATTAACAAATGT
1381 SEQ ID N0:5229 -5 -15.8 51.4 -8 -2.8 -8.5
TCCAGTTAAATGTGCTCATT
1398 SEQ ID N0:5230 -5 -21.8 65.1 -15.3 -1.4 -3.7
GGGTTTCGACCAGCCTTCAC
1528 SEQ ID N0:5231 -5 -28.6 79.1 -20.9 -2.7 -6
AGCTTGTGTAGCCATAGTTG
1548 SEQ ID N0:5232 -5 -24.4 73.1 -17.8 -1.5 -4.6
CTGGTAAAGATTTTCCCAAT
1622 SEQ ID N0:5233 -5 -20.9 61.2 -15.9 0 -4.8
TCTTTAGCACCTTTGGAACT
1945 SEQ TD N0:5234 -5 -23.2 68 -18.2 0 -4.l
GAAAATGCTTGTTTTGCTAT
2186 SEQ ID N0:5235 -5 -19.2 58.6 -13.3 -0.8 -4.8
AGAATGCTGGCTATGCTCAC
2587 SEQ ID N0:5236 -5 -24.2 70.4 -18.5 -0.4 -5.2
TATACCAGCATGGCGGACAT
2646 SEQ ID N0:5237 -5 -25.3 69.9 -18.3 -2 -7.4
ACCATTTCTGCTGTGAAAAT
2875 SEQ ID N0:5238 -5 -20.8 61.3 -14.9 -0.7 -5
CAACTTGAAAACTCTAAGCA
3035 SEQ ID N0:5239 -5 -17.6 54.2 -12.6 0 -4.1
GCACGCGGAACACAATCAGG
3270 SEQ ID N0:5240 -5 -24.6 66.7 -19.1 0 -7.9
CAGCACGCGGAACACAATCA
3272 5EQ ID N0:5241 -5 -24.1 65.5 -19.1 0 -7
TGAACTCAATAATAAGGCCA
3410 SEQ ID N0:5242 -5 -19.1 57 -13.6 0 -7.7
AATCTGCAGATTATTCATTT
3470 SEQ ID N0:5243 -5 -18.9 59.1 -11.2 -0.2 -13.6
AGCTGGTTGCATTTAATTTC
3864 SEQ ID N0:5244 -5 -21.5 65.5 -14.9 -1.5 -5.1
ATCAACTGTGCTTCCTTCAG
3887 SEQ ID N0:5245 -5 -24 70.8 -19 0.6 -3.6
AGTCTTTCGCTGTTCAATGT
4157 SEQ ID N0:5246 -5 -23.5 70.5 -18.5 0 I -3.1
CTAGCCAGCACCAGGCATTA
4278 SEQ ID N0:5247 -5 -28 77.4 -20.3 -2.7 -7.4
268
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AATCTAGCCAGCACCAGGCA
4281 SEQ ID N0:5248 -5 -27.9 76.8 -20.2 -2.7 -7.4
ACCAGGCTAACCAAAGAAAC
4315 SEQ TD N0:5249 -5 -20.7 59.2 -14.3 -1.3 -5
AGTAGCCAAGAGCATTGGCT
4335 SEQ ID N0:5250 -5 -25.8 74.1 -15.6 -5.2 -14.4
TCCGTAATGATTTGATGGCA
4365 SEQ ID N0:5251 -5 -22.5 64.6 -17.5 0 -4
ACAGTGGTAGAACTTGCCAG
4544 SEQ ID N0:5252 -5 -23.8 69.5 -17.5 -1.2 -5.1
AGCCTTTAAATGTGGCCACT
4707 SEQ ID N0:5253 -5 -25.2 70.5 -17.7 -1.8 -13
TACAGGCTGAAGTTTAACAT
4763 SEQ ID N0:5254 -5 -19.7 60 -14.7 0 -4.1
ATACATGTACAGATTTTCTT
4787 SEQ ID N0:5255 -5 -18.7 59.2 -13 0 -9.1
AAATACATGTACAGATTTTC
4789 SEQ ID N0:5256 -5 -16.3 53 -10.8 0 -8.2
AGTATAAATACATGTACAGA
4794 SEQ TD N0:5257 -5 -16.2 52.7 -10.5 -0.5 -8.2
GTCATAAAGATGTCTTGACC
4909 SEQ ID N0:5258 -5 -20.6 62.5 -14.1 -1.4 -7.7
TGTCATAAAGATGTCTTGAC
4910 SEQ ID N0:5259 -5 -18.6 58.5 -12.7 -0.8 -8.3
GGACAAAACTAGGGTCATGT
5129 SEQ ID N0:5260 -5 -21.3 63.1 -15 -1.2 -5
GGGACAAAACTAGGGTCATG
5130 SEQ ID N0:5261 -5 -21.3 62.6 -l5 -1.2 -5
ATGTTCCAGCCTATAGTGAA
5224 SEQ ID N0:5262 -5 -23.6 69 -18.6 0 -5.1
CGGAACAAGGTAGGGGACAC
5314 SEQ ID N0:5263 -5 -23.5 66.3 -17.9 -0.3 -3.2
CCCTTTGCTCCTTTGATCAG
5371 SEQ ID N0:5264 -5 -27 75.9 -22 0 -6.5
AGTTGAACATGTCATCAATT
5526 SEQ ID N0:5265 -5 -18.9 58.8 -12.6 -1 -9.9
GCACTATTAAGAATAGGTGC
5617 SEQ ID N0:5266 -5 -20.2 61.4 -12.6 -2.6 -8.1
AGAGAGTTTAGAGAACTCTA
5894 SEQ ID N0:5267 -5 -18.9 60.3 -9.7 -4.2 -9.6
CAGCTGCAAAATCAGAGAGT
5907 SEQ ID N0:5268 -5 -21.3 63.2 -15.6 -0.4 -7.2
CCAGGGCAGCTGCAAAATCA
5913 SEQ ID N0:5269 -5 -25.8 70.8 -18.3 -1 -13.2
GGCAGACACCTCCTCTTGTT
6164 SEQ ID N0:5270 -5 -28.3 80.2 -23.3 0 -4
AAATTACGCTGAATGATAGC
6184 SEQ ID N0:5271 -5 -18.1 55.2 -12.3 -0.6 -4.4
GTGTCAGCTGGTAATAAAAA
6682 SEQ ID N0:5272 -5 -18.5 57 -12.9 0 -8.6
ACCATGGAAATGCACTAGAA
6846 SEQ ID N0:5273 -5 -20.5 59.7 -14.1 -1.3 -8.8
TCTGGTTTTGAGCAAAAATT
6993 SEQ ID N0:5274 -5 -18.4 56.7 -12.8 -0.3 -7.6
GCAGAAGATGGCAAAGCAAT
7322 SEQ ID N0:5275 -5 -21.1 61.2 -15.2 -0.7 -4.9
GTGTTTGTAAATAGCTTCAA
7687 SEQ ID N0:5276 -5 -19 59.3 -14 0 -4.9
269
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AACAAGTTTTAGACATATTT
7820 SEQ ID N0:5277 -5 -16.1 52.6 -11.1 0,4 -3.1
TAAACAAGTTTTAGACATAT
7822 SEQ ID N0:5278 -5 -14.9 49.7 -9.2 -0.4 -5.5
TTGGAATTGTGATTAAAAAT
7956 SEQ ID N0:5279 -5 -14.1 47.4 -9.1 0 -3.1
ATGTTAGGTAATTGCACAAC
8295 SEQ ID N0:5280 -5 -19.4 59.6 -14.4 0 -5.6
ATCATGTTAGGTAATTGCAC
8298 SEQ ID N0:5281 -5 -20.3 62.5 -15.3 0 -5.3
TAAACTGCCAACAGCAAAAA
8521 SEQ ID N0:5282 -5 -17.8 53.2 -11.2 -1.5 -4.5
TAACTATATCATTAATACCT
8908 SEQ ID N0:5283 -5 -16.5 52.9 -11.5 0 -4.2
CTTTCCAGAATCCTCTCTGC
19 SEQ ID N0:5284 -4.9 -25.8 74.6 -20.2 -0.4 -4
TCCGGAAAAGCTCCAGGTCC
379 SEQ ID N0:5285 -4.9 -27.5 73.9 -20.7 -1.9 -7.8
CAACAGTGCCTGTGCCATCT
470 SEQ ID N0:5286 -4.9 -27.8 77.1 -21.3 -1.5 -8.7
AAAGGCGGAAGCTTTCAGGT
501 SEQ ID N0:5287 -4.9 -23.9 68 -16.6 -2.4 -7.6
AATGGAAGGTTCTTTCCAGC
640 SEQ ID N0:5288 -4.9 -23.3 68.5 -15.3 -3.1 -9.4
TAAAATATACAAGGCAGAGG
785 SEQ ID N0:5289 -4.9 -16.7 52.7 -11.8 0 -4
TCAAAATAGTGCACATGATA -
870 SEQ ID N0:5290 -4.9 -17.6 54.9 -11.7 0 -9.9
ACTCTGTCACATATGCCATC
1068 SEQ ID N0:5291 -4.9 -24.2 71.3 -19.3 0 -6.5
ATCAGAAAGCTTCTTTACCG
1199 SEQ ID N0:5292 -4.9 -21.3 &2.6 -15.6 -0.6 -7
ATGTGCTCATTGTTACATTA
1389 SEQ ID N0:5293 -4.g -20.8 64.1 -15.4 -0.1 -1.1
AAGCTTGTGTAGCCATAGTT
1549 SEQ ID N0:5294 -4.9 -23.7 70.7 -17.2 -1.5 -7.5
AGGACAAAAAATATCATGTA
1669 SEQ ID N0:5295 -4.9 -14.9 49 -10 0 -4.7
GTCTCTCCTGCTTTCGCCGT
2279 SEQ TD N0:5296 -4.9 -31 85.3 -25.4 -0.5 -3.6
CAAGATGTTTTACTTTTAAC
2709 SEQ ID N0:5297 -4.9 -16.4 53.3 -11.5 0 -2.9
GCTCCATTAAACTGAGGCTG
2967 SEQ ID N0:5298 -4.9 -23.8 68.1 -18.4 -0.1 -4.1
CACAGCAAAAATGAAGACGA
3146 SEQ ID N0:5299 -4.9 -17.4 52.6 -12.5 0 -4.1
ATGTGCCACCGTGGGAGCGT
3229 SEQ ID N0:5300 -4.9 -30.7 81 -24.6 -1.1 -8.8
TTGTCATCATCAGTAGCAGC
3448 SEQ ID N0:5301 -4.9 -23.8 72,9 -18.9 0 -4.1
AAAAAGGCTTTTTGGAAACA
3544 SEQ ID N0:5302 -4.9 -16.8 52.3 -10.8 -1 -7.9
TTCTAAAAAAGGCTTTTTGG
3548 SEQ TD N0:5303 -4.9 -17.1 53.8 -10.7 -1.4 -7.7
AAGCTCTTAATGTCCGTAAT
4377 SEQ ID N0:5304 -4.9 -2l 62.1 -16.1 0 -5
AGTCACTCAAATTGTTAACA
4602 SEQ ID N0:5305 -4.9 -18.4 57.5 -l3 0 -8
270
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGACCCAAAGATGATAAAGA
4820 SEQ ID N0:5306 -4.9 -18.2 54.7 -13.3 0 -1.9
TGTTCCTCTGTCATAAAGAT
4918 SEQ ID N0:5307 -4.9 -21.1 64.1 -16.2 0 -3.5
CTTGGATCCAAGTTTCTTCA
4958 SEQ ID N0:5308 -4.9 -23.1 68.7 -15.1 -0.7 -14.3
GCTCCTTTGATCAGACGTAG
5365 SEQ ID N0:5309 -4.9 -24.4 71 -19.5 0 -6.5
AGGGACATCATCAAAGCAAA
5407 SEQ ID N0:5310 -4.9 -19.8 58.9 -14.3 -0.3 -4.4
CCAAAGATGGCATAGATAAA
5470 SEQ ID N0:5311 -4.9 -18.2 54.9 -12.4 -0.8 -5
CAAAGTCATCCTCACTCAGG
5823 SEQ ID N0:5312 -4.9 -23.4 68.5 -17.8 -0.4 -3.1
AACATCTCAAAGTCATCCTC
5830 SEQ ID N0:5313 -4.9 -21.2 63.8 -16.3 0 -2.8
TTTTCCCAAACCTCATAGAA
5848 SEQ ID N0:5314 -4.9 -21.8 62.5 -16.9 0 -2.8
TCCACTCTCACACAAAACAC
6047 SEQ ID N0:5315 -4.9 -21.4 62.3 -16.5 0 0
TCATAAGAGACTTTGGAGGG
6118 SEQ ID N0:5316 -4.9 -20.8 63.1 -15.9 0 -3.4
AATTGCCTCTTTGTTATAGT
6248 SEQ ID N0:5317 -4.9 -21.5 65.5 -16.6 0 -3
TTGTCAACGTTGATACCCTG
6652 SEQ ID N0:5318 -4.9 -23.4 66.5 -16.2 -0.1 -12.8
TTAAATATTAGAGGAGACTT
7126 SEQ ID N0:5319 -4.9 -16.1 52.6 -10.3 -0.7 -5.9
CTAAATTAAATATAGAGCTC
7206 SEQ ID N0:5320 -4.9 -14.7 49.3 -9.3 0 -8
TAAACTATGTTTAATGAATG
7523 SEQ ID N0:5321 -4.9 -13.4 46.3 -7.6 -0.8 -5.5
ATAGCTTCAAATTATTCTGC
7677 SEQ ID N0:5322 -4.9 -19.2 59.7 -14.3 0 -4.6
CAAGTTTTAGACATATTTTT
7818 SEQ ID N0:5323 -4.9 -16.8 54.6 -11.2 -0.4 -2.9
AACCATAGTTGGTAGAAAAT
8116 SEQ ID N0:5324 -4.9 -17.8 55 -10.5 -2.4 -6.3
CAGTTCTTCAATACACTACA
8382 SEQ ID N0:5325 -4.9 -20.1 61.8 -15.2 0 -3.1
TTCCCTGCATGCAGTTCTTC
8393 SEQ ID N0:5326 -4.9 -27.5 79.4 -19.5 -0.2 -14.3
GGTTTTGACCTCACATAAAT
8967 SEQ ID N0:5327 -4.9 -20.7 61.6 -14:2 -1.6 -4.2
TATATAATTTATTATGGGAG
9069 SEQ ID N0:5328 -4.9 -15.1 50.5 -9.4 -0.6 -4.9
GCAGCTGTTCAGCTTTTTTT
124 SEQ ID N0:5329 -4.8 -24.9 75 -18.2 -1.8 -11
TAACGTGTCTTCCTCTGGCA
141 SEQ ID N0:5330 -4.8 -26.1 74.4 -21.3 0 -5.3
CAATATCCCTAGAAGAGATT
331 SEQ ID N0:5331 -4.8 -19.9 59.6 -15.1 0 -0.4
CTTTTTCCGGAAAAGCTCCA
384 SEQ ID N0:5332 -4.8 -24 66.6 -16.1 -1.6 -14.4
TCCTTTATTCATTACTATAA
740 SEQ ID N0:5333 -4.8 -18 57 -13.2 0 -2.3
GTGGCACTGAATCGGAAAAT
766 SEQ ID N0:5334 -4.8 -20.8 60 -16 0 -4.3
271
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AATCTTCTAAGCAAAACCCT
999 SEQ ID N0:5335 -4.8 -20.5 59.7 -15.7 0 -4.1
ACAGCTGCAGCCCAATGAGA
1257 SEQ ID N0:5336 -4.8 -27.1 74.4 -19.8 0 -13.2
TAAATGTGCTCATTGTTACA
1392 SEQ ID N0:5337 -4.8 -19.3 59.5 -12.9 -1.6 -4
TTTTTGCCCATCCAAAACAT
1448 SEQ ID N0:5338 -4.8 -22.8 63.7 -16.5 -1.4 -5.4
GATTCTGCTCCTCATAGGCC
1746 SEQ ID N0:5339 -4.8 -27.8 79.5 -22.3 -0.5 -6.4
CTTTGGAACTCAACTTTGAT
1935 SEQ ID N0:5340 -4.8 -19.6 59.6 -14.2 -0.3 -5
AGAGCCCCCACAGAATTGCC
3097 SEQ TD N0:5341 -4.8 -29.8 78 -25 0 -3.2
GCTGCATGCCGACCACAGCA
3159 SEQ ID N0:5342 -4.8 -30.7 80.3 -23.3 -2.6 -9.7
TCGTTCATGTGCCACCGTGG
3235 SEQ ID N0:5343 -4.8 -28.7 77.5 -23.1 -0.6 -8.4
ATGAACTCAATAATAAGGCC
3411 SEQ ID N0:5344 -4.8 -18.4 55.8 -13.6 0 -6.4
TCATCATCAGTAGCAGCAAG
3445 SEQ ID N0:5345 -4.8 -22.5 68 -17.7 0 -5.4
AACTGTGCTTCCTTCAGATG
3884 SEQ ID NO:5346 -4.8 -23.5 69.2 -17.8 -0.7 -4
AAGGATCATGAACACAATGA
4103 SEQ ID N0:5347 -4.8 -17.8 54.8 -12.5 -0.1 -7.4
TATATATCTTCAAAGGCCAA
4138 SEQ ID N0:5348 -4.8 -19.2 58.2 -13.9 0 -7.7
ATTCATGATAGAGGGAATTG
4463 SEQ ID N0:5349 -4.8 -18.5 57.7 -13.7 0 -6.4
GATGACAAAGTATAAATACA
4802 SEQ ID N0:5350 -4.8 -14.5 48.3 -9 -0.5 -5.8
AGATGACAAAGTATAAATAC
4803 SEQ ID N0:5351 -4.8 -13.8 47.1 -9 0 -4.5
ATGACCCAAAGATGATAAAG
4821 SEQ ID N0:5352 -4.8 -17.6 53.5 -12.8 0 -2.1
TCAAAGACCATTCCTTGGAA
5014 SEQ ID N0:5353 -4.8 -21.8 62.8 -15.4 -1.5 -6.9
TGAATTGTGTCAGGGTCACA
5647 SEQ ID N0:5354 -4.8 -23.1 69.1 -17.1 -1.1 -5.6
CACTTTCTTCAGTAGCAACA
5796 SEQ ID N0:5355 -4.8 -22.1 66.7 -16.6 -0.5 -0.8
TCAAAGTCATCCTCACTCAG
5824 SEQ ID N0:5356 -4.8 -22.6 67.5 -17.8 0 -2.6
AGAAGAGGAGGATCCAGGGC
5926 SEQ ID N0:5357 -4.8 -25.4 73.1 -18 -2.6 -9
GGAGGGGTTTGATGCCATAA
6104 SEQ ID N0:5358 -4.8 -24.9 70.8 -19.4 -0.5 -4
GACTTTGGAGGGGTTTGATG
6110 SEQ ID N0:5359 -4.8 -23.3 69.1 -18.5 0 -2.6
TCTCAAACTTTTCCTTGTCT
6399 SEQ ID N0:5360 -4.8 -22.3 67.1 -17.5 0 -2.8
CTGGTTTGTCTTTCTCAAAC
6411 SEQ ID N0:5361 -4.8 -21.4 65.6 -14.2 -2.4 -7.4
CCTCTTGAAGTCCAGTTGAC
6537 SEQ ID N0:5362 -4.8 -24.6 71.8 -18.9 -0.7 -3.7
AGTATTTGTTAAAACAGTCA
6572 SEQ ID N0:5363 -4.8 -17.2 55.3 -12.4 0 -5.9
272
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GAGGTCACTTCACTGTCTTG
6609 SEQ ID N0:5364 -4.8 -24.1 73.3 -19.3 0 -3
ACTTTGCACAACTATCCCTA
6735 SEQ ID N0:5365 -4.8 -23.8 67.9 -19 0 -5
TAAAAATATGGCAGATATGG
6817 SEQ ID N0:5366 -4.8 -15.8 50.7 -9.6 -1.3 -4.7
TCAACGTAAACCTCATTTAC
6908 SEQ ID N0:5367 -4.8 -19.2 57.6 -13.2 -1.1 -5.3
ACTGAAACTGTAGCCATTAC
7022 SEQ ID N0:5368 -4.8 -20.8 61.9 -16 0 -3.3
TAACTGAAACTGTAGCCATT
7024 SEQ ID N0:5369 -4.8 -19.9 59.4 -15.1 0 -3.3
GTATCCAGTGTGTTTCCTTG
7763 5EQ ID N0:5370 -4.8 -25.2 75.3 -20.4 0 -3.2
GCTGACAAATAAAGTTGATT
7864 SEQ ID N0:5371 -4.8 -17.1 53.7 -12.3 0.8 -3.2
AAAAAAACATCTATGAATAA
8152 SEQ ID N0:5372 -4.8 -10.6 40.6 -5.8 0 -3.8
TACGTAAATACTACAAAAGT
8179 SEQ ID N0:5373 -4.8 -14.7 48.4 -9.2 -0.4 -5.8
AGGTAATTGCACAACTTTGC
8290 SEQ ID N0:5374 -4.8 -21.3 63.4 -15.8 -0.5 -5.3
ATAATGACGTAGCTCACCAT
8431 SEQ ID N0:5375 -4.8 -22.2 64.2 -17.4 0 -5.3
AATTATGAAATACATATTTA
9049 SEQ ID N0:5376 -4.8 -12.5 44.6 -6.6 -1 -5.2
AAAGAGACCTTTCCAGAATC
27 SEQ ID N0:5377 -4.7 -20.5 60.9 -14.9 -0.8 -3.7
CAAACCTTGATGTGGCTTGG
250 SEQ ID N0:5378 -4.7 -23.5 66.7 -18.8 0 -3.7
AAGGCGGAAGCTTTCAGGTC
500 SEQ ID N0:5379 -4.7 -25 71.8 -17.9 -2.4 -7.4
TTCCTTTATTCATTACTATA
741 SEQ ID N0:5380 -4.7 -18.8 59.3 -14.1 0 -1.5
TCCACAAACTCTGTCACATA
1075 SEQ ID N0:5381 -4.7 -21.9 64.4 -16.7 -0.1 -4.2
CTGAATGTTCTCAACGCTGA
1108 SEQ ID N0:5382 -4.7 -22.1 64.3 -16.5 -0.8 -4.8
CCTGGAATGACTGAAATTGT
1147 SEQ ID N0:5383 -4.7 -20.2 59.5 -15.5 0 -3.6
AGCTGCAGCCCAATGAGAGC
1255 SEQ TD N0:5384 -4.7 -28 77.3 -20.8 -0.7 -13.2
CAGAATCGCTTGGGGGCCAC
1308 SEQ ID N0:5385 -4.7 -28.1 75.8 -22.7 -0.5 -7.6
TGTGCTCATTGTTACATTAA
1388 SEQ ID NO:5386 -4.7 -20.1 61.9 -15.4 0 -4.1
TTTTGCCCATCCAAAACATA
1447 5EQ ID N0:5387 -4.7 -22.4 62.8 -16.5 -1.1 -5
TCCAAGGTGGCCTGATTCTG
1759 SEQ ID N0:5388 -4.7 -26.7 75.2 -21.1 -0.7 -7.2
CTGCTTCTTCCAAGGTGGCC
1767 SEQ ID N0:5389 -4.7 -28.9 80.8 -23.3 -0.7 -6.3
TTCGGCCTCTTTTTGTTCTG
1784 SEQ ID N0:5390 -4.7 -25.5 74.2 -20.8 0 -6.7
TCTGCTGAAATTCGGCCTCT
1794 SEQ ID N0:5391 -4.7 -25.7 71.7 -19 -2 -10.2
TTCTGAAGAACTTTCCAACA
1913 SEQ ID N0:5392 -4.7 -19.8 59.5 -14.4 -0.4 -4.7
273
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Tnter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGTGGTGGTGCCCTCTGGGG
2483 SEQ ID N0:5393 -4.7 -31.6 88.3 -25.1 -1.8 -6.6
TCCGTTTCAGTGGTGGTGCC
2491 SEQ TD N0:5394 -4.7 -29.5 83.3 -24.8 0 -4.7
CCAGGTTTCCTACAGTCAAC
2844 SEQ ID N0:5395 -4.7 -25 72.4 -19.8 -0.1 -3.9
AGACCAGGTTTCCTACAGTC
2847 SEQ ID N0:5396 -4.7 -25.6 75.5 -20.2 -0.5 -5.9
AACCATTTCTGCTGTGAAAA
2876 SEQ ID N0:5397 -4.7 -20.1 59.4 -14.9 -0.2 -4.5
CCACTCTCCACACAGCACGC
3284 SEQ ID N0:5398 -4.7 -29.3 78.6 -24.6 0 -4.1
CATGGTCTCTATCCACTCTC
3296 SEQ ID N0:5399 -4.7 -25.3 75.6 -19.7 -0.7 -3.9
CATACAGTCCCACATGGTCT
3308 SEQ ID N0:5400 -4.7 -26.2 74.7 -21.5 0 -5.2
TCCATACAGTCCCACATGGT
3310 SEQ ID N0:5401 -4.7 -27.3 76.3 -21.4 -1.1 -5.2
CTAAATGAACTCAATAATAA
3415 SEQ ID N0:5402 -4.7 -12.6 44.4 -7.9 0 -3.4
ACACCACTGGTGGTTCCATT
3673 SEQ ID N0:5403 -4.7 -27 76 -19.7 -2.6 -12
AAACCAGTTGTGCTCAACAA
4076 SEQ ID N0:5404 -4.7 -21.3 62 -13.3 -3.3 -6.6
TCATGAACACAATGAAAGTC
4098 SEQ ID N0:5405 -4.7 -16.9 53.3 -11.6 -0.3 -6.9
CTGTTCAATGTATATATCTT
4148 SEQ ID N0:5406 -4.7 -18.3 58.4 -13.6 0 -3.9
CCCATTTGAGAAGCATTTCC
4230 SEQ ID N0:5407 -4.7 -24.5 69 -19 -0.6 -4.1
AGTGAAATATGTTTGAAATC
4259 SEQ TD N0:5408 -4.7 -15.1 50.1 -10.4 0 -4.1
TCATGCCTTCAAACCGGGAT
4416 5EQ ID N0:5409 -4.7 -25.6 69.4 -20.9 0 -7.1
ATACAGGCTGAAGTTTAACA
4764 SEQ ID N0:5410 -4.7 -19.7 60 -15 0 -4.l
TCCGTTTCCACCATCATGGT
5095 SEQ TD N0:5411 -4.7 -28.1 77.1 -21.8 -1.5 -6.9
AGCACAAATTCTCCAGTGAA
5176 SEQ ID N0:5412 -4.7 -21.6 63.4 -16.1 -0.6 -4.6
TCGGAACAAGGTAGGGGACA
5315 SEQ ID N0:5413 -4.7 -23.7 67.2 -18.4 -0.3 -3.3
CAGGGTCACAGTCGGGTGGT
5637 SEQ ID N0:5414 -4.7 -28.7 82.3 -23.2 -0.6 -5.6
AAAATCCCAACAGATGGGTC
5698 SEQ ID N0:5415 -4.7 -21.8 62.4 -14.5 -2.6 -7.5
GTTTGATGCCATAAACCTGT
6098 SEQ ID N0:5416 -4.7 -23.1 66.1 -17.9 -0.1 -4.2
AGAGAGGTCACTTCACTGTC
6612 SEQ ID N0:5417 -4.7 -23.7 73.1 -18.5 -0.2 -4.1
TGCAAGGACTGTACTAAAGG
6778 SEQ ID N0:5418 -4.7 -20.2 60.5 -15.5 0 -4.8
ATGAATTGGGGACCATGGAA
6857 SEQ ID N0:5419 -4.7 -22.2 63.3 -15.1 -2.4 -8.8
TATGAATTGGGGACCATGGA
6858 SEQ ID N0:5420 -4.7 -22.6 64.7 -15.5 -2.4 -8.8
TTCTGGTTTTGAGCAAAAAT
6994 SEQ ID N0:5421 -4.7 -18.4 56.7 -12.8 -0.8 -8.1
274
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTTTCTGGTTTTGAGCAAAA
6996 SEQ ID N0:5422 -4.7 -19.3 59.3 -14.1 -0.1 -7.9
TACAGGCACATAACTGTTCA
7106 SEQ ID N0:5423 -4.7 -21.7 64.7 -15.4 -1.5 -5.2
TACTCATGTTGAATTAAAAG ,
7720 SEQ ID N0:5424 -4.7 -14.8 49.3 -10.1 0 -4.7
GCACAACTTTGCCACTTTGT
8282 SEQ ID N0:5425 -4.7 -25 71.1 -19.8 -0.2 -3.8
AATTAACATTAAACTTTTGG
8342 SEQ ID N0:5426 -4.7 -14.3 48.1 -9.6 0 -3.5
ATGACGTAGCTCACCATTCT
8428 SEQ ID N0:5427 -4.7 -24.6 70.7 -19.9 0 -5.3
ATATAAATTCTCAATAACTA
8922 SEQ ID N0:5428 -4.7 -13.6 46.9 -8.9 0 -2.6
CTTTCCCAGTAAGCCACTCT
303 SEQ ID N0:5429 -4.6 -27.3 76.5 -22.7 0 -3.4
ACCATCTCTGGAGGAATGTC
670 SEQ ID N0:5430 -4.6 -24 70.5 -17.8 -l.5 -6
GAGAACTCTGAATGTTCTCA
1115 SEQ ID N0:5431 -4.6 -20.5 62.8 -11.8 -4.1 -12
TGAAATTGTTTTCAGTGCTC
1136 SEQ ID N0:5432 -4.6 -20.2 62.5 -13.5 -2.1 -7.7
CAGAGTAAAGGGTCTTTTTG
1462 SEQ ID N0:5433 -4.6 -20.1 62.1 -14.8 -0.4 -4.1
CTTGTGTAGCCATAGTTGGG
1546 SEQ ID N0:5434 -4.6 -25 73.7 -18.9 -1.4 -4.3
TGAAATTCGGCCTCTTTTTG
1789 SEQ ID N0:5435 -4.6 -22.1 63.9 -17.5 0 -6.7
CCATTCTTTAGCACCTTTGG
1949 SEQ ID N0:5436 -4.6 -25 71.6 -20.4 0 -4.1
AGAGAGACTGATGAGGGGAG
2130 SEQ ID N0:5437 -4.6 -22.3 66.9 -17.7 0 -2.l
GCACAAACAGTGAGTCTCTC
2292 SEQ ID N0:5438 -4.6 -22.9 68.9 -16.7 -1.5 -5.2
TTCAGTGGTGGTGCCCTCTG
2486 SEQ ID N0:5439 -4.6 -29.2 83.5 -23.4 -1.1 -5.6
AAAGAGGGTATTTAAGACAA
2780 SEQ ID N0:5440 -4.6 -16.5 52.7 -11.9 0 -2.9
ATTTAGTGTGGGCCAGGATT
3059 SEQ ID N0:5441 -4.6 -25.1 73.3 -20 0 -7.6
ATCTTAATTAGCATATTTAG
3073 SEQ ID N0:5442 -4.6 -16.3 53.6 -11.7 0 -4.1
CCCCCACAGAATTGCCAATG
3093 SEQ ID N0:5443 -4.6 -27.4 71.1 -22.8 0 -4.3
AAACAATAAGGCACATGGTT
3342 SEQ TD N0:5444 -4.6 -18.9 56.8 -14.3 0 -5.2
AGAAAGAGGTTCAGAACCAC
3391 SEQ ID N0:5445 -4.6 -20.4 61.1 -13.1 -2.7 -12
ACTGTGCTTCCTTCAGATGA
3883 SEQ ID N0:5446 -4.6 -24.8 73 -19.3 -0.7 -4.2
CTTCCGGTTTAAAGTCTTCT
3951 SEQ ID N0:5447 -4.6 -23 67.7 -18.4 0 -6.6
AGAAGGATCATGAACACAAT
4105 SEQ ID N0:5448 -4.6 -17.8 55 -12.5 -0.5 -6.9
TCAATGTATATATCTTCAAA
4144 SEQ ID N0:5449 -4.6 -15.8 51.9 -11.2 0 -3.9
CATTTGAGAAGCATTTCCAG
4228 SEQ'ID N0:5450 -4.6 -21.2 63.2 -15.8 -0.6 -4.1
275
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GAAATCCATAAGCAACCCAT
4245 SEQ ID N0:5451 -4.6 -22 61.5 -17.4 0 -4.1
TTGAAATCCATAAGCAACCC
4247 SEQ ID N0:5452 -4.6 -21.4 60.7 -16.8 0 -4.1
TTTGAAATCCATAAGCAACC
424$ SEQ ID N0:5453 -4.6 -19.5 57.5 -14.9 0 -4.1
GGCACCGAGTTCTGAGTAGC
4349 SEQ ID N0:5454 -4.6 -27.2 77.8 -22.6 0 -4
CTCTTAATGTCCGTAATGAT
4374 SEQ ID N0:5455 -4.6 -20.5 61.1 -15.9 0 -2.6
AACCGGGATAAGGCTCTTAG
4405 5EQ ID N0:5456 -4.6 -23.3 66.2 -18.2 -0.2 -7.4
GACCCAAAGATGATAAAGAT
4819 SEQ ID N0:5457 -4.6 -18.2 54.7 -13.6 0 -2.1
CAAGTTTCTTCATTGCATTG
4950 SEQ ID N0:5458 -4.6 -20.6 63.1 -16 0 -5.6
ACATCATCAAAGCAAAGAGC
5403 SEQ ID N0:5459 -4.6 -19.2 58.1 -13.9 -0.5 -4.1
AAGGGACATCATCAAAGCAA
5408 SEQ ID N0:5460 -4.6 -19.8 58.9 -14.6 -0.3 -4.4
CCAGGATGACCGCGATGTAC
5766 SEQ ID N0:5461 -4.6 -26.4 70.8 -20.4 -1.3 -7.2
TCCAGGATGACCGCGATGTA
5767 SEQ ID N0:5462 -4.6 -26.6 71.8 -20.6 -1.3 -7.2
GCAGCTGCAAAATCAGAGAG
5908 SEQ ID N0:5463 -4.6 -21.9 64.2 -14.7 -0.4 -13.4
TCCAGGGCAGCTGCAAAATC
5914 SEQ ID N0:5464 -4.6 -25.5 71.2 -18 -1 -14
CACGCTTTGTAAAGGCAAAT
6030 SEQ ID N0:5465 -4.6 -20.4 59.2 -13.8 -2 -7.2
ATCTCTCCACTCTCACACAA
6052 SEQ ID N0:5466 -4.6 -24.3 71.1 -19.7 0 -0.3
CTCTTTGTTATAGTTACTTG
6242 SEQ ID N0:5467 -4.6 -19.3 61.7 -14.7 0 -2.5
TTTTGTTACACTATCATAGG
6377 SEQ ID N0:5468 -4.6 -19 60 -14.4 0 -3.3
GGGACCATGGAAATGCACTA
6849 SEQ ID N0:5469 -4.6 -23.6 66.2 -18.1 -0.8 -8.8
TGTTTCTTCAACGTAAACCT
6915 SEQ ID N0:5470 -4.6 -20.8 61.4 -15.1 -1 -6.6
CATCTAGAAAATGGAAGTAA
7041 SEQ ID N0:5471 -4.6 -15.5 50.4 -10.9 0 -6.2
GTTTAATGAATGATACAGGA
7515 SEQ ID N0:5472 -4.6 -17.3 54.7 -12.7 0 -2.5
AAAGTGCAAAAGTAAAGGTG
7704 SEQ ID N0:5473 -4.6 -16.1 51.3 -11.5 0 -5.4
AAATTGTGATGTCATCAACC
7911 SEQ ID N0:5474 -4.6 -19.4 58.8 -13.7 -1 -7.2
CAGTAAATAGTTTTGTAAAA
8364 SEQ ID N0:5475 -4.6 -14.2 48.2 -9.6 0 -4.1
ATGCAGTTCTTCAATACACT
8385 SEQ ID N0:5476 -4.6 -21.3 64.7 -16.7 0 -5.5
AAACTGCCAACAGCAAAAAA
8520 5EQ ID N0:5477 -4.6 -17.4 52.2 -11.2 -1.5 -4.5
TTAGATGCTTATAGCCAAGG
8779 SEQ ID N0:5478 -4.6 -21.6 64.2 -15.7 -1.2 -4.9
AATAAGAGTTTGGTTTTGAC
8978 SEQ ID N0:5479 -4.6 -17.8 56.8 -13.2 0 -2.5
276
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TACAACTGGAGTTTTCCACT
9001 SEQ ID N0:5480 -4.6 -22.5 66.4 -15.8 -2.1 -5.6
AATATGCATTACAACTGGAG
9010 SEQ ID N0:5481 -4.6 -18.4 56.5 -13.8 0 -6.8
GAATTATGAAATACATATTT
9050 SEQ 2D N0:5482 -4.6 -13.4 46.3 -7.7 -l -5.l
AACGTGTCTTCCTCTGGCAG
140 SEQ ID N0:5483 -4.5 -26.4 75.3 -21.9 0 -5.3
TGCTCCATAATCTCTGATAA
218 SEQ ID N0:5484 -4.5 -2l 62.7 -16.5 0 -3.6
AGTCACAGCACCTTTTTCCG
395 SEQ ID N0:5485 -4.5 -26.4 74.4 -21.9 0 -4.1
TTTCAGGTCCTGGGGGTACC
489 SEQ ID N0:5486 -4.5 -28.9 82.4 -21.1 -3.3 -12.6
GGTGGCACTGAATCGGAAAA
767 SEQ ID N0:5487 -4.5 -22 62.3 -17.5 0 -4.5
CCAGTGAATGTGTACTCTAC
940 SEQ ID N0:5488 -4.5 -22.2 66.6 -17.7 0 -4.9
AAAATCTTCTAAGCAAAACC
1001 SEQ ID N0:5489 -4.5 -16.2 51.1 -11.7 0 -4.1
AGAAACGTAAAATCTTCTAA
1009 SEQ ID N0:5490 -4.5 -14.7 48.5 -10.2 0 -5.3
GGTCCACAAACTCTGTCACA
1077 SEQ ID N0:5491 -4.5 -24.6 70.8 -19.4 -0.5 -3
GAGTCATGAGTCGAAATAGA
1596 SEQ ID N0:5492 -4.5 -19.4 59.5 -13.4 0 -10.9
CACCACAGCCAGGATCAAAT
1721 SEQ ID N0:5493 -4.5 -24.5 67.7 -20 0 -5.3
CTGTCTCTCTCTCCTTTGTT
2017 SEQ ID N0:5494 -4.5 -26.1 79.7 -21.6 0 0
TTCAGATTCGGATTTGGGAA
2039 SEQ ID N0:5495 -4.5 -21.4 63.2 -16.9 0 -5
AAAGGAAGCTGCTTCTTTTG
2067 SEQ ID N0:5496 -4.5 -20.8 62.5 -13.1 -2 -14.4
CTGGTCAGTCTGTTTCCATC
2095 SEQ ID N0:5497 -4.5 -25.8 78 -20.8 -0.1 -4.4
CCCTGGCACCATCCTGGATG
2363 SEQ ID N0:5498 -4.5 -30.6 80.2 -24.4 -1,2 -11.2
GAGCTGAAGGTCCACCCACC
2439 SEQ ID N0:5499 -4.5 -29.8 79,8 -24.4 -0.8 -5.8
CAATGATCTTGAGAACCATT
2889 SEQ ID N0:5500 -4.5 -19.5 58.5 -15 0 -7.1
CAATCCCTCCACATTTGACA '
2993 SEQ ID N0:5501 -4.5 -25 69.2 -20.5 0 -2.4
GAGCCCCCACAGAATTGCCA
3096 SEQ ID N0:5502 -4.5 -30.5 78,7 -26 0 -3.2
GCATGCCGACCACAGCAAAA
3156 SEQ ID N0:5503 -4.5 -25.9 68.3 -20.3 -1 -8.1
ATACAGTCCCACATGGTCTC
3307 SEQ ID N0:5504 -4.5 -25.9 75.3 -21.4 0 -5.2
TTTCGCTGTTCAATGTATAT
4153 SEQ ID N0:5505 -4,5 -20.4 62.1 -15.9 0 -3.1
AAGCATTTCCAGAATGAATA
4220 SEQ ID N0:5506 -4.5 -18.6 56.6 -12.5 -1.6 -4.9
CTTAATGTCCGTAATGATTT
4372 SEQ ID N0:5507 -4.5 -19.4 58.5 -14.9 0 -2.6
GCTCTTAATGTCCGTAATGA
4375 SEQ ID N0:5508 -4.5 -22.3 65.1 -17.8 0 -2.8
277
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ACATTCATGATAGAGGGAAT
4465 5EQ ID N0:5509 -4.5 -19.3 59.2 -14.8 0 -6.4
GTTAACATCACTAATGTCAA
4589 SEQ ID N0:5510 -4.5 -18 56.4 -11.9 -1.5 -6.6
GCAGGAAGGGACATCATCAA
5413 SEQ ID N0:5511 -4.5 -23 66.6 -17.9 -0.3 -3.7
TCAAAGTTGAACATGTCATC
5530 SEQ ID N0:5512 -4.5 -18.5 57.8 -13.4 -0.3 -7
AAAAAGAAAATCCCAACAGA
5704 SEQ ID N0:5513 -4.5 -15.6 49 -11.1 0 -2
ACATGTTCACCACAACCAGG
5748 SEQ ID N0:5514 -4.5 -24.5 68.8 -19.3 -0.4 -6.1
ACACAAAACACGCTTTGTAA
6038 SEQ ID N0:5515 -4.5 -18.7 55.7 -12.7 -1.4 -6.6
TAAGTCAATCCTCCCTTTAA
6266 SEQ ID N0:5516 -4.5 -22.4 64.9 -17.9 0 -2.4
TTTTCCTTTGCTTTCTTTTT
6431 SEQ ID N0:5517 -4.5 -22.4 68.4 -17.9 0 -3.6
CAAAGATAATTCTTTGTTTC
6478 SEQ ID N0:5518 -4.5 -16.3 53.2 -8.4 -3.4 -8.4
TGACTATGAGTATTTGTTAA
6580 SEQ ID N0:5519 -4.5 -17.4 56 -12.4 -0.1 -3
CTTCACAGAGTTGCAGTGAC
6632 5EQ ID N0:5520 -4.5 -23.4 70.7 -17.4 -1.4 -7.4
AAAAATAGTGACATAGCATT
6888 SEQ ID N0:5521 -4.5 -15.9 51.2 -11.4 0 -4.1
CTAGAAAATGGAAGTAACTG
7038 SEQ ID N0:5522 -4.5 -15.5 50.3 -11 0 -3
ACAGGCACATAACTGTTCAG
7105 SEQ ID N0:5523 -4.5 -22 65.5 -16.2 -1.2 -6.7
ATGTGACATTCTTTAACCAA
7613 SEQ ID N0:5524 -4.5 -19.5 59 -15 0 -3.5
TGAATTAAAAGTGCAAAAGT
7711 SEQ ID N0:5525 -4.5 -14.4 47.8 -9.9 0 -5.4
TGTCATCAACCTGAAAATAA
7902 SEQ ID N0:5526 -4.5 -17.3 53.5 -12.8 0.4 -3
TACTACAAAAGTTGAATAAA
8171 SEQ ID N0:5527 -4.5 -12.8 44.9 -7.7 -0.3 -4.2
GTTCACAAAGCTGCTTTTAA
8661 SEQ ID N0:5528 -4.5 -20.6 62 -14.6 -0.3 -10.9
ATTAGTTACAATTTTTTTTC
72 SEQ ID N0:5529 -4.4 -16.1 53.7 -11.7 0 -2.6
CTGATAAAACAGAGCCTTAT
205 SEQ ID N0:5530 -4.4 -19.1 57.5 -14.7 0 -4.5
GAATGTCTCCATAAATAAAT
657 SEQ ID N0:5531 -4.4 -16.1 51.3 -11.1 -0.3 -2.8
AATAGTGCACATGATAAGCA
866 SEQ ID N0:5532 -4.4 -19.7 59.6 -14.3 -0.4 -9.9
GCCCAATGAGAGCAAACACG
1248 SEQ ID N0:5533 -4.4 -24 65 -19.6 0 -4.1
GCTCATTGTTACATTAACAA
1385 SEQ ID N0:5534 -4.4 -19.1 58.7 -12.6 -2.1 -8
CGAAATAGAGACAGGAAAGC
1585 SEQ ID N0:5535 -4.4 -18 54.7 -13.6 0 -2.8
CTGCTGAAATTCGGCCTCTT
1793 SEQ ID N0:5536 -4.4 -25.4 70.6 -19 -2 -10.2
CTGGATGACATACTGGCCTG
2350 SEQ ID N0:5537 -4.4 -24.9 70.4 -20.5 0 -7.2
278
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TAGATTCTTCAAGTTCTTCC
2619 SEQ ID N0:5538 -4.4 -21.3 66.2 -16.4 -0.2 -3.6
TAAATTCACAAGATGTTTTA
2717 SEQ ID N0:5539 -4.4 -15.5 51 -11.1 0 -4.3
CACTACTGAATTGCTCAGTC
2823 SEQ ID N0:5540 -4.4 -22 66.4 -14.8 -2.8 -8.2
CTGAGGCTGACAATAATTCC
2956 SEQ ID N0:5541 -4.4 -21.7 63.5 -17.3 0 -2.9
TTTTCACATAATCAATTCCC
3510 SEQ ID N0:5542 -4.4 -20.2 60.4 -15.8 0 -2.5
CAGTATTATTGGACATGCAG
3612 SEQ ID N0:5543 -4.4 -20.7 62.8 -16.3 0 -5.5
AGGATCATGAACACAATGAA
4102 SEQ ID N0:5544 -4.4 -17.8 54.8 -12.5 -0.8 -7.4
ATGTATATATCTTCAAAGGC
4141 SEQ ID N0:5545 -4.4 -18.4 58 -14 0 -4.2
CCAGCCTTTAAATGTGGCCA
4709 SEQ ID N0:5546 -4.4 -26.8 72.6 -20.6 -1.8 -8.8
CCATGTTGAGGCAGATGAGG
5073 SEQ ID N0:5547 -4.4 -24.7 71.1 -20.3 0 -4.3
CAAAGATGTTCCAGCCTATA
5229 SEQ ID N0:5548 -4.4 -22.4 64.9 -18 0 -3.2
CCTTTGCTCCTTTGATCAGA
5370 SEQ ID N0:5549 -4.4 -25.6 73.6 -21.2 0 -6.5
GCCGATGTTAAACAACGCAG
5429 SEQ ID N0:5550 -4.4 -22.5 62.2 -18.1 2.6 -6
CTTTTTAACATAGGCAAAGT
5498 SEQ ID N0:5551 -4.4 -18.4 57 -14 0 -4
GGTG~GTGCACTATTAAGAAT
5623 SEQ ID N0:5552 -4.4 -21.1 63.3 -15.1 -1.1 -10.8
ATGTACATGTTCACCACAAC
5752 SEQ ID N0:5553 -4.4 -21.5 63.7 -16.4 -0.4 -7.6
ATCAAACTTTT'CCCAAACCT
5855 SEQ ID N0:5554 -4.4 -21.9 62 -17.5 0 -2.5
AGCTGCAAAATCAGAGAGTT
5906 SEQ ID N0:5555 -4.4 -20.7 62.3 -15.6 -0.4 -6.5
TCTCTCCACTCTCACACAAA
6051 SEQ ID N0:5556 -4.4 -23.6 68.8 -19.2 0 0
AGACTTTGGAGGGGTTTGAT
6111 SEQ ID N0:5557 -4.4 -23.3 69.5 -18.9 0 -2.6
CCTTTGCTTTAAAAGATAAC
6209 SEQ ID N0:5558 -4.4 -17.4 54.1 -12.2 -0.6 -4.8
CTTGATATATTTTTTAACCT
6226 SEQ ID N0:5559 -4.4 -17.6 55.6 -13.2 0 -4.3
TGGTTTGTCTTTCTCAAACT
6410 SEQ ID N0:5560 -4.4 -21.4 65.6 -13.8 -3.2 -8.3
CCATTGGGTTTCTCCTCAGC
6703 SEQ ID N0:5561 -4.4 -28.1 80.5 -22.8 -0.8 -5
ACAACTATCCCTATAGTCTA
6728 SEQ ID N0:5562 -4.4 -21.9 65.3 -15.5 -2 -5.4
TACTGTTTCTTCAACGTAAA
6918 SEQ ID N0:5563 -4.4 -18.5 57.2 -13 -l -5.3
AATATTAGAGGAGACTTTAC
7123 SEQ ID N0:5564 -4.4 -17 55 -11.7 -0.7 -6.7
ATATTTGATTTAATAGAAGT
7450 SEQ ID N0:5565 -4.4 -14.5 49.3 -10.1 0 -2.6
AAACAAGTTTTAGACATATT
7821 SEQ ID N0:5566 -4.4 -15.3 50.5 -10.2 -0.4 -5.l
279
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTGCAGCAGGAATTAAAAAA
8215 SEQ ID N0:5567 -4.4 -17.6 53.9 -13.2 0 -6.6
TTTTATTAATTATATATATT
8542 SEQ ID N0:5568 -4.4 -12.1 44.3 -7.7 0 -5.2
TTATTATCAAACCTGAAAGT
8717 SEQ ID N0:5569 -4.4 -16.8 53.1 -11.7 -0.4 -2.9
ATCAATTATATTGAAAGAAG
8805 SEQ ID N0:5570 -4.4 -13.1 45.8 -6.7 -2 -6.6
AATGTAACATTTATTAGCCA
8845 SEQ ID N0:5571 -4.4 -18.6 57.2 -13.7 -0.2 -5.5
TATATAATGCATTTAAGTAA
8870 SEQ ID N0:5572 -4.4 -14.3 48.4 -9.3 0 -8.5
CTCTGTGGATAAGAAAACAA
45 5EQ ID N0:5573 -4.3 -16.9 53 -12.6 0 -2.9
CTTCCAAGTCACTATTTGGC
621 SEQ ID N0:5574 -4.3 -23.7 69.8 -17.9 -1.4 -5.1
GCACTGAATCGGAAAATTGC
763 SEQ ID N0:5575 -4.3 -20.3 58.9 -16 0 -4.3
CTCTACATTCTTTGTCCAGT
926 SEQ ID N0:5576 -4.3 -23.9 72.3 -19 -0.3 -3.5
GTGTACTCTACATTCTTTGT
931 SEQ ID N0:5577 -4.3 -21.9 68.4 -16.7 -0.8 -5
GTTCTCAACGCTGAGACATT
1102 SEQ ID N0:5578 -4.3 -22.9 67 -15.8 -2.8 -8.2
TTCCAAGGTGGCCTGATTCT
1760 SEQ ID N0:5579 -4.3 -26.8 75.7 -21.6 -0.7 -7.2
GCTGAAATTCGGCCTCTTTT
1791 SEQ ID N0:5580 -4.3 -24.7 69.5 -19 -1.3 -9.2
CTTCAGATTCGGATTTGGGA
2040 SEQ ID N0:5581 -4.3 -23 67.3 -18.7 0 -5
CCCGACCTCTGAAACTGAAA
2202 SEQ TD N0:5582 -4.3 -23.3 63.1 -19 0 -2.8
AAGAGCTTAACCTTCTCTTT
2517 SEQ ID N0:5583 -4.3 -21.7 65.2 -15.8 -1.5 -5.5
GCGGACATTTCTGTCTAGAT
2634 SEQ ID N0:5584 -4.3 -23.6 69.6 -16.6 -2.7 -8
AGATGTTTTACTTTTAACCA
2707 SEQ ID N0:5585 -4.3 -19.1 59.1 -14.8 0 -2.8
ATGATCTTGAGAACCATTTC
2887 SEQ ID N0:5586 -4.3 -20 61 -15.7 0 -5.1
GAAAACTCTAAGCAGTCTGA
3029 SEQ ID N0:5587 -4.3 -19.5 59.5 -15.2 0 -4.1
AAAGAGCTGCATGCCGACCA
3164 SEQ ID N0:5588 -4.3 -26.5 70.8 -21.5 0 -9.1
ACAGTCCCACATGGTCTCTA
3305 SEQ ID N0:5589 -4.3 -26.8 77.4 -22.5 0 -5.2
TACAGTCCCACATGGTCTCT
3306 SEQ ID N0:5590 -4.3 -26.8 77.4 -22.5 0 -5.2
CTACACCACTGGTGGTTCCA
3675 SEQ ID N0:5591 -4.3 -27.5 77 -20.6 -2.6 -12
GAAACTTTTTAATACACCCT
3984 SEQ ID N0:5592 -4.3 -19.4 57.8 -15.1 0 -2.5
TCAAAGGCCAATGCACCACT
4129 SEQ ID N0:5593 -4.3 -25.2 68.7 -19.4 -1.4 -6.9
AGCATTGGCTACCAGGCTAA
4325 SEQ ID N0:5594 -4.3 -26 73.3 -20.1 -1.5 -7.1
TTAGAGGTCTTAAAGCTCTT
4389 SEQ ID N0:5595 -4.3 -20.6 64 -15.1 -1.1 -5.2
280
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CATGCCTTCAAACCGGGATA
4415 SEQ ID N0:5596 -4.3 -24.9 67.5 -20.6 0 -7.1
CATCTCGTGAATCAACAGCT
4746 SEQ TD N0:5597 -4.3 -22.3 64.9 -18 0 -4.6
TAAATACATGTACAGATTTT
4790 SEQ ID N0:5598 -4.3 -15.6 51.2 -10.8 0 -8.2
TCCAAGTTTCTTCATTGCAT
4952 SEQ ID N0:5599 -4.3 -22.9 68.2 -18.6 0 -5.1
ATCAAAGACCATTCCTTGGA
5015 SEQ TD N0:5600 -4.3 -22.5 64.8 -16.6 -1.5 -4.8
GTGAACAGAACAATGAACAC
5161 SEQ ID N0:5601 -4.3 -17.1 53.2 -12.8 0 -3.2
ATCATCTCAGCCAGAAACAT
5281 SEQ TD N0:5602 -4.3 -22.1 64.8 -17.8 0 -3.6
AGGAAGGGACATCATCAAAG
5411 SEQ ID N0:5603 -4.3 -19.8 59.6 -14.9 -0.3 -2.9
AACATGTCATCAATTCCAGC
5521 SEQ ID N0:5604 -4.3 -21.9 64.7 -17.6 0 -6.9
TTGAACATGTCATCAATTCC
5524 SEQ ID N0:5605 -4.3 -20.1 60.7 -14.9 -0.5 -9.1
GAAAATCCCAACAGATGGGT
5699 SEQ ID N0:5606 -4.3 -22 62.3 -14.5 -3.2 -7.9
GGGTTTTGCTATGAGAAGAG
5939 SEQ ID N0:5607 -4.3 -21.4 64.9 -17.1 0 -3.6
GGTTTGATGCCATAAACCTG
6099 SEQ ID N0:5608 -4.3 -23.1 65.5 -16.5 -2.3 -8.6
AATTACGCTGAATGATAGCG
6183 SEQ ID N0:5609 -4.3 -19.6 57.6 -l3 -2.3 -7.6
ACTGTTTCTTCAACGTAAAC
6917 SEQ ID N0:5610 -4.3 -19 58.2 -13.6 -1 -6.2
TGTGATGTCATCAACCTGAA
7907 SEQ ID N0:5611 -4.3 -21.5 63.5 -16.1 -1 -6.9
AAATTATCCATTGAAAAATC
7992 SEQ ID N0:5612 -4.3 -13.8 46.6 -8.8 -0.5 -4
GGAATGGTAGAAAATATATT
8058 SEQ ID N0:5613 -4.3 -15.2 49.9 -10.9 0 -5.9
TTGGAATGGTAGAAAATATA
8060 SEQ ID N0:5614 -4.3 -15.2 49.9 -10.9 0 -2.7
AAAAATAAGACTAGTCTGCA
8199 SEQ ID N0:5615 -4.3 -16.6 52.8 -10.6 0 -11.5
TAAAAAGAACAAAGTCCATG
8255 SEQ ID N0:5616 -4.3 -14.6 47.9 -10.3 0 -3.9
TP~AAAAATGAAATTTATTCT '
8460 SEQ ID N0:5617 -4.3 -10.7 41 -5.1 -1.2 -5.2
ATAGCATCAATTATATTGAA
8810 SEQ TD N0:5618 -4.3 -16.1 52.2 -9.8 -2 -8.1
CTCAATAACTATATCATTAA
8913 SEQ ID N0:5619 -4.3 -15 49.8 -10.7 0 -2.6
AAAAATATGCATTACAACTG
9013 SEQ ID N0:5620 -4.3 -14.5 47.9 -10.2 0 -6.8
TATGGGAGAATTATGAAATA
9057 SEQ ID N0:5621 -4.3 -15.3 50.1 -11 0 -3.2
CAGAATCCTCTCTGCTTATG
14 SEQ ID N0:5622 -4.2 -23 68 -18.1 -0.4 -3.7
TTTCCAGAATCCTCTCTGCT
l8 SEQ ID N0:5623 -4.2 -25.8 74.6 -20.6 -0.9 -4.5
GCATCCAAGATGGTTAGGGT
162 SEQ ID N0:5624 -4.2 -25.3 73.1 -19.6 -1.4 -6.2
281
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGCCCAGCATCCAAGATGGT
168 SEQ ID N0:5625 -4.2 -28.4 77.5 -22.6 -1.5 -7
TCTGATAAAACAGAGCCTTA
206 SEQ ID N0:5626 -4.2 -19.5 58.8 -14.1 -1.1 -5.9
TAAAAAGGCGGAAGCTTTCA
504 SEQ ID N0:5627 -4.2 -19.8 58.1 -13.2 -2.4 -7.6
ATAGTGCACATGATAAGCAT
865 SEQ ID N0:5628 -4.2 -20.4 61.6 -14.9 -1.1 -9.4
ATTCCAGTGAATGTGTACTC
943 SEQ ID N0:5629 -4.2 -21.9 66.5 -16.8 -0.7 -6.2
ATATGCCATCACAATGACAC
1058 SEQ ID N0:5630 -4.2 -21.2 62 -16.3 -0.4 -4.2
TGCAGCCCAATGAGAGCAAA
1252 SEQ ID N0:5631 -4.2 -24.6 67.6 -19.6 -0.6 -5.4
TGCTCATTGTTACATTAACA
1386 SEQ ID N0:5632 -4.2 -19.8 60.7 -14.1 -1.4 -6.4
TTAAATGTGCTCATTGTTAC
1393 SEQ ID N0:5633 -4.2 -18.7 58.6 -12.9 -1.6 -4
ATAAAATGAGCCCAAGAAAA
1694 SEQ ID N0:5634 -4.2 -16.5 50.8 -12.3 0 -3.2
TTCTTTAGCACCTTTGGAAC
1946 SEQ ID N0:5635 -4.2 -22.4 66.4 -18.2 0 -4.1
TCTTCAGATTCGGATTTGGG
2041 SEQ ID N0:5636 -4.2 -22.8 67.5 -18.6 0 -5
AAAAGGAAGCTGCTTCTTTT
2068 SEQ ID N0:5637 -4.2 -20.1 60.5 -12.4 -2.3 -l5
GGCACCATCCTGGATGACAT
2359 SEQ ID N0:5638 -4.2 -27.2 74.7 -21.3 -1.2 -11.3
CCACACCATTGCAATCCACA
2412 SEQ ID N0:5639 -4.2 -26.4 70.9 -21.6 0 -8.6
AAGATGTTTTACTTTTAACC
2708 SEQ ID N0:5640 -4.2 -17.7 55.9 -13.5 0 -2.8
TTTCTGCTGTGAAAATCCCA
2871 SEQ ID N0:5641 -4.2 -23 65.7 -18.3 -0.2 -4
TATTTAGTGTGGGCCAGGAT
3060 SEQ ID N0:5642 -4.2 -24.7 72.3 -20 0 -7.6
TTGCATTTAATTTCTCTTTG
3858 SEQ ID N0:5643 -4.2 -18.8 59.3 -14.6 0 -5.1
GTAAAGACTTTGTCAGCATA
4195 SEQ ID N0:5644 -4.2 -19.9 61.4 -l5 -0.4 -4.6
TGGATCCAAGTTTCTTCATT
4956 SEQ ID N0:5645 -4.2 -22.2 66.7 -17.1 0 -9.6
TGCTGATATCAAAGACTTGT
5046 SEQ ID N0:5646 -4.2 -19.7 60.2 -14.9 -0.3 -7.7
TACTTTTCTATCATCTCAGC
5290 SEQ ID N0:5647 -4.2 -21.4 66.9 -17.2 0 -2.8
ATTCCAGCTTCCTTTTTAAC
5509 SEQ ID N0:5648 -4.2 -22.9 67.6 -18.7 0 -4.3
AGGGTCACAGTCGGGTGGTG
5636 SEQ TD N0:5649 -4.2 -28 81 -23.8 0 -5.6
CCAAACCTCATAGAACATCT
5843 SEQ ID N0:5650 -4.2 -21.3 61.5 -17.1 0 -2.6
CTCTATAAACTGGGTCGCAT
5879 SEQ ID N0:5651 -4.2 -22.6 65.4 -18.4 0 -3.6
CTCCCTTTAATTGCCTCTTT
6256 SEQ ID N0:5652 -4.2 -25.7 72.6 -21.5 0 -3
GGTTTGTCTTTCTCAAACTT
6409 SEQ ID N0:5653 -4.2 -21.5 66.1 -14.1 -3.2 -8.3
282
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAGTCCAGTTGACACATATA
6530 SEQ ID N0:5654 -4.2 -20.7 62.7 -14.7 -1.8 -4.9
ACATAACAGACTAAAATACT
7075 SEQ ID N0:5655 -4.2 -14.9 49 -10.7 0 -2
TAGATTACTTTTTGGAAAGC
7233 SEQ ID N0:5656 -4.2 -17.8 56.3 -12 -1.6 -5.2
AGAAGATGGCAAAGCAATAC
7320 SEQ ID N0:5657 -4.2 -18.5 56.2 -13.4 -0.7 -4.3
AAGCTTGCAAAAGACACATA
7481 SEQ ID N0:5658 -4.2 -18.6 56.3 -12.3 -2.1 -6.9
TGAATGATACAGGATACATC
7509 SEQ ID N0:5659 -4.2 -17.9 56.1 -13.7 0 -3.2
AAGTGCAAAAGTAAAGGTGT
7703 SEQ ID N0:5660 -4.2 -18 55.7 -13.8 0 -5.4
TAAAGTTGATTATATTTTTA
7855 SEQ ID N0:5661 -4.2 -13.8 47.9 -9.6 0 -2.6
TGCTGACAAATAAAGTTGAT
7865 SEQ ID N0:5662 -4.2 -17 53.3 -12.3 -0.1 -3.7
ATGCTGACAAATAAAGTTGA
7866 SEQ ID N0:5663 -4.2 -17 53.3 -12.3 -0.1 -3.7
TTCAAAAGTTTGGAATTGTG
7965 SEQ ID N0:5664 -4.2 -16.9 53.8 -12.2 -O.l -6.9
TGGAATGGTAGAAAATATAT
8059 SEQ ID N0:5665 -4.2 -15.1 49.6 -10.9 0 -3.9
AAAATAAGACTAGTCTGCAT
8198 SEQ ID N0:5666 -4.2 -17.3 54.5 -11.4 0 -11.5
ACTGGAGTTTTCCACTGAGA
8997 SEQ ID N0:5667 -4.2 -23.8 70.4 -17.5 -2.1 -6.3
CTGTCAAACCTTGATGTGGC
254 SEQ ID N0:5668 -4.l -23.8 68.5 -18.5 -1.1 -5
CCAACAGTGCCTGTGCCATC
471 SEQ ID N0:5669 -4.1 -28.9 78.6 -23.2 -1.5 -8.7
TGCCAAGATTTTTATAAGTG
977 SEQ ID N0:5670 -4.1 -18.7 57.7 -14.6 0 -4.l
CTCATTGTTACATTAACAAA
1384 SEQ ID N0:5671 -4.1 -16.6 53 -9.7 -2.8 -8.5
AATTCACCAAATAAAATGAG
1704 SEQ ID N0:5672 -4.1 -14.2 47.1 -10.1 0 -3
AGCTCTCCTAACCCACCTAC
1894 SEQ ID N0:5673 -4.1 -28.2 77 -24.1 0 -4.3
GTTTCCTTCAAGGTGCTCTC
1997 SEQ ID N0:5674 -4.1, -26 77.8 -21.1 -0.6 -5.3
TTCAGATCCAACATCCTTTG
2222 SEQ ID N0:5675 -4.1 -22.6 66 -18 -0.1 -4.5
TACCAGCATGGCGGACATTT
2644 SEQ ID N0:5676 -4.1 -25.8 71.2 -19.7 -2 -7.4
AAATCTATACCAGCATGGCG
2651 SEQ ID N0:5677 -4.1 -22.5 63.8 -16.4 -2 -7.4
GTTTCCTACAGTCAACACAC
2840 SEQ ID N0:5678 -4.1 -22.9 68.1 -18.3 -0.1 -3
AGGTTTCCTACAGTCAACAC
2842 SEQ ID N0:5679 -4.l -23.2 69.2 -18.6 -0.2 -3.6
AAAGACCAGGTTTCCTACAG
2849 SEQ ID N0:5680 -4.1 -22.6 65.7 -18 -0.1 -5.9
CCATTTCTGCTGTGAAAATC
2874 SEQ ID N0:5681 -4.1 -21 62.1 -16 -0.7 -5
CTTCTTGGAAATAGTAATAA
2919 SEQ ID N0:5682 -4.1 -15.7 51.3 -11.6 0 -3.2
283
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CTAAGCAGTCTGAATGATCG
3022 SEQ ID N0:5683 -4.1 -20.6 61.5 -15.8 -0.4 -5.6
GGAGCGTACAGTCATCATTG
3216 SEQ ID N0:5684 -4.1 -23.7 69.9 -19.6 0 -5
TCTAAAAAAGGCTTTTTGGA
3548 SEQ ID N0:5685 -4.1 -17.6 54.7 -11.4 -2.1 -7.7
AACATCAACTGTGCTTCCTT
3890 SEQ ID N0:5686 -4.1 -23.1 67.2 -18.3 -0.4 -4.1
GGGTAGAACAACATCAACTG
3899 SEQ ID N0:5687 -4.1 -19.8 59.4 -15.7 0 -2.9
TGGAAACTTTTTAATACACC
3986 SEQ ID N0:5688 -4.1 -17.7 54.7 -13.6 0 -2.8
GAGTAGCCAAGAGCATTGGC
4336 SEQ ID N0:5689 -4.1 -25.5 73.4 -17.8 -3.6 -12
TGATGGCACCGAGTTCTGAG
4353 SEQ ID N0:5690 -4.1 -25.1 71.2 -21 0 -3.9
AAAGATGACAAAGTATAAAT
4805 SEQ ID N0:5691 -4.1 -12.5 44.2 -8.4 0 -2.8
CCGTTTCCACCATCATGGTG
5094 SEQ ID N0:5692 -4.1 -27.7 75.3 -20.3 -3.3 -10.5
CAAGCAGATCATGCTGTTGC
5558 SEQ ID N0:5693 -4.1 -24 70.2 -17.1 -2.8 -10.6
TAGCAATCCATCCCAGCCAG
5597 SEQ ID N0:5694 -4.l -28.2 76.2 -24.1 0 -4.1
AACTTTTCCCAAACCTCATA
5851 5EQ TD N0:5695 -4.1 -22.3 63.4 -18.2 0 -1.7
GACAGTGGATCCGGTCACCA
6000 SEQ ID N0:5696 -4.1 -28.1 77.3 -22.8 -0.7 -10.1
CTGAAATTACGCTGAATGAT
6187 SEQ ID N0:5697 -4.1 -18.1 54.8 -14 0 -3.3
.
GGACTGTACTAAAGGTGTTT
6773 5EQ ID N0:5698 -4.1 -21 63.9 -16.9 0 -4.1
ATTTACAAAAATAGTGACAT
6894 SEQ ID N0:5699 -4.1 -14.4 48.2 -9.7 -0.3 -4.8
TAAAATAAATTGTGATGTCA
7917 SEQ ID N0:5700 -4.1 -14.1 47.6 -10 0 -4.9
CAATAATGACGTAGCTCACC
8433 SEQ ID N0:5701 -4.l -21.5 62.2 -17.4 0 -5.3
ATAACTATATCATTAATACC
8909 SEQ ID N0:5702 -4.1 -15.6 51 -11.5 0 -4.2
TTATGAAATACATATTTAGA
9047 SEQ ID N0:5703 -4.1 -13.8 47.4 -8.6 -1 -4.6
ATAACAAAGCCCAGCATCCA
175 SEQ ID N0:5704 -4 -24.6 67.2 -19.7 -0.7 -4.1
TTATGAATTACAGCATAACA
189 SEQ ID N0:5705 -4 -16.8 53.3 -11.9 -0.8 -4.9
CTGGAGGAATGTCTCCATAA
663 SEQ ID N0:5706 -4 -22.4 65.5 -15.1 -3.3 -8.5
ACTGAATCGGAAAATTGCCT
761 SEQ ID N0:5707 -4 -20.7 59.3 -16.7 0 -4.4
CCGACTGGATCAGGGCCCCC
1182 SEQ ID N0:5708 -4 -33.6 84.5 -28.2 -0.7 -10.5
AGAACACAGTCAGGATCATC
1221 SEQ ID N0:5709 -4 -21.3 65 -17.3 0 -5.3
TGTAATCCTTCCAGTTAAAT
1407 SEQ ID N0:5710 -4 -20.3 60.9 -16.3 0 -2.8
ACTGTCATCTCCAATGTAAT
1421 SEQ ID N0:5711 -4 -21.3 63.9 -17.3 0.3 -3
284
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTTGCCCATCCAAAACATAA
1446 SEQ ID N0:5712 -4 -21.6 60.7 -17.1 -O.l -3.4
ATAGTTGGGGTTTCGACCAG
1535 SEQ ID N0:5713 -4 -24.7 71.3 -18 -2.7 -6.4
AACTGGTAAAGATTTTCCCA
1624 SEQ ID N0:5714 -4 -21.1 61.8 -17.1 0 -4.6
TGCCGCAACTGCCTGAGCTT
1844 SEQ ID N0:5715 -4 -29.6 78.3 -24.4 -1.1 -7.1
AACTTTGATGCTTCTGAAGA
1924 SEQ ID N0:5716 -4 -19.8 60.4 -15.3 0 -8.3
GCGGCACAAACAGTGAGTCT
2295 SEQ ID N0:5717 -4 -25 70.7 -19.4 -1.5 -7
TGGCACCATCCTGGATGACA
2360 SEQ ID N0:5718 -4 -27.2 74.6 -21.3 -1.2 -11.8
TTAAGACAATGCAAATAGTG
2769 SEQ ID N0:5719 -4 -15.9 51.2 -11.4 -0.1 -5.6
TAGTAATAAGGATCCATGGC
2908 SEQ TD N0:5720 -4 -20.8 62.3 -15.9 0 -9.5
TCTTAATTAGCATATTTAGT
3072 SEQ ID N0:5721 -4 -17.5 56.7 -13.5 0 -4.1
AAGAGGTTCAGAACCACAAG
3388 SEQ ID N0:5722 -4 -20.5 61 -13.8 -2.7 -12
ATCTGCAGATTATTCATTTC
3469 SEQ ID N0:5723 -4 -20 62.7 -14.3 -0.2 -11.6
TTTGCATTCTTCCTACTGCA
3489 SEQ ID N0:5724 -4 -24.8 72.4 -19.3 -1.4 -5.4
CTGTCTATCTTATTGCCTTC
3592 SEQ ID N0:5725 -4 -23.5 71.2 -19.5 0 -3
TACCTACACCACTGGTGGTT
3678 SEQ ID N0:5726 -4 -26.3 74.2 -19.7 -2.6 -12
TCATCGATTACGTATTTTTC
3712 SEQ ID N0:5727 -4 -19.4 59.6 -14.5 -0.7 -6.3
GTTTATGAATGACATATAAT
3737 5EQ ID N0:5728 -4 -15.2 50.3 -10.1 -1 -5.1
GATGAGCTGGTTGCATTTAA
3868 SEQ ID N0:5729 -4 -22.1 65.8 -17.2 -0.7 -5.1
CAGATGAGCTGGTTGCATTT
3870 SEQ ID N0:5730 -4 -23.8 70.2 -18.2 -1.5 -6.1
TTCCTTCAGATGAGCTGGTT
3876 SEQ ID N0:5731 -4 -25 74 -19.8 -1.1 -5
TCAACTGTGCTTCCTTCAGA
3886 SEQ TD N0:5732 -4 -24.6 72.2 -19.7 -0.7 -4
CATCAACTGTGCTTCCTTCA
3888 SEQ ID N0:5733 -4 -24.7 71.7 -20.7 0 -3.6
CAACATCAACTGTGCTTCCT
3891 SEQ ID N0:5734 -4 -23.7 68 -19 -0.4 -4.1
CGGGGTAGAACAACATCAAC
3901 SEQ ID N0:5735 -4 -20.9 60.6 -16.9 0 -2.9
TGAACACAATGAAAGTCTCA
4095 SEQ TD N0:5736 -4 -17.8 55.1 -13.3 -0.1 -3.3
TATAGGTAAAGACTTTGTCA
4200 SEQ ID N0:5737 -4 -18.3 58 -13 -1.2 -5.2
TCCATAAGCAACCCATTTGA
4241 SEQ ID N0:5738 -4 -23.6 65.9 -18.9 -0.4 -4.1
GCATTGGCTACCAGGCTAAC
4324 SEQ ID N0:5739 -4 -26.2 73.6 -20.9 -1.2 -7.2
AGCTCTTAATGTCCGTAATG
4376 SEQ ID N0:5740 -4 -21.7 64 -17.7 0 -4.3
285
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGTCATGTTAACACAGTGGT
4556 SEQ ID N0:5741 -4 -22 66.8 -17.3 -0.3 -8.2
TCATAAAGATGTCTTGACCT
4908 SEQ ID N0:5742 -4 -20.3 61.4 -15.5 -0.6 -6.3
TGAACAGAACAATGAACACT
5160 SEQ ID N0:5743 -4 -16.8 52.3 -12.8 0 -3.l
CATCTCAGCCAGAAACATAC
5279 SEQ ID N0:5744 -4 -21.6 63.4 -17.6 0 -3.6
TGCTCCTTTGATCAGACGTA
5366 SEQ ID N0:5745 -4 -24.4 70.6 -20.4 0 -6.5
ACATAGGCAAAGTTGGACAT
5491 SEQ ID N0:5746 -4 -20.9 62.1 -16.9 0 -4.2
CAAACTTTTCCCAAACCTCA
5853 SEQ ID N0:5747 -4 -22.6 63.1 -18.6 0 -2.4
ATATCAAGACAGTGGATCCG
6007 SEQ ID N0:5748 -4 -21.8 63.7 -17.1 0 -8.9
TCAGTTTGGCATGGACCTCC
6555 SEQ ID N0:5749 -4 -27.5 78 -23 -0.1 -5.4
TGTCAGCTGGTAATAAAAAC
6681 SEQ ID N0:5750 -4 -17.5 54.7 -12.9 0 -8.6
AAAATAGAATGGATGCAAGG
6791 SEQ ID N0:5751 -4 -16.3 51.4 -7.2.3 0 -5.6
TCTGGCAAAACACCTTTGTC
6966 SEQ ID N0:5752 -4 -22.7 65.7 -17.1 -1.5 -6.6
TTTCTGGTTTTGAGCAAAAA
6995 SEQ ID N0:5753 -4 -18.5 57 -13.7 -0.6 -8.1
TCAAAATTAAAGCCATCTAG
7054 SEQ ID N0:5754 -4 -16.9 52.9 -12.9 0 -3.4
AACTATTTACATAACATAGG
7378 SEQ ID N0:5755 -4 -15.7 51.3 -11.2 -0.1 -4.2
TTAAAAGTGCAAAAGTAAAG
7707 SEQ ID N0:5756 -4 -12.8 44.8 -8.8 0 -5.4
CATATTTTTAGCAAAATATG
7807 SEQ ID N0:5757 -4 -14.6 48.7 -6.8 -3.8 -10.4
GAAAATATATTATAACAAAG
8049 SEQ ID N0:5758 -4 -10.2 40 -6.2 0 -6.2
TGGAACATGTGAACTTGATC
8697 SEQ TD N0:5759 -4 -19.3 58.9 -14.6 -0.4 -7
TACTATTATTATCAAACCTG
8722 SEQ ID N0:5760 -4 -16.9 53.7 -12.9 0 -1.5
TAAAAATATGCATTACAACT
9014 SEQ ID N0:5761 -4 -14.2 47.4 -10.2 0 -6.8
AATTGTCTTTAAAAATATGC
9023 SEQ ID N0:5762 -4 -14.5 48.6 -10.5 0 -4.3
CTCTCTGCTTATGCCTCCGC
7 SEQ TD N0:5763 -3.9 -29.7 81.9 -24.9 -0.8 -4.6
TTTTTTTGACCACAGAGGTT
97 SEQ ID N0:5764 -3.9 -22.1 66.2 -16.6 -1.5 -4.7
ACCAACAGTGCCTGTGCCAT
472 SEQ ID N0:5765 -3.9 -28.7 77,5 -23.2 -1.5 -8.7
TTGTTCTCATCATCATTATC
595 SEQ ID N0:5766 -3.9 -20.2 64.1 -16.3 0 -1.9
TGATAGCAATTTTCCTAACA
819 SEQ ID N0:5767 -3.9 -19.6 59.2 -15.7 0 -3.3
ACTCTACATTCTTTGTCCAG
927 SEQ ID N0:5768 -3.9 -22.9 69.3 -19 0 -2,9
ACTCAAAGGTATAGATTCCA
957 SEQ ID N0:5769 -3.9 -20.4 61.7 -15.8 -0.4 -3.6
286
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGTCACATATGCCATCACAA
1064 SEQ TD N0:5770 -3.9 -22.7 65.8 -18.8 0 -5.6
AGAACTCTGAATGTTCTCAA
1114 SEQ ID N0:5771 -3.9 -19.2 59.4 -13.3 -2 -7.7
AAAGCTTCTTTACCGACTGG
1194 SEQ ID N0:5772 -3.9 -22.5 64.6 -17.9 -0.4 -7.6
TTCCTCAGATTGCCCATGAA
1276 SEQ TD N0:5773 -3.9 -25.6 71.3 -21.7 0 -4.5
GCCCAAGAAAATGACCAGGA
1685 SEQ ID N0:5774 -3.9 -23.6 64.4 -19.7 0 -4
ACCACAGCCAGGATCAAATT
1720 SEQ ID N0:5775 -3.9 -23.9 67 -20 0 -5.3
CTGAAATTCGGCCTCTTTTT
1790 SEQ ID N0:5776 -3.9 -23 65.9 -19.1 0 -6.7
CCTTTGGAACTCAACTTTGA
1936 SEQ TD N0:5777 -3.9 -21.6 63.2 -17.1 -0.3 -4.7
CTTTGTTGTTTCCTTCAAGG
2004 SEQ ID N0:5778 -3.9 -22.8 68.6 -18.3 -0.3 -4.6
TCAAGAGAGACTGATGAGGG
2133 SEQ ID N0:5779 -3.9 -20.9 63.2 -17 0 -2.8
ATCATCAGCAAAGTCATTTT
2240 SEQ ID N0:5780 -3.9 -19.9 61.3 -16 0 -4.1
TCCTGGATGACATACTGGCC
2352 SEQ ID N0:5781 -3.9 -26.4 73.8 -22.5 0 -6.2
CTTCCCATTTGCTGGAAGCC
2381 SEQ ID N0:5782 -3.9 -27.9 76.2 -21.8 -2.2 -7.9
TTAAATTCACAAGATGTTTT
2718 SEQ ID N0:5783 -3.9 -15.9 51.9 -12 0 -4.3
AACAATTAAATTCACAAGAT
2723 SEQ ID N0:5784 -3.9 -13.9 46.9 -10 0 -3.1
GACCAGGTTTCCTACAGTCA
2846 SEQ ID N0:5785 -3.9 -26.3 76.3 -21.5 -0.8 -5.9
TAAAGACCAGGTTTCCTACA
2850 SEQ ID N0:5786 -3.9 -22.3 64.9 -17.9 -0.1 -5.3
AATGATCTTGAGAACCATTT
2888 SEQ ID N0:5787 -3.9 -18.9 57.7 -15 0 -7.1
AATCCCTCCACATTTGACAG
2992 SEQ ID N0:5788 -3.9 -24.3 68.3 -20.4 0 -2.4
TTGAAAACTCTAAGCAGTCT
3031 SEQ ID N0:5789 -3.9 -19 58.5 -15.1 0 -4.1
CAAAAATGAAGACGATGATG
3141 SEQ ID N0:5790 -3.9 -14.6 47.5 -10.7 0 -3.5
AAGAGCTGCATGCCGACCAC
3163 SEQ ID N0:5791 -3.9 -27.4 73.5 -22.5 -0.8 -9.1
ACACAGCACGCGGAACACAA
3275 SEQ ID N0:5792 -3.9 -24.1 65.2 -19.7 0 -7.9
GTAGCCAAGAGCATTGGCTA
4334 SEQ ID N0:5793 -3.9 -25.5 73.2 -15.6 -6 -16
GAGTTCTGAGTAGCCAAGAG
4343 SEQ ID N0:5794 -3.9 -23.1 69.6 -19.2 0 -3.2
TTTGATGGCACCGAGTTCTG
4355 SEQ ID N0:5795 -3.9 -24.7 70.4 -20.8 0 -4
AGAGGGAATTGCTCCAACAA
4454 SEQ ID N0:5796 -3.9 -22.3 64 -16.6 -1.8 -6.1
GGAACAAGGTAGGGGACACA
5313 SEQ ID N0:5797 -3.9 -23.4 67.2 -18.9 -0.3 -3.2
CAGTAGCAACACTGAAGTTC
57g7 SEQ ID N0:5798 -3.9 -21 63.7 -16.2 -0.8 -5.8
287
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GATCCATGGCAATAAGCTGG
5967 SEQ ID N0:5799 -3.9 -23.6 67 -18.3 -1.3 -8
TTTTGTAAAAATATGGCAGA
6822 SEQ ID N0:5800 -3.9 -16.4 52.3 -11.2 -1.2 -6.3
ACTATTCTAAAGCAATACTT
7281 SEQ ID N0:5801 -3.9 -17.2 54.6 -12.7 -0.3 -4.1
AACATAGGGTATTTAATTGA
7366 SEQ ID N0:5802 -3.9 -17.1 54.5 -13.2 0 -2.9
GATACCATATGATACTCATG
7732 SEQ ID N0:5803 -3.9 -19.4 59.2 -14.6 -0.8 -5.5
AAAAAAAACATCTATGAATA
8153 SEQ TD N0:5804 -3.9 -10.6 40.6 -6.7 0 -3.8
TCATGTTAGGTAATTGCACA
8297 SEQ ID N0:5805 -3.9 -21 63.8 -17.1 0 -5.3
AAAAAACAAAAATTTATATC
8315 SEQ ID N0:5806 -3.9 -8.6 37.2 -4.7 0 -5.2
CTTCAATACACTACAGTAAA
8377 SEQ ID N0:5807 -3.9 -17.2 54.4 -13.3 0 -3.6
ATATTTTAAACTGCCAACAG
8527 SEQ ID N0:5808 -3.9 -18.1 55.4 -12.8 -1.3 -7.3
CTGGAGTTTTCCACTGAGAA
8996 SEQ ID N0:5809 -3.9 -22.9 67.5 -16.9 -2.1 -6.3
GCTCCATAATCTCTGATAAA
217 SEQ ID N0:5810 -3.8 -20.3 60.8 -16.5 0 -3.3
CCTGTCAAACCTTGATGTGG
255 SEQ ID N0:5811 -3.8 -24 68 -19 -1.1 -4.5
GTCCTGGGGGTACCAACAGT
483 SEQ ID N0:5812 -3.8 -28.5 79.7 -21.9 -2.8 -10.6
CAATTTTCCTAACAGGGTTT
813 SEQ ID N0:5813 -3.8 -21.3 63.3 -16.6 -0.7 -4.1
AATGAGAGCAAACACGCTCA
1244 SEQ ID N0:5814 -3.8 -21.3 61.3 -15 -2.5 -7.7
AGGATCAAATTCACCAAATA
1711 SEQ ID N0:5815 -3.8 -17.9 54.8 -13.5 -0.3 -5.3
CTGCTCCTCATAGGCCATGG
1742 SEQ ID N0:5816 -3.8 -28.6 79.4 -23.6 -0.3 -10.3
CTGATTCTGCTCCTCATAGG
1748 SEQ ID N0:5817 -3.8 -24.9 73.1 -20.5 -0.3 -4
ATCTGCTGAAATTCGGCCTC
1795 SEQ ID N0:5818 -3.8 -24.8 69.9 -19 -2 -10.2
TTTGTTGTTTCCTTCAAGGT
2003 SEQ ID N0:5819 -3.8 -23.1 70 -18.5 -0.6 -5.2
GTGAGTCTCTCCTGCTTTCG
2283 SEQ ID N0:5820 -3.8 -27 79.2 -22.6 -0.3 -4.3
CCTGGCACCATCCTGGATGA
2362 SEQ ID N0:5821 -3.8 -29.2 78.2 -23.5 -1.2 -11.8
CCGTTTCAGTGGTGGTGCCC
2490 SEQ ID N0:5822 -3.8 -31.1 84.8 -26.7 -0.3 -5.1
CGGACATTTCTGTCTAGATT
2633 SEQ ID N0:5823 -3.8 -21.9 65.6 -15.4 -2.7 -8.7
GGCAAATCTATACCAGCATG
2654 SEQ ID N0:5824 -3.8 -22.4 64.6 -17.9 -0.5 -4.3
AGCACGCGGAACACAATCAG
3271 SEQ ID N0:5825 -3.8 -23.4 64.7 -19.1 0 -7.9
GAACTCAATAATAAGGCCAG
3409 SEQ ID N0:5826 -3.8 -19.1 57.2 -14.8 0 -7.7
CATGCAGCTGTCTATCTTAT
3599 SEQ ID N0:5827 -3.8 -23.2 70 -18.7 0 -8.7
288
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GCTTCCGGTTTAAAGTCTTC
3952 SEQ ID N0:5828 -3.8 -23.9 70.1 -20.1 0 -6.6
ATGAACACAATGAAAGTCTC
4096 SEQ ID N0:5829 -3.8 -17.1 53.9 -13.3 0 -3.1
TACCAGGCTAACCAAAGAAA
4316 , SEQ ID N0:5830-3.8 -20.2 58.2 -15.7 -0.5 -4.3
AGCCAAGAGCATTGGCTACC
4332 SEQ ID N0:5831 -3.8 -26.8 74.5 -17.8 -5.2 -14.3
TTCATGATAGAGGGAATTGC
4462 SEQ ID N0:5832 -3.8 -20.3 61.8 -16.5 0 -6.4
TTGTCATGTTAACACAGTGG
4557 SEQ ID N0:5833 -3.8 -20.9 63.8 -16.3 -0.5 -8.7
AATACATGTACAGATTTTCT
4788 SEQ ID N0:5834 -3.8 -17.9 56.9 -13.6 0 -8.2
GATTCGGCCAATCCTGGCAA
5345 SEQ ID N0:5835 -3.8 -27.2 72.8 -19.1 -4.3 -10.3
AACAACGCAGGAAGGGACAT
5419 SEQ ID N0:5836 -3.8 -22 62.1 -18.2 0 -3.6
AGGAAGGATATGATGATGTA
5731 SEQ ID N0:5837 -3.8 -18.7 58.1 -14.9 0 -2.6
CACTGAAGTTCTCCAGGATG
5778 SEQ ID N0:5838 -3.8 -23.2 68.1 -18.6 -0.6 -6.3
GCAAATAAAATATCAAGACA
6016 SEQ ID N0:5839 -3.8 -14.3 47.5 -10.5 0 -3.4
ACTCTCACACAAAACACGCT
6044 SEQ ID N0:5840 -3.8 -21.8 62.3 -l8 0 -3.3
ATAACATCTGAAATTACGCT
6194 SEQ ID N0:5841 -3.8 -17.9 54.8 -14.1 0 -3.3
TTTAACCTTTGCTTTAAAAG
6214 SEQ ID N0:5842 -3.8 -17 53.5 -12.7 -0.2 -4.3
CATAGGCTGTAAACAATTGA
6501 SEQ ID N0:5843 -3.8 -18.7 57 -14.9 0 -7.2
CTCAGCAGTGTCAGCTGGTA
6689 SEQ ID N0:5844 -3.8 -26.8 80.4 -20.2 -2.8 -10
GAAAATGGAAGTAACTGAAA
7035 SEQ ID N0:5845 -3.8 -14.1 47.1 -10.3 0 -3
TTGATTATATTTTTACATTA
7850 SEQ ID N0:5846 -3.8 -15 50.7 -11.2 0 -2.2
TTCTTATGTACAAAATGCTG
7880 SEQ ID N0:5847 -3.8 -17.6 55.3 -13.8 0 -6.8
AAAAAATGAAATTTATTCTT
8459 SEQ 2D N0:5848 -3.8 -11.1 41.7 -6 -1.2 -5.2
GATAGCATCAATTATATTGA
8811 SEQ ID N0:5849 -3.8 -17.4 55.3 -11.8 -1.8 -7.5
AATTCTCAATAACTATATCA
8917 SEQ ID N0:5850 -3.8 -15.7 51.5 -11.9 0 -2.4
TTGTCTTTAAAAATATGCAT
9021 SEQ ID N0:5851 -3.8 -15.9 51.5 -12.1 0 -6.6
GAAATACATATTTAGATCCA
9043 SEQ ID N0:5852 -3.8 -17.1 53.9 -12.7 -0.3 -5.8
CCACAGAGGTTTACAAATTA
88 SEQ ID N0:5853 -3.7 -19.8 59.5 -16.1 0 -3.2
GCATAACAAAGCCCAGCATC
177 SEQ ID N0:5854 -3.7 -24.4 67.7 -19.8 -0.7 -4.9
GCCACTCTACTATGAATCCT
291 SEQ ID N0:5855 -3.7 -24.6 70.2 -20.9 0 -2.2
ATCCCTAGAAGAGATTCTTT
327 SEQ ID N0:5856 -3.7 -21.7 65 -15.7 -2.3 -4.9
289
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GGCACTGAATCGGAAAATTG
764 SEQ ID N0:5857 -3.7 -19.7 57.6 -16 0 -4.3
TGGCACTGAATCGGAAAATT
765 SEQ ID N0:5858 -3.7 -19.7 57.6 -16 0 -4
ACCTGGAATGACTGAAATTG
1148 SEQ TD N0:5859 -3.7 -19.2 57.2 -15.5 0 -5.l
CCATGGAGAAAAGGAAGCTG
2076 SEQ ID N0:5860 -3.7 -20.8 60.2 -17.1 0 -7.3
ACTCAAGAGAGACTGATGAG
2135 SEQ ID N0:5861 -3.7 -19.6 60.5 -14.3 -1.5 -6.3
TTTCAGATCCAACATCCTTT
2223 SEQ ID N0:5862 -3.7 -22.7 66.5 -19 0.7 -3.7
TCTTCCCATTTGCTGGAAGC
2382 SEQ ID N0:5863 -3.7 -26.3 74.4 -19.9 -2.7 -8
ACACCATTGCAATCCACAGT
2410 SEQ ID N0:5864 -3.7 -24.9 69.8 -20.6 0 -8.4
ACCACACCATTGCAATCCAC
2413 SEQ ID N0:5865 -3.7 -25.9 70.4 -21.6 0 -8.6
GTGGTGCCCTCTGGGGGAAG
2479 SEQ ID N0:5866 -3.7 -30.3 83.3 -24.4 -2.2 -8.7
GTAAGAGCTTAACCTTCTCT
2519 SEQ ID N0:5867 -3.7 -22.4 67.2 -17.8 -0.8 -4.9
AATGCTGGCTATGCTCACGG
2585 SEQ ID N0:5868 -3.7 -25.6 71.4 -21.2 -0.4 -5.9
TTCTTCCATTGTGTTGGTCA
2606 SEQ ID N0:5869 -3.7 -24.7 74.3 -21 0.2 -3.7
ACAGACCAAGCTCCATTAAA
2976 SEQ ID N0:5870 -3.7 -21.9 62.8 -18.2 0 -5
TTAATTAGCATATTTAGTGT
3070 SEQ ID N0:5871 -3.7 -17.4 56.3 -13.7 0 -6.1
CCCACATGGTCTCTATCCAC
3300 SEQ ID N0:5872 -3.7 -27.6 77.1 -23 -0.7 -5.2
GTCATCATCAGTAGCAGCAA
3446 SEQ ID N0:5873 -3.7 -23.7 71.3 -20 0 -5.4
AGATGAGCTGGTTGCATTTA
3869 SEQ ID N0:5874 -3.7 -22.8 68.4 -17.5 -1.5 -5.1
AGTCTTCTTCGGGTTCAGTT
3939 SEQ ID N0:5875 -3.7 -25.3 77.1 -21.6 0 -3
TGTCCGTAATGATTTGATGG
4367 SEQ ID N0:5876 -3.7 -21.2 62.4 -17.5 0 -3.2
CAACAAGAGCATTCACAACC
4440 SEQ ID N0:5877 -3.7 -20.9 60.8 -16.6 -0.3 -4.l
GCAAACAAATTCACACCCAT
4525 SEQ ID N0:5878 -3.7 -21.6 60.8 -17.9 0 -3.4
GTCACTCAAATTGTTAACAT
4601 SEQ ID N0:5879 -3.7 -18.4 57.3 -14.2 0 -8.3
ACCCAAAGATGATAAAGATG
4818 SEQ ID N0:5880 -3.7 -17.6 53.5 -13.9 0 -2.1
TAGGATTCGGCCAATCCTGG
5348 SEQ ID N0:5881 -3.7 -26.3 72.1 -18.7 -3.5 -15.6
TTCCAGCTTCCTTTTTAACA
5508 SEQ ID N0:5882 -3.7 -23.6 68.8 -19.9 0 -4.5
GTTGTAATTTGGAACAAGCA
5572 SEQ ID N0:5883 -3.7 -19.5 59.2 -14.2 -1.6 -7.3
AAAAGAAAATCCCAACAGAT
5703 SEQ ID N0:5884 -3.7 -16.3 50.5 -12.6 0 -2.9
GGCTCTGCACTTTCTTCAGT
5803 SEQ ID N0:5885 -3.7 -26.7 79.8 -22.1 -0.7 -6.4
290
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TCAAACTTTTCCCAAACCTC
5854 SEQ ID N0:5886 -3.7 -22.3 63.3 -18.6 0 -2.5
TTTGTTACACTATCATAGGA
6376 SEQ ID N0:5887 -3.7 -19.5 61 -15.8 0 -3.3
CTTTCTCAAACTTTTCCTTG
6402 SEQ ID N0:5888 -3.7 -20.9 63.1 -I7.2 0 -2.5
TTTCCTTTGCTTTCTTTTTC
6430 SEQ ID N0:5889 -3.7 -22.7 69.7 -19 0 -3.6
CAGCAGTGTCAGCTGGTAAT
6687 SEQ ID N0:5890 -3.7 -24.8 73.5 -I8.9 -2.2 -9.2
TCAGATAGAAACAAACATAA
7089 SEQ ID N0:5891 -3.7 -14 47.1 -10.3 0 -2.4
AACTATTCTAAAGCAATACT
7282 SEQ ID N0:5892 -3.7 -16.4 52.5 -12.7 0 -4.1
CTGCAGCAGAAAGTGGAACA
7301 SEQ ID N0:5893 -3.7 -22.3 64.5 -17.2 -0.9 -10.4
GGAATTGTGATTAAAAATCA
7954 SEQ ID N0:5894 -3.7 -15.1 49.4 -9.6 -1.8 -6.9
ATTGGAATGGTAGAAAATAT
8061 SEQ ID N0:5895 -3.7 -15.5 50.4 -11.8 0 -2.4
TACTACTATTATTATCAAAC
8725 SEQ ID N0:5896 -3.7 -14.8 49.8 -11.1 0 -1.3
AAATCCAAGGGTTCTTGAAA
8952 SEQ ID N0:5897 -3.7 -19.3 57.8 -14 -1.6 -6.7
ATAAATCCAAGGGTTCTTGA
8953 SEQ ID N0:5898 -3.7 -20.4 61.1 -14.6 -2.1 -6.7
CCTAGAAGAGATTCTTTGCT
324 SEQ ID N0:5899 -3.6 -22 65.8 -16.1 -2.3 -8.3
GAATTACCTTAGATAGTCAC
409 SEQ ID N0:5900 -3.6 -19.4 60.2 -15.8 0 -3.2
GATAGCAATTTTCCTAACAG
818 SEQ ID N0:5901 -3.6 -19.6 59.5 -16 0 -4.1
CTGAAATCCAGCCAGTTCCA
1039 5EQ ID N0:5902 -3.6 -26.1 72.1 -22 -0.2 -4.9
TCTGTCACATATGCCATCAC
1066 SEQ ID N0:5903 -3.6 -24 70.5 -20.4 0 -6.5
TAATCCTTCCAGTTAAATGT
1405 SEQ ID N0:5904 -3.6 -20.3 60.9 -16.7 0 -5.6
AAAGCTTGTGTAGCCATAGT
1550 SEQ ID N0:5905 -3.6 -22.9 67.9 -17.7 -1.5 -7.9
TCAAATTCACCAAATAAAAT
1707 SEQ ID N0:5906 -3.6 -14 46.6 -10.4 0 -3.1
CAGGATCAAATTCACCAAAT '
1712 SEQ ID N0:5907 -3.6 -18.9 56.5 -14.7 -0.3 -5.3
TGCTGAAATTCGGCCTCTTT
1792 SEQ ID N0:5908 -3.6 -24.6 69.1 -19 -2 -10.2
TGTTTCCTTCAAGGTGCTCT
1998 SEQ ID N0:5909 -3.6 -25.6 75.7 -22 0 -5.3
GCTGTCTCTCTCTCCTTTGT
2018 SEQ ID N0:5910 -3.6 -27.8 84.3 -24.2 p -2,g
CTGAAAATGCTTGTTTTGCT
2188 SEQ ID N0:5911 -3.6 -20.4 61 -15.9 -0.8 -4.8
TAAGAGCTTAACCTTCTCTT
2518 SEQ ID N0:5912 -3.6 -21.3 64.3 -16.1 -I.6 -5.7
TAACAATTAAATTCACAAGA
2724 SEQ ID N0:5913 -3.6 -13.6 46.4 -10 0 -3.1
TCAACACACTACTGAATTGC
.2829 SEQ ID N0:5914 -3.6 -19.9 59.8 -15.8 -0.1 -3.1
291
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CCTACAGTCAACACACTACT
2836 SEQ ID N0:5915 -3.6 -22.8 66.5 -18.7 -0.1 -2.9
GAACCATTTCTGCTGTGAAA
2877 SEQ ID N0:5916 -3.6 -21.4 62.6 -17.1 -0.5 -4.6
TTCTTGGAAATAGTAATAAG
2918 SEQ ID N0:5917 -3.6 -14.8 49.6 -11.2 0 -3.1
ATTAAACTGAGGCTGACAAT
2962 SEQ ID N0:5918 -3.6 -18.8 57.1 -15.2 0 -3.7
AACTCAATAATAAGGCCAGA
3408 SEQ ID N0:5919 -3.6 -19.1 57.2 -15 0 -7.7
TCGATTACGTATTTTTCAAC
3709 SEQ ID N0:5920 -3.6 -18.5 56.9 -14 -0.7 -5.8
TTTATGAATGACATATAATC
3736 SEQ ID N0:5921 -3.6 -14.4 48.7 -9.7 -1 -4
AGCAATTGGCACTGTGACGG
3770 SEQ ID N0:5922 -3.6 -24.7 69.4 -19.5 -1.5 -7.1
CTTTCTTCTAGTTCTGACTC
3838 SEQ ID N0:5923 -3.6 -22.2 70 -17.9 -0.4 -4
GTTGCATTTAATTTCTCTTT
3859 SEQ ID N0:5924 -3.6 -20 62.6 -16.4 0 -5.1
GCCAAGAGCATTGGCTACCA
4331 SEQ ID N0:5925 -3.6 -27.5 75.3 -19.5 -4.4 -12.8
TCTTCATATACAGGCTGAAG
4771 SEQ ID N0:5926 -3.6 -20.6 62.9 -15.3 -1.7 -6.5
GTTGAAGTTATCTATGATGA
4868 SEQ ID N0:5927 -3.6 -18.4 58.4 -14.8 0 -3.2
GATGTACATGTTCACCACAA
5753 SEQ ID N0:5928 -3.6 -21.9 64.5 -17.6 -0.4 -8.4
TCTCCAGGATGACCGCGATG
5769 SEQ ID N0:5929 -3.6 -27 72.5 -22 -1.3 -7.2
AAACCTCATAGAACATCTCA
5841 5EQ ID N0:5930 -3.6 -19.7 59.3 -16.1 0 -2.8
CAGTGGATCCGGTCACCACT
5998 SEQ ID N0:5931 -3.6 -28.4 77.9 -21.7 -3 -13.5
CATCTCTCCACTCTCACACA
6053 SEQ ID N0:5932 -3.6 -25.7 74.8 -22.1 0 -0.5
ACTTTGGAGGGGTTTGATGC
6109 SEQ ID N0:5933 -3.6 -24.5 72.2 -20.9 0 -2.6
CCTCCCTTTAATTGCCTCTT
6257 SEQ ID N0:5934 -3.6 -27.6 75.8 -24 0 -3
CTGACTATGAGTATTTGTTA
6581 SEQ ID N0:5935 -3.6 -19 60.1 -14.9 -0.1 -3
CACAACTATCCCTATAGTCT
6729 SEQ ID N0:5936 -3.6 -22.9 67 -17.3 -2 -5.4
CCATGGAAATGCACTAGAAC
6845 SEQ ID N0:5937 -3.6 -20.5 59.7 -15.5 -1.3 -7.3
AATACTTTCAAAATTAAAGC
7061 SEQ TD N0:5938 -3.6 -13.5 46.4 -9 -0.7 -5.6
GGTGTTTGTAAATAGCTTCA
7688 SEQ ID N0:5939 -3.6 -20.9 64.1 -17.3 0 -4.9
AAATAAAGTTGATTATATTT
7858 SEQ ID N0:5940 -3.6 -12.5 44.7 -8.9 0 -3.2
TTTGGAATTGTGATTAAAAA
7957 SEQ ID N0:5941 -3.6 -14.2 47.7 -10.6 0 -3
ATACGTAAATACTACAAAAG
8180 SEQ ID N0:5942 -3.6 -13.5 46 -9.2 -0.4 -6.6
AAAAAGAACAAAGTCCATGT
8254 SEQ ID N0:5943 -3.6 -16.1 50.8 -12.5 0 -4.3
292
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAAAATGAAATTTATTCTTT
8458 SEQ ID N0:5944 -3.6 -11.9 43.3 -7 -1.2 -5.2
CACAGGTTTTATTAATTATA
8548 SEQ ID N0:5945 -3.6 -16.6 53.9 -13 0 -4.2
CAAATTAGTTACAATTTTTT
75 SEQ ID N0:5946 -3.5 -14.8 49,5 -10.6 -0.5 -4
TTGCTCCATAATCTCTGATA
219 SEQ ID N0:5947 -3.5 -21.8 65.2 -18.3 0 -3.6
TACCAACAGTGCCTGTGCCA
473 SEQ ID N0:5948 -3.5 -28.4 77 -23.8 -1 -8.2
CACCATCTCTGGAGGAATGT
671 SEQ ID N0:5949 -3.5 -24,3 70.1 -19.2 -1.5 -6.1
ACTATAAAAGTTTTCTTATT
727 SEQ ID N0:5950 -3.5 -15.1 50.7 -10.5 -1 -6
CCACAAACTCTGTCACATAT
1074 SEQ ID N0:5951 -3.5 -21.5 63 -17.5 -0.1 -4.2
CAGACAGAACACAGTCAGGA
1226 SEQ ID N0:5952 -3.5 -22 65.4 -17 -1.4 -4.6
CAAACACGCTCAGACAGAAC
1236 SEQ ID N0:5953 -3.5 -20.6 59.8 -17.1 0 -3.4
TCCAATGTAATCCTTCCAGT
1412 SEQ ID N0:5954 -3.5 -24.3 69.6 -20.8 0 -2.2
ATAAAAGTGACTGTCATCTC
1430 SEQ ID N0:5955 -3.5 -18.5 58.3 -14.3 -0.1 -8.8
AGCATCTGCTGAAATTCGGC
1798 SEQ ID N0:5956 -3.5 -24 68.4 -18.9 -1.6 -9.8
TGAGTCTCTCCTGCTTTCGC
2282 SEQ ID N0:5957 -3.5 -27.6 80.1 -23.4 -0.4 -4.5
TCTTGAGAACCATTTCTGCT
2883 SEQ ID N0:5958 -3.5 -23 67.7 -18.6 -0.7 -5.2
TGGGCCAGGATTTTGCCAAC
3051 SEQ ID N0:5959 -3.5 -27 74 -21.2 -2.3 -7.9
ATATTTAGTGTGGGCCAGGA
3061 SEQ ID N0:5960 -3.5 -24.7 72.3 -20.7 0 -7.6
CACTCTCCACACAGCACGCG
3283 SEQ ID N0:5961 -3.5 -28.1 75 -24.6 0 -7.4
CAGCGACCTCCATACAGTCC
3318 SEQ ID N0:5962 -3.5 -28.3 77.1 -24.3 -0.1 -3.5
CAGATTATTCATTTCATTGT
3464 SEQ ID N0:5963 -3.5 -18.9 59.7 -14.9 -0.2 -3
TTTTGCATTCTTCCTACTGC
3490 SEQ ID N0:5964 -3.5 -24.2 71.7 -20.1 -0.3 -5.1
AAAGGCTTTTTGGAAACACT
3542 SEQ ID N0:5965 -3.5 -19.3 58 -15 -0.6 -7.3
TTTCTTCTAGTTCTGACTCA
3837 SEQ ID N0:5966 -3.5 -22 69.1 -17.8 -0.4 -4
CAGTTGTGCTCAACAATACT
4072 SEQ ID N0:5967 -3.5 -21.3 63.8 -14.5 -3.3 -6.6
GCATTAGTGAAATATGTTTG
4264 SEQ ID N0:5968 -3.5 -17.8 56.2 -14.3 0 -4.1
CCTTTAAATGTGGCCACTTG
4705 SEQ ID N0:5969 -3.5 -23.5 66.5 -17.6 0 -l3
ATGACAAAGTATAAATACAT
4801 SEQ ID N0:5970 -3.5 -13.9 47.1 -9.7 -0.5 -5.8
AAGTTATCTATGATGACACC
4864 SEQ ID N0:5971 -3.5 -19.6 60 -14.6 -1.4 -5.8
ATCAAAGACTTGTCTGGTTA
5039 SEQ ID N0:5972 -3.5 -20.2 62.3 -15.7 -0,9 -6.5
293
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ACGCAGGAAGGGACATCATC
5415 SEQ ID N0:5973 -3.5 -24 68.4 -20.5 0 -3.6
GGGTCACAGTCGGGTGGTGC
5635 SEQ ID N0:5974 -3.5 -29.8 85.4 -25.5 -0.6 -5.6
CCAGGAAGGATATGATGATG
5733 SEQ ID N0:5975 -3.5 -20.5 60.6 -l7 0 -3.1
ACTCTATAAACTGGGTCGCA
5880 SEQ ID N0:5976 -3.5 -22.8 66 -19.3 0 -3.6
CAAAATCAGAGAGTTTAGAG
5901 SEQ ID N0:5977 -3.5 -16.6 53.6 -12.6 -0.1 -4.4
CTGCAAAATCAGAGAGTTTA
5904 SEQ ID N0:5978 -3.5 -18.7 57.8 -14.7 -0.1 -4.9
ACAGTGGATCCGGTCACCAC
5999 SEQ ID N0:5979 -3.5 -27.7 76.5 -21.9 -2.2 -12
ATGCAAGGACTGTACTAAAG
6779 SEQ TD N0:5980 -3.5 -19 58 -15.5 0 -5.6
ACCTTTGTCTGATCATTTGA
6955 SEQ ID N0:5981 -3.5 -22.3 67 -18.8 0 -6.2
CATAAAAATAATCCTTTAAA
7141 SEQ ID N0:5982 -3.5 -12.4 43.9 -8.9 0 -4
CAACTATTCTAAAGCAATAC
7283 SEQ ID N0:5983 -3.5 -16.2 51.9 -12.7 0 -4.1
GAATTGTGATTAAAAATCAA
7953 SEQ ID N0:5984 -3.5 -13.2 45.6 -7.7 -2 -8.2
ACAGGTTTTATTAATTATAT
8547 5EQ ID N0:5985 -3.5 -15.9 52.5 -12.4 0 -4.2
TAGCCAAGGGAGTTAATTGA
8768 SEQ ID N0:5986 -3.5 -21.5 63.6 -18 0 -3.7
AACATTTATTAGCCACCAAG
8840 SEQ ID N0:5987 -3.5 -20.6 60.4 -17.1 0 -3.2
ACCTCACATAAATCCAAGGG
8960 SEQ ID N0:5988 -3.5 -22.2 63.3 -18.1 -0.3 -3.9
TATGAATCCTTGACAGGTAT
281 SEQ ID N0:5989 -3.4 -20.6 62.1 -16.2 -0.9 -3.4
ACTATGAATCCTTGACAGGT
283 SEQ ID N0:5990 -3.4 -22 65.1 -17.6 -0.9 -3.4
CTTCTTGGCTTTCTCTTCTG
560 SEQ ID N0:5991 -3.4 -24.5 74.6 -21.1 0 -3.7
TTCCAGCTTCCAAGTCACTA
627 SEQ ID N0:5992 -3.4 -25.5 73.8 -22.1 0 -4.5
GGAAGGTTCTTTCCAGCTTC
637 SEQ ID N0:5993 -3.4 -25.4 75.3 -20 -2 -8.6
ACAAGGCAGAGGTGGCACTG
777 SEQ ID N0:5994 -3.4 -25.7 73.4 -21.7 -0.3 -4.5
ATGACACTGAAATCCAGCCA
1045 SEQ ID N0:5995 -3.4 -23.4 65.7 -18.8 -1.1 -4.9
GCCCAGGTCCACAAACTCTG
1082 SEQ ID N0:5996 -3.4 -27.9 75.7 -24.5 0 -3.4
GAATGTTCTCAACGCTGAGA
1106 SEQ ID N0:5997 -3.4 -21.8 64 -15.8 -2.6 -8
CTTTACCGACTGGATCAGGG
1187 SEQ ID N0:5998 -3.4 -24.8 69.9 -20.5 -0.7 -5.3
CAGAACACAGTCAGGATCAT
1222 SEQ ID N0:5999 -3.4 -21.6 64.7 -18.2 0 -5.3
CTTTTTGCCCATCCAAAACA
1449 SEQ ID N0:6000 -3.4 -23.7 65.4 -18.8 -1.4 -5.4
GAAATAGAGACAGGAAAGCC
1584 5EQ ID N0:6001 -3.4 -19.2 57.5 -15.8 0 -3.2
294
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CATGGAGAAAAGGAAGCTGC
2075 SEQ ID N0:6002 -3.4 -20.6 60.4 -17.2 0 -5.2
TAAGACAATGCAAATAGTGA
2768 SEQ ID NO:6003 -3.4 -16.4 52.1 -12.1 -0.7 -5.6
CCTTCTTGGAAATAGTAATA
2920 5EQ ID N0:6004 -3.4 -18.4 56.8 -15 0 -3.2
CCATTAAACTGAGGCTGACA
2964 SEQ TD N0:6005 -3.4 -22.2 63.8 -18.8 0 -3.7
CTTAATTAGCATATTTAGTG
3071 SEQ ID N0:6006 -3.4 -17.1 55.3 -13.7 0 -5
TCCACACAGCACGCGGAACA
3278 SEQ ID NO:6007 -3.4 -27 71.3 -23.1 0 -7.9
ATTTTTCACATAATCAATTC
3512 SEQ ID N0:6008 -3.4 -16.3 53.2 -12.9 0 -2.5
CATCTTATTTTTCACATAAT
3518 SEQ ID N0:6009 -3.4 -17.2 55.1 -13.8 0 -2.2
GCACTGTGACGGTGAGGCTG
3762 SEQ ID N0:6010 -3.4 -27.3 76.6 -22.1 -1.8 -7.6
AAAACAAGCTTCCGGTTTAA
3959 SEQ ID N0:6011 -3.4 -19.7 57.7 -15.4 -0.7 -8.9
TAAAACAAGCTTCCGGTTTA
3960 SEQ TD N0:6012 -3.4 -20.1 59 -15.8 -0.7 -8.9
TCATGATAGAGGGAATTGCT
4461 SEQ ID NO:6013 -3.4 -21.1 63.4 -17.7 0 -5.9
CACAGTGGTAGAACTTGCCA
4545 SEQ ID NO:6014 -3.4 -24.5 70.4 -20.4 -0.5 -5.2
TGACAGTCACTCAAATTGTT
4606 SEQ ID NO:6015 -3.4 -20 61.3 -16.6 0 -7
TGAACACTAGGTTGATCCGG
5148 SEQ ID N0:6016 -3.4 -23.1 66 -18.5 -1.1 -6.8
GGGGACACAGAATACTTTTC
5302 SEQ ID NO:6017 -3.4 -21.4 64.1 -18 0 -3.5
AGAAAATCCCAACAGATGGG
5700 SEQ ID N0:6018 -3.4 -20.8 59.7 -14.5 -2.9 -7.4
GATCCGGTCACCACTGACCA
5993 SEQ ID NO:6019 -3.4 -28.8 77 -21.5 -3.9 -11.8
TTTGGAGGGGTTTGATGCCA
6107 SEQ ID N0:6020 -3.4 -26.1 74.4 -21.6 -1 -4.7
ATCTGAAATTACGCTGAATG
6189 SEQ ID NO:6021 -3.4 -17.9 54.7 -14.5 0 -3.3
GATATATTTTTTAACCTTTG
6223 SEQ ID N0:6022 -3.4 -16.8 54 -13.4 0 -4.3
CCTTCATAGGCTGTAAACAA
6505 SEQ ID N0:6023 -3.4 -21.4 62.6 -17.5 -0.2 -5.7
ACAGAGTTGCAGTGACAGAG
6628 SEQ ID N0:6024 -3.4 -22.6 68.5 -19.2 0 -4.9
CTGTAGCCATTACAATTCTT
7015 SEQ ID N0:6025 -3.4 -21.8 65 -17.4 -0.9 -3.9
TTTGCACTTGCTGAAACAGA
7169 SEQ ID N0:6026 -3.4 -21.3 62.8 -17.2 -0.5 -6.5
AGAGCAGAAGATGGCAAAGC
7325 SEQ ID N0:6027 -3.4 -21.7 63.7 -17.4 -0.8 -4.7
TTTAATGAATGATACAGGAT
7514 SEQ ID N0:6028 -3.4 -16.1 51.9 -12.7 0 -2.5
CCTTTAAACTATGTTTAATG
7527 SEQ ID NO:6029 -3.4 -16.6 52.9 -11.1 -2.1 -8
CAAATAAAGTTGATTATATT
7859 SEQ ID N0:6030 -3.4 -13.1 45.7 -9,7 0 -2.9
295
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkoal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AATGCTGACAAATAAAGTTG
7867 SEQ ID N0:6031 -3.4 -15.7 50.5 -12.3 0 -3.6
TCTATGAATAAAAGGTTATA
8143 SEQ ID N0:6032 -3.4 -14.4 48.6 -10.4 -0.3 -3.1
GTCTGCATACGTAAATACTA
8186 SEQ ID N0:6033 -3.4 -19.7 59.6 -16.3 0 -6.6
AAAATGAAATTTATTCTTTT
8457 SEQ ID N0:6034 -3.4 -12.7 45 -7.8 -1.4 -6.5
TGCATTTAAGTAACAAAGAA
8863 SEQ ID N0:6035 -3.4 -15.3 49.9 -11.9 0 -4.7
AAGATGGTTAGGGTATAACG
156 SEQ ID N0:6036 -3.3 -19.4 58.8 -14.1 -2 -4.6
TCCAAGATGGTTAGGGTATA
159 SEQ ID N0:6037 -3.3 -22.2 66.4 -18 -0.8 -4.9
CATCCAAGATGGTTAGGGTA
161 SEQ ID N0:6038 -3.3 -23.2 68.2 -19 -0.8 -4.9
CCCTAGAAGAGATTCTTTGC
325 SEQ ID N0:6039 -3.3 -23.1 67.6 -17.5 -2.3 -7.5
CCTTTTTCCGGAAAAGCTCC
385 SEQ ID N0:6040 -3.3 -25.3 68.9 -18.8 -2.1 -14.4
AAAAGGCGGAAGCTTTCAGG
502 SEQ ID N0:6041 -3.3 -22 62.9 -16.6 -2.1 -7.6
GGCTCTGACACCATCTCTGG
679 SEQ ID N0:6042 -3.3 -27.4 78.1 -22.9 -1.1 -5.9
AGTGCTCGGAGAACTCTGAA
1123 SEQ ID N0:6043 -3.3 -23.1 67.2 -19 -0.6 -8
TCCTCAGATTGCCCATGAAC
1275 SEQ ID N0:6044 -3.3 -25.7 71.5 -22.4 0 -4.5
AAAATGACCAGGACAAAAAA
1678 SEQ ID N0:6045 -3.3 -14.6 47.2 -11.3 0 -4
TGGAGAAAAGGAAGCTGCTT
2073 SEQ ID N0:6046 -3.3 -20.9 61.4 -16.8 0 -9.4
TGATCTTGAGAACCATTTCT
2886 SEQ ID N0:6047 -3.3 -20.9 62.9 -16.4 -1.1 -7.1
GCCAGGATTTTGCCAACTTG
3048 SEQ ID N0:6048 -3.3 -25.6 71.3 -21.7 -0.3 -3.8
TGTGGGCCAGGATTTTGCCA
3053 SEQ ID N0:6049 -3.3 -28.7 79.1 -23.1 -2.3 -7.9
AAGAAGTCGTTCATGTGCCA
3241 SEQ ID N0:6050 -3.3 -23.7 68.4 -19.1 -1.2 -4.7
GGTCTCTATCCACTCTCCAC
3293 SEQ ID N0:6051 -3.3 -27.5 80.3 -24.2 0 -2.8
CACATGGTCTCTATCCACTC
3298 SEQ ID N0:6052 -3.3 -24.9 73.5 -20.7 -0.7 -5.2
CAATGACCATGACCAACATG
3363 SEQ ID N0:6053 -3.3 -21.2 60.2 -16 -1.9 -5.4
CATTAGTGAAATATGTTTGA
4263 SEQ ID N0:6054 -3.3 -16.6 53.5 -13.3 0 -4.1
GTTGATCCGGGACAAAACTA
5138 SEQ ID N0:6055 -3.3 -21.7 61.9 -17.7 0 -8.7
ACACTAGGTTGATCCGGGAC
5145 SEQ ID N0:6056 -3.3 -25.2 71.4 -20.7 -1.1 -6.8
ATGAACACTAGGTTGATCCG
5149 SEQ ID N0:6057 -3.3 -21.9 63.6 -17.4 -1.1 -6
AGGTTGTAATTTGGAACAAG
5574 SEQ ID N0:6058 -3.3 -18.2 56.7 -13.3 -1.6 -7.3
AAGAAAATCCCAACAGATGG
5701 SEQ ID N0:6059 -3.3 -18.9 55.8 -14.5 -1 -4.3
296
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GAACATCTCAAAGTCATCCT
5831 SEQ ID N0:6060 -3.3 -21.4 63.6 -18.1 0 -2.8
CCACTGACCATGGGCAGATC
5983 SEQ ID N0:6061 -3.3 -27.2 75 -22.1 -1.8 -8.8
ACGCTGAATGATAGCGGCAG
6179 SEQ ID N0:6062 -3.3 -24.2 67.1 -17.3 -3.6 -10.6
CTTTAAAAGATAACATCTGA
6203 SEQ ID N0:6063 -3.3 -15.1 49.7 -10.9 -0.8 -6.5
ACTTGATATATTTTTTAACC
6227 SEQ ID N0:6064 -3.3 -16.9 54.2 -13.6 0 -3.7
GGAACTCCCATCTGTTTTTT
6338 SEQ ID N0:6065 -3.3 -24.3 70.4 -20.5 -0.1 -3.9
AAAACAGTCAGTTTGGCATG
6562 SEQ ID N0:6066 -3.3 -20.2 60.9 -15.3 -1.6 -7.7
AAGGACTGTACTAAAGGTGT
6775 SEQ ID N0:6067 -3.3 -20.1 61.3 -16.8 0 -4.8
AAAATACTTTCAAAATTAAA
7063 SEQ ID N0:6068 -3.3 -10.3 40.2 -7 0 -3.2
TTGCATAAAAATAATCCTTT
7144 SEQ ID N0:6069 -3.3 -16 50.9 -12.7 0 -5.1
TTTGCATAAAAATAATCCTT
7145 SEQ TD N0:6070 -3.3 -16 50.9 -12.7 0 -5.1
ACTGCAGCAGAAAGTGGAAC
7302 SEQ ID N0:6071 -3.3 -21.8 63.9 -17.2 -0.7 -10.4
ACATAACATAGGGTATTTAA
7370 SEQ ID N0:6072 -3.3 -17 54.1 -13.7 0 -2.9
AGAATGGATTGAGTAAAATA
7584 SEQ ID N0:6073 -3.3 -14.9 49.3 -11.6 0 -2.3
AAGGTGTTTGTAAATAGCTT
7690 SEQ ID N0:6074 -3.3 -19.1 59.5 -15.8 0 -4.9
AAAATATATTATAACAAAGA
8048 SEQ ID N0:6075 -3.3 -10.2 40 -6.9 0 -6.2
AAGACTAGTCTGCATACGTA
8193 SEQ ID N0:6076 -3.3 -21.3 64 -16.3 0 -11.5
TAAGACTAGTCTGCATACGT
8194 SEQ TD N0:6077 -3.3 -21.3 64 -16.3 0 -11.5
TGCAGTTCTTCAATACACTA
8384 SEQ ID N0:6078 -3.3 -21 64.1 -17.7 0 -4.7
CAATAGCAATTCCCTGCATG
8402 SEQ TD N0:6079 -3.3 -23.4 65.9 -19.1 -0.9 -4.9
AAACAAAAAACCCCAGAGCC
8497 SEQ ID N0:6080 -3.3 -21.3 58.5 -18 0 -3.2
TTTGTTGTAAAATTCATGTA '
8598 SEQ ID N0:6081 -3.3 -16.4 53.4 -12.4 -0.4 -6.6
ATATAATTTATTATGGGAGA
9068 SEQ ID N0:6082 -3.3 -16 52.3 -11.9 -0.6 -4.9
ACCACAGAGGTTTACAAATT
89 SEQ ID N0:6083 -3.2 -20.3 60.6 -16.1 -0.9 -4.7
GCAAGAGATTCTCTAGTAAA
520 SEQ ID N0:6084 -3.2 -18.9 59.1 -14.4 -1.2 -9.3
CCTAACAGGGTTTAGTGGAG
8,06 SEQ ID N0:6085 -3.2 -23.3 68.6 -19.6 -0.1 -3.6
CTCAAGGTCATAAATACACA
895 SEQ ID N0:6086 -3.2 -18.6 57.2 -15.4 0 -2.8
ATTCTTTGTCCAGTCAGGAG
920 SEQ TD N0:6087 -3.2 -24 72.9 -19.4 -1.3 -4.4
GTAAAATCTTCTAAGCAAAA
1003 SEQ ID N0:6088 -3.2 -14.9 49.1 -11.7 0 -4.1
297
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TATGCCATCACAATGACACT
1057 SEQ ID N0:6089 -3.2 -22.1 63.9 -18.4 -0.1 -4.2
TAAAATGAGCCCAAGAAAAT
1693 5EQ ID N0:6090 -3.2 -16.5 50.8 -13.3 0 -3.2
ATGGAGAAAAGGAAGCTGCT
2074 SEQ ID N0:6091 -3.2 -20.8 61.1 -17.6 0 -7.2
TGGTCAGTCTGTTTCCATCC
2094 5EQ ID N0:6092 -3.2 -26.9 79.8 -23.7 0 -4.2
GAGACTGATGAGGGGAGCAG
2127 SEQ ID N0:6093 -3.2 -24.2 70.8 -20.5 -O.l -4.1
CAGAATGCTGGCTATGCTCA
2588 SEQ ID N0:6094 -3.2 -24.7 71 -20.7 -0.6 -5.9
TACAGTCAACACACTACTGA
2834 SEQ ID N0:6095 -3.2 -20.5 62 -15.6 -1.7 -5.6
TTAGTGTGGGCCAGGATTTT
3057 SEQ ID N0:6096 -3.2 -25.2 73.8 -21.5 0 -7.6
GGGAGCGTACAGTCATCATT
3217 SEQ ID N0:6097 -3.2 -24.9 72.7 -21.7 0 -4.8
GAAGAAGTCGTTCATGTGCC
3242 SEQ ID N0:6098 -3.2 -23.6 68.5 -19.1 -1.2 -4.7
CCACACAGCACGCGGAACAC
3277 SEQ ID NO:6099 -3.2 -26.8 70.4 -23.1 0 -7.9
AGCGACCTCCATACAGTCCC
3317 SEQ ID N0:6100 -3.2 -29.6 79.4 -25.9 -O.l -3.5
TTCCTACTGCAATCTGCAGA
3480 SEQ ID N0:6101 -3.2 -24.4 70.5 -16.8 -4.4 -11.4
AAAAGGCTTTTTGGAAACAC
3543 SEQ ID N0:6102 -3.2 -17.7 54.4 -13.6 -0.7 -7.2
ACCACTGGTGGTTCCATTCC
3671 SEQ ID N0:6103 -3.2 -28.5 79.6 -23.4 -1.5 -11.7
TAGCCAAGAGCATTGGCTAC
4333 SEQ ID N0:6104 -3.2 -24.5 70.4 -15.6 -5.7 -15.4
CGAGTTCTGAGTAGCCAAGA
4344 SEQ ID N0:6105 -3.2 -23.9 69.4 -20.7 0 -3.2
ATCCAGCCTTTAAATGTGGC
4711 SEQ ID N0:6106 -3.2 -24.5 69.6 -20.5 -0.6 -7.4
AGAAACATACCTACAATGGA
5269 SEQ ID N0:6107 -3.2 -18.6 56.1 -15.4 0.2 -4
CCGCGATGTACATGTTCACC
5757 SEQ ID N0:6108 -3.2 -26.4 71.7 -22.7 0 -7.8
AAAGTCATCCTCACTCAGGG
5822 SEQ ID N0:6109 -3.2 -23.9 70 -19.8 -0.8 -3.4
ACTTTGTTGGGTTTTGCTAT
5947 SEQ ID N0:6110 -3.2 -22.9 69.3 -19.7 0 -3.6
ATCCGGTCACCACTGACCAT
5992 SEQ ID N0:6111 -3.2 -28.2 75.7 -20.6 -4.4 -9.6
AAGACAGTGGATCCGGTCAC
6002 SEQ ID N0:6112 -3.2 -24.7 70.5 -19.9 -1.1 -10.8
CCCTTTAATTGCCTCTTTGT
6254 SEQ ID N0:6113 -3.2 -25.6 72.3 -22.4 0 -3
TCCCTTTAATTGCCTCTTTG
6255 SEQ ID N0:6114 -3.2 -24.8 70.6 -21.6 0 -3
TTTTTCTGGAGTGGAGTTCC
6323 SEQ ID N0:6115 -3.2 -24.2 73.3 -20.5 -0.1 -4
TAATTCTTTGTTTCTTTTTA
6472 SEQ ID N0:6116 -3.2 -17.4 57 -14.2 0 -2.9
TCAGCAGTGTCAGCTGGTAA
6688 SEQ ID N0:6117 -3.2 -25.2 75.4 -19.2 -2.8 -10
298
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ACTTTCAAAATTAAAGCCAT
7058 SEQ ID N0:6118 -3.2 -17.2 53.2 -13.1 -0.7 -5.6
TGAGAGCAGAAGATGGCAAA
7327 SEQ TD N0:6119 -3.2 -20.5 60.7 -17.3 0 -4.l
CTGAGAGCAGAAGATGGCAA
7328 SEQ ID N0:6120 -3.2 -22.1 64.6 -18 -0.8 -5.2
ATATATTTGCCCAAACATGC
7413 SEQ TD N0:6121 -3.2 -21.4 61.7 -18.2 0 -5
AAACATCTATGAATAAAAGG
8148 SEQ ID N0:6122 -3.2 -13.2 45.5 -10 0 -3.8
GCAGTTCTTCAATACACTAC
8383 SEQ ID N0:6123 -3.2 -21.2 64.8 -18 0 -3.4
CATGCAGTTCTTCAATACAC
8386 SEQ ID N0:6124 -3.2 -21.1 63.9 -17.9 0 -5.5
CAATTCCCTGCATGCAGTTC
8396 SEQ TD N0:6125 -3.2 -26.1 73.7 -19.8 -0.2 -14.3
TATTTTAAACTGCCAACAGC
8526 SEQ ID N0:6126 -3.2 -19.9 59.2 -15.1 -l.5 -7.3
ACTACTATTATTATCAAACC
8724 SEQ ID N0:6127 -3.2 -17.1 54.2 -13.9 0 -1.3
CAGCATCCAAGATGGTTAGG
164 SEQ ID N0:6128 -3.1 -23.6 68.5 -19 -1.4 -6.2
TACAGCATAACAAAGCCCAG
l81 SEQ ID N0:6129 -3.1 -22.1 62.7 -18.5 -0.2 -4.l
GGAGGAATGTCTCCATAAAT
661 SEQ ID N0:6130 -3.1 -20.8 61.7 -15.2 -2.5 -7
TTGCCAAGATTTTTATAAGT
978 SEQ ID N0:6131 -3.1 -18.8 58.1 -15.7 0 -4.1
GAACACAGTCAGGATCATCA
1220 SEQ ID N0:6132 -3.l -22 66 -18.9 0 -5.3
TTGGGGTTTCGACCAGCCTT
1531 SEQ ID N0:6133 -3.1 -28.6 78.4 -22.8 -2.7 -7.8
ATGAGCCCAAGAAAATGACC
1689 SEQ ID N0:6134 -3.1 -21.7 61 -18.6 0 -3.2
CAGCTGATGCTGCCGCAACT
1854 SEQ ID N0:6135 -3.1 -28.2 75.6 -22.4 -2.7 -12
CCAACAGCTCTCCTAACCCA
1899 SEQ ID N0:6136 -3.1 -28.1 74.9 -25 0 -4.2
CCACGGATACTCAAGAGAGA
2143 SEQ ID N0:6137 -3.1 -22.5 64.5 -17.8 -l.5 -6.2
TGACATACTGGCCTGACTAA
2345 SEQ ID N0:6138 -3.1 -22.9 65.9 -19.8 0 -7.2
ATGACATACTGGCCTGACTA
2346 SEQ ID N0:6139 -3.1 -23.6 68 -20.5 0 -7.2
TTCTGCTGTGAAAATCCCAG
2870 SEQ ID N0:6140 -3.1 -22.9 65.6 -19.8 0 -3.6
CATTAAACTGAGGCTGACAA
2963 SEQ ID NO:6141 -3.1 -19.5 58.3 -16.4 0 -3.7
CCAGGATTTTGCCAACTTGA
3047 SEQ ID N0:6142 -3.1 -24.4 68.5 -20.7 -0.3 -3.5
ATTGTCATCATCAGTAGCAG
3449 SEQ ID N0:6143 -3.1 -22 68.1 -18.9 0 -4.1
TCTTCTAGTTCTGACTCACT
3835 SEQ ID N0:6144 -3.1 -22.9 71.2 -19.1 -0.4 -4
AAACAAGCTTCCGGTTTAAA
3958 SEQ ID N0:6145 -3.1 -19.7 57.7 -16 -0.2 -8
TGAAATCCATAAGCAACCCA
4246 SEQ ID N0:6146 -3.1 -22 61.4 -18.9 0 -4.1
299
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATTGGCTACCAGGCTAACCA
4322 SEQ ID N0:6147 -3.1 -26.4 72.9 -21.7 -1.5 -7.2
ATAAAGATGACAAAGTATAA
4807 SEQ ID N0:6148 -3.1 -12.9 45.2 -9.8 0 -2.8
ATAGTGAAGTAGTAGTGTCT
5212 SEQ ID N0:6149 -3.1 -20.3 65.2 -17.2 0 -1.9
GGAAGGATATGATGATGTAA
5730 SEQ ID N0:6150 -3.1 -18 56 -14.9 0 -2.6
CGATGTACATGTTCACCACA
5754 SEQ ID N0:6151 -3.1 -23.4 66.9 -19.6 -0.2 -8.4
CAAACCTCATAGAACATCTC
5842 SEQ ID N0:6152 -3.1 -19.7 59.3 -16.6 0 -2.8
AAATAAAATATCAAGACAGT
6014 SEQ ID N0:6153 -3.1 -13 45.3 -9.9 0 -2.9
GGGGTTTGATGCCATAAACC
6101 SEQ ID N0:6154 -3.1 -24.6 68.7 -19.2 -2.3 -8.6
CTTTGTTTCTTTTTACTTTT
6467 SEQ ID N0:6155 -3.1 -19.3 61.7 -16.2 0 -2.2
TTTACAAAAATAGTGACATA
6893 SEQ ID N0:6156 -3.1 -14.1 47.7 -11 0 -3.5
GGTTTTGAGCAAAAATTTTA
6990 SEQ ID N0:6157 -3.1 -17 53.8 -13 -0.8 -8.1
CATAACAGACTAAAATACTT
7074 SEQ ID N0:6158 -3.1 -14.8 48.9 -11.7 0 -2
GAAGATGGCAAAGCAATACT
7319 SEQ ID N0:6159 -3.1 -19.4 57.9 -15.4 -0.7 -4.3
ATTTAATTGACATAGACTAT
7356 SEQ ID N0:6160 -3.1 -15.9 52.1 -12.8 0 -3.3
TAATGAATGATACAGGATAC
7512 SEQ 2D N0:6161 -3.1 -15.8 51.3 -12.7 0 -2.4
AGCATAAAGTAAAATAAATT
7926 SEQ ID N0:6162 -3.1 -12 43.3 -8.9 0 -4.1
ATTCAAAAGTTTGGAATTGT
7966 SEQ ID N0:6163 -3.1 -16.9 53.8 -13.3 -0.2 -6.5
TTTGACCAATGTATCTCCTA
8080 SEQ ID N0:6164 -3.1 -22.2 65.5 -19.1 0 -3.4
TGTTTGACCAATGTATCTCC
8082 SEQ ID N0:6165 -3.1 -22.8 67.2 -19.7 0 -3.4
TCTTCAATACACTACAGTAA
8378 SEQ ID N0:6166 -3.1 -18.3 57.5 -15.2 0 -3.6
AATAATGACGTAGCTCACCA
8432 SEQ ID N0:6167 -3.1 -21.5 62.2 -18.4 0 -5.3
AGCCAAGGGAGTTAATTGAA
8767 SEQ ID N0:6168 -3.1 -21.1 62.1 -18 0 -3.7
AAATACATATTTAGATCCAA
9042 SEQ ID N0:6169 -3.1 -15.8 51 -12.7 0 -5.7
TTTTTTGACCACAGAGGTTT
96 SEQ ID N0:6170 -3 -22.1 66.2 -17.5 -1.5 -4.7
CTTCCTCTGGCAGCTGTTCA
133 SEQ ID N0:6171 -3 -28.4 82.2 -24.7 0 -8.9
AAACCTTGATGTGGCTTGGC
249 SEQ ID N0:6172 -3 -24.6 69.7 -21.6 0 -3.7
TCTACTATGAATCCTTGACA
2g6 SEQ ID N0:6173 -3 -20.6 62 -17.6 0 -2.3
TTCAGGTCCTGGGGGTACCA
4gg SEQ ID N0:6174 -3 -29.5 83 -23.2 -3.3 -12.6
GAGTTAAAATATACAAGGCA
7gg SEQ ID N0:6175 -3 -16.8 53.1 -13.8 0 -4
300
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TAGTGCACATGATAAGCATG
864 SEQ ID N0:6176 -3 -20.4 61.5 -15.3 -2.1 -9.9
TACTCTACATTCTTTGTCCA
928 SEQ ID N0:6177 -3 -22.6 68.4 -19 -0.3 -2.9
AACCTGGAATGACTGAAATT
1149 SEQ ID N0:6178 -3 -18.5 55.5 -15.5 0 -5.1
TTGTTACATTAACAAATGTC
1380 SEQ ID N0:6179 -3 -16.2 52.6 -10.9 -2.3 -7.5
AAGTGACTGTCATCTCCAAT
1426 SEQ ID N0:6180 -3 -22.2 66.1 -18.5 -0.1 -8.8
CATAGTTGGGGTTTCGACCA
1536 SEQ ID N0:6181 -3 -25.4 72.2 -19.7 -2.7 -6.4
CACTGAAATCTCTTGAAGCA
1872 SEQ ID N0:6182 -3 -20.1 60.3 -17.1 0 -4.1
ACTTTCCAACAGCTCTCCTA
1904 SEQ ID N0:6183 -3 -25.6 73.5 -22.6 0 -4.4
GAGAGACTGATGAGGGGAGC
2129 SEQ ID N0:6184 -3 -24.1 71 -21.1 0 -2.8
TAATAAGGATCCATGGCAAT
2905 SEQ ID N0:6185 -3 -19.9 58.9 -16.2 0 -9
TGAAAACTCTAAGCAGTCTG
3030 SEQ ID N0:6186 -3 -18.9 58.1 -15.9 0 -4.1
CTTGAAAACTCTAAGCAGTC
3032 SEQ ID N0:6187 -3 -19 58.5 -16 0 -4.1
CCTAGAGCCCCCACAGAATT
3100 SEQ ID N0:6188 -3 -28.6 75.5 -25.6 0 -3.8
AAAACAATAAGGCACATGGT
3343 SEQ ID N0:6189 -3 -18.1 54.8 -15.1 0 -5.2
CCTTTTGCATTCTTCCTACT
3492 SEQ ID N0:6190 -3 -25.3 73.1 -22.3 0 -4.8
CAAAGGCCAATGCACCACTA
4128 5EQ ID N0:6191 -3 -24.5 66.8 -20.7 -0.6 -7.7
TTCAAACCGGGATAAGGCTC
4409 SEQ ID N0:6192 -3 -23.1 65.1 -20.1 0 -7.1
ACTAATGTCAAACATGTTAC
4580 SEQ ID N0:6193 -3 -17.1 54.4 -12.9 -1.1 -9
CTTTAAATGTGGCCACTTGA
4704 SEQ ID N0:6194 -3 -22.1 64.2 -16.7 0 -Z3
TAAAGATGACAAAGTATAAA
4806 SEQ ID N0:6195 -3 -12.2 43.7 -9.2 0 -2.8
TATCAAAGACTTGTCTGGTT
5040 SEQ ID N0:6196 -3 -20.2 62.3 -15.7 -1.4 -7
GACAAAACTAGGGTCATGTA
5128 SEQ ID N0:6197 -3 -19.8 60 -15.9 -0.7 -4.7
CGGGTGGTGCACTATTAAGA
5625 SEQ ID N0:6198 -3 -23.8 68.3 -19.5 -1.1 -9.5
TTACCTTCATAGGCTGTAAA
6508 SEQ ID N0:6199 -3 -21.2 63.3 -17 -1.1 -4.4
GTAAAAATATGGCAGATATG
6818 SEQ ID N0:6200 -3 -15.8 50.9 -11.8 -0.9 -4.5
GCCATTACAATTCTTTTTCT
7010 SEQ ID N0:6201 -3 -21.6 64.8 -18.6 0 -2.5
GCATAAAAATAATCCTTTAA
7142 SEQ ID N0:6202 -3 -14.9 48.6 -11.9 0 -3.4
TGCAAAAGACACATACACTG
7476 5EQ ID N0:6203 -3 -18.5 56 -15.5 0 -4.7
TTAATGAATGATACAGGATA
7513 SEQ ID N0:6204 -3 -15.7 51.1 -12.7 0 -2.4
301
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTACAAAATGCTGACAAATA
7873 SEQ ID N0:6205 -3 -16.2 51.3 -13.2 0 -4.6
GTGATGTCATCAACCTGAAA
7906 SEQ ID N0:6206 -3 -20.8 61.6 -16.7 -1 -6.9
TGACCAATGTATCTCCTATT
8078 SEQ Ib N0:6207 -3 -22.1 65.1 -19.1 0 -2.4
TTGACCAATGTATCTCCTAT
8079 SEQ ID N0:6208 -3 -22.1 65.1 -19.1 0 -2.9
TCAATAATGACGTAGCTCAC
8434 SEQ ID N0:6209 -3 -19.9 59.9 -16.3 -0.3 -5.4
AGTTCACAAAGCTGCTTTTA
8662 SEQ ID N0:6210 -3 -21.3 64.4 -16.8 -0.3 -10.9
GAATGTAACATTTATTAGCC
8846 SEQ ID N0:6211 -3 -18.5 57,2 -14.6 -0.8 -6.5
CAACTGGAGTTTTCCACTGA
8999 SEQ ID N0:6212 -3 -23.2 67,6 -18.1 -2.1 -7.1
CATTACAACTGGAGTTTTCC
9004 SEQ ID N0:6213 -3 -21.5 64.3 -17.5 -0.9 -5.2
TATGAAATACATATTTAGAT
9046 5EQ ID N0:6214 -3 -13.7 47.2 -9.8 -0.7 -5.2
AACCTTGATGTGGCTTGGCT
248 SEQ ID N0:6215 -2.9 -26.2 73.9 -22.6 -0.4 -3.8
AATTACCTTAGATAGTCACA
408 SEQ ID N0:6216 -2.9 -19.5 60.1 -16.6 0 -2.7
GGCTTTCTCTTCTGCAGCAC
554 SEQ ID N0:6217 -2.9 -27.3 80.7 -23.1 -1.2 -8.3
AGTGCACATGATAAGCATGC
863 SEQ ID N0:6218 -2.9 -22.5 66.2 -17.3 -2.3 -9.9
AGTAAAGGGTCTTTTTGCCC
1459 SEQ ID N0:6219 -2.9 -24.6 71.3 -20.5 -1.1 -4.8
AGAGTAAAGGGTCTTTTTGC
1461 SEQ ID N0:6220 -2.9 -21.2 65.2 -17.8 -0.1 -3.8
CTTCCAAGGTGGCCTGATTC
1761 SEQ ID N0:6221 -2.9 -26.8 75.7 -23 -0.7 -7.2
AAGCTGTCTCTCTCTCCTTT
2020 SEQ ID N0:6222 -2.9 -25.9 77.9 -23 0 -5.1
ACTGAAAATGCTTGTTTTGC
2189 SEQ ID N0:6223 -2.9 -19.7 59.6 -15.9 -0.8 -4.7
GATGACATACTGGCCTGACT
2347 SEQ ID N0:6224 -2.9 -24.5 69.9 -21.6 0 -7.2
ACAATTAAATTCACAAGATG
2722 SEQ ID N0:6225 -2.9 -14.6 48.5 -11.7 0 -3.1
GTCAACACACTACTGAATTG
2830 SEQ ID N0:6226 -2.9 -19.3 58.8 -16.4 0 -3.6
GTGAAAATCCCAGTAAAGAC
2863 SEQ ID N0:6227 -2.9 -19.1 57.1 -16.2 0 -2.1
CCAACTTGAAAACTCTAAGC
3036 SEQ ID N0:6228 -2.9 -18.9 56.6 -16 0 -2.g
GCCCCCACAGAATTGCCAAT
3094 SEQ ID N0:6229 -2.9 -29.2 75 -26.3 0 -4.2
CCACAGCAAAAATGAAGACG
3147 SEQ ID N0:6230 -2.9 -18.8 54.8 -15.9 0 -3.3
ATGACCAACATGAAAACAAT
3355 SEQ ID N0:6231 -2.9 -16.4 50.8 -13 -0.1 -5.2
CGATTACGTATTTTTCAACA
3708 SEQ ID N0:6232 -2.g -18.8 56.9 -15.4 -0.1 -6.1
_ TTATGAATGACATATAATCA
3735 SEQ ID N0:6233 -2.9 -15 49.7 -11 -1 -4
302
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal)
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CTTCTAGTTCTGACTCACTG
3834 SEQ ID N0:6234 -2.9 -22.5 69.2 -19.1 -0.1 -4
TTCTTCTAGTTCTGACTCAC
3836 SEQ ID N0:6235 -2.9 -22.1 69,4 -18.5 -0.4 -3.4
GAATGAATATATAGGTAAAG
4209 5EQ ID N0:6236 -2.9 -13.6 46.8 -10.7 0 -4.2
TGTTAACATCACTAATGTCA
4590 SEQ ID N0:6237 -2.9 -18.7 58.3 -14.7 -1 -7.9
ACTCAAATTGTTAACATCAC
4598 SEQ ID N0:6238 -2.9 -17.4 54.9 -14 0 -8.3
GATAAAGATGACAAAGTATA
4808 SEQ ID N0:6239 -2.9 -7.4.2 47.9 -11.3 0 -2.8
ATATCAAAGACTTGTCTGGT
5041 SEQ ID N0:6240 -2.9 -20.1 61.9 -15.7 -1.4 -7
ATTAAGAATAGGTGCTAGCA
5612 SEQ ID N0:6241 -2.9 -20 61.1 -15.8 0 -10.6
GAGAAGAGGAGGATCCAGGG
5927 SEQ ID N0:6242 -2.9 -24.2 70.1 -18.7 -2.6 -9
ACACTATCATAGGAAGGAGG
6370 SEQ ID N0:6243 -2.9 -20.6 62.4 -17.7 0 -3.4
CAAAAATAGTGACATAGCAT
6889 SEQ ID N0:6244 -2.9 -16.5 52.2 -13.6 0 -4.1
ATTTGCACTTGCTGAAACAG
7170 SEQ ID N0:6245 -2.9 -20.7 61.5 -17.2 -0.3 -6.5
ATGAATGATACAGGATACAT
7510 SEQ ID N0:6246 -2.9 -17.5 54.8 -14.6 0 -3.2
AGGTGTTTGTAAATAGCTTC
7689 SEQ ID N0:6247 -2.9 -20.2 63.1 -17.3 0 -4.9
GAATTAAAAGTGCAAAAGTA
7710 SEQ ID N0:6248 -2.9 -14.1 47.3 -11.2 0 -5.4
GTAAAATAAATTGTGATGTC
7918 SEQ ID N0:6249 -2.9 -14.6 49 -11.7 0 -3.2
AAATAAGACTAGTCTGCATA
8197 SEQ ID N0:6250 -2.9 -17.7 55.8 -13.3 0 -11
AAAAAATAAGACTAGTCTGC
8200 SEQ ID N0:6251 -2.9 -15.2 49.9 -10.6 0 -12.5
TA~1AAAATAAGACTAGTCT
8202 SEQ ID N0:6252 -2.9 -12.4 44.3 -7.9 0 -11.2
TTAAAAAAATAAGACTAGTC
8203 SEQ ID N0:6253 -2.9 -11.6 42.8 -7.9 0 -9.2
AATAGCTTTAGTGCAGCAGG
8225 SEQ ID N0:6254 -2.9 -23 68.7 -18.5 -1.5 -6.6
GGCTAAAAAGAACAAAGTCC
8258 SEQ ID N0:6255 -2.9 -17.8 54.1 -14.9 0 -3.7
ATAGCCAAGGGAGTTAATTG
8769 SEQ ID N0:6256 -2.9 -20.9 62.3 -18 0 -3.7
ACAACTGGAGTTTTCCACTG
9000 SEQ ID N0:6257 -2.9 -22.8 66.9 -18 -1.9 -5.9
CCAGCATCCAAGATGGTTAG
165 SEQ ID N0:6258 -2.8 -24.4 69.6 -20.1 -1.4 -6.2
AAAGCCCAGCATCCAAGATG
170 SEQ ID N0:6259 -2.8 -24.6 67.5 -20.7 -1 -5.5
GAGCCTTATGAATTACAGCA
194 SEQ ID N0:6260 -2.8 -22.2 65.1 -18.7 -0.4 -4.1
AGCCACTCTACTATGAATCC
292 SEQ ID N0:6261 -2.8 -23.7 68.6 -20.9 0 -3.2
ACAATATCCCTAGAAGAGAT
332 SEQ ID N0:6262 -2.8 -20 59.8 -17.2 0 -3.8
303
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTCACAGCACCTTTTTCCGG
394 5EQ ID N0:6263 -2.8 -27.6 76.6 -24.8 0 -6
AAAAAGGCGGAAGCTTTCAG
503 SEQ ID N0:6264 -2.8 -20.1 58.7 -14.9 -2.4 -7.6
GTGCACATGATAAGCATGCT
862 SEQ ID N0:6265 -2.8 -23.4 67.9 -18.8 -1.7 -10.9
CAAAATAGTGCACATGATAA
869 SEQ ID N0:6266 -2.8 -16.5 52 -12.7 0 -9.9
CAGGTCCACAAACTCTGTCA
1079 SEQ ID N0:6267 -2.8 -24.4 70.5 -21.1 -0.1 -3.6
CTGAAATTGTTTTCAGTGCT
1137 SEQ ID N0:6268 -2.8 -20.7 63 -14.5 -3.4 -11.5
CGACTGGATCAGGGCCCCCA
1181 SEQ ID N0:6269 -2.8 -32.3 82.3 -28.1 -0.7 -10.5
CCAATGTAATCCTTCCAGTT
1411 SEQ ID N0:6270 -2.B -24 68.4 -21.2 0 -2.2
TGACTGTCATCTCCAATGTA
1423 SEQ ID N0:6271 -2.8 -22.6 67.4 -19.1 -0.3 -8.1
GTGACTGTCATCTCCAATGT
1424 5EQ ID N0:6272 -2.8 -24.1 71.4 -20.6 -0.3 -$.8
CAAAACATAAAAGTGACTGT
1436 SEQ ID N0:6273 -2.8 -15.2 49.3 -12.4 0 -3.2
TTGCCCATCCAAAACATAAA
1445 SEQ ID N0:6274 -2.8 -20.8 58.7 -18 0 -3
AAGGAAGCTGCTTCTTTTGA
2066 SEQ ID N0:6275 -2.8 -22.1 65,9 -16.7 -1.8 -13.3
TGAAAATGCTTGTTTTGCTA
2187 SEQ ID N0:6276 -2.8 -19.2 58.6 -15.5 -0.8 -4.8
TTTCCTACAGTCAACACACT
2839 SEQ ID N0:6277 -2.8 -22.6 66.7 -19.3 -0.1 -2.9
CTTGAGAACCATTTCTGCTG
2882 SEQ ID N0:6278 -2.8 -22.6 66.1 -18.4 -1.3 -S.8
TCAAAGATATTCCAGCCTTC
2935 SEQ ID N0:6279 -2.8 -22.4 65.7 -18.9 -0.4 -3.8
ATTTTGCCAACTTGAAAACT
3042 SEQ ID N0:6280 -2.8 -18.9 56.6 -16.1 0 -4
TCTATCCACTCTCCACACAG
3289 SEQ ID N0:6281 -2.8 -25.4 73.3 -22.6 0 -1.6
AATAAGGCCAGAAAGAGGTT
3400 SEQ ID N0:6282 -2.8 -20.3 60.1 -17.5 0 -6.9
CTCTCCAACAGCAATTGGCA
3779 SEQ ID N0:6283 -2.8 -25.1 70.5 -20.7 -1.5 -8.1
CTTCCTTCAGATGAGCTGGT
3877 SEQ ID N0:6284 -2.8 -25.8 75.6 -21.8 -1.1 -5
TCCGGTTTAAAGTCTTCTTC
3949 SEQ ID N0:6285 -2.8 -22.5 67.3 -19 -0.5 -7.4
TGAGAAGGATCATGAACACA
4107 SEQ ID N0:6286 -2.8 -19.1 58 -15.6 -0.5 -6.9
AAAGACTTTGTCAGCATATT
4193 SEQ ID N0:6287 -2.8 -19.1 59.2 -15 -1.2 -5.3
ATAAATACATGTACAGATTT
4791 SEQ ID N0:6288 -2.8 -15.5 50.9 -12.2 0 -7,7
AGTTATCTATGATGACACCA
4863 SEQ ID N0:6289 -2.8 -21 63.4 -26.7 -1.4 -5.8
TTTTTAACATAGGCAAAGTT
5497 SEQ ID N0:6290 -2.8 -17.6 55.4 -14.8 0 -4
TCAGGGTCACAGTCGGGTGG
5638 SEQ ID N0:6291 -2.8 -27.9 80.5 -24.3 -0.6 -5.6
304
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GCACTTTCTTCAGTAGCAAC
5797 SEQ TD N0:6292 -2.8 -23.2 69.9 -19.5 -0.7 -4.2
TTTGTTGGGTTTTGCTATGA
5945 SEQ ID N0:6293 -2.8 -22.4 67.9 -19.6 0 -3.6
GGATCCGGTCACCACTGACC
5994 SEQ ID N0:6294 -2.8 -29.3 78.4 -23.2 -3.3 0
AATTGATCACAAAGATAATT
6487 SEQ ID N0:6295 -2.8 -14.3 47.9 -10.6 -0.8 -6.3
TGCACAACTATCCCTATAGT
6731 SEQ ID N0:6296 -2.8 -23.4 67.6 -18.8 -1.8 -8.3
CTTTGTCTGATCATTTGAGA
6953 SEQ ID N0:6297 -2.8 -20.7 64.1 -17.9 0 -6.2
AGATAGAAACAAACATAACA
7087 SEQ ID N0:6298 -2.8 -13.8 46.6 -1l 0 -1.2
CTTTGCATAAAAATAATCCT
7146 SEQ ID N0:6299 -2.8 -16.8 52.4 -14 0 -5.1
AGCAGAAAGTGGAACAACTA
7297 SEQ ID N0:6300 -2.8 -19 57.6 -15.2 -0.9 -5.6
TACTGCAGCAGAAAGTGGAA
7303 SEQ ID N0:6301 -2.8 -21.3 62.8 -17.2 -0.7 -10.4
GAATGGTAGAAAATATATTA
8057 SEQ ID N0:6302 -2.8 -13.7 47 -10.9 0 -6.2
ATCTATGAATAAAAGGTTAT
8144 SEQ ID N0:6303 -2.8 -14.7 49.2 -11.4 -0.1 -2.9
CTAGTCTGCATACGTAAATA
8189 5EQ ID N0:6304 -2.8 -19.5 59.3 -16.7 0 -6.6
ATAGCTTTAGTGCAGCAGGA
8224 SEQ ID N0:6305 -2.8 -24.3 72.6 -19.9 -1.5 -6.6
CTTATAGCCAAGGGAGTTAA
8772 SEQ ID N0:6306 -2.8 -21.5 63.8 -18.7 0 -3.7
TAAATCCAAGGGTTCTTGAA
8952 SEQ ID N0:6307 -2.8 -19.7 59.1 -14.8 -2.1 -6.7
ATGCATTACAACTGGAGTTT
9007 SEQ ID N0:6308 -2.8 -20.8 62.7 -18 0 -6.4
AACAGAGCCTTATGAATTAC
198 SEQ ID N0:6309 -2.7 -19.2 58.4 -16.5 0 -3.2
TTCTTGGCTTTCTCTTCTGC
559 SEQ ID N0:6310 -2.7 -25.4 77.3 -22.7 0 -3.7
TCTCTGGAGGAATGTCTCCA
666 SEQ ID N0:6311 -2.7 -25.1 73.7 -19.3 -3.1 -8.2
AGTTAAAATATACAAGGCAG
788 SEQ ID N0:6312 -2.7 -16.2 52 -13.5 0 -4
GTGCTCGGAGAACTCTGAAT
1122 SEQ ID N0:6313 -2.7 -23.1 66.9 -19.7 -0.4 -8.2
TTAAACCTGGAATGACTGAA
1152 SEQ ID N0:6314 -2.7 -18.2 55 -15.5 0 -4.2
TCAGGATCATCACATCAGAA
1212 SEQ ID N0:6315 -2.7 -21 63.6 -17.8 -0.1 -5.3
GTGCTCATTGTTACATTAAC
1387 SEQ ID N0:6316 -2.7 -20.3 62.6 -l7 -0.3 -4.2
GGGTCTTTTTGCCCATCCAA
1453 SEQ ID N0:6317 -2.7 -28.2 77,7 -24 -1.4 -5.4
GAAAATGACCAGGACAAAAA
1679 SEQ ID N0:6318 -2.7 -15.9 49.7 -13.2 0 -4
ATCAAATTCACCAAATAAAA
1708 SEQ ID N0:6319 -2.7 -14 46.6 -11.3 0 -3.1
AATOTATACCAGCATGGCGG
2650 SEQ ID N0:6320 -2.7 -24.4 68.2 -19.7 -2 -7.4
305
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ACTGAATTGCTCAGTCATGG
2819 SEQ ID N0:6321 -2.7 -22.4 66.9 -17.2 -2.5 -10.5
CACAGCACGCGGAACACAAT
3274 SEQ ID N0:6322 -2.7 -23.9 64.7 -20.7 0 -7.9
ACTGCAATCTGCAGATTATT
3475 SEQ ID N0:6323 -2.7 -21.2 63.6 -14.1 -4.4 -13.8
AACAAGCTTCCGGTTTAAAG
3957 SEQ ID N0:6324 -2.7 -20.4 59.7 -17.7 0 -6.6
ATTAGTGAAATATGTTTGAA
4262 SEQ ID N0:6325 -2.7 -15.2 50.4 -12.5 0 -4.1
AAGATGACAAAGTATAAATA
4804 SEQ TD N0:6326 -2.7 -12.9 45.2 -10.2 0 -2.8
AGTGAAGAATGACCCAAAGA
4829 SEQ TD N0:6327 -2.7 -19.7 58 -17 0 -2.1
GATCCGGGACAAAACTAGGG
5135 SEQ ID N0:6328 -2.7 -22.8 63.7 -20.1 0 -6.8
GAACAGAACAATGAACACTA
5159 SEQ ID N0:6329 -2.7 -16.5 51.9 -13.8 0 -3.1
GGGACATCATCAAAGCAAAG
5406 SEQ TD N0:6330 -2.7 -19.8 58.9 -16.5 -0.3 -4.4
GAATTGTGTCAGGGTCACAG
5646 SEQ ID N0:6331 -2.7 -23.1 69.6 -18.8 -1.6 -5.8
TTTTGCTATGAGAAGAGGAG
5936 SEQ ID N0:6332 -2.7 -19.6 60.6 -16.9 0 -3.6
AATATCAAGACAGTGGATCC
6008 SEQ ID N0:6333 -2.7 -20.3 61.2 -17.1 0 -7.5
CTTTGTAAAGGCAAATAAAA
6026 SEQ ID N0:6334 -2.7 -14.5 47.9 -10.2 -1.6 -5
CTCTCACACAAAACACGCTT
6043 SEQ ID N0:6335 -2.7 -21.7 62.1 -19 0 -3.3
CATAAGAGACTTTGGAGGGG
6117 SEQ ID N0:6336 -2.7 -21.6 64.2 -18.9 0 -2.9
AACCTTTGCTTTAAAAGATA
6211 SEQ ID N0:6337 -2.7 -17.4 54.1 -13.9 -0.6 -4.8
TTGATATATTTTTTAACCTT
6225 SEQ ID N0:6338 -2.7 -16.8 54 -14.1 0 -4.3
CTTCATAGGCTGTAAACAAT
6504 SEQ ID N0:6339 -2.7 -19.4 59 -16.7 0 -3.7
AACAGTCAGTTTGGCATGGA
6560 SEQ ID N0:6340 -2.7 -23.4 69.3 -20 -0.5 -5.5
TTCTATCACCAATATGTGAC
7626 SEQ ID N0:6341 -2.7 -20.1 61.2 -16.4 -0.9 -6
CTCATGTTGAATTAAAAGTG
7718 SEQ ID N0:6342 -2.7 -16.1 52 -13.4 0 -4.7
AAATGCTGACAAATAAAGTT
7868 SEQ TD N0:6343 -2.7 -15 48.9 -12.3 0 -3.6
AAAAGAACAAAGTCCATGTT
8253 SEQ ID N0:6344 -2.7 -16.9 52.7 -13.5 -0.4 -4.3
ATTCCCTGCATGCAGTTCTT
8394 SEQ ID N0:6345 -2.7 -27.1 77.5 -21.6 0.3 -13.8
TAATGACGTAGCTCACCATT
8430 SEQ ID N0:6346 -2.7 -22.3 64.5 -19.6 0 -4.8
CAATAAAAAATGAAATTTAT
8463 SEQ ID N0:6347 -2.7 -9.3 38.3 -5.3 -1.2 -5.2
GTAACAAAGAATGTAACATT
8854 SEQ ID N0:6348 -2.7 -14.8 48.9 -11.2 -0.8 -7.2
GAGTTTTCCACTGAGAATAA
8993 SEQ TD N0:6349 -2.7 -19.8 60.3 -16.5 -0.3 -3.3
306
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CAGAGCCTTATGAATTACAG
196 SEQ ID N0:6350 -2.6 -20.4 61.2 -17.8 0 -3.2
CTACTATGAATCCTTGACAG
285 SEQ ID N0:6351 -2.6 -20.2 60.9 -17.6 0 -2.4
TCGATAGCAGCAAGAGATTC
529 SEQ ID N0:6352 -2.6 -21.5 64.2 -18.9 0 -5.4
TCACGAAGAAACGTAAAATC
1015 SEQ ID N0:6353 -2.6 -15.4 49.1 -11.9 -0.8 -5.3
TGAATGTTCTCAACGCTGAG
1107 SEQ ID N0:6354 -2.6 -21.2 62.6 -17 -1.6 -6
TGAGCCCAAGAAAATGACCA
1688 SEQ TD N0:6355 -2.6 -22.4 62 -19.8 0 -3.2
TGAAATCTCTTGAAGCAGCT
1869 SEQ ID N0:6356 -2.6 -21 62.8 -18.4 0 -6.1
AACAGCTCTCCTAACCCACC
1897 SEQ ID N0:6357 -2.6 -27.6 74.4 -25 0 -4.4
TCCAGTAGGTGACGTTAGAG
2456 SEQ ID N0:6358 -2.6 -23.6 70.1 -20.4 -0.3 -7
TCATTGATCTTGCAGACACA
3202 SEQ ID N0:6359 -2.6 -22.1 66.1 -19.5 0 -5.2
TACTGCAATCTGCAGATTAT
3476 SEQ ID N0:6360 -2.6 -20.8 62.7 -13.8 -4.4 -Z4
CTTTTGCATTCTTCCTACTG
3491 SEQ ID N0:6361 -2.6 -23.3 69.2 -20.7 0 -5.1
GGGGTAGAACAACATCAACT
3900 SEQ ID N0:6362 -2.6 -21 61.9 -18.4 0 -2.9
ATAGGTAAAGACTTTGTCAG
4199 SEQ ID N0:6363 -2.6 -18.6 58.7 -14.7 -1.2 -5.2
ACCCATTTGAGAAGCATTTC
4231 SEQ ID N0:6364 -2.6 -22.7 66 -19.6 -0.2 -4.1
ACAAGAGCATTCACAACCAC
4438 SEQ TD N0:6365 -2.6 -21.8 63.2 -18.6 -0.3 -4.1
TTAACATCACTAATGTCAAA
4588 SEQ ID N0:6366 -2.6 -16.1 51.8 -11.9 -1.5 -4.9
CTGTTCCTCTGTCATAAAGA
4919 SEQ ID N0:6367 -2.6 -22 66.1 -19.4 0 -2.7
TGTTCCAGCCTATAGTGAAG
5223 SEQ ID N0:6368 -2.6 -23.6 69.3 -21 0 -5.1
AAGTCATCCTCACTCAGGGG
5821 SEQ ID N0:6369 -2.6 -25.8 75.1 -22.3 -0.8 -3.5
AACCTCATAGAACATCTCAA
5840 SEQ ID N0:6370 -2.6 -19.7 59.3 -17.1 0 -2.8
TGCAAAATCAGAGAGTTTAG
5903 SEQ ID N0:6371 -2.6 -17.8 56.1 -14.7 -0.1 -4.7
TCCGGTCACCACTGACCATG
5991 SEQ ID N0:6372 -2.6 -28.2 75.6 -21.2 -4.4 -9.6
AATAAAATATCAAGACAGTG
6013 SEQ ID N0:6373 -2.6 -13.7 46.8 -11.1 0 -4.1
GAAATTACGCTGAATGATAG
6185 SEQ ID N0:6374 -2.6 -16.9 52.7 -14.3 0 -3.3
CTCTGGCAAAACACCTTTGT
6967 SEQ ID N0:6375 -2.6 -23.2 66.1 -19.2 -1.3 -6.6
TGGTTTTGAGCAAAAATTTT
6991 SEQ ID N0:6376 -2.6 -17.3 54.3 -13.8 -0.8 -8.1
AAACTGTAGCCATTACAATT
7018 SEQ ID N0:6377 -2.6 -19.2 57.9 -15.6 -0.9 -3.9
GAAACAAACATAACAGACTA
7082 SEQ ID N0:6378 -2.6 -14.9 48.7 -12.3 0 -2
307
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTGCACTTGCTGAAACAGAA
7168 SEQ ID N0:6379 -2.6 -20.5 60.5 -17.2 -0.5 -6.5
ATTCTATCACCAATATGTGA
7627 SEQ Ib NO:6380 -2.6 -19.9 60.6 -16 -1.2 -6.2
CCAGTGTGTTTCCTTGAAAT
7759 SEQ TD N0:6381 -2.6 -23.1 67.3 -19.7 -0.6 -4.7
TGTACAAAATGCTGACAAAT
7874 SEQ ID N0:6382 -2.6 -16.5 51.8 -13.9 0 -5.9
AAAAAAAAACATCTATGAAT
8154 SEQ ID NO:6383 -2.6 -10.2 39.9 -7.6 0 -3.8
ACGTAAATACTACAAAAGTT
8178 SEQ ID NO:6384 -2.6 -15.1 49.2 -11.8 -0.4 -4.8
CTGCATACGTAAATACTACA
8184 SEQ ID N0:6385 -2.6 -19 57.2 -15.7 -0.4 -6.1
GGTAATTGCACAACTTTGCC
82$9 SEQ ID N0:6386 -2.6 -23.3 66.9 -19.7 -0.9 -5.3
GGTTTGTGCP~AAAAACAAAA
8324 SEQ ID N0:6387 -2.6 -15.6 49.6 -11 -2 -10
GCTTATAGCCAAGGGAGTTA
8773 SEQ ID N0:6388 -2.6 -24 70.3 -20.7 -0.5 -4.2
AGTAACAAAGAATGTAACAT
8855 SEQ ID NO:6389 -2.6 -14.7 48.7 -11.2 -0.8 -6.1
AATTACAGCATAACAAAGCC
184 SEQ ID N0:6390 -2.5 -18.8 56.4 -15.8 -0.2 -4.1
TAGTCACAGCACCTTTTTCC
396 SEQ ID N0:6391 -2.5 -25.3 73.9 -22.8 0 -4.1
ATACGAATTACCTTAGATAG
413 SEQ ID N0:6392 -2.5 -17.6 54.8 -15.1 0 -3.5
CAAGAGATTCTCTAGTAAAA
519 SEQ ID N0:6393 -2.5 -16.4 53.1 -12.6 -1.2 -9.3
ACAGAACACAGTCAGGATCA
1223 SEQ ID N0:6394 -2.5 -2I.8 65.3 -19.3 0 -5.3
CATCTCCAATGTAATCCTTC
1416 SEQ TD N0:6395 -2.5 -22.4 65.9 -19.9 0 -2.4
AGCTGTCTCTCTCTCCTTTG
2019 SEQ ID N0:6396 -2.5 -26.6 80.6 -24.1 0 -4.3
TCCATGGAGAAAAGGAAGCT
2077 SEQ ID N0:6397 -2.5 -21.2 61.5 -17.8 0 -9.5
ATCTTGAGAACCATTTCTGC
2884 SEQ ID N0:6398 -2.5 -22.1 65.8 -18.2 -1.3 -5.5
CGACCTCCATACAGTCCCAC
3315 SEQ ID N0:6399 -2.S -28.7 76.6 -25.7 -0.1 -3.4
GCTGTTCAATGTATATATCT "
4149 SEQ ID N0:6400 -2.5 -20 62.3 -17.5 0 -3.9
ATTTGATGGCACCGAGTTCT
4356 SEQ ID N0:6401 -2.5 -24.7 70.5 -22.2 0 -4
CTGACAGTCACTCAAATTGT
4607 SEQ ID NO:6402 -2.5 -20.8 62.9 -18.3 0 -7.1
GATGATAAAGATGACAAAGT
4811 SEQ ID N0:6403 -2.5 -15.4 50.1 -12.9 0 -2.9
CGGGACAAAACTAGGGTCAT
5131 SEQ ID N0:6404 -2.5 -22.1 63.1 -18.3 -1.2 -S
CGCAGGAAGGGACATCATCA
5414 SEQ ID N0:6405 -2.5 -24.5 69 -21.4 -0.3 -3.9
AGTAGCAACACTGAAGTTCT
5786 SEQ ID N0:6406 -2.5 -21.2 64.5 -18 -0.5 -6.8
GATCAAACTTTTCCCAAACC
5856 SEQ ID N0:6407 -2.5 -21.6 61.5 -19.1 0 -4.7
308
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTGCTATGAGAAGAGGAGGA
5934 SEQ ID N0:6408 -2.5 -21.2 63.9 -18.7 0 -3.6
TAAGCTGGACTTTGTTGGGT
5955 SEQ ID N0:6409 -2.5 -23.7 70.2 -20.6 -0.3 -5.1
ACCTTTGCTTTAAAAGATAA
6210 5EQ ID N0:6410 -2.5 -17.4 54.1 -14.1 -0.6 -4.8
TGATATATTTTTTAACCTTT
6224 SEQ ID N0:6411 -2.5 -16.8 54 -14.3 0 -4.3
GTTACTTGATATATTTTTTA
6230 SEQ ID N0:6412 -2.5 -16.4 54.3 -13.9 0 -4.3
TCACAAAGATAATTCTTTGT
6481 SEQ ID N0:6413 -2.5 -17 54.4 -9.8 -4.7 -11
TTCATAGGCTGTAAACAATT
6503 SEQ ID N0:6414 -2.5 -18.6 57.4 -16.1 0 -3.7
AAACAGTCAGTTTGGCATGG
6561 SEQ TD N0:6415 -2.5 -22.1 65.6 -18.4 -1.1 -7.2
CGTAAACCTCATTTACAAAA
6904 SEQ ID N0:6416 -2.5 -17.2 52.6 -12 -2.7 -6.1
TTTGTCTGATCATTTGAGAG
6952 SEQ ID N0:6417 -2.5 -19.8 62.3 -17.3 0 -6.2
ATAAAAATAATCCTTTAAAT
7140 SEQ ID N0:6418 -2.5 -11.7 42.7 -9.2 0 -4.3
TGCATAAAAATAATCCTTTA
7143 SEQ ID N0:6419 -2.5 '15.6 50.2 -13.1 0 -4.7
AAAGGTGTTTGTAAATAGCT
7691 SEQ ID N0:6420 -2.5 -18.3 57.1 -15.8 0 -4.7
ACAAGTTTTAGACATATTTT
7819 SEQ ID N0:6421 -2.5 -16.9 54.8 -13.7 -0.4 -2.9
TGATTATATTTTTACATTAT
7849 SEQ ID N0:6422 -2.5 -14.9 50.3 -12.4 0 -2
AAAGTTGATTATATTTTTAC
7854 SEQ ID N0:6423 -2.5 -14.3 49 -11.8 0 -2.6
GACCAATGTATCTCCTATTG
8077 SEQ ID N0:6424 -2.5 -22.1 65.1 -19.1 -0.1 -3.4
ATTAAAAAAATAAGACTAGT
8204 SEQ ID N0:6425 -2.5 -11.2 41.9 -8.7 0 -6.2
TGCAGCAGGAATTAAAAAAA
8214 SEQ ID N0:6426 -2.5 -15.7 49.8 -13.2 0 -6
AATTCCCTGCATGCAGTTCT
8395 SEQ ID N0:6427 -2.5 -26.3 74.6 -20.7 -0.2 -14.3
CTACTATTATTATCAAACCT
8723 5EQ ID N0:6428 -2.5 -17.8 55.6 -15.3 0 -1.3
CTTGATGTGGCTTGGCTTCA
245 SEQ ID N0:6429 -2.4 -25.9 75.3 -22.8 -0.4 -6
ACCTTGATGTGGCTTGGCTT
247 SEQ ID N0:6430 -2.4 -27 76.7 -23.9 -0.4 -3.8
AATGTGTACTCTACATTCTT
934 SEQ ID N0:6431 -2.4 -19.9 62.2 -16.1 -1.3 -7.4
GTGAATGTGTACTCTACATT
937 SEQ ID N0:6432 -2.4 -20.3 62.8 -16.2 -1.7 -8.2
CTTGCCAAGATTTTTATAAG
979 SEQ ID N0:6433 -2.4 -18.5 57 -16.1 0 -4.1
CATTGTTACATTAACAAATG
1382 SEQ ID N0:6434 -2.4 -15.3 50 -10.1 -2.8 -8.5
AATGTGCTCATTGTTACATT
1390 SEQ ID N0:6435 -2.4 -20.4 62.5 -16.8 -1.1 -3.1
ATGTAATCCTTCCAGTTAAA
1408 5EQ ID N0:6436 -2.4 -20.3 60.9 -179 0 -2.8
309
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Tnter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AATGTAATCCTTCCAGTTAA
1409 SEQ ID N0:6437 -2.4 -20.3 60.9 -17.9 0 -2.6
CCATAGTTGGGGTTTCGACC
1537 SEQ ID N0:6438 -2.4 -26.7 74.7 -21.4 -2.9 -7
AATCTCTTGAAGCAGCTGAT
1866 SEQ ID N0:6439 -2.4 -21.7 64.9 -18.6 0 -8.7
CTTTCCAACAGCTCTCCTAA
1903 SEQ ID N0:6440 -2.4 -24.7 70.5 -22.3 0 -4.4
CAACACACTACTGAATTGCT
2828 SEQ ID N0:6441 -2.4 -20.4 60.4 -18 0 -3.6
GGCCAGGATTTTGCCAACTT
3049 SEQ ID N0:6442 -2.4 -26.8 73.9 -22.8 -1.5 -7.4
CATCATTGATCTTGCAGACA
3204 SEQ ID N0:6443 -2.4 -21.9 65.5 -19.5 0 -5.6
GCCACCGTGGGAGCGTACAG
3225 SEQ ID N0:6444 -2.4 -30.1 79.4 -26.6 -1 -9.1
GGAAGAAGTCGTTCATGTGC
3243 SEQ ID N0:6445 -2.4 -22.8 67.4 -19.1 -1.2 -4.9
GACCAACATGAAAACAATAA
3353 SEQ ID N0:6446 -2.4 -15.4 48.9 -13 0 -5.2
CCCTTTTGCATTCTTCCTAC
3493 SEQ ID N0:6447 -2.4 -26.4 74.8 -24 0 -5.1
AATGACATATAATCATTTTC
3730 SEQ ID N0:6448 -2.4 -15.3 50.7 -11.5 -1.3 -7.1
TCCTTCAGATGAGCTGGTTG
3875 SEQ ID N0:6449 -2.4 -24.9 73.4 -21.8 -0.5 -5
CCAGTTGTGCTCAACAATAC
4073 SEQ ID N0:6450 -2.4 -22.4 65.6 -16.7 -3.3 -6.6
ACTTTGTCAGCATATTCTAG
4189 SEQ ID N0:6451 -2.4 -20.9 65.1 -18.5 0 -4.1
TAAAGACTTTGTCAGCATAT
4194 SEQ ID N0:6452 -2.4 -18.7 58.3 -15 -1.2 -5.3
TTGGCTACCAGGCTAACCAA
4321 SEQ ID N0:6453 -2.4 -25.7 70.7 -21.7 -1.5 -7.2
CAAATTGTTAACATCACTAA
4595 SEQ ID N0:6454 -2.4 -15.8 51 -12.9 0 -8
TCAAATTGTTAACATCACTA
4596 SEQ ID N0:6455 -2.4 -16.9 53.9 -14 0 -8.3
AATGACCCAAAGATGATAAA
4822 SEQ ID N0:6456 -2.4 -16.9 51.8 -14.5 0 -2.1
TTGATCCGGGACAAAACTAG
5137 5EQ TD N0:6457 -2.4 -20.5 59.4 -17.6 0 -7.9
CAGAAACATACCTACAATGG
5270 SEQ ID N0:6458 -2.4 -18.7 56 -15.8 -0.1 -3.3
TCCCCTTTGCTCCTTTGATC
5373 SEQ ID N0:6459 -2.4 -28.7 79.8 -26.3 0 -3.9
CAACCAGGAAGGATATGATG
5736 SEQ TD N0:6460 -2.4 -20.1 59.3 -16.9 -0.6 -4
AGAACATCTCAAAGTCATCC
5832 SEQ ID N0:6461 -2.4 -20.5 61.9 -18.1 0 -2.8
GGCAATAAGCTGGACTTTGT
5960 SEQ TD N0:6462 -2.4 -23 67.1 -19.2 -1.3 -5.9
CTCCACTCTCACACAAAACA
6048 SEQ ID N0:6463 -2.4 -22.1 63.6 -19.7 0 0
ATTACGCTGAATGATAGCGG
6182 SEQ ID N0:6464 -2.4 -21.5 61.7 -15.5 -3.6 -8.9
TAACATCTGAAATTACGCTG
6193 SEQ ID N0:6465 -2.4 -17.9 54.7 -15.5 0 -3.3
310
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol koal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGTTACTTGATATATTTTTT
6231 SEQ ID N0:6466 -2.4 -16.7 55 -14.3 0 -4.3
AACAATTGATCACAAAGATA
6490 SEQ ID N0:6467 -2.4 -15.1 49.4 -l2 -0.5 -7.3
ACCTTCATAGGCTGTAAACA
6506 SEQ ID N0:6468 -2.4 -22.3 65.2 -18.7 -1.1 -5.4
GCACAACTATCCCTATAGTC
6730 SEQ ID N0:6469 -2.4 -23.8 69.3 -19.8 -1.5 -7.2
GATGCAAGGACTGTACTAAA
6780 SEQ ID N0:6470 -2.4 -19.6 59.1 -17.2 0 -5.6
CAGACTAAAATACTTTCAAA
7069 SEQ ID N0:6471 -2.4 -14.7 48.7 -12.3 0 -2.5
ACAGACTAAAATACTTTCAA
7070 SEQ ID N0:6472 -2.4 -15.6 50.7 -13.2 0 -2.5
CAGCAGAAAGTGGAACAACT
7298 SEQ ID N0:6473 -2.4 -20 59.3 -16.6 -0.9 -5.6
TGTTTGTAAATAGCTTCAAA
7686 SEQ ID N0:6474 -2.4 -17.1 54.4 -14 -0.5 -4.9
AAAATAATTTTCTTATGTAC
7889 SEQ ID N0:6475 -2.4 -13.4 46.7 -11 0 -4.1
CTACAAAAGTTGAATAAAAA
8169 SEQ ID N0:6476 -2.4 -11.5 42.3 -8.4 -0.4 -3.4
GTAAATACTACAAAAGTTGA
8176 SEQ ID N0:6477 -2.4 -14.7 48.9 -11.6 -0.4 -4.2
TCTGCATACGTAAATACTAC
8185 SEQ ID N0:6478 -2.4 -18.7 57.3 -16.3 0 -6.6
ACTGCCAACAGCAAAAAACA
8518 SEQ ID N0:6479 -2.4 -19.7 56.8 -15.7 -1.5 -4.5
CTATTATTATCAAACCTGAA
8720 SEQ ID N0:6480 -2.4 -16.9 53.2 -13.8 -0.4 -2.9
ACTATTATTATCAAACCTGA
8721 SEQ ID N0:6481 -2.4 -17.8 55.5 -14.9 -0.2 -2.7
AGGGAGTTAATTGAAATTGA
8762 SEQ ID N0:6482 -2.4 -17.3 54.6 -14.9 0 -3.9
GCATTTAAGTAACAAAGAAT
8862 SEQ ID N0:6483 -2.4 -15.3 49.9 -12.9 0 -3.4
TGCATTACAACTGGAGTTTT
9006 SEQ ID N0:6484 -2.4 -20.9 63.1 -18.5 0 -5.2
TGTCTTTAAAAATATGCATT
9020 SEQ ID N0:6485 -2.4 -15.9 51.5 -13.5 0 -6.8
ACAGAGCCTTATGAATTACA
197 SEQ ID N0:6486 -2.3 -20.6 61.5 -18.3 0 -3.2
CCTTGATGTGGCTTGGCTTC
246 SEQ ID N0:6487 -2.3 -27.2 77.9 -24.2 -0.4 -3.8
TTTCCCAGTAAGCCACTCTA
302 SEQ ID N0:6488 -2.3 -26.1 74 -23.8 0 -3.4
AGAAGAGATTCTTTGCTCCT
321 SEQ ID N0:6489 -2.3 -22.7 68 -18.3 -2.1 -8.1
GCTCTGACACCATCTCTGGA
67g SEQ ID N0:6490 -2.3 -26.8 76.8 -22.9 -1.5 -5.5
TTAAAATATACAAGGCAGAG
7g6 SEQ ID N0:6491 -2.3 -15.6 50.6 -13.3 0 -4
GGAGTTAAAATATACAAGGC
790 SEQ ID N0:6492 -2.3 -17.3 54.3 -15 0 -2.8
CAATGTAATCCTTCCAGTTA
1410 SEQ ID N0:6493 -2.3 -21.7 64.2 -19.4 0 -1.9
TGATTCTGCTCCTCATAGGC
1747 SEQ TD N0:6494 -2.3 -25.8 75.6 -22.8 -0.5 -5
311
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Tnter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAGTCATTTTCAGATCCAAC
2230 SEQ ID N0:6495 -2.3 -20.2 61.7 -17.9 0 -4.5
CGTTTCAGTGGTGGTGCCCT
2489 SEQ ID N0:6496 -2.3 -30 83.3 -27.1 -0.3 -5.1
CAAAGATATTCCAGCCTTCT
2934 SEQ ID N0:6497 -2.3 -22.9 66.1 -19.9 -0.4 -3.8
GGGCCAGGATTTTGCCAACT
3050 SEQ ID N0:6498 -2.3 -27.9 76.1 -23.3 -2.3 -7.9
CAGTCATCATTGATCTTGCA
3208 SEQ ID N0:6499 -2.3 -22.7 68.4 -19.7 -0.5 -5.8
CGTACAGTCATCATTGATCT
3212 SEQ ID N0:6500 -2.3 -22 66.1 -19 -0.5 -5,6
TGGGAGCGTACAGTCATCAT
3218 SEQ ID N0:6501 -2.3 -24.8 72.2 -22.5 0 -4.8
CATGACCAACATGAAAACAA
3356 SEQ ID N0:6502 -2.3 -17.1 52 -13 -1.8 -5.2
ATAAGGCCAGAAAGAGGTTC
3399 5EQ ID N0:6503 -2.3 -21.4 63.5 -18.6 -0.1 -7.8
ATTTCATTGTCATCATCAGT
3454 SEQ ID N0:6504 -2.3 -21.1 66 -18.8 0 -2.4
CTAAAAAAGGCTTTTTGGAA
3547 SEQ ID N0:6505 -2.3 -16.5 51.9 -12.7 -1.4 -7.7
ACTCTTCAGTATTTAAGTTT
3810 SEQ ID N0:6506 -2.3 -19.1 61.3 -16.8 0 -2.7
TTCCGGTTTAAAGTCTTCTT
3950 SEQ ID N0:6507 -2.3 -22.2 66.1 -19.3 -0.3 -7.2
ACTGAGAAGGATCATGAACA
4109 SEQ ID N0:6508 -2.3 -19.3 58.6 -16.1 -0.8 -8.2
TGAATATATAGGTAAAGACT
4206 SEQ ID N0:6509 -2.3 -15.4 50.7 -12.6 -0.1 -4.3
CGTAATGATTTGATGGCACC
4363 SEQ ID N0:6510 -2.3 -22.3 63.8 -20 0 -4
AGCAGTGCAAGATAGCCAGC
4684 SEQ ID N0:6511 -2.3 -26.1 74.9 -22.8 -0.7 -9.6
AATCAAAGACCATTCCTTGG
5016 SEQ ID N0:6512 -2.3 -21.2 61.5 -17.7 -1.1 -3.9
GATATCAAAGACTTGTCTGG
5042 SEQ TD N0:6513 -2.3 -19.5 60.1 -15.7 -1.4 -8.9
GGTTGATCCGGGACAAAACT
5139 SEQ ID N0:6514 -2.3 -23.2 64.8 -20.2 -0.3 -8.7
TGTAACTGACAAAAAAGAAA
5715 SEQ ID N0:6515 -2.3 -12.5 44 -9.7 -0.2 -2.9
TTGTAAAGGCAAATAAAATA
6024 SEQ ID N0:6516 -2.3 -13.2 45.4 -10.2 -0.4 -4.8
GTATTTGTTAAAACAGTCAG
6571 SEQ ID N0:6517 -2.3 -17.2 55.3 -14.9 0 -5.6
CAGCAACCTCTTGTCAACGT
6662 SEQ ID N0:6518 -2.3 -24.8 69.8 -21.9 -0.3 -5.5
GTTTTGAGCAAAAATTTTAT
6989 SEQ ID N0:6519 -2.3 -15.8 51.3 -12.6 -0.8 -8.1
GAAGTAACTGAAACTGTAGC
7028 SEQ ID N0:6520 -2.3 -18.2 56.6 -15.9 0 -3.3
AAAATGGAAGTAACTGAAAC
7034 SEQ ID N0:6521 -2.3 -13.7 46.4 -11.4 0 -3
TAGAAAATGGAAGTAACTGA
7037 SEQ ID N0:6522 -2.3 -15.2 49.7 -12.9 0 -3
TAAAATACTTTCAAAATTAA
7064 SEQ ID N0:6523 -2.3 -10.7 41 -8.4 0 -3.2
312
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkoal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATAGAAACAAACATAACAGA
7085 SEQ ID N0:6524 -2.3 -13.8 46.6 -11.5 0 -1
TAAAATTTGCACTTGCTGAA
7174 SEQ ID N0:6525 -2.3 -18.1 55.4 -15.2 -0.3 -6.5
CTAAAGCAATACTTTAGATA
7275 SEQ ID N0:6526 -2.3 -16 51.9 -10.6 -3.1 -7.9
GAGAGCAGAAGATGGCAAAG
7326 SEQ ID N0:6527 -2.3 -20.5 61 -17.3 -0.8 -4.1
GAATF~1AAP~AACATCTAT
8158 SEQ ID N0:6528 -2.3 -9.9 39.4 -7.6 0 -1.8
TGAATF~AACATCTA
8159 SEQ ID N0:6529 -2.3 -9.9 39.4 -7.6 0 -2.5
AAATACTACAAAAGTTGAAT
8174 SEQ ID N0:6530 -2.3 -13.1 45.4 -10.1 -0.4 -4.2
TATAGCCAAGGGAGTTAATT
8770 SEQ ID N0:6531 -2.3 -20.6 61.8 -18.3 0 -3.7
ACTATATCATTAATACCTTA
8906 SEQ ID N0:6532 -2.3 -17.3 55 -15 0 -4.2
AACTATATCATTAATACCTT
8907 SEQ ID N0:6533 -2.3 -16.9 53.7 -14.6 0 -4.2
GTTCTTGAAAAAAAAGTTAA
8941 SEQ ID N0:6534 -2.3 -12.7 44.8 -10.4 0 -3.5
ATGGGAGAATTATGAAATAC
9056 SEQ ID N0:6535 -2.3 -15.8 51.1 -13.5 0 -3.2
ACAGAGGTTTACAAATTAGT
86 SEQ ID N0:6536 -2.2 -18.3 57.6 -16.1 0 -3.2
TATCCCTAGAAGAGATTCTT
328 SEQ ID N0:6537 -2.2 -21.3 64.1 -16.8 -2.3 -5.3
AAATCTTCTAAGCAAAACCC
1000 SEQ ID N0:6538 -2.2 -18.9 56.2 -16.7 0 -4.1
TAAAATCTTCTAAGCAAAAC
1002 5EQ ID N0:6539 -2.2 -13.9 47.1 -11.7 0 -4.1
AAACCTGGAATGACTGAAAT
1150 SEQ ID N0:6540 -2.2 -17.7 53.6 -15.5 0 -5.1
ACTGGATCAGGGCCCCCACA
1179 SEQ ID N0:6541 -2.2 -31.8 83.1 -28.3 -0.7 -10.4
AATCCTTCCAGTTAAATGTG
1404 SEQ ID N0:6542 -2.2 -20.6 61.4 -18.4 0 -5.6
GTAATCCTTCCAGTTAAATG
1406 SEQ ID N0:6543 -2.2 -20.3 60.9 -18.1 0 -5.2
GAGCCCAAGAAAATGACCAG
1687 SEQ ID N0:6544 -2.2 -22.4 62.3 -20.2 0 -3.2
CCAGGATCAAATTCACCAAA
1713 SEQ ID N0:6545 -2.2 -20.9 59.9 -18.1 -0.3 -5.3
GCATCTGCTGAAATTCGGCC
1797 SEQ ID N0:6546 -2.2 -26 71.6 -21.8 -2 -10.2
ATCCATGGAGAAAAGGAAGC
2078 SEQ ID N0:6547 -2.2 -20.3 59.7 -16.8 -0.4 -10.4
GGTCCACCCACCAAGGAAAC
2431 SEQ ID N0:6548 -2.2 -27.2 72 -24.3 -0.5 -5
TTCCGTTTCAGTGGTGGTGC
2492 SEQ ID N0:6549 -2.2 -27.6 80 -25.4 0 -4.1
CATTGTGTTGGTCAGAATGC
2600 SEQ ID N0:6550 -2.2 -22.5 67.6 -20.3 2.5 -1.2
CAAGTTCTTCCATTGTGTTG
2610 5EQ ID N0:6551 -2.2 -22.4 67.5 -20.2 0 -2.9
TTCTTCAAGTTCTTCCATTG
2615 SEQ ID N0:6552 -2.2 -21.8 66.7 -19.6 0 -2.9
313
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GGACATTTCTGTCTAGATTC
2632 SEQ ID N0:6553 -2.2 -21.5 67 -16.6 -2.7 -6.8
ACAATGCAAATAGTGATGGC
2764 SEQ ID N0:6554 -2.2 -19.8 59.2 -17 -0.3 -5.6
ACAGTCAACACACTACTGAA
2833 SEQ ID N0:6555 -2.2 -20.1 60.5 -16.2 -1.7 -5.6
TTTAGTGTGGGCCAGGATTT
3058 SEQ ID N0:6556 -2.2 -25.2 73.8 -22.5 0 -7.6
ATGCCGACCACAGCAAAAAT
3154 5EQ ID N0:6557 -2.2 -22.7 61.9 -19.4 -1 -4.6
CATTGATCTTGCAGACACAT
3201 SEQ ID N0:6558 -2.2 -21.7 64.5 -19.5 0 -5.2
CGTTCATGTGCCACCGTGGG
3234 SEQ ID N0:6559 -2.2 -29.5 78.3 -26.2 -1 -9.1
AAAGAGGTTCAGAACCACAA
3389 SEQ ID N0:6560 -2.2 -19.8 58.9 -15.6 -1.9 -11.2
CTCTTCAGTATTTAAGTTTT
3809 5EQ ID N0:6561 -2.2 -19 61 -16.8 0 -2.7
GGTAGAACAACATCAACTGT
3898 SEQ ID N0:6562 -2.2 -19.8 59.8 -17.1 -0.2 -3.3
ACACAATGAAAGTCTCAAAC
4092 SEQ ID N0:6563 -2.2 -16.7 52.7 -13.9 -0.3 -3.1
ACACAGTGGTAGAACTTGCC
4546 SEQ ID N0:6564 -2.2 -24 69.8 -21.8 0 -6.2
CCAAGTTTCTTCATTGCATT
4951 SEQ ID N0:6565 -2.2 -22.6 67 -20.4 0 -5.1
AATGAACACTAGGTTGATCC
5150 SEQ ID N0:6566 -2.2 -20.4 61.1 -17.4 -0.6 -6
TCAAAGATGTTCCAGCCTAT
5230 SEQ ID N0:6567 -2.2 -23.1 66.9 -20.9 0 -3.2
CCAGCTTCCTTTTTAACATA
5506 SEQ ID N0:6568 -2.2 -22.8 66.3 -20.6 0 -4.5
TTTGCTATGAGAAGAGGAGG
5935 SEQ ID N0:6569 -2.2 -20.7 62.9 -18.5 0 -3.6
TCTGAAATTACGCTGAATGA
6188 SEQ ID N0:6570 -2.2 -18.5 55.9 -16.3 0 -3.3
CAGAGTTGCAGTGACAGAGA
6627 SEQ ID N0:6571 -2.2 -23 69.3 -20.8 0 -5.5
AGCCATTACAATTCTTTTTC
7011 SEQ ID N0:6572 -2.2 -20.7 63 -18.5 0 -3.2
ATGGAAGTAACTGAAACTGT
7031 SEQ ID N0:6573 -2.2 -17.9 55.5 -15.7 , 0 -3
CTATTCTAAAGCAATACTTT
7280 SEQ ID N0:6574 -2.2 -17.1 54.4 -13.7 -1.1 -4.1
TTTAATTGACATAGACTATC
7355 SEQ ID N0:6575 -2.2 -16.3 53.3 -14.1 0 -3.3
TTTTACATTATTTATATTTA
7840 SEQ ID N0:6576 -2.2 -14.2 49.1 -12 0 -2.2
AATGGTAGAAAATATATTAT
8056 SEQ ID N0:6577 -2.2 -13.1 45.8 -10.9 0 -6.2
ACTACAAAAGTTGAATAAAA
8170 SEQ ID N0:6578 -2.2 -12.4 44 -9.5 -0.4 -4.1
TATTATTATCAAACCTGAAA
8719 SEQ ID N0:6579 -2.2 -15.3 49.8 -12.4 -0.4 -2.9
AAGTAACAAAGAATGTAACA
8856 SEQ ID N0:6580 -2.2 -14 47.2 -11.2 -0.3 -5.2
TCAATAACTATATCATTAAT
8912 SEQ ID N0:6581 -2.2 -14.1 48 -11.9 0 -3.8
314
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGGGTTCTTGAAAAAAAAGT
8944 SEQ ID N0:6582 -2.2 -16 51.2 -13.8 0 -3.5
GGCAGCTGTTCAGCTTTTTT
125 SEQ ID N0:6583 -2.1 -26 77.4 -22 -1.8 -11
CTATGAATCCTTGACAGGTA
282 SEQ ID N0:6584 -2.1 -21.5 64 -18.4 -0.9 -3.4
TACTATGAATCCTTGACAGG
284 SEQ ID N0:6585 -2.1 -20.5 61.5 -17.6 -0.6 -3.1
CTCAAAGGTATAGATTCCAG
956 SEQ ID N0:6586 -2.1 -20.2 61.4 -17.4 -0.4 -3.6
CACGAAGAAACGTAAAATCT
1014 SEQ ID N0:6587 -2.1 -15.9 49.7 -12.9 -0.8 -5.3
TGACACTGAAATCCAGCCAG
1044 SEQ ID N0:6588 -2.1 -23.4 66 -20.8 -0.2 -5.5
GATCAAATTCACCAAATAAA
1709 SEQ TD N0:6589 -2.1 -15.3 49.2 -13.2 0 -4.7
CTTTAGCACCTTTGGAACTC
1944 SEQ ID N0:6590 -2.1 -23.2 68 -21.1 0 -3.3
TTTTCAGATCCAACATCCTT
2224 SEQ ID N0:6591 -2.1 -22.7 66.5 -20.1 -0.1 -4.5
ACGTTAGAGCTGAAGGTCCA
2445 SEQ ID N0:6592 -2.1 -24.7 70.9 -22.6 0 -5.8
GTGACGTTAGAGCTGAAGGT
2448 SEQ ID N0:6593 -2.1 -23.4 69 -21.3 0 -6.6
GGTGGTGCCCTCTGGGGGAA
2480 SEQ ID N0:6594 -2.1 -31.5 85.5 -27.2 -2.2 -8.7
TTCAAGTTCTTCCATTGTGT
2612 SEQ ID N0:6595 -2.1 -22.8 69.3 -20.7 0 -3.1
TCTTCAAGTTCTTCCATTGT
2614 5EQ ID N0:6596 -2.l -22.9 69.8 -20.8 0 -3.1
TATTTAAGACAATGCAAATA
2772 SEQ ID N0:6597 -2.1 -14.5 48.3 -11.8 -0.3 -5.6
TAGTGTGGGCCAGGATTTTG
3056 SEQ ID N0:6598 -2.1 -25.1 73.2 -22.5 0 -7.6
AGCCCCCACAGAATTGCCAA
3095 SEQ ID N0:6599 -2.1 -29.2 75.3 -27.1 0 -3.2
TAGAGCCCCCACAGAATTGC
3098 5EQ ID N0:6600 -2.1 -27.5 74.2 -25.4 0 -3.2
TCATCATTGATCTTGCAGAC
3205 SEQ ID N0:6601 -2.1 -21.6 65.8 -19.5 0 -5.6
TGTGCCACCGTGGGAGCGTA
3228 SEQ ID N0:6602 -2.1 -30.4 80.5 -27.1 -1.1 -9.1
CCAGAAAGAGGTTCAGAACC
3393 SEQ ID N0:6603 -2.1 -22.2 64.2 -18.4 -1.6 -10.7
ATCTTATTTTTCACATAATC
3517 SEQ ID N0:6604 -2.1 -16.9 55.1 -14.8 0 -2.2
ATGGAAACTTTTTAATACAC
3987 SEQ ID N0:6605 -2.1 -15.7 51.1 -13.6 0 -2.5
TACTTACTTGACAGAATGGA
4002 SEQ ID N0:6606 -2.1 -19 58.5 -16.2 -0.4 -3.2
TTAGTGAAATATGTTTGAAA
4261 SEQ ID N0:6607 -2.1 -14.5 48.8 -12.4 0 -4.1
CCAGGCATTAGTGAAATATG
4268 SEQ ID N0:6608 -2.1 -20.3 60.4 -18.2 0 -4
TGAGTAGCCAAGAGCATTGG
4337 SEQ ID N0:6609 -2.1 -23.7 68.9 -19.5 -2.1 -8.2
CTTCAAACCGGGATAAGGCT
4410 SEQ ID N0:6610 -2.1 -23.6 65.5 -21.5 0 -7.1
315
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mot kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTGAATCAACAGCTGCATAC
4740 SEQ ID N0:6611 -2.1 -21.5. 63.8 -18.7 0 -9
AGATGATAAAGATGACAAAG
4812 SEQ ID N0:6612 -2.1 -14.2 47.7 -12.1 0 -2.5
CCAATGAATAGATTCAGAGT
4846 SEQ ID N0:6613 -2.1 -19.2 58.6 -15.9 -1.1 -7.8
GAAGTTATCTATGATGACAC
4865 SEQ ID N0:6614 -2.1 -18.2 57.5 -14.6 -1.4 -5.8
TGATCCGGGACAAAACTAGG
5136 SEQ ID N0:6615 -2.1 -21.6 61.4 -19.5 0 -6.8
CCAGAAACATACCTACAATG
5271 SEQ ID N0:6616 -2.1 -19.5 57.2 -17.4 0 -3
GTTGAACATGTCATCAATTC
5525 SEQ ID N0:6617 -2.l -19.3 60 -15.9 -1 -9.9
TTAAGAATAGGTGCTAGCAA
5611 SEQ ID N0:6618 -2.1 -19.3 59.1 -15.8 0 -10.8
CCCAAACCTCATAGAACATC
5844 SEQ ID N0:6619 -2.1 -22.4 63.2 -20.3 0 -2.5
AGGCAAATAAAATATCAAGA
6018 SEQ ID N0:6620 -2.1 -14.6 48.2 -12.5 0 -4
TAAAGGCAAATAAAATATCA
6021 SEQ TD N0:6621 -2.1 -13 45 -10.9 0 -3.2
GATAACATCTGAAATTACGC
6195 5EQ ID N0:6622 -2.1 -17.6 54.2 -15.5 0 -3.3
TTTGTTTCTTTTTACTTTTG
6466 SEQ ID N0:6623 -2.1 -18.4 59.5 -16.3 0 -2.2
TTGTCTGATCATTTGAGAGA
6951 SEQ 2D N0:6624 -2.1 -20.3 63.3 -18.2 0 -6
CTGGTTTTGAGCAAAAATTT
6992 SEQ ID N0:6625 -2.1 -18.1 55.8 -15.1 -0.8 -8.l
TACTTTCAAAATTAAAGCCA
7059 SEQ ID N0:6626 -2.1 -16.9 52.7 -13.9 -0.7 -5.6
ATAAAATTTGCACTTGCTGA
7175 SEQ ID N0:6627 -2.1 -18.8 57.2 -16.1 -0.3 -6.5
TATATATTTGCCCAAACATG
7414 5EQ ID N0:6628 -2.1 -19.3 57.4 -17.2 0 -5.4
ACTCATGTTGAATTAAAAGT
7719 SEQ ID N0:6629 -2.1 -16.3 52.6 -14.2 0 -4.7
TATTGGAATGGTAGAAAATA
8062 SEQ ID N0:6630 -2.1 -15.2 49.9 -13.1 0 -2.2
TTGGCTCAATAATGACGTAG
8439 SEQ ID N0:6631 -2.1 -19.9 59.6 -17.2 -0.3 -5.3
GTTTTATTAATTATATATAT
8543 SEQ ID N0:6632 -2.1 -13.2 46.8 -11.1 0 -5.4
TTATAGCCAAGGGAGTTAAT
8771 SEQ ID N0:6633 -2.1 -20.6 61.8 -18.5 0 -3.7
AACTGGAGTTTTCCACTGAG
ggg8 SEQ ID N0:6634 -2.1 -22.5 66.7 -18.3 -2.1 -6.3
ATGAAATACATATTTAGATC
9045 SEQ ID N0:6635 -2.1 -14.4 48.8 -11.7 -0.3 -5.2
CAAGATGGTTAGGGTATAAC
157 SEQ ID N0:6636 -2 -19.3 59.5 -16.3 -0.9 -3.8
CCAGTAAGCCACTCTACTAT
2g8 SEQ ID N0:6637 -2 -24.3 70 -22.3 0 -4.7
TTACAATATCCCTAGAAGAG
334 SEQ ID N0:6638 -2 -19.2 58.3 -17.2 0 -3.8
TCCTGGGGGTACCAACAGTG
482 SEQ ID N0:6639 -2 -27.3 76 -22.5 -2.8 -10.6
316
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GCAGCAAGAGATTCTCTAGT
523 SEQ ID N0:6640 -2 -23.1 70.1 -19.8 -1.2 -9.3
CACTGAATCGGAAAATTGCC
762 SEQ ID N0:6641 -2 -20.5 58.7 -18.5 0 -4.3
AGTGAATGTGTACTCTACAT
938 SEQ ID N0:6642 -2 -20.2 62.7 -17.3 -0.8 -5.5
ATAGATTCCAGTGAATGTGT
947 SEQ ID N0:6643 -2 -2l 64 -17.6 -1.3 -4.1
AGGTCCACAAACTCTGTCAC
1078 SEQ ID N0:6644 -2 -23.9 69.9 -21.4 -0.1 -3.6
TGAGAGCAAACACGCTCAGA
1242 SEQ ID N0:6645 -2 -22.6 64.7 -17.3 -3.3 -8.5
ATGAGAGCAAACACGCTCAG
1243 SEQ ID N0:6646 -2 -22 63.5 -16.7 -3.3 -8.5
GTAAAGGGTCTTTTTGCCCA
1458 SEQ ID N0:6647 -2 -25.3 72.1 -21.8 -1.4 -5.3
TGGGGTTTCGACCAGCCTTC
1530 SEQ ID N0:6648 -2 -28.9 79.8 -24.2 -2.7 -7.8
TTGTTGTTTCCTTCAAGGTG
2002 SEQ ID N0:6649 -2 -23 69.5 -20.2 -0.6 -5.2
CCACAGTGCTGTGCATCTTC
2397 SEQ ID N0:6650 -2 -27 78.3 -22.8 -1.7 -12.4
TCTGGTAAGAGCTTAACCTT
2523 SEQ ID N0:6651 -2 -22.3 66.2 -19.2 -1 -8
GAGCGTACAGTCATCATTGA
3215 SEQ ID N0:6652 -2 -23.1 68.6 -20.5 -0.3 -5.5
CACACAGCACGCGGAACACA
3276 5EQ ID N0:6653 -2 -25.5 68.2 -23 0 -7.9
ATGGTCTCTATCCACTCTCC
3295 SEQ ID N0:6654 -2 -26.6 78.3 -23.7 -0.7 -3.9
TCTTCCTACTGCAATCTGCA
3482 SEQ ID N0:6655 -2 -25.1 72.5 -21 -2.1 -7
TCAATTCCCTTTTGCATTCT
3499 SEQ ID N0:6656 -2 -24 69.6 -22 0 -5.l
AGTATTATTGGACATGCAGC
3611 SEQ ID N0:6657 -2 -21.8 65.9 -19.8 0 -5.5
TTTCAAAGTCAGACTCTCCA
3792 SEQ ID N0:6658 -2 -22.3 66.8 -20.3 0 -7.3
TCTAGTTCTGACTCACTGCT
3832 SEQ ID N0:6659 -2 -24.2 73.5 -21.5 -0.4 -4.4
CAACTGTGCTTCCTTCAGAT
3885 SEQ ID N0:6660 -2 -24.2 70.5 -21.3 -0.7 -4
TAGTGAAATATGTTTGAAAT
4260 SEQ ID N0:6661 -2 -14.4 48.5 -12.4 0 -3.5
CATTGGCTACCAGGCTAACC
4323 SEQ ID N0:6662 -2 -26.4 72.9 -23.1 -1.2 -7.2
ATGCCTTCAAACCGGGATAA
4414 SEQ ID N0:6663 -2 -23.5 64.5 -21.5 0 -7.l
AAAGTATAAATACATGTACA
4796 SEQ ID N0:6664 -2 -14.2 47.9 -11.5 -0.5 -8.2
GCTGATATCAAAGACTTGTC
5045 SEQ ID N0:6665 -2 -20.1 61.7 -17.4 -0.3 -8.1
AGGGGACACAGAATACTTTT
5303 SEQ ID N0:6666 -2 -21 62.9 -19 0 -1.9
CTCGGAACAAGGTAGGGGAC
5316 SEQ ID N0:6667 -2 -23.9 67.9 -21.9 0 -3
AACATAGGCAAAGTTGGACA
5492 SEQ ID N0:6668 -2 -20.2 60.1 -18.2 0 -4.2
317
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATCCATCCCAGCCAGCAGAG
5592 SEQ ID N0:6669 -2 -29.8 80.8 -27.8 0 -4.6
TAAGAATAGGTGCTAGCAAT
5610 SEQ ID N0:6670 -2 -19.2 58.7 -15.8 0 -10.8
AAAAE~1GAAAATCCCAACAG
5705 SEQ ID N0:6671 -2 -14.3 46.6 -12.3 0 -2.2
ACATCTCAAAGTCATCCTCA
5829 SEQ ID N0:6672 -2 -22.6 67.2 -20.6 0 -2.5
AACACGCTTTGTAAAGGCAA
6032 SEQ ID NO:6673 -2 -20.6 59.7 -17 -l.5 -5.9
CTTTGGAGGGGTTTGATGCC
6108 SEQ TD N0:6674 -2 -26.3 75.3 -24.3 0 -3
CACAAAGATAATTCTTTGTT
6480 SEQ ID N0:6675 -2 -16.7 53.5 -9.8 -4.9 -11.3
GAAACTTAGAATAAAATTTG
7185 SEQ ID N0:6676 -2 -11.8 43 -9.8 0 -5.2
TGAAACTTAGAATAAAATTT
7186 SEQ ID N0:6677 -2 -11.8 43 -9.8 0 -4.9
CTTTAAACTATGTTTAATGA
7526 SEQ ID N0:6678 -2 -15.2 50.3 -11.1 -2.1 -8
ATATGAAGAATAGGTTTTGT
7792 SEQ ID N0:6679 -2 -17.1 55 -15.1 0 -l.8
TGCACAACTTTGCCACTTTG
8283 SEQ ID N0:6680 -2 -23.8 67.8 -20.8 -0.9 -4.7
AATGACGTAGCTCACCATTC
8429 SEQ ID N0:6681 -2 -23 66.5 -21 0 -5.3
AACTGCCAACAGCAAAAAAC
8519 SEQ ID NO:6682 -2 -18.3 54.1 -14.7 -1.5 -4.5
TGGAGTTTTCCACTGAGAAT
8995 SEQ ID N0:6683 -2 -22 65.5 -18 -2 -6.2
AGAATTATGAAATACATATT
9051 SEQ ID N0:6684 -2 -13.3 46.1 -10.4 -0.7 -4.6
CAAAGAGACCTTTCCAGAAT
28 SEQ ID N0:6685 -1.9 -20.8 60.8 -17.8 -1 -3.9
GACCACAGAGGTTTACAAAT
90 SEQ ID N0:6686 -1.9 -20.8 61.5 -17.3 -1.5 -7.1
TAACAAAGCCCAGCATCCAA
174 SEQ ID N0:6687 -1.9 -23.9 65.3 -21.1 -0.7 -4.1
TTTCTTGCTCCATAATCTCT
223 SEQ ID N0:6688 -1.9 -23 68.9 -21.1 0 -3.6
CAGCAAGAGATTCTCTAGTA
522 SEQ ID N0:6689 -1.9 -21 64.9 -18.2 -0.7 -8.8
TGTACCAAAATCTTGATAGC
832 SEQ ID N0:6690 -1.9 -19.2 58.3 -17.3 0.2 -4.8
TAAAGAATGTACCAAAATCT
839 SEQ ID N0:6691 -1.9 -15.2 49.3 -13.3 0 -4.2
TCTACATTCTTTGTCCAGTC
925 SEQ ID N0:6692 -1.9 -23.4 71.9 -20.9 -0.3 -3.1
TAAACCTGGAATGACTGAAA
1151 SEQ ID N0:6693 -1.9 -17.4 53.1 -15.5 0 -5.1
GAAAGCTTCTTTACCGACTG
1195 SEQ ID N0:6694 -1.9 -21.9 63.4 -19.1 -0.7 -7
CCACAGCCAGGATCAAATTC
1719 SEQ ID N0:6695 -1.9 -24.1 67.9 -22.2 0 -5.3
ATCTGGTAAGAGCTTAACCT
2524 SEQ ID N0:6696 -1.9 -22.2 65.8 -19.2 -1 -8
TCAAGTTCTTCCATTGTGTT
2611 SEQ ID N0:6697 -1.9 -22.8 69.3 -20.9 0 -3.1
318
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal)
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATCATTGATCTTGCAGACAC
3203 SEQ ID N0:6698 -1.9 -21.4 64.8 -19.5 0 -5.4
CCACATGGTCTCTATCCACT
3299 SEQ ID N0:6699 -1.9 -26.5 75.5 -24.1 -0.2 -5.2
TAATAAGGCCAGAAAGAGGT
3401 SEQ ID N0:6700 -1.9 -19.9 59.3 -17.5 0 -7.7
ACATGCAGCTGTCTATCTTA
3600 SEQ ID N0:6701 -1.9 -23.4 70.6 -20.9 0 -8.6
TCAGTATTTAAGTTTTCAAA
3805 SEQ ID N0:6702 -1.9 -16.4 53.8 -14.5 0 -2.7
ACAAGCTTCCGGTTTAAAGT
3956 SEQ ID N0:6703 -1.9 -22.3 64.5 -20.4 0 -6.6
CAGAATGGAAACTTTTTAAT
3991 SEQ ID N0:6704 -1.9 -15.5 50.3 -13.6 0 -2.5
CATGATAGAGGGAATTGCTC
4460 SEQ TD N0:6705 -1.9 -21.1 63.4 -18.7 -0.2 -5.7
CTCAAATTGTTAACATCACT
4597 SEQ ID N0:6706 -1.9 -18.1 56.3 -15.7 0 -8.3
CAAAGATGATAAAGATGACA
4815 SEQ ID N0:6707 -1.9 -14.9 48.8 -13 0 -2.3
TGAAGTTATCTATGATGACA
4866 SEQ ID N0:6708 -1.9 -18 56.9 -14.6 -1.4 -5.8
TATAGTGAAGTAGTAGTGTC
5213 SEQ ID N0:6709 -1.9 -19.1 62.3 -17.2 0 -1.7
TCCAGCTTCCTTTTTAACAT
5507 SEQ ID N0:6710 -1.9 -23.5 68.4 -21.6 0 -4.5
CTCAAAGTTGAACATGTCAT
5531 SEQ ID N0:6711 -1.9 -19 58.4 -16.5 -0.3 -7
ATGTAACTGACAAAAAAGAA
5716 SEQ ID N0:6712 -1.9 -13.2 45.4 -10.5 -0.6 -3.4
GCAAAATCAGAGAGTTTAGA
5902 SEQ ID N0:6713 -1.9 -18.4 57.5 -16 -0.1 -4.4
TTGTTGGGTTTTGCTATGAG
5944 SEQ ID N0:6714 -1.9 -22.3 67.8 -20.4 0 -3.6
TTTGTAAAGGCAAATAAAAT
6025 SEQ ID N0:6715 -1.9 -13.6 46.2 -10.2 -1.4 -4.8
TCTCACACAAAACACGCTTT
6042 SEQ ID N0:6716 -1.9 -20.9 60.7 -19 0 -3.3
GAGGGGTTTGATGCCATAAA
6103 SEQ TD N0:6717 -1.9 -23 66.1 -20 -1 -3.7
TTACTTGATATATTTTTTAA
6229 SEQ ID N0:6718 -1.9 -14.5 49.5 -12.6 0 -4.3
ACGTAAACCTCATTTACAAA
6905 SEQ ID N0:6719 -1.9 -18.1 54.7 -13.5 -2.7 -6.1
ATACTTTCAAAATTAAAGCC
7060 SEQ ID N0:6720 -1.9 -16.2 51.5 -13.4 -0.7 -5.6
GCAGAAAGTGGAACAACTAT
7296 SEQ ID N0:6721 -1.9 -19 57.4 -16.1 -0.9 -4.9
TAACTATTTACATAACATAG
7379 5EQ ID N0:6722 -1.9 -14.2 48.3 -12.3 0 -3.7
TTTACATTATTTATATTTAA
7839 SEQ ID N0:6723 -1.9 -13.4 47.1 -11.5 0 -2.2
AAAATGCTGACAAATAAAGT
7869 SEQ ID N0:6724 -1.9 -14.2 47.2 -12.3 0 -2.9
AAATCCATAAAACCCATTAT
8029 SEQ ID N0:6725 -1.9 -18 53.7 -16.1 0 -2.4
AAATATATTATAACAAAGAA
8047 SEQ ID N0:6726 -1.9 -10.2 40 -8.3 0 -6.2
319
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTTTGACCAATGTATCTCCT
8081 SEQ ID N0:6727 -1.9 -23.7 69.3 -21.8 0 -3.4
ACTAGTCTGCATACGTAAAT
8190 SEQ ID N0:6728 -1.9 -20 60.4 -18.1 0 -6.6
AATAAGACTAGTCTGCATAC
8196 SEQ ID N0:6729 -1.9 -18.6 58.3 -l5 0 -11.5
CATGGCTAAAAAGAACAAAG
8261 SEQ ID N0:6730 -1.9 -14.9 48.3 -13 0 -3.7
CCAAGGGTTCTTGAAAAAAA
8947 SEQ ID N0:6731 -1.9 -17.5 53.3 -13.5 -2.1 -5.7
TTTAGATCCAAATTGTCTTT
9033 SEQ ID N0:6732 -1.9 -19 59 -17.1 0 -4.5
AAACAGAGCCTTATGAATTA
199 SEQ ID N0:6733 -1.8 -18.3 56 -16.5 0 -3.2
TGATAAAACAGAGCCTTATG
204 SEQ ID N0:6734 -1.8 -18.2 55.7 -16.4 0 -3.2
TAGAAGAGATTCTTTGCTCC
322 SEQ ID N0:6735 -l.8 -21.5 65.4 -17.4 -2.3 -8.3
AGCAAGAGATTCTCTAGTAA
521 SEQ ID N0:6736 -1.8 -19.6 61.4 -16.5 -1.2 -9.3
ATGTACCAAAATCTTGATAG
833 SEQ ID N0:6737 -1.8 -17.4 54.5 -15 -0.3 -4.8
AATGTACCAAAATCTTGATA
834 SEQ ID N0:6738 -1.8 -16.7 52.6 -14.3 -0.3 -4.8
GAATGTACCAAAATCTTGAT
835 SEQ TD N0:6739 -1.8 -17.6 54.3 -15.2 -0.3 -4.8
GGAATGACTGAAATTGTTTT
1144 SEQ ID N0:6740 -1.8 -17.6 55 -15.8 0 -3.2
AACTTTCCAACAGCTCTCCT
1905 5EQ ID N0:6741 -1.8 -25.2 71.6 -23.4 0 -4.4
TCCTTCAAGGTGCTCTCTCT
1994 SEQ ID N0:6742 -1.8 -26.8 79.3 -24.2 -0.6 -5.3
TCATCAGCAAAGTCATTTTC
2239 SEQ ID N0:6743 -1.8 -20.3 62.8 -18.5 0 -4.1
CTGGCACCATCCTGGATGAC
2361 SEQ ID N0:6744 -1.8 -27.4 75.4 -23.7 -1.2 -11.8
AGCTGAAGGTCCACCCACCA
2438 SEQ ID N0:6745 -1.8 -29.9 79.5 -26.9 -1.1 -5.6
GGTGACGTTAGAGCTGAAGG
2449 SEQ ID N0:6746 -1.8 -23.4 68.3 -21.6 0 -5.4
TAATTAGCATATTTAGTGTG
3069 SEQ ID N0:6747 -1.8 -17.3 55.9 -15.5 0 -5.4
GTACCTACACCACTGGTGGT
3679 SEQ ID N0:6748 -1.8 -27.4 77.3 -23 -2.6 -11.7
ATGAGCTGGTTGCATTTAAT
3867 SEQ ID N0:6749 -1.8 -21.5 64.4 -18.1 -1.5 -5.1
AACCCATTTGAGAAGCATTT
4232 SEQ ID N0:6750 -1.8 -21.6 62.5 -19.8 0 -4.1
AATCCATAAGCAACCCATTT
4243 SEQ ID N0:6751 -1.8 -22.3 62.8 -20.5 0 -4.1
GCTAAAGATCAACCAGAAGA
4502 SEQ ID N0:6752 -1.8 -19.4 58 -17.6 0 -5.4
TCCAGTGAACAGAACAATGA
5165 SEQ ID N0:6753 -1.8 -19.8 58.9 -17.3 -0.5 -3.9
ACAAGCAGATCATGCTGTTG
5559 SEQ ID N0:6754 -1.8 -22.4 66.5 -17.8 -2.8 -10.6
TAGAACATCTCAAAGTCATC
5833 SEQ ID N0:6755 -1.8 -18.2 57.5 -16.4 0 -2.8
320
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CTATGAGAAGAGGAGGATCC
5931 SEQ ID N0:6756 -1.8 -21.7 64.7 -18.3 -1.5 -7.7
AAAGGCAAATAAAATATCAA
6020 SEQ ID N0:6757 -1.8 -12.6 44.1 -10.8 0 -4
GTAAAGGCAAATAAAATATC
6022 SEQ ID N0:6758 -1.8 -13.5 46.1 -11.7 0 -4
ACAAAACACGCTTTGTAAAG
6036 SEQ ID N0:6759 -1.8 -17.1 52.6 -14 -1.2 -6.2
CTCTCCACTCTCACACAAAA
6050 SEQ ID N0:6760 -1.8 -22.5 65.1 -20.7 0 0
CCTTTAATTGCCTCTTTGTT
6253 SEQ ID N0:6761 -1.8 -23.7 69 -21.9 0 -3
TTTCTCAAACTTTTCCTTGT
6401 SEQ ID N0:6762 -l.8 -21.2 64.3 -19.4 0 -2.8
AAACAATTGATCACAAAGAT
6491 SEQ ID N0:6763 -1.8 -14.7 48.3 -12 -0.8 -7.2
AGGACTGTACTAAAGGTGTT
6774 SEQ ID N0:6764 -1.8 -20.9 63.8 -19.1 0 -4.8
TGGAAGTAACTGAAACTGTA
7030 SEQ ID N0:6765 -1.8 -17.6 55 -15.8 0 -3.3
TAAATATTAGAGGAGACTTT
7125 SEQ ID N0:6766 -1.8 -16.1 52.6 -13.4 -0.7 -7.1
AATTTGCACTTGCTGAAACA
7171 SEQ ID N0:6767 -1.8 -20 59.4 -18.2 0.4 -5.8
GCAGCAGAAAGTGGAACAAC
7299 SEQ ID N0:6768 -1.8 -20.9 61.3 -18.1 -0.9 -6.2
AAATATGAAGAATAGGTTTT
7794 SEQ ID N0:6769 -1.8 -14.5 48.7 -12.7 0 -2.7
ACAAAAGTTGAATAAAAAAA
8167 SEQ ID N0:6770 -1.8 -9.5 38.7 -7 -0.4 -3.4
AATACTACAAAAGTTGAATA
8173 SEQ ID N0:6771 -l.8 -13.5 46.4 -11 -0.4 -4.2
TAAATACTACAAAAGTTGAA
8175 SEQ ID N0:6772 -1.8 -12.8 44.9 -10.3 -0.4 -4.2
TGCCAACAGCAAAAAACAAA
8516 SEQ ID N0:6773 -1.8 -17.2 51.7 -14 -1.3 -4.1
ATTTAGATCCAAATTGTCTT
9034 SEQ ID N0:6774 -1.8 -18.9 58.7 -17.1 0 -2
CACAGAGGTTTACAAATTAG
87 SEQ ID N0:6775 -1.7 -17.8 55.9 -16.1 0 -3.2
AATCTCTGATAAAACAGAGC
210 SEQ ID N0:6776 -1.7 -17.4 54.7 -12.7 -3 -8.7
TGATGTGGCTTGGCTTCAGT
243 SEQ ID N0:6777 -1.7 -26.1 76.9 -23.7 -0.4 -6
CCCAGTAAGCCACTCTACTA
299 SEQ ID N0:6778 -l.7 -26.3 73.6 -24.6 0 -4.7
TTCCCAGTAAGCCACTCTAC
301 SEQ ID N0:6779 -1.7 -26.2 74.2 -24.5 0 -3.2
ACGAATTACCTTAGATAGTC
411 SEQ ID N0:6780 -1.7 -19.5 59.5 -17.8 0 -3.5
TGGAAGGTTCTTTCCAGCTT
638 SEQ ID N0:6781 -1.7 -25 73.3 -20.6 -2.7 -9.2
TTTCCTAACAGGGTTTAGTG
gOg SEQ ID N0:6782 -1.7 -22.1 66.7 -19.5 -0.7 -4.1
AAAGAATGTACCAAAATCTT
gag SEQ ID N0:6783 -1.7 -15.6 50 -13.3 -0.3 -4.2
CAGTGAATGTGTACTCTACA
gag SEQ ID N0:6784 -1.7 -20.9 64 -18.4 -0.6 -4.8
321
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Tntra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TAGATTCCAGTGAATGTGTA
946 SEQ ID N0:6785 -1.7 -20.7 63.4 -17.6 -1.3 -6
AGTGACTGTCATCTCCAATG
1425 SEQ ID N0:6786 -1.7 -22.9 68.3 -20.5 -0.1 -8.8
CACCTTTGGAACTCAACTTT
1938 SEQ ID N0:6787 -l.7 -21.9 63.8 -20.2 0 -4
TGGATGACATACTGGCCTGA
2349 SEQ ID N0:6788 -1.7 -24.6 69.8 -22.9 0 -7.2
ATTGTGTTGGTCAGAATGCT
2599 SEQ ID N0:6789 -1.7 -22.7 68.4 -21 0 0
GTACAGTCATCATTGATCTT
3211 SEQ ID N0:6790 -1.7 -21.3 66.3 -18.9 -0.5 -5.8
TTTCATTGTCATCATCAGTA
3453 SEQ ID N0:6791 -1.7 -20.8 65.4 -19.1 0 -2.4
AGTACCTACACCACTGGTGG
3680 SEQ ID N0:6792 -l.7 -26.2 74.2 -21.9 -2.6 -11
CAGTATTTAAGTTTTCAAAG
3804 SEQ ID N0:6793 -1.7 -16 52.7 -14.3 0 -2.7
TTCAGTATTTAAGTTTTCAA
3806 SEQ TD N0:6794 -1.7 -17.2 56.1 -15.5 0 -2.7
TCTTCAGTATTTAAGTTTTC
3808 SEQ ID N0:6795 -1.7 -18.5 60.4 -16.8 0 -2.7
CTACTGAGAAGGATCATGAA
4111 SEQ ID N0:6796 -1.7 -19 58.2 -16.4 -0.8 -8.2
CATAAGCAACCCATTTGAGA
4239 SEQ ID N0:6797 -1.7 -21.8 62.5 -19.4 -0.4 -3.3
GTTATCTATGATGACACCAA
4862 SEQ ID N0:6798 -1.7 -20.3 61.1 -17.8 -0.6 -5.1
CAAAATCAAAGACCATTCCT
5019 SEQ ID N0:6799 -1.7 -19.2 56.5 -17.5 0 -2.8
AGAACAATGAACACTAGGTT
5155 SEQ ID N0:6800 -1.7 -18.2 56.2 -15.8 -0.4 -6
TGGAACAAGCAGATCATGCT
5563 SEQ ID N0:6801 -1.7 -22.2 64.7 -17.1 -3.4 -11.7
TTGGAACAAGCAGATCATGC
5564 SEQ ID N0:6802 -1.7 -21.4 63.2 -16.3 -3.4 -11.9
GGTGCTAGCAATCCATCCCA
5602 SEQ ID N0:6803 -1.7 -28.8 78.6 -25.6 0 -10.9
TCGGGTGGTGCACTATTAAG
5626 SEQ ID N0:6804 -1.7 -23.6 68.5 -20.6 -1.1 -9.5
TGTGTCAGGGTCACAGTCGG
5642 SEQ ID N0:6805 -1.7 -26.7 78.5 -23.5 -1.4 -5.7
TTAAAAGATAACATCTGAAA
6201 SEQ ID N0:6806 -1.7 -12.7 44.7 -10.4 -0.3 -3.7
TAACCTTTGCTTTAAAAGAT
6212 SEQ ID N0:6807 -1.7 -17.4 54.1 -14.9 -0.6 -4.8
AGCAACCTCTTGTCAACGTT
6661 SEQ ID N0:6808 -1.7 -24.2 69.1 -21.9 -0.3 -6.9
TTGCACAACTATCCCTATAG
6732 SEQ ID N0:6809 -1.7 -22.3 64.8 -19.7 -0.8 -6.6
TTTGCACAACTATCCCTATA
6733 SEQ ID N0:6810 -1.7 -22.4 64.9 -20.7 0 -5
ATTTTGTAAAAATATGGCAG
6823 SEQ ID N0:6811 -1.7 -15.8 51.1 -12.4 -1.7 -7.4
GATTATATTTTTACATTATT
7848 SEQ ID N0:6812 -1.7 -15 50.7 -13.3 0 -2.2
AATTGTGATTAAAAATCAAA
7g52 SEQ ID N0:6813 -1.7 -11.9 43.1 -8.6 -1.5 -7.5
322
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CATCTATGAATAAAAGGTTA
8145 SEQ ID N0:6814 -1.7 -15.4 50.4 -13.7 0 -2.5
AAACTTTTGGTTTGTGCAAA
8332 SEQ ID N0:6815 -1.7 -18.9 57.7 -16.1 -1 -8.8
GAATTAACATTAAACTTTTG
8343 5EQ ID N0:6816 -1.7 -13.7 46.9 -12 0 -3.5
GCCAACAGCAAAAAACAAAA
8515 SEQ ID N0:6817 -1.7 -16.5 50.2 -14 -0.6 -4.1
AAGTTCACAAAGCTGCTTTT
8663 SEQ ID N0:6818 -1.7 -20.9 62.8 -17.7 -0.3 -10.9
GGGAGTTAATTGAAATTGAA
8761 SEQ ID N0:6819 -1.7 -16.6 52.7 -14.9 0 -3.9
AAGAATGTACCAAAATCTTG
837 SEQ ID N0:6820 -1.6 -16.3 51.6 -14.7 0 -4.8
TTGCTCAAGGTCATAAATAC
898 SEQ ID N0:6821 -1.6 -18.9 58.4 -17.3 0 -3.6
ACACGCTCAGACAGAACACA
1233 5EQ ID N0:6822 -1.6 -22.9 65.3 -21.3 0 -3.4
GGGGTTTCGACCAGCCTTCA
1529 SEQ ID N0:6823 -l.6 -29.6 81 -25.3 -2.7 -7.7
TGAGTCATGAGTCGAAATAG
1597 SEQ ID N0:6824 -1.6 -18.8 58.1 -15.5 0 -11.5
CAGCTCTCCTAACCCACCTA
1895 SEQ ID N0:6825 -1.6 -28.7 77.5 -27.1 0 -4.4
AGAGACTGATGAGGGGAGCA
2128 SEQ ID N0:6826 -1.6 -24.2 70.8 -22.6 0 -4.1
GTGGTGGTGCCCTCTGGGGG
2482 SEQ ID N0:6827 -1.6 -32.8 90.6 -29 -2.2 -8.2
CATCTCCATTGAAATCTGGT
2537 SEQ ID N0:6828 -1.6 -22.1 65 -20.5 0.3 -3.1
GGCGGACATTTCTGTCTAGA
2635 SEQ ID N0:6829 -1.6 -24.8 72.3 -20.5 -2.7 -8.6
CAATTAAATTCACAAGATGT
2721 SEQ ID N0:6830 -1.6 -15.6 50.6 -14 0 -3.1
CTACAGTCAACACACTACTG
2835 SEQ ID N0:6831 -1.6 -20.8 62.6 -17.8 -1.3 -5.1
GGCAATGATCTTGAGAACCA
2891 SEQ ID N0:6832 -1.6 -22.4 64.6 -20.1 -0.4 -6.2
TTTTGCCAACTTGAAAACTC
3041 SEQ ID N0:6833 -1.6 -19.3 57.8 -17.7 0 -3.1
TGGTCTCTATCCACTCTCCA
3294 SEQ ID N0:6834 -1.6 -27.3 79.4 -25.1 -0.3 -3.7
ACCAACATGAAAACAATAAG
3352 SEQ ID N0:6835 -l.6 -14.8 47.9 -13.2 0 -4.3
TAGCAGGTTTTTCGAAGATT
4051 SEQ ID N0:6836 -1.6 -20.8 62.9 -18.5 -0.4 -6.8
AGTTGTGCTCAACAATACTG
4071 SEQ ID N0:6837 -1.6 -20.6 62.4 -15.7 -3.3 -6.6
GGATCATGAACACAATGAAA
4101 SEQ ID N0:6838 -1.6 -17.1 52.9 -14.6 -0.8 -7.4
CCATAAGCAACCCATTTGAG
4240 SEQ ID N0:6839 -1.6 -23.2 64.7 -20.9 -0.4 -4.1
GCCTTCAAACCGGGATAAGG
4412 SEQ ID N0:6840 -1.6 -24.7 67.1 -22.2 -0.8 -8.6
~
ATAGAGGGAATTGCTCCAAC
4456 SEQ ID N0:6841 -1.6 -22 64.4 -18.6 -1.8 -6.1
AAATTGTTAACATCACTAAT
4594 SEQ ID N0:6842 -1.6 -15.1 49.7 -13 0 -8.3
323
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformation,Duplexstructureoligo oligo
GAATCAACAGCTGCATACAT
4738 SEQ ID N0:6843 -1.6 -21 62 -18.7 0 -8.9
TGAATCAACAGCTGCATACA
4739 SEQ ID N0:6844 -l.6 -21 61.9 -18.7 0 -8.9
AAAGTCAAAGATGTTCCAGC
5234 SEQ ID N0:6845 -l.6 -20.3 6l -18.7 0 -2.9
CTTTGCTCCTTTGATCAGAC
5369 SEQ ID N0:6846 -1.6 -23.8 70.5 -22.2 0 -6.5
TGAACATGTCATCAATTCCA
5523 SEQ ID N0:6847 -1.6 -20.7 61.6 -18.4 -0.5 -7.2
CTTTGTTGGGTTTTGCTATG
5946 SEQ ID N0:6848 -1.6 -22.7 68.6 -21.1 0 -3.6
TACGCTGAATGATAGCGGCA
6180 SEQ ID N0:6849 -1.6 -23.9 66.3 -18.7 -3.6 -10.6
TTTAAAAGATAACATCTGAA
6202 SEQ ID N0:6850 -1.6 -13.5 46.4 -11 -0.8 -6.5
AGCAGTGTCAGCTGGTAATA
6686 SEQ ID N0:6851 -l.6 -23.8 71.7 -20.6 -1.6 -8.6
AGATGGCAAAGCAATACTGC
7317 SEQ ID N0:6852 -1.6 -21.3 62.3 -18.2 -1.4 -6
TTAATTGACATAGACTATCA
7354 SEQ ID N0:6853 -1.6 -16.9 54.3 -15.3 0 -3.3
TATATTTGCCCAAACATGCA
7412 SEQ ID N0:6854 -1.6 -22.1 62.9 -19.8 -0.5 -5.4
TCTATCACCAATATGTGACA
7625 SEQ ID N0:6855 -1.6 -20.7 62 -17.6 -1.4 -6.5
TGTAAATAGCTTCAAATTAT
7682 SEQ ID N0:6856 -1.6 -15.5 50.8 -13.9 0 -4.6
TTTTTACATTATTTATATTT
7841 SEQ ID N0:6857 -1.6 -14.6 50 -13 0 -2.2
ATTGTGATTAAAAATCAAAA
7951 SEQ ID N0:6858 -1.6 -11.9 43.1 -8.3 -2 -7
ATGGTAGAAAATATATTATA
8055 SEQ ID N0:6859 -1.6 -13.5 46.8 -11.9 0 -6.2
TACAAAAGTTGAATAAAAAA
8168 SEQ ID N0:6860 -l.6 -9.9 39.4 -7.6 -0.4 -3.4
CAGGTTTTATTAATTATATA
8546 SEQ ID N0:6861 -1.6 -15.4 51.4 -13.8 0 -4.2
TTGTTGTAAAATTCATGTAA
8597 SEQ ID N0:6862 -1.6 -15.6 51.3 -13.3 -0.4 -6.6
GGGTTCTTGAAAAAAAAGTT
8943 SEQ ID N0:6863 -1.6 -16.1 51.4 -14.5 0 -3.5
TTTTTCGATAGCAGCAAGAG
533 SEQ ID N0:6864 -1.5 -20.8 62.5 -19.3 0 -5.4
CAGAGGTGGCACTGAATCGG
771 SEQ ID N0:6865 -1.5 -24.8 70 -23.3 0 -4
GGTTTAGTGGAGTTAAAATA
798 SEQ ID N0:6866 -1.5 -17.9 56.8 -16.4 0 -2.8
TCTGAATGTTCTCAACGCTG
1109 SEQ ID N0:6867 -1.5 -21.9 64.4 -19.5 -0.8 -5.3
GAAATCTCTTGAAGCAGCTG
1868 SEQ ID N0:6868 -1.5 -21 62.8 -19 0 -8.2
GTTCTTCCATTGTGTTGGTC
2607 5EQ ID N0:6869 -1.5 -25.2 76.9 -23 -0.4 -3.7
ATCCATAACAATTAAATTCA
2729 SEQ ID N0:6870 -1.5 -15.9 50.9 -14.4 0 -3.1
CATGGCAATGATCTTGAGAA
2894 SEQ ID N0:6871 -1.5 -20.2 60.3 -18.7 0 -5.5
324
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GCGTACAGTCATCATTGATC
3213 SEQ ID N0:6872 -1.5 -22.9 68.5 -20.7 -0.5 -5.7
CTCTATCCACTCTCCACACA
3290 SEQ ID N0:6873 -1.5 -26.3 75 -24.8 0 -0.9
GCTTCCTTCAGATGAGCTGG
3878 SEQ ID N0:6874 -1.5 -26.4 76.6 -23.7 -1.1 -5.2
GAATATATAGGTAAAGACTT
4205 SEQ ID N0:6875 -1.5 -15.5 51 -13.5 -0.1 -4.3
AGATGAGACAGACCAACAGC
4485 SEQ ID N0:6876 -1.5 -22.2 64.8 -20.7 0 -2.8
CTAAAGATCAACCAGAAGAT
4501 SEQ ID N0:6877 -1.5 -17.6 54.2 -16.1 0 -4.6
CGTGAATCAACAGCTGCATA
4741 SEQ ID N0:6878 -1.5 -22.1 63.6 -19.9 0 -9
GAACAATGAACACTAGGTTG
5154 SEQ ID N0:6879 -1.5 -18.2 56 -15.9 -0.6 -6
TTGTTACACTATCATAGGAA
6375 SEQ ID N0:6880 -l.5 -18.7 58.6 -17.2 0 -3.4
ATTCTTTGTTTCTTTTTACT
6470 SEQ ID N0:6881 -1.5 -19.5 62.5 -18 0 -2.2
TAAACAATTGATCACAAAGA
6492 SEQ ID N0:6882 -1.5 -14.4 47.8 -l2 -0.8 -7.2
CTGGTAATAAAAACAGCAAC
6675 5EQ ID N0:6883 -1.5 -16.1 50.9 -14.6 0 -4.1
CAAGGACTGTACTAAAGGTG
6776 SEQ ID N0:6884 -1.5 -19.6 59.5 -18.1 0 -4.8
TGCAGCAGAAAGTGGAACAA
7300 SEQ ID N0:6885 -1.5 -20.7 60.7 -18.2 -0.9 -7.5
CTATCACCAATATGTGACAT
7624 SEQ ID N0:6886 -1.5 -20.3 60.7 -17.3 -1.4 -6.5
ATGTACAAAATGCTGACAAA
7875 SEQ ID N0:6887 -1.5 -16.5 51.8 -15 0 -6.8
AAGCATAAAGTAAAATAAAT
7927 SEQ ID N0:6888 -1.5 -11.2 41.7 -9.7 0 -4.1
ACAAAAACAAAAAACCCCAG
8501 SEQ ID N0:6889 -l.5 -16.4 49.6 -14.9 0 0
AGATAGCATCAATTATATTG
8812 SEQ ID N0:6890 -1.5 -16.8 54.2 -14.4 -0.7 -5.7
GTAACATTTATTAGCCACCA
8842 SEQ ID N0:6891 -l.5 -22.2 64.7 -20.7 0 -3.2
TTCCACTGAGAATAAGAGTT
8988 SEQ ID N0:6892 -1.5 -19.7 60.2 -18.2 0 -2.8
TATGCATTACAACTGGAGTT
9008 SEQ ID N0:6893 -1.5 -20.4 61.8 -18.9 0 -6.8
TTAGATCCAAATTGTCTTTA
9032 SEQ ID N0:6894 -1.5 -18.6 58.1 -17.1 0 -4.6
AAAACAGAGCCTTATGAATT
200 SEQ ID N0:6895 -l.4 -17.9 54.8 -16.5 0 -3.2
CTAGAAGAGATTCTTTGCTC
323 SEQ ID N0:6896 -1.4 -20.4 63.5 -16.7 -2.3 -8.3
CATACGAATTACCTTAGATA
414 SEQ ID N0:6897 -1.4 -18.3 55.8 -16.9 0 -3.5
GGTCCTGGGGGTACCAACAG
484 SEQ ID N0:6898 -1.4 -28.5 78.7 -24.6 -2.5 -10.2
CGATAGCAGCAAGAGATTCT
528 SEQ ID N0:6899 -1.4 -22 64.7 -20.6 0 -4.6
GATTCCAGTGAATGTGTACT
944 SEQ ID N0:6900 -1.4 -22.1 66.3 -19.3 -1.3 -7
325
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TGCTCGGAGAACTCTGAATG
1121 SEQ ID N0:6901 -1.4 -21.9 63.7 -19.8 -0.4 -8.2
CAGTGCTCGGAGAACTCTGA
1124 SEQ TD N0:6902 -l.4 -24.5 70.6 -22.2 -0.7 -7.9
CACGCTCAGACAGAACACAG
1232 SEQ ID N0:6903 -1.4 -22.7 65 -21.3 0 -3.4
CTGTCATCTCCAATGTAATC
1420 SEQ ID N0:6904 -1.4 -21.5 64.8 -19.5 -0.3 -3
GAGTAAAGGGTCTTTTTGCC
1460 SEQ ID N0:6905 -1.4 -23.2 68.9 -21.1 -0.4 -4.l
CAAAGCTTGTGTAGCCATAG
1551 SEQ ID N0:6906 -1.4 -22.4 65.8 -19.4 -l.5 -7.9
CCCAAGAAAATGACCAGGAC
1684 SEQ ID N0:6907 -1.4 -22 61.3 -20.6 0 -4
AGCCCAAGAAAATGACCAGG
1686 SEQ ID N0:6908 -1.4 -23 63.4 -21.6 0 -3.6
TCTCTTGAAGCAGCTGATGC
1864 SEQ ID N0:6909 -1.4 -24.2 71.5 -21.2 -1.6 -8.7
ATTCTTTAGCACCTTTGGAA
1947 5EQ ID N0:6910 -1.4 -22.2 65.8 -20.8 0 -4.1
CATTCTTTAGCACCTTTGGA
1948 SEQ ID N0:6911 -1.4 -23.6 69.2 -22.2 0 -4.1
AGGTCCACCCACCAAGGAAA
2432 SEQ ID N0:6912 -1.4 -27 71.7 -24.4 -1.1 -5.8
TCTTCCATTGTGTTGGTCAG
2605 SEQ ID N0:6913 -1.4 -24.6 74.2 -22.5 -0.4 -3.7
CTTCAAGTTCTTCCATTGTG
2613 SEQ ID N0:6914 -1.4 -22.5 67.9 -21.1 0 -3.1
CAGCATGGCGGACATTTCTG
2641 SEQ ID N0:6915 -l.4 -25.2 70.9 -22.9 -0.7 -5.4
GATTTTGCCAACTTGAAAAC
3043 5EQ ID N0:6916 -1.4 -18.6 56 -17.2 0 -4
CATGTGCCACCGTGGGAGCG
3230 SEQ ID N0:6917 -1.4 -30.2 78.7 -27.7 -1 -9.1
CAGAAAGAGGTTCAGAACCA
3392 SEQ ID N0:6918 -1.4 -20.9 61.7 -16.8 -2.7 -12
TTGCATTCTTCCTACTGCAA
3488 SEQ ID N0:6919 -1.4 -24 69.7 -20.5 -2.1 -6.8
TACTGAGAAGGATCATGAAC
4110 SEQ ID N0:6920 -l.4 -18.3 56.9 -16 -0.8 -8.2
CCTTCAAACCGGGATAAGGC
4411 SEQ ID N0:6921 -1.4 -24.7 67.1 -22.7 -0.3 -7.6
ATCTCAGCCAGAAACATACC
5278 SEQ ID N0:6922 -1.4 -22.9 65.8 -21.5 0 -3.6
CAATCCATCCCAGCCAGCAG
5594 SEQ ID N0:6923 -1.4 -29.2 77.7 -27.8 0 -4.6
GTCACAGTCGGGTGGTGCAC
5633 SEQ ID N0:6924 -l.4 -28.3 81.6 -25.8 -0.6 -9.9
GCTGTAAACAATTGATCACA
6496 SEQ ID N0:6925 -1.4 -19.1 57.9 -17.7 0 -7.2
GTCTTGTATAGGCACTGACT
6595 SEQ ID N0:6926 -1.4 -23.7 71.5 -21.3 -0.9 -4.3
TAGAAACAAACATAACAGAC
7084 SEQ ID N0:6927 -1.4 -14 47 -12.6 0 -1
ATACTGCAGCAGAAAGTGGA
7304 SEQ ID N0:6928 -1.4 -22 64.9 -19.3 -0.7 -10.4
TGGCAAAGCAATACTGCAGC
7314 SEQ ID N0:6929 -l.4 -23.2 66.2 -19.3 -2.5 -9.6
326
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGATACCATATGATACTCAT
7733 SEQ ID N0:6930 -1.4 -19.4 59.4 -17.2 -0.6 -6
CAAAAGTTGAAT~
8166 SEQ ID N0:6931 -1.4 -8.6 37.2 -7.2 0 -2.6
TAGTCTGCATACGTAAATAC
8188 SEQ ID N0:6932 -1.4 -18.8 57.9 -17.4 0 -6.6
AAAAAAATAAGACTAGTCTG
8201 SEQ ID N0:6933 -1.4 -12.7 44.8 -9.6 0 -11.5
CAAAAAACAAAAATTTATAT
8316 SEQ ID N0:6934 -1.4 -8.9 37.6 -7.5 0 -5.2
ATGTGAACTTGATCCTTTGC
8691 SEQ ID N0:6935 -1.4 -22.2 65.8 -20.8 0 -4.3
TAACATTTATTAGCCACCAA
8841 SEQ ID N0:6936 -1.4 -20.3 59.7 -18.9 0 -3.2
ACAAATTAGTTACAATTTTT
76 SEQ 2D N0:6937 -1.3 -14.9 49.7 -12.9 -0.5 -4
AGAGCCTTATGAATTACAGC
195 SEQ ID N0:6938 -1.3 -21.5 64.1 -20.2 0 -3.2
CTCCATAATCTCTGATAAAA
216 SEQ ID N0:6939 -l.3 -17.8 55.1 -16.5 0 -3.3
TCCCAGTAAGCCACTCTACT
300 SEQ ID N0:6940 -1.3 -27 75.8 -25.7 0 -4.5
TGGCTTTCTCTTCTGCAGCA
555 SEQ ID N0:6941 -1.3 -27.1 79.8 -24.5 -1.2 -8.3
GAGACAGGAAAGCCCAGCTA
1578 SEQ ID N0:6942 -1.3 -25.4 70.8 -23.1 -0.9 -6
AAAATGAGCCCAAGAAAATG
1692 SEQ ID N0:6943 -1.3 -16.8 51.2 -15.5 0 -3.2
AAATCTCTTGAAGCAGCTGA
1867 SEQ ID N0:6944 -1.3 -21 62.8 -19 0 -8.7
CAACAGCTCTCCTAACCCAC
1898 SEQ ID N0:6945 -1.3 -26.3 72.1 -25 0 -4.4
GTTGTTTCCTTCAAGGTGCT
2000 SEQ ID N0:6946 -1.3 -25.6 75.9 -23.5 -0.6 -5.3
ATTTTCAGATCCAACATCCT
2225 SEQ ID N0:6947 -1.3 -22.6 66.1 -20.8 -0.1 -4.5
CACACCATTGCAATCCACAG
2411 SEQ ID N0:6948 -1.3 -24.4 67.8 -22.5 0 -8.6
GGTTTCCTACAGTCAACACA
2841 SEQ ID N0:6949 -1.3 -23.9 70.1 -22.1 -0.2 -3.6
AGATATTCCAGCCTTCTTGG
2931 SEQ ID N0:6950 -1.3 -24.9 72.4 -23.1 -0.2 -6.7
GCCGACCACAGCAAAAATGA
3152 SEQ ID N0:6951 -1.3 -23.3 63 -22 0 -4.1
AGTCATCATTGATCTTGCAG
3207 SEQ ID N0:6952 -1.3 -22 67.5 -20 -0.5 -6.4
TTCTTCCTACTGCAATCTGC
3483 SEQ ID N0:6953 -1.3 -24.5 71.7 -22.1 -1 -4.9
CACCACTGGTGGTTCCATTC
3672 SEQ ID N0:6954 -l.3 -27.2 77.1 -23.8 -1.7 -12
TCAAAGTCAGACTCTCCAAC
3790 SEQ ID N0:6955 -1.3 -21.6 64.5 -20.3 0 -7.3
GTTGTGCTCAACAATACTGT
4070 SEQ ID N0:6956 -1.3 -21.8 65.4 -18 ~ -2.5 -8.8
CATCACTAATGTCAAACATG
4584 SEQ ID N0:6957 -1.3 -17.7 55 -15.2 -1.1 -5
CCTGACAGTCACTCAAATTG
4608 SEQ ID N0:6958 -1.3 -21.6 63.6 -20.3 0 -7.1
327
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATCTCGTGAATCAACAGCTG
4745 SEQ ID N0:6959 -1.3 -21.6 63.7 -19.7 0 -8.6
CCGGGACAAAACTAGGGTCA
5132 SEQ ID N0:6960 -1.3 -24.1 66.5 -21.5 -1.2 -7.1
AAGACGGATCACTCGGAACA
5327 SEQ ID N0:6961 -1.3 -22.1 62.6 -20.1 -0.4 -5.3
AATCCATCCCAGCCAGCAGA
5593 SEQ ID N0:6962 -1.3 -29.1 78 -27.8 0 -4.6
AAAGAAAATCCCAACAGATG
5702 SEQ ID NO:6963 -1.3 -l7 52 -15.7 0 -3
CGCGATGTACATGTTCACCA
5756 SEQ ID NO:6964 -l.3 -25.1 69.3 -23.2 0 -8.4
ATCCATGGCAATAAGCTGGA
5966 SEQ ID N0:6965 -1.3 -23.6 67 -19.8 -2.5 -8
ATAAAATATCAAGACAGTGG
6012 SEQ ID N0:6966 -1.3 -15.6 50.7 -14.3 0 -4.6
ATCACAAAGATAATTCTTTG
6482 SEQ ID N0:6967 -1.3 -15.8 51.6 -10.5 -4 -9.6
ACAAATTTTGTAAAAATATG
6827 SEQ ID N0:6968 -l.3 -11.6 42.6 -7.7 -2.6 -7.8
GGACCATGGAAATGCACTAG
6848 SEQ ID N0:6969 -1.3 -22.4 64 -19.7 -1.3 -8.8
AAACAAACATAACAGACTAA
7081 SEQ ID N0:6970 -1.3 -13.6 46.1 -12.3 0 -2
AGAAACAAACATAACAGACT
7083 SEQ 2D N0:6971 -l.3 -15.2 49.3 -13.9 0 -1.8
GATAGAAACAAACATAACAG
7086 SEQ ID N0:6972 -1.3 -13.8 46.6 -12.5 0 -1.2
AAATATTAGAGGAGACTTTA
7124 SEQ ID N0:6973 -1.3 -16.1 52.6 -13.9 -0.7 -7.1
AGCTCTGAAACTTAGAATAA
7191 SEQ ID N0:6974 -1.3 -l7 53.9 -15.7 0 -4.3
GATGGCAAAGCAATACTGCA
7316 SEQ ID N0:6975 -l.3 -22 63.2 -18.2 -2.5 -8.1
CTATGTTTAATGAATGATAC
7519 SEQ ID N0:6976 -1.3 -15.4 50.8 -14.1 0 -2.5
ACTATGTTTAATGAATGATA
7520 SEQ ID N0:6977 -1.3 -15.4 50.8 -14.1 0 -2.5
GTGTGTTTCCTTGAAATCCA
7756 SEQ ID N0:6978 -1.3 -23.5 68.5 -21.7 -0.1 -3.8
CAGTGTGTTTCCTTGAAATC
7758 5EQ ID N0:6979 -1.3 -21.5 65 -19.4 -0.6 -5.1
ACCAATGTATCTCCTATTGG
8076 SEQ ID N0:6980 -1.3 -22.7 66.3 -19.1 -2.3 -7.1
TAAACTTTTGGTTTGTGCAA
8333 SEQ ID NO:6981 -1.3 -19.3 59 -16.1 -1.3 -11.8
TCTGTGGATAAGAAAACAAA
44 SEQ ID N0:6982 -1.2 -15.3 49.6 -14.1 0 -2.9
TGCTGAATAAAGAATGTACC
846 SEQ ID N0:6983 -1.2 -17.9 54.9 -16.7 0 -4.2
ATCATCACATCAGAAAGCTT
1207 SEQ ID N0:6984 -1.2 -20.2 61.4 -19 0 -6.8
GTCAGGATCATCACATCAGA
1213 SEQ ID N0:6985 -1.2 -22.9 69.3 -21.7 0.7 -4.5
ACGCTCAGACAGAACACAGT
1231 SEQ ID N0:6986 -1.2 -23.2 67 -22 0 -3.4
GCCCATCCAAAACATAAAAG
1443 SEQ ID N0:6987 -1.2 -20 57 -18.8 0 -2
328
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GAGTCGAAATAGAGACAGGA
1589 SEQ ID N0:6988 -1.2 -19.8 59.8 -17.1 -1.4 -5
AGAAAATGACCAGGACAAAA
1680 SEQ ID N0:6989 -1.2 -16.6 51.3 -15.4 0 -4
TCTGAAGAACTTTCCAACAG
1912 SEQ TD N0:6990 -1.2 -19.7 59.3 -17.8 -0.4 -4.1
TGGTGGTGCCCTCTGGGGGA
2481 SEQ ID N0:6991 -1.2 -32.2 88.1 -28.8 -2.2 -8.7
AGTCAACACACTACTGAATT
2831 SEQ ID N0:6992 -1.2 -19.3 59.1 -17.6 -0.1 -3.2
CTGTGAAAATCCCAGTAAAG
2865 SEQ ID N0:6993 -1.2 -19.2 57.1 -18 0 -2.9
ATAGTAATAAGGATCCATGG
2909 SEQ ID N0:6994 -1.2 -19 58.2 -16.9 0 -9.5
GTGCCACCGTGGGAGCGTAC
3227 SEQ ID N0:6995 -1.2 -30.6 81.3 -28.2 -1.1 -9.1
TTCAAAGTCAGACTCTCCAA
3791 SEQ ID N0:6996 -1.2 -21.5 64.2 -20.3 0 -6.8
GTATTTAAGTTTTCAAAGTC
3802 SEQ ID N0:6997 -1.2 -16.9 55.5 -15.7 0 -2.7
CTTCAGTATTTAAGTTTTCA
3807 SEQ ID N0:6998 -1.2 -18.8 60.3 -17.6 0 -2.6
CTGCTGAACTCTTCAGTATT
3817 SEQ ID N0:6999 -1.2 -22.1 66.9 -18.2 -2.7 -10.1
ACTGCTGAACTCTTCAGTAT
3818 SEQ ID N0:7000 -1.2 -22.2 67.2 -18.3 -2.7 -10.1
AATGGAAACTTTTTAATACA
3988 SEQ ID N0:7001 -1.2 -14.8 49 -13.6 0 -2.5
GCTCAACAATACTGTAGCAG
4065 SEQ 2D N0:7002 -1.2 -21.5 64.2 -18.2 -2.1 -6.6
CTACCAGGCTAACCAAAGAA
4317 SEQ ID N0:7003 -1.2 -21.8 61.7 -19.2 -1.3 -5
GTAATGATTTGATGGCACCG
4362 SEQ 2D N0:7004 -1.2 -22.3 63.8 -21.1 0 -4
CACCCATGATGCTAAAGATC
4512 SEQ ID N0:7005 -1.2 -22.2 63.6 -21 0 -4.5
GGTTACAAAATCAAAGACCA
5024 SEQ ID N0:7006 -1.2 -18.2 55.1 -16.5 -0.2 -4.1
GCAATCCATCCCAGCCAGCA
5595 SEQ ID N0:7007 -1.2 -31 81.5 -29.8 0 -4.6
GCGATGTACATGTTCACCAC
5755 SEQ ID N0:7008 -1.2 -24.5 69.8 -22.7 0 -8.4
ACCTCATAGAACATCTCAAA
5839 SEQ ID N0:7009 -1.2 -19.7 59.3 -18.5 0 -2.8
CCTTTGTCTGATCATTTGAG
6954 SEQ ID N0:7010 -1.2 -22.1 66.7 -20.9 0 -6.2
ACAAATAAAGTTGATTATAT
7860 SEQ ID N0:7011 -1.2 -13.2 45.9 -11.5 -0.1 -3.7
AGTAAATAGTTTTGTAAAAA
8363 SEQ ID N0:7012 -1.2 -12.8 45.3 -10.4 -1.1 -4.3
AATAAAAAATGAAATTTATT
8462 SEQ ID N0:7013 -1.2 -8.7 37.3 -6.2 -1.2 -5.5
ATATAATGCATTTAAGTAAC
8869 SEQ ID N0:7014 -1.2 -14.8 49.5 -12.9 0 -8.8
TTAAAAATATGCATTACAAC
9015 SEQ ID N0:7015 -1.2 -13.4 46 -12.2 0 -6.8
AAGCCCAGCATCCAAGATGG
l69 SEQ ID N0:7016 -1.1 -26.5 72 -23.9 -1.4 -6.9
329
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TCCCTAGAAGAGATTCTTTG
326 SEQ ID N0:7017 -1.1 -21.7 64.9 -18.6 -2 -4.7
GTACCAACAGTGCCTGTGCC
474 SEQ ID N0:7018 -1.1 -28.9 79.4 -26.2 -1.5 -8.7
AGATTCTCTAGTAAAAAGGC
515 SEQ ID N0:7019 -1.1 -18.1 57 -l7 0 -4
AAGAGATTCTCTAGTAAAAA
518 5EQ ID N0:7020 -1.1 -15 50 -12.6 -1.2 -9.3
GATAGCAGCAAGAGATTCTC
527 SEQ ID N0:7021 -1.1 -21.6 65.9 -20.5 0 -7
CATTCTTTGTCCAGTCAGGA
921 SEQ ID N0:7022 -1.1 -24.7 73.8 -22.4 -1.1 -4.5
ATGCCATCACAATGACACTG
1056 SEQ ID N0:7023 -1.1 -22.4 64.3 -20.6 -0.4 -3.8
ATCCAAAACATAAAAGTGAC
1439 SEQ ID N0:7024 -1.1 -15.5 49.7 -14.4 0 -2.9
GACGTTAGAGCTGAAGGTCC
2446 SEQ ID N0:7025 -1.1 -24.6 71.1 -22.6 -0.7 -8.8
AAGTTCTTCCATTGTGTTGG
2609 SEQ ID N0:7026 -1.1 -22.9 69 -21.3 -0.1 -4.3
CTAGATTCTTCAAGTTCTTC
2620 SEQ ID N0:7027 -1.l -20.2 64.2 -18.6 -0.2 -3.6
ACATTTCTGTCTAGATTCTT
2630 SEQ ID N0:7028 -1.1 -20.7 65.2 -19.6 0 -6
CCATAACAATTAAATTCACA
2727 SEQ ID N0:7029 -1.1 -16.4 51.5 -15.3 0 -3.1
AACACACTACTGAATTGCTC
2827 SEQ ID N0:7030 -1.1 -20.1 60.5 -19 0 -3.6
CCAAAGAGCTGCATGCCGAC
3166 SEQ ID N0:7031 -1.1 -26.5 70.8 -24.4 -0.8 -9.1
GTCATCATTGATCTTGCAGA
3206 SEQ ID N0:7032 -1.1 -22.6 68.6 -20.8 -0.5 -6.4
CAATTCCCTTTTGCATTCTT
3498 SEQ ID N0:7033 -1.1 -23.7 68.4 -22.6 0 -5.1
TGGACATGCAGCTGTCTATC
3603 SEQ ID N0:7034 -1.1 -24.5 72.8 -21.5 -1.9 -10.5
GTTCTGACTCACTGCTGAAC
3828 SEQ ID N0:7035 -1.1 -23.3 69.4 -22.2 0 -4.2
ACAACATCAACTGTGCTTCC
3892 SEQ ID N0:7036 -1.1 -23 66.7 -21.2 -0.4 -4.1
GAATGGAAACTTTTTAATAC
3989 SEQ ID N0:7037 -1.1 -14.7 48.9 -13.6 0 -2.5
CCTTCTTCTGTACTTACTTG
4012 SEQ ID N0:7038 -1.1 -22.7 68.7 -21.6 0 -4.8
AACACAATGAAAGTCTCAAA
4093 5EQ ID N0:7039 -1.1 -15.8 50.6 -14.1 -0.3 -3.1
TCAGAGTGAAGAATGACCCA
4833 SEQ ID N0:7040 -1.1 -22.2 64.3 -21.1 0 -2.7
AGCTTCCTTTTTAACATAGG
5504 SEQ ID N0:7041 -1.1 -21.3 64.2 -20.2 0 -4.3
TATTAAGAATAGGTGCTAGC
5613 SEQ ID N0:7042 -1.1 -19 59.3 -17.4 0 -8
GGTTTTGCTATGAGAAGAGG
5938 SEQ ID N0:7043 -1.1 -21.4 64.9 -20.3 0 -3.6
AACGTAAACCTCATTTACAA
6906 SEQ ID N0:7044 -1.1 -18.1 54.7 -14.3 -2.7 -6.1
ATGTTTAATGAATGATACAG
7517 SEQ ID N0:7045 -1.1 -15.5 50.9 -14.4 0 -3
330
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TATGTTTAATGAATGATACA
7518 SEQ ID N0:7046 -l.1 -15.2 50.2 -14.1 0 -2.9
TACAAAATGCTGACAAATAA
7872 SEQ ID N0:7047 -1.1 -14.3 47.3 -13.2 0 -3.6
CATGTGAACTTGATCCTTTG
8692 SEQ ID N0:7048 -1.1 -21.1 62.9 -20 0 -4.3
AAGGGAGTTAATTGAAATTG
8763 SEQ ID N0:7049 -1.1 -16 51.6 -14.9 0 -3.9
TCTTGAAAAAAAAGTTAATA
8939 SEQ ID N0:7050 -1.1 -11.1 41.7 -l0 0 -2.9
TAAAACAGAGCCTTATGAAT
201 SEQ ID N0:7051 -1 -17.5 54 -16.5 0 -3.2
ATAAAACAGAGCCTTATGAA
202 SEQ ID N0:7052 -1 -17.5 54 -16.5 0 -3.2
TTTTCTTGCTCCATAATCTC
224 SEQ TD N0:7053 -1 -22.2 67.2 -21.2 0 -3.6
TACGAATTACCTTAGATAGT
412 SEQ ID N0:7054 -1 -18.8 57.6 -17.8 0 -3.5
GGTACCAACAGTGCCTGTGC
475 SEQ ID N0:7055 -1 -28.1 78.5 -25.2 -1.5 -11.6
ATAGCAGCAAGAGATTCTCT
526 SEQ ID N0:7056 -1 -21.9 66.6 -19.8 -1 -9
TGGAGGAATGTCTCCATAAA
662 SEQ ID N0:7057 -1 -20.8 61.6 -16.6 -3.2 -8.3
GGGTTTAGTGGAGTTAAAAT
799 SEQ ID N0:7058 -1 -19.4 60 -18.4 0 -2.8
TATAGATTCCAGTGAATGTG
948 SEQ TD N0:7059 -1 -19.5 60.2 -17.6 -0.7 -5.3
GAAACGTAAAATCTTCTAAG
1008 SEQ ID N0:7060 -1 -14.7 48.5 -13.7 0 -5.3
ACTGAAATCCAGCCAGTTCC
1040 SEQ ID N0:7061 -1 -25.6 71.6 -23.4 -1.1 -6.2
CCCAGGTCCACAAACTCTGT
1081 SEQ ID N0:7062 -1 -27.3 74.8 -25.8 -0.2 -3.7
GTCTTTAAACCTGGAATGAC
1156 SEQ 2D N0:7063 -1 -20 60 -19 0 -5.1
GGATCATCACATCAGAAAGC
1209 SEQ ID N0:7064 -1 -21 63 -19.5 -0.1 -5.3
GACTGTCATCTCCAATGTAA
1422 SEQ ID N0:7065 -1 -21.9 65.3 -20.3 -0.3 -6.8
TGCCCATCCAAAACATAAAA
1444 SEQ ID N0:7066 -1 -20 56.8 -19 0 -3
TTTAGCACCTTTGGAACTCA
1943 SEQ ID N0:7067 -1 -23 67.2 -22 0 -4.1
CCAGCATGGCGGACATTTCT
2642 SEQ ID N0:7068 -1 -27.2 74.6 -25 -1.1 -7.4
TGTGAAAATCCCAGTAAAGA
2864 SEQ ID N0:7069 -1 -18.9 56.6 -17.9 0 -2.1
GATCTTGAGAACCATTTCTG
2885 SEQ ID N0:7070 -1 -20.9 62.9 -18.5 -1.3 -6.3
GCCTTCTTGGAAATAGTAAT
2921 SEQ ID N0:7071 -1 -20.5 61.3 -18.9 -0.3 -3.2
CAGGATTTTGCCAACTTGAA
3046 SEQ 2D N0:7072 -1 -21.7 62.9 -20.1 -0.3 -3.5
CCAACATGAAAACAATAAGG
3351 SEQ ID N0:7073 -1 -15.8 49.6 -14.8 0 -5.2
TGACCAACATGAAAACAATA
3354 SEQ ID N0:7074 -1 -16.1 50.4 -15.1 0 -5.2
331
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Tnter-
total dupleac Tm target molecularmolecular
of
Positionoligo bindingformationDupleacstructureoligo oligo
GATTACGTATTTTTCAACAC
3707 SEQ ID N0:7075 -1 -18.2 56.7 -17.2 0 -6.1
CTCAACAATACTGTAGCAGG
4064 SEQ ID N0:7076 -1 -20.9 62.6 -l9 -0.7 -5.3
CTGAGAAGGATCATGAACAC
4108 SEQ ID N0:7077 -1 -19.3 58.6 -17.6 -0.5 -6.9
AATGAATATATAGGTAAAGA
4208 SEQ ID N0:7078 -1 -13.6 46.8 -12.6 0 -3.9
ACACCCATGATGCTAAAGAT
4513 SEQ ID N0:7079 -1 -22 62.7 -21 0 -4.4
GCCTGACAGTCACTCAAATT
4609 SEQ ID N0:7080 -1 -23.4 67.8 -22.4 0 -7.1
ACAAAATCAAAGACCATTCC
5020 SEQ ID N0:7081 -1 -18.5 55.3 -17.5 0 -2.8
TAGTGAAGTAGTAGTGTCTG
5211 SEQ TD N0:7082 -1 -20.3 65.1 -19.3 0 -2.3
TCACTCGGAACAAGGTAGGG
5319 SEQ ID N0:7083 -1 -23.2 66.7 -22.2 0 -2.9
TTTTAACATAGGCAAAGTTG
5496 SEQ ID N0:7084 -1 -17.5 55.1 -16.5 0 -4
GGAACAAGCAGATCATGCTG
5562 SEQ ID N0:7085 -l -22.2 64.7 -18.4 -2.8 -10.6
AGTTCTCCAGGATGACCGCG
5772 SEQ ID N0:7086 -1 -27.7 75.3 -25.3 -1.3 -6.6
TTATAGTTACTTGATATATT
6235 SEQ ID N0:7087 -1 -15.8 52.8 -14.8 0 -4.3
AGACTAAAATACTTTCAAAA
7068 SEQ ID N0:7088 -1 -13.3 45.9 -12.3 0 -2.5
AACAGACTAAAATACTTTCA
7071 SEQ ID N0:7089 -1 -15.6 50.7 -14.6 0 -2.5
TCTAAAGCAATACTTTAGAT
7276 5EQ ID N0:7090 -1 -16.7 53.6 -11.5 -4.2 -9.9
TTACATAACATAGGGTATTT
7372 SEQ ID N0:7091 -1 -17.8 56.3 -16.8 0 -3.3
TTTACATAACATAGGGTATT
7373 SEQ ID N0:7092 -1 -17.8 56.3 -16.8 0 -3.3
GACAAATAAAGTTGATTATA
7861 SEQ ID N0:7093 -1 -13.8 47.1 -12.3 -0.1 -3.7
TAAAAAAAAACATCTATGAA
8155 SEQ ID N0:7094 -1 -9.9 39.4 -8.9 0 -3.8
ATGGCTAAAAAGAACAAAGT
8260 SEQ ID N0:7095 -1 -15.4 49.5 -14.4 0 -3.7
TGTGAACTTGATCCTTTGCA
8690 SEQ ID N0:7096 -1 -22.9 67 -21.9 0 -4.8
AGAATGTAACATTTATTAGC
8847 SEQ ID N0:7097 -1 -16.5 53.5 -14.6 -0.8 -6.5
TCCACTGAGAATAAGAGTTT
8987 SEQ ID N0:7098 -1 -19.7 60.2 -18.7 0 -2.8
ATATCCCTAGAAGAGATTCT
329 SEQ ID N0:7099 -0.9 -21.2 63.7 -18.2 -2.1 -6
TCACAGCACCTTTTTCCGGA
393 SEQ ID N0:7100 -0.9 -27 74.6 -25.6 0 -8
GCTCAAGGTCATAAATACAC
896 SEQ ID N0:7101 -0.9 -19.7 59.9 -18.8 0 -2.8
AGTCGAAATAGAGACAGGAA
1588 SEQ ID N0:7102 -0.9 -18.5 56.6 -16.1 -1.4 -5
CAAATTCACCAAATAAAATG
1706 SEQ ID N0:7103 -0.9 -13.6 45.7 -12.7 0 -3.1
332
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGTGAGTCTCTCCTGCTTTC
2284 SEQ ID N0:7104 -0.9 -26.2 80.1 -24.7 -0.3 -4.6
CACAGTGCTGTGCATCTTCC
2396 SEQ ID N0:7105 -0.9 -27 78.3 -24.3 -1.2 -11.5
AGTTCTTCCATTGTGTTGGT
2608 SEQ ID N0:7106 -0.9 -24.8 75.3 -23.2 -0.4 -3.7
TGGCAATGATCTTGAGAACC
2892 SEQ ID N0:7107 -0.9 -21.7 63.3 -20.1 -0.4 -6.2
TTACCAAAGAGCTGCATGCC
3169 SEQ ID N0:7108 -0.9 -24.9 69.4 -23 -0.8 -9.1
ATGAAAACAATAAGGCACAT
3346 SEQ ID N0:7109 -0.9 -16.3 51.1 -15.4 0 -4
GACCATGACCAACATGAAAA
3359 SEQ ID N0:7110 -0.9 -19.7 56.9 -16.5 -2.3 -5.9
TTCATTGTCATCATCAGTAG
3452 SEQ ID N0:7111 -0.9 -20.7 65.3 -19.8 0 -2.4
CTGCAATCTGCAGATTATTC
3474 SEQ ID N0:7112 -0.9 -21.4 64.5 -17 -3.5 -14
CACTGCTGAACTCTTCAGTA
3819 SEQ ID N0:7113 -0.9 -22.9 68.4 -19.4 -2.6 -7.7
ACATCAACTGTGCTTCCTTC
3889 SEQ ID N0:7114 -0.9 -24.2 71.1 -23.3 0 -3.9
GCAACCCATTTGAGAAGCAT
4234 SEQ ID N0:7115 -0.9 -23.9 66.9 -22.3 -0.4 -4.6
AGCAACCCATTTGAGAAGCA
4235 SEQ ID N0:7116 -0.9 -23.9 67.1 -22.3 -0.4 -4.6
CCATGATGCTAAAGATCAAC
4509 SEQ ID N0:7117 -0.9 -19.5 58.1 -17.8 -0.6 -5.4
AACAATGAACACTAGGTTGA
5153 SEQ ID N0:7118 -0.9 -18.2 56 -16.5 -0.6 -6
GGTAGGGGACACAGAATACT
5306 SEQ ID N0:7119 -0.9 -22.8 67 -21.3 -0.3 -3.2
ACAAGGTAGGGGACACAGAA
5310 SEQ ID N0:7120 -0.9 -22.2 64.9 -21.3 0.5 -2.1
ATTCGGCCAATCCTGGCAAG
5344 SEQ ID N0:7121 -0.9 -26.6 71.8 -22.2 -3.5 -10.3
ATCCCCTTTGCTCCTTTGAT
5374 SEQ ID N0:7122 -0.9 -28.3 78 -27.4 0 -3.6
AACTGACAAAAAAGAAAATC
5712 SEQ ID N0:7123 -0.9 -11.3 41.8 -10.4 0 -2.2
AATTCTTTGTTTCTTTTTAC
6471 SEQ ID N0:7124 -0.9 -17.9 58.2 -17 0 -2.3
ACAAAGATAATTCTTTGTTT
6479 SEQ ID N0:7125 -0.9 -16.1 52.5 -10.5 -4.7 -11
AACATAACAGACTAAAATAC
7076 SEQ ID N0:7126 -0.9 -13.3 45.8 -12.4 0 -2
GAGATACCATATGATACTCA
7734 SEQ ID N0:7127 -0.9 -20 60.7 -19.1 0 -6.6
AATATATTATAACAAAGAAA
8046 SEQ ID N0:7128 -0.9 -10.2 40 -9.3 0 -5.3
GACTAGTCTGCATACGTAAA
8191 SEQ ID N0:7129 -0.9 -20.6 61.7 -18.9 0 -9.4
ATAAGACTAGTCTGCATACG
8195 SEQ ID N0:7130 -0.9 -20.1 60.9 -17.5 0 -11.5
AATAGTTTTGTAAAAAGAAT
8359 SEQ ID N0:7131 -0.9 -12.5 44.6 -10.3 -1.2 -4.3
AATAGCAATTCCCTGCATGC
8401 SEQ ID N0:7132 -0.9 -24.5 68.8 -21.9 -1.7 -8.7
333
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TTTTTGACCACAGAGGTTTA
95 SEQ ID N0:7133 -0.8 -21.7 65.3 -19.3 -1.5 -7.1
TCTGGCAGCTGTTCAGCTTT
128 SEQ ID N0:7134 -0.8 -27 80 -24.3 -1.8 -Z1
TATGAATTACAGCATAACAA
188 SEQ ID N0:7135 -0.8 -16 51.3 -15.2 0 -4.1
AAGAGATTCTTTGCTCCTTT
319 SEQ ID N0:7136 -0.8 -22.3 67.1 -20.8 -0.4 -5.3
TGGGGGTACCAACAGTGCCT
479 SEQ ID N0:7137 -0.8 -28.7 78.5 -25.6 -2.3 -8.8
TCAGGTCCTGGGGGTACCAA
487 SEQ ID NO:7138 -0.8 -28.7 79.9 -24.6 -3.3 -12.6
AGCAGCAAGAGATTCTCTAG
524 SEQ ID N0:7139 -0.8 -21.9 66.8 -19.8 -1.2 -9.3
AGAATGTACCAAAATCTTGA
836 SEQ ID N0:7I40 -0.8 -17.6 54.5 -16.2 -0.3 -4
GAATGTGTACTCTACATTCT
935 SEQ TD N0:7141 -0.8 -20.4 63.2 -16.4 -3.2 -11.2
GAATGACTGAAATTGTTTTC
1143 SEQ ID N0:7142 -0.8 -16.8 53.8 -14.9 -1 -3.6
CTGGATCAGGGCCCCCACAA
1178 SEQ ID NO:7143 -0.8 -30.9 80.1 -28.9 -0.3 -10.4
AAACACGCTCAGACAGAACA
1235 SEQ ID N0:7144 -0.8 -20.6 59.8 -19.8 0 -3.1
AGACAGGAAAGCCCAGCTAA
1577 SEQ ID N0:7145 -0.8 -24.1 67.3 -22.4 -0.8 -5
GTCGAAATAGAGACAGGAAA
1587 SEQ ID N0:7146 -0.8 -17.8 54.7 -I6.2 -0.6 -5
GCCAGGATCAAATTCACCAA
1714 SEQ ID N0:7147 -0.8 -23.4 65.6 -22 -0.3 -4.5
ACAGCTCTCCTAACCCACCT
1896 SEQ ID N0:7148 -0.8 -29.2 78.6 -28.4 0 -4.4
TTTCCAACAGCTCTCCTAAC
1902 SEQ ID N0:7149 -0.8 -24 69.2 -23.2 0 -4.4
AAAGCTGTCTCTCTCTCCTT
2021 SEQ ID N0:7150 -0.8 -25.1 74.8 -24.3 0 -5.1
AAAGTCATTTTCAGATCCAA
2231 SEQ ID N0:7151 -0.8 -19.3 59.1 -18.5 0 -4.5
ATTCTTCAAGTTCTTCCATT
2616 SEQ ID NO:7152 -0.8 -21.8 66.8 -21 0 -2.9
TCTTGGAAATAGTAATAAGG
2917 SEQ ID N0:7153 -0.8 -15.9 51.7 -15.1 0 -2.8
CCAGCCTTCTTGGAAATAGT '
2924 SEQ ID N0:7154 -0.8 -24.2 69 -22.8 -0.3 -4.9
TACCAAAGAGCTGCATGCCG
3168 SEQ ID N0:7155 -0.8 -25.6 69.1 -23.8 -0.8 -9.1
TCCACTCTCCACACAGCACG
3285 SEQ ID N0:7156 -0.8 -27.9 76.1 -27.1 0 -4.1
TTCTGACTCACTGCTGAACT
3827 SEQ ID N0:7157 -0.8 -23 68 -22.2 0 -3.6
ATGAATATATAGGTAAAGAC
4207 SEQ ID N0:7158 -0.8 -14.5 48,g -13.7 0 -4.2
CATGATGCTAAAGATCAACC
4508 SEQ ID N0:7159 -0.8 -19.5 58,1 -17.9 -0.6 -5.4
AATTGTTAACATCACTAATG
4593 SEQ ID N0:7160 -0.8 -15.8 51.4 -14.3 -0.3 -8.3
TTGCCAAGAGCCTGACAGTC
4618 SEQ ID N0:7161 -0.8 -26.3 74.5 -24.7 -0.6 -5.7
334
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGCTTGCTTGCCAAGAGCCT
4625 SEQ ID N0:7162 -0.8 -28.7 79.3 -25.9 -2 -7.4
AAGATGATAAAGATGACAAA
4813 SEQ ID N0:7163 -0.8 -13.5 46.1 -12.7 0 -2.5
GAATGACCCAAAGATGATAA
4823 SEQ ID N0:7164 -0.8 -18.2 54.5 -17.4 0 -2.1
TGATATCAAAGACTTGTCTG
5043 SEQ ID N0:7165 -0.8 -18.3 57.5 -15.7 -1.4 -11.5
GAACACTAGGTTGATCCGGG
5147 SEQ ID N0:7166 -0.8 -24.3 68.6 -22.3 -1.1 -7.4
TATCATCTCAGCCAGAAACA
5282 SEQ ID N0:7167 -0.8 -21.8 64.2 -21 0 -3.1
CAGGAAGGGACATCATCAAA
5412 SEQ ID N0:7168 -0.8 -20.5 60.6 -19.1 -0.3 -2.9
AGGTGCTAGCAATCCATCCC
5603 SEQ ID N0:7169 -0.8 -28.1 77.9 -25.6 -0.2 -11.5
GTGTCAGGGTCACAGTCGGG
5641 SEQ ID N0:7170 -0.8 -27.9 81.5 -26.2 -0.7 -4.4
TGCCAGGGTGAATTGTGTCA
5655 SEQ ID N0:7171 -0.8 -25.6 73.7 -24.8 0 -3.8
AAGTTCTCCAGGATGACCGC
5773 SEQ ID N0:7172 -0.8 -26.2 73.1 -24 -1.3 -5.6
AGACAGTGGATCCGGTCACC
6001 SEQ ID N0:7173 -0.8 -27.4 76.5 -25 -1.1 -10.8
GTTATAGTTACTTGATATAT
6236 SEQ ID N0:7174 -0.8 -16.9 55.6 -16.1 0 -4.1
ACAGTCAGTTTGGCATGGAC
6559 SEQ ID N0:7175 -0.8 -24.3 72.4 -22.8 -0.5 -5.4
TTACAAAAATAGTGACATAG
6892 SEQ ID NO:7176 -0.8 -14 47.5 -13.2 0 -3.5
GAAACTGTAGCCATTACAAT
7019 SEQ ID N0:7177 -0.8 -19.7 58.8 -18 -0.7 -3.7
TAATTGACATAGACTATCAG
7353 SEQ ID N0:7178 -0.8 -16.8 54.1 -16 0 -3.3
ATAACTATTTACATAACATA
7380 SEQ ID N0:7179 -0.8 -14.2 48.2 -13.4 0 -1.7
AATGAATGATACAGGATACA
7511 SEQ ID N0:7180 -0.8 -16.8 53.1 -16 0 -2.4
ATACTACAAAAGTTGAATAA
8172 SEQ ID N0:7181 -0.8 -13.5 46.4 -12 -0.4 -4.2
CATACGTAAATACTACAAAA
8181 SEQ ID N0:7182 -0.8 -14.2 47.1 -13.4 0.1 -6.6
TTGTGCAAAP.AACAAAAATT
8321 SEQ ID N0:7183 -0.8 -12.5 43.8 -11 -0.5 -5.4
AACAAAAACAAAAAACCCCA
8502 SEQ ID N0:7184 -0.8 -15.7 48.3 -14.9 0 0
TAACAAAGAATGTAACATTT
8853 SEQ ID N0:7185 -0.8 -13.7 46.6 -12 -0.8 -7.2
CACTGAGAATAAGAGTTTGG
8985 SEQ ID N0:7186 -0.8 -18.5 57.5 -17.7 0 -2.8
CTGGCAGCTGTTCAGCTTTT
127 SEQ ID N0:7187 -0.7 -26.7 78.5 -24.3 -l.6 -10.8
CTAACAGGGTTTAGTGGAGT
805 SEQ ID N0:7188 -0.7 -22.5 68.2 -21.8 0 -3.6
TGCTCAAGGTCATAAATACA
897 SEQ ID N0:7189 -0.7 -19.5 59.3 -18.8 0 -3.6
AATGACACTGAAATCCAGCC
1046 SEQ ID N0:7190 -0.7 -22 62.7 -20.1 -1.1 -4
335
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAACTCTGTCACATATGCCA
1070 SEQ ID N0:7191 -0.7 -22.4 65.2 -21.7 0 -6.5
GACTGGATCAGGGCCCCCAC
1180 SEQ ID N0:7192 -0.7 -31.7 83.5 -29.6 -0.7 -10.5
CATTTTCAGATCCAACATCC
2226 SEQ ID N0:7193 -0.7 -22.4 65.4 -21.2 -0.1 -4.5
GCCCTGGCACCATCCTGGAT
2364 SEQ ID N0:7194 -0.7 -32.4 84.6 -29.9 -1.8 -10.4
AACCACACCATTGCAATCCA
2414 SEQ ID N0:7195 -0.7 -25 67.8 -23.7 0 -8.6
AATCTGGTAAGAGCTTAACC
2525 SEQ ID N0:7196 -0.7 -20.6 61.8 -19.2 -0.5 -6.3
ATTTAAGACAATGCAAATAG
2771 SEQ ID N0:7197 -0.7 -14.8 48.9 -13.5 -0.3 -5.6
AGTGTGGGCCAGGATTTTGC
3055 SEQ ID N0:7198 -0.7 -27.2 78.3 -26 0 -7.6
CTAGAGCCCCCACAGAATTG
3099 SEQ ID N0:7199 -0.7 -26.6 72 -25.9 0 -3.1
ATGACCATGACCAACATGAA
3361 SEQ ID N0:7200 -0.7 -21.1 60.3 -18.6 -1.8 -5.4
ATTCATTTCATTGTCATCAT
3458 SEQ ID N0:7201 -0.7 -20 62.7 -19.3 0 -2.4
CTTCCTACTGCAATCTGCAG
3481 SEQ ID N0:7202 -0.7 -24.7 71.2 -20 -4 -10.9
AAATCCATAAGCAACCCATT
4244 SEQ ID N0:7203 -0.7 -21.5 60.7 -20.8 0 -4.1
CAACCAGAAGATGAGACAGA
4493 5EQ ID N0:7204 -0.7 -20.1 59.6 -19.4 0 -2.4
TTGTTAACATCACTAATGTC
4591 SEQ ID N0:7205 -0.7 -18.1 57.3 -15.8 -1.5 -9.5
ATTGTTAACATCACTAATGT
4592 SEQ TD N0:7206 -0.7 -17.7 56 -15.6 -1.3 -9.5
GCATACATAATATCCATCCA
4726 SEQ ID N0:7207 -0.7 -22 63.8 -21.3 0 -3.4
AAATCAAAGACCATTCCTTG
5017 SEQ ID N0:7208 -0.7 -19.3 57.3 -18.6 0 -2.8
TCAAAGACTTGTCTGGTTAC
5038 SEQ TD N0:7209 -0.7 -20.4 62.9 -18.2 -1.4 -7
AAGAATAGGTGCTAGCAATC
5609 SEQ ID N0:7210 -0.7 -19.9 60.7 -17.8 0 -10.8
CACTATTAAGAATAGGTGCT
5616 SEQ ID N0:7211 -0.7 -19.3 59.3 -16.9 -1.7 -6.7
AGTCGGGTGGTGCACTATTA
5628 5EQ TD N0:7212 -0.7 -25.5 74.3 -23.5 -1.1 -9.5
GATGTAACTGACAAAAAAGA
5717 SEQ TD N0:7213 -0.7 -14.5 47.9 -13 -0.6 -3.4
TGCTATGAGAAGAGGAGGAT
5933 SEQ ID N0:7214 -0.7 -21.1 63.5 -20.4 0 -3.6
AAGGCAAATAAAATATCAAG
6019 SEQ ID N0:7215 -0.7 -13.3 45.6 -12.6 0 -4
ACACGCTTTGTAAAGGCAAA
6031 SEQ ID N0:7216 -0.7 -20.6 59.7 -17.9 -2 -6.4
TCTCCACTCTCACACAAAAC
6049 SEQ ID N0:7217 -0.7 -21.8 63.8 -21.1 0 0
TACTTGATATATTTTTTAAC
6228 SEQ TD N0:7218 -0.7 -14.6 49.7 -13.9 0 -4.3
TTCTTTGTTTCTTTTTACTT
6469 SEQ ID N0:7219 -0.7 -19,6 62.9 -18.9 0 -2.2
336
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total dupleac Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
CTTGTCAACGTTGATACCCT
6653 SEQ ID N0:7220 -0.7 -24.3 68.4 -21.3 -0.1 -12.8
AACAAATTTTGTAAAAATAT
6828 SEQ TD N0:7221 -0.7 -10.9 41.2 -8.5 -1.7 -8.7
ATAACAGACTAAAATACTTT
7073 SEQ ID N0:7222 -0.7 -14.2 47.9 -13.5 0 -2
ATGGCAAAGCAATACTGCAG
7315 SEQ ID N0:7223 -0.7 -21.4 62.2 -18.2 -2.5 -9.3
ATTTACATAACATAGGGTAT
7374 SEQ ID N0:7224 -0.7 -17.7 56 -l7 0 -3.3
TTGTAAATAGCTTCAAATTA
7683 SEQ ID N0:7225 -0.7 -15.6 51.7.-14.9 0 -4.6
AGTTTGGAATTGTGATTAAA
7959 SEQ ID N0:7226 -0.7 -16.8 53.8 -16.1 0 -3.2
AAGTTTGGAATTGTGATTAA
7960 SEQ ID N0:7227 -0.7 -16.8 53.8 -16.1 0 -3.1
GTTTGTGCAAAAAACAAAAA
8323 SEQ ID N0:7228 -0.7 -13.7 46 -11 -2 -9.4
GCATTACAACTGGAGTTTTC
9005 SEQ ID N0:7229 -0.7 -21.3 64.7 -20.6 0 -5.2
TAGATCCAAATTGTCTTTAA
9031 SEQ ID N0:7230 -0.7 -17.8 55,8 -17.1 0 -4.6
TTCCTCTGGCAGCTGTTCAG
132 SEQ ID N0:7231 -0.6 -27.5 80.5 -26.3 0 -8.5
TCCATAATCTCTGATAAAAC
215 SEQ ID N0:7232 -0.6 -17.1 53.8 -16.5 0 -3.3
CCACTCTACTATGAATCCTT
290 SEQ ID N0:7233 -0.6 -22.9 66.5 -22.3 0 -2.2
CAGTAAGCCACTCTACTATG
297 SEQ ID N0:7234 -0.6 -22.3 66.1 -21.7 0 -4.7
CGAATTACCTTAGATAGTCA
410 SEQ ID N0:7235 -0.6 -20 60.2 -19.4 0 -3.2
ACATTCTTTGTCCAGTCAGG
922 SEQ ID N0:7236 -0.6 -24.3 73 -23.7 0 -3.8
CAAAGGTATAGATTCCAGTG
954 SEQ ID N0:7237 -0.6 -20.1 61 -18.8 -0.4 -3.6
TCAGGGCCCCCACAATGGTC
1173 SEQ ID N0:7238 -0.6 -31 82.1 -28.6 -0.7 -11.8
AAGGTCCACCCACCAAGGAA
2433 SEQ ID N0:7239 -0.6 -27 71.7 -25.2 -1.1 -5.8
CATGGCGGACATTTCTGTCT
2638 SEQ ID N0:7240 -0.6 -25.2 72.2 -21.9 -2.7 -8.6
AGCATGGCGGACATTTCTGT
2640 SEQ ID N0:7241 -0.6 -25.7 73.1 -23.9 -1.1 -6.5
TCCATAACAATTAAATTCAC
2728 SEQ ID N0:7242 -0.6 -16.1 51.4 -15.5 0 -3.1
AAAAATGAAGACGATGATGG
3140 SEQ ID N0:7243 -0.6 -15.1 48.5 -14.5 0 -3.5
CAAAGAGCTGCATGCCGACC
3165 SEQ ID N0:7244 -0.6 -26.5 70.8 -24.9 -0.8 -9.1
ACCAAAGAGCTGCATGCCGA
3167 SEQ ID N0:7245 -0.6 -26.5 70.8 -24.9 -0.8 -9.1
CATGAAAACAATAAGGCACA
3347 SEQ ID N0:7246 -0.6 -17 52.3 -16.4 0 -4
CAACCCATTTGAGAAGCATT
4233 SEQ ID N0:7247 -0.6 -22.2 63.3 -21.6 0 -4.1
GATGAGACAGACCAACAGCA
4484 SEQ ID N0:7248 -0.6 -22.9 65.8 -22.3 0 -4.1
337
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AAGATGAGACAGACCAACAG
4486 SEQ ID N0:7249 -0.6 -19.7 58.9 -19.1 0 -2.4
CTGCATACATAATATCCATC
4728 SEQ ID N0:7250 -0.6 -20.2 60.7 -19.6 0 -4.9
AGAATGACCCAAAGATGATA
4824 SEQ ID N0:7251 -0.6 -18.9 56.4 -18.3 0 -2.1
CCAGTGAACAGAACAATGAA
5164 SEQ TD N0:7252 -0.6 -18.7 55.9 -17.4 -0.5 -3.9
GAAACATACCTACAATGGAG
5268 SEQ ID N0:7253 -0.6 -18.6 56.1 -17.5 -0.1 -4
CTATOATCTCAGCCAGAAAC
5283 SEQ ID N0:7254 -0.6 -22 65 -21.4 0 -3.6
TCTATCATCTCAGCCAGAAA
5284 SEQ ID NO:7255 -0.6 -22.2 65.9 -21.6 0 -3.6
AATTGTGTCAGGGTCACAGT
5645 SEQ ID N0:7256 -0.6 -23.7 71.7 -21.5 -1.6 -5.8
CAAATAAAATATCAAGACAG
6015 SEQ ID N0:7257 -0.6 -12.5 44.1 -11.9 0 -2.8
AAACACGCTTTGTAAAGGCA
6033 SEQ ID N0:7258 -0.6 -20.6 59.7 -18 -2 -5.8
AAAAGATAACATCTGAAATT
6199 SEQ ID NO:7259 -0.6 -13 45.2 -11.5 -0.8 -4.4
TAAAAGATAACATCTGAAAT
6200 SEQ ID N0:7260 -0.6 -12.6 44.4 -11.1 -0.8 -4.2
TCTTGTATAGGCACTGACTA
6594 SEQ ID N0:7261 -0.6 -22.2 67.4 -20.9 -0.4 -4.8
CTAAAATACTTTCAAAATTA
7065 SEQ ID N0:7262 -0.6 -12.3 44 -11.7 0 -3.2
GAATACTTTGCATAAAAATA
7151 SEQ ID N0:7263 -0.6 -14 47.2 -13.4 0 -5.1
TCTGAAACTTAGAATAAAAT
7188 SEQ ID N0:7264 -0.6 -12.9 45.2 -12.3 0 -2.3
GCTCTGAAACTTAGAATAAA
7190 SEQ ID N0:7265 -0.6 -16.3 52 -15.7 0 -2.8
CTATTTACATAACATAGGGT
7376 SEQ ID N0:7266 -0.6 -18.6 58 -18 0 -2.8
CATATTTGATTTAATAGAAG
7451 SEQ ID N0:7267 -0.6 -14 47.9 -13.4 0 -2.6
AATTAAAAGTGCAAAAGTAA
7709 SEQ ID N0:7268 -0.6 -12.8 44.7 -12.2 0 -5.4
TATGTACAAAATGCTGACAA
7876 SEQ ID N0:7269 -0.6 -16.9 52.9 -16.3 0 -6.8
TGATGTCATCAACCTGAAAA
7905 SEQ ID N0:7270 -0.6 -18.9 56.9 -17.5 -0.6 -6.2
ATTATCCATTGAAAAATCTT
7990 SEQ ID N0:7271 -0.6 -16.2 51.7 -14.9 -0.5 -3.4
ATAAAAAAAAACATCTATGA
8156 SEQ ID N0:7272 -0.6 -10.6 40.6 -10 0 -3.8
CGTAAATACTACAAAAGTTG
8177 SEQ ID N0:7273 -0.6 -14.9 48.7 -13.6 -0.4 -3.5
GTCAGATCAAGCACAGGTTT
8559 SEQ ID N0:7274 -0.6 -23.3 70 -22.7 0 -5.4
AAACAAAGAGACCTTTCCAG
31 SEQ ID N0:7275 -0.5 -19.7 58.2 -18.1 -1 -4.1
CTCTGGCAGCTGTTCAGCTT
129 SEQ ID N0:7276 -0.5 -27.8 81.7 -25.4 -1.8 -11
TAGCAGCAAGAGATTCTCTA
525 SEQ ID N0:7277 -0.5 -21.6 66 -19.8 -1.2 -9.3
338
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTATAGATTCCAGTGAATGT
949 SEQ ID N0:7278 -0.5 -20.7 63.5 -18.8 -1.3 -5.5
AAGGTATAGATTCCAGTGAA
952 SEQ ID N0:7279 -0.5 -20 61.1 -18.8 -0.4 -3.9
AAAGGTATAGATTCCAGTGA
953 SEQ ID N0:7280 -0.5 -20 61.1 -18.8 -0.4 -3.9
ACAATGACACTGAAATCCAG
1048 SEQ ID N0:7281 -0.5 -19.1 57.1 -17.6 -0.9 -4.9
TCATCACATCAGAAAGCTTC
1206 SEQ ID N0:7282 -0.5 -20.6 62.8 -20.1 0 -7
CCAAAACATAAAAGTGACTG
1437 SEQ ID N0:7283 -0.5 -16 50.3 -15.5 0 -3.1
ATCTCTTGAAGCAGCTGATG
1865 SEQ ID N0:7284 -0.5 -22.4 67.1 -21.2 0 -8.7
CCGACCTCTGAAACTGAAAA
2201 SEQ ID N0:7285 -0.5 -20.6 58.2 -20.1 0 -2.8
CACAAACAGTGAGTCTCTCC
2291 SEQ ID N0:7286 -0.5 -23.1 68.3 -21.7 -0.8 -4.8
GCATCTCCATTGAAATCTGG
2538 SEQ ID N0:7287 -0.5 -22.7 66 -22.2 0 -3.4
ACCATGACCAACATGAAAAC
3358 SEQ ID N0:7288 -0.5 -19.3 56.2 -16.5 -2.3 -5.9
TGACCATGACCAACATGAAA
3360 SEQ ID N0:7289 -0.5 -20.4 58.5 -17.6 -2.3 -5.9
TAAATGAACTCAATAATAAG
3414 SEQ ID N0:7290 -0.5 -11.7 42.8 -11.2 0 -3.9
ACCTACACCACTGGTGGTTC
3677 SEQ ID N0:7291 -0.5 -27 76.5 -24.4 -l.7 -12
TAGGTAAAGACTTTGTCAGC
4198 SEQ ID N0:7292 -0.5 -20.4 63.1 -18.6 -1.2 -5.2
TAACATCACTAATGTCAAAC
4587 SEQ ID N0:7293 -0.5 -16.2 52 -14.1 -1.5 -4.3
TCACTCAAATTGTTAACATC
4600 SEQ ID N0:7294 -0.5 -17.6 55.7 -16.6 0 -8.3
GTCGGGTGGTGCACTATTAA
5627 5EQ ID N0:7295 -0.5 -24.8 71.5 -23.4 -0.3 -9.5
TGAGAAGAGGAGGATCCAGG
5928 SEQ ID N0:7296 -0.5 -23 67.4 -19.9 -2.6 -9
CAATTGATCACAAAGATAAT
6488 SEQ ID N0:7297 -0.5 -14.9 48.9 -13.5 -0.8 -6.6
TGGTAATAAAAACAGCAACC
6674 SEQ ID N0:7298 -0.5 -17.2 52.7 -16.7 0 -4.1
CAAACATAACAGACTAAAAT
7078 SEQ ID N0:7299 -0.5 -13.4 45.6 -12.9 0 -2
AAAATTTGCACTTGCTGAAA
7173 SEQ ID N0:7300 -0.5 -17.7 54.2 -16.6 -0.3 -6.5
TCCAGAGAGATACCATATGA
7740 SEQ ID N0:7301 -0.5 -21.8 64.3 -21.3 0 -6
AATATGAAGAATAGGTTTTG
7793 SEQ ID N0:7302 -0.5 -15.2 50.3 -14.7 0 -2.7
CAAAATGCTGACAAATAAAG
7870 SEQ ID N0:7303 -0.5 -13.7 46 -13.2 0 -3.6
GCATGCAGTTCTTCAATACA
8387 SEQ ID N0:7304 -0.5 -22.7 67.6 -21.3 0 -9.5
CAAAAAACCCCAGA
8500 SEQ ID N0:7305 -0.5 -16.8 50.3 -16.3 0 0
GGTTTTATTAATTATATATA
8544 SEQ ID N0:7306 -0.5 -14.4 49.4 -13.9 0 -5.2
339
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
AGTTAATATAAATTCTCAAT
8927 SEQ ID N0:7307 -0.5 -14.1 48.2 -13.6 0 -3.1
TTTCCACTGAGAATAAGAGT
8989 SEQ ID N0:7308 -0.5 -19.7 60.2 -19.2 0 -2.9
TCAAAGGTATAGATTCCAGT
955 SEQ ID N0:7309 -0.4 -20.5 62.5 -20.1 0.4 -2.8
GACACTGAAATCCAGCCAGT
1043 SEQ ID N0:7310 -0.4 -24.6 69.2 -23 -1.1 -6.2
CACAATGACACTGAAATCCA
1049 SEQ ID N0:7311 -0.4 -19.8 58.1 -19.4 0 -3.1
ATCAGGGCCCCCACAATGGT
1174 SEQ ID N0:7312 -0.4 -30.6 80.3 -28.4 -0.7 -11.8
CATCAGAAAGCTTCTTTACC
1200 SEQ ID N0:7313 -0.4 -21.2 63.4 -19.9 -0.7 -7
GACAGAACACAGTCAGGATC
1224 SEQ ID N0:7314 -0.4 -21.7 65.4 -20.5 -0.6 -5.3
CATCCAAAACATAAAAGTGA
1440 SEQ ID N0:7315 -0.4 -16 50.4 -15.6 0 -2.9
AATGAGCCCAAGAAAATGAC
1690 SEQ ID N0:7316 -0.4 -l9 55.9 -18.6 0 -2.4
TTGTTTCCTTCAAGGTGCTC
1999 SEQ ID N0:7317 -0.4 -24.8 74.1 -23.6 -0.6 -5.3
GGTAAGAGCTTAACCTTCTC
2520 SEQ ID N0:7318 -0.4 -22.7 67.9 -21.7 -0.3 -7.2
ATCTCCATTGAAATCTGGTA
2536 SEQ ID N0:7319 -0.4 -21.1 63.2 -20.1 -0.3 -3.7
AATGGATCCATAACAATTAA
2734 SEQ ID N0:7320 -0.4 -16.5 51.8 -14.1 0 -12.2
AAATGGATCCATAACAATTA
2735 SEQ ID N0:7321 -0.4 -16.5 51.8 -14.1 0 -12.2
ATTTCTGCTGTGAAAATCCC
2872 SEQ ID N0:7322 -0.4 -22.3 64.6 -21 -0.7 -5
GCCAGAAAGAGGTTCAGAAC
3394 SEQ ID N0:7323 -0.4 -22 64.6 -20.3 -1.2 -7.1
AATGAACTCAATAATAAGGC
3412 SEQ ID N0:7324 -0.4 -15.7 50.6 -15.3 0 -3.9
GATTATTCATTTCATTGTCA
3462 SEQ ID N0:7325 -0.4 -19.3 61 -18.9 0 -2.4
AGATTATTCATTTCATTGTC
3463 SEQ ID N0:7326 -0.4 -18.6 59.9 -17.7 -0.2 -3
GTATTATTGGACATGCAGCT
3610 SEQ ID N0:7327 -0.4 -22.7 67.7 -22.3 0 -5.5
AGTATTTAAGTTTTCAAAGT
3803 SEQ ID N0:7328 -0.4 -16.5 54.3 -16.1 0 -2.4
AACTCTTCAGTATTTAAGTT
3811 SEQ ID N0:7329 -0.4 -18.3 58.7 -17.4 -0.2 -3.6
AAGTCTTCTTCGGGTTCAGT
3940 SEQ TD N0:7330 -0.4 -24.5 73.9 -24.1 0 -4.4
GACTTTGTCAGCATATTCTA
4190 SEQ ID N0:7331 -0.4 -21.5 66.3 -20.4 -0.4 -5.1
GTTTGAAATCCATAAGCAAC
4249 SEQ ID N0:7332 -0.4 -18.7 56.7 -18.3 0 -4.1
ATATGTTTGAAATCCATAAG
4253 SEQ ID N0:7333 -0.4 -16.4 52.4 -16 0 -3.5
GCTACCAGGCTAACCAAAGA
4318 SEQ ID N0:7334 -0.4 -24.3 67.5 -22.5 -1.3 -5
CAGAGTGAAGAATGACCCAA
4832 SEQ ID NO:7335 -0.4 -21.1 60.9 -20.7 0 -2.1
340
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ACAATGAACACTAGGTTGAT
5152 SEQ ID N0:7336 -0.4 -18.9 57.8 -17.7 -0.6 -6
AACAGAACAATGAACACTAG
5158 SEQ ID N0:7337 -0.4 -15.9 50.8 -15.5 0 -4
GCCAGAAACATACCTACAAT
5272 SEQ ID N0:7338 -0.4 -21.3 60.9 -20.9 0 -2
TTGTAATTTGGAACAAGCAG
5571 SEQ ID N0:7339 -0.4 -18.3 56.5 -16.3 -1.6 -7.1
TAACTGACAAAAAAGAAAAT
5713 SEQ ID N0:7340 -0.4 -10.6 40.5 -10.2 0 -2.2
CAGGAAGGATATGATGATGT
5732 SEQ ID N0:7341 -0.4 -19.7 59.9 -19.3 0 -2.6
ACCGCGATGTACATGTTCAC
5758 SEQ TD N0:7342 -0.4 -24.6 68.8 -23.6 0 -8.4
TGTAAAGGCAAATAAAATAT
6023 SEQ ID N0:7343 -0.4 -13.1 45.2 -12.7 0 -4
TGAAATTACGCTGAATGATA
6186 SEQ ID N0:7344 -0.4 -16.9 52.5 -16.5 0 -3.3
GTCAGTTTGGCATGGACCTC
6556 SEQ ID N0:7345 -0.4 -26.7 78 -25.8 -0.1 -5.4
TCTTGTCAACGTTGATACCC
6654 SEQ ID N0:7346 -0.4 -23.8 68.1 -21.3 0.4 -12.3
ACAGCAACCTCTTGTCAACG
6663 SEQ ID N0:7347 -0.4 -23.8 67.3 -22.8 -0.3 -4.6
GAACAACTATTCTAAAGCAA
7286 SEQ ID N0:7348 -0.4 -16.4 52 -16 0 -4.l
GCAAAAGACACATACACTGT
7475 SEQ ID N0:7349 -0.4 -19.7 58.8 -19.3 0 -3.4
ATTTTTACATTATTTATATT
7842 SEQ ID N0:7350 -0.4 -14.5 49.7 -14.1 0 -2.2
CTGACAAATAAAGTTGATTA
7863 SEQ ID N0:7351 -0.4 -15 49.4 -14.1 -0.1 -3.3
TTATGTACAAAATGCTGACA
7877 SEQ ID N0:7352 -0.4 -17.7 54.9 -17.3 0 -6.8
CTGCCAACAGCAA<~AAACAA
8517 SEQ ID N0:7353 -0.4 -18.8 54.7 -16.9 -1.4 -4.2
TATAATGCATTTAAGTAACA
8868 SEQ ID N0:7354 -0.4 -15.5 50.8 -14.4 0 -8.8
CCAAATTGTCTTTAAAAATA
9026 SEQ ID N0:7355 -0.4 -14.7 48.4 -14.3 0 -4.3
GAGAATTATGAAATACATAT
9052 SEQ ID N0:7356 -0.4 -13.8 47.1 -12.3 -1 -4.6
AGAGATTCTTTGCTCCTTTC
318 SEQ ID N0:7357 -0.3 -23.4 71.2 -22.4 -0.4 -4.2
AATATCCCTAGAAGAGATTC
330 SEQ ID N0:7358 -0.3 -19.6 59.7 -17.9 -1.3 -5.2
ATTACCTTAGATAGTCACAG
407 SEQ ID N0:7359 -0.3 -20.2 62.5 -19.9 0 -2.7
TTGGCTTTCTCTTCTGCAGC
556 SEQ ID N0:7360 -0.3 -26.5 79.1 -25.4 -0.6 -8.3
ACACCATCTCTGGAGGAATG
672 SEQ ID N0:7361 -0.3 -23.3 67.4 -21.4 -1.5 -6.1
CCAGGTCCTCCAGGGGCTCT
693 SEQ ID N0:7362 -0.3 -33.1 90.9 -31.4 -1.3 -5.6
GTTAAAATATACAAGGCAGA
787 SEQ ID N0:7363 -0.3 -16.8 53.1 -16.5 0 -4
GTTTAGTGGAGTTAAAATAT
797 SEQ ID N0:7364 -0.3 -16.7 54.2 -16.4 0 -2.8
341
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
ATAAAGAATGTACCAAAATC
840 SEQ ID N0:7365 -0.3 -14.3 47.6 -14 0 -4.2
TGCCATCACAATGACACTGA
1055 SEQ ID N0:7366 -0.3 -23 65.6 -22 -0.4 -3.8
AGTTAAATGTGCTCATTGTT
1395 SEQ ID N0:7367 -0.3 -20 61.9 -18.5 -1.1 -3.5
CCATCCAAAACATAAAAGTG
1441 SEQ TD N0:7368 -0.3 -17.4 52.7 -17.1 0 -2.9
AAATAGAGACAGGAAAGCCC
1583 SEQ ID N0:7369 -0.3 -20.6 59.9 -19.6 -0.4 -3.2
CTCAAGAGAGACTGATGAGG
2134 SEQ ID N0:7370 -0.3 -20.6 62.5 -19.2 -1 -5.1
ATAACAATTAAATTCACAAG
2725 SEQ ID N0:7371 -0.3 -13 45.3 -12.7 0 -3.1
CAATGCAAATAGTGATGGCA
2763 SEQ ID N0:7372 -0.3 -20.3 59.9 -19.2 -0.6 -5.6
GCTGTGAAAATCCCAGTAAA
2866 SEQ ID N0:7373 -0.3 -21 60.7 -20.2 -0.1 -3.5
ATGGCAATGATCTTGAGAAC
2893 SEQ ID N0:7374 -0.3 -19.7 59.6 -18.7 -0.4 -6.2
CCATGGCAATGATCTTGAGA
2895 SEQ ID N0:7375 -0.3 -22.9 66 -21.9 -0.5 0
AAAGATATTCCAGCCTTCTT
2933 SEQ TD N0:7376 -0.3 -22.3 65.3 -21.3 -0.4 -4
CTTGCAGACACATTCTTTGT
3194 SEQ ID N0:7377 -0.3 -22.7 68 -21.9 0 -8.2
ATTGATCTTGCAGACACATT
3200 SEQ ID N0:7378 -0.3 -21.1 63.7 -20.8 0 -5.2
TCATTGTCATCATCAGTAGC
3451 5EQ ID N0:7379 -0.3 -22.4 69.6 -22.1 0 -2.8
ATCCATAAGCAACCCATTTG
4242 SEQ ID N0:7380 -0.3 -23 64.6 -22.7 0 -4.1
CCACTTGAAGCAGTGCAAGA
4692 5EQ ID N0:7381 -0.3 -23.9 68.1 -21.9 -1.7 -9.6
TTCAGAGTGAAGAATGACCC
4834 SEQ ID N0:7382 -0.3 -21.6 63.4 -20.5 -0.6 -3.9
GATGTTAAACAACGCAGGAA
5426 SEQ ID N0:7383 -0.3 -19 56.4 -18.2 -0.2 -4.7
GTAGCAACACTGAAGTTCTC
5785 SEQ ID N0:7384 -0.3 -21.6 65.8 -21.3 0 -6.3
TTACGCTGAATGATAGCGGC
6181 SEQ ID N0:7385 -0.3 -23.3 65.5 -19.4 -3.6 -9.4
TTGTTATAGTTACTTGATAT
6238 SEQ ID N0:7386 -0.3 -17.3 56.5 -17 0 -2.6
CAACGTAAACCTCATTTACA
6907 SEQ ID N0:7387 -0.3 -19.5 57.5 -16.5 -2.7 -6.1
AAACTTAGAATAAAATTTGC
7184 SEQ ID N0:7388 -0.3 -13 45.3 -12.7 0 -5.2
TCACCAATATGTGACATTCT
7621 SEQ ID N0:7389 -0.3 -21.1 62.9 -19.8 -0.9 -5.6
TAAAGGTGTTTGTAAATAGC
7692 SEQ ID N0:7390 -0.3 -17.1 54.7 -16.8 0 0
AGTGTGTTTCCTTGAAATCC
7757 SEQ ID N0:7391 -0.3 -22.8 67.6 -21.7 -0.6 -4.3
ATTATATTTTTACATTATTT
7847 SEQ ID NO:7392 -0.3 -14.5 49.7 -14.2 0 -2.2
ATAGTTTTGTAAAAAGAATT
8358 SEQ ID N0:7393 -0.3 -13.3 46.3 -11.6 -1.3 -9.3
342
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mot kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GCACAGGTTTTATTAATTAT
8549 SEQ ID N0:7394 -0.3 -18.7 58.6 -18.4 0 -4.2
AAAAAAAAGTTAATATAAAT
8934 SEQ TD N0:7395 -0.3 -7.4 35.1 -7.1 0 -2.8
CACATAAATCCAAGGGTTCT
8956 SEQ ID No:7396 -0.3 -21.3 62.4 -21 0 -4.3
ACTGAGAATAAGAGTTTGGT
8984 SEQ ID N0:7397 -0.3 -Z9 59.3 -18.7 0 -2.7
AGATCCAAATTGTCTTTAAA
9030 5EQ ID N0:7398 -0.3 -17.4 54.6 -17.1 0 -4.6
TCAGTGCTCGGAGAACTCTG
1125 SEQ ID N0:7399 -0.2 -24.3 70.8 -23.2 -0.7 -6.4
CAGTCAGGATCATCACATCA
1215 SEQ ID N0:7400 -0.2 -23 69.1 -22.3 -0.1 -5.3
AAATGTGCTCATTGTTACAT
1391 SEQ ID N0:7401 -0.2 -19.6 60 -17.8 -1.6 -4
CAGTTAAATGTGCTCATTGT
1396 SEQ ID N0:7402 -0.2 -20.6 62.8 -18.8 -1.6 -4
CATCTGCTGAAATTCGGCCT
1796 SEQ ID N0:7403 -0.2 -25.1 69.4 -23.5 -1.3 -9.5
GATTCTTCAAGTTCTTCCAT
2617 SEQ TD N0:7404 -0.2 -22.3 67.8 -22.1 0 -2.9
GACAATGCAAATAGTGATGG
2765 SEQ ID N0:7405 -0.2 -18.6 56.6 -17.5 -0.7 -5.1
TTTGCCAACTTGAAAACTCT
3040 SEQ ID N0:7406 -0.2 -20.1 59.3 -19.9 0 -3
CTATCCACTCTCCACACAGC
3288 SEQ ID N0:7407 -0.2 -26.8 76 -26.6 0 -2.8
CATTCTTCCTACTGCAATCT
3485 SEQ ID N0:7408 -0.2 -23.4 68.7 -23.2 0 -4.9
TGCATTCTTCCTACTGCAAT
3487 SEQ ID N0:7409 -0.2 -23.9 69.3 -22.2 -1.4 -5.3
GACATGCAGCTGTCTATCTT
3601 SEQ ID N0:7410 -0.2 -24.3 72.7 -22.8 -1.1 -9.6
CAAAGTCAGACTCTCCAACA
3789 SEQ ID N0:7411 -0.2 -21.9 64.2 -21.7 0 -7.3
ACCAGTTGTGCTCAACAATA
4074 SEQ ID N0:7412 -0.2 -22.4 65.6 -18.9 -3.3 -6.6
CATGAACACAATGAAAGTCT
4097 SEQ TD N0:7413 -0.2 -17.4 54 -17.2 0 -3.7
TGCCTTCAAACCGGGATAAG
4413 SEQ ID N0:7414 -0.2 -23.5 64.7 -23.3 0 -7.1
CATACATAATATCCATCCAG
4725 SEQ ID N0:7415 -0.2 -20.2 60 -20 0 -2.6
TCTCAGCCAGAAACATACCT
5277 SEQ ID N0:7416 -0.2 -23.8 67.7 -23.6 0 -2.7
GGCTGTAAACAATTGATCAC
6497 SEQ ID N0:7417 -0.2 -19.6 59.2 -19.4 0 -7.2
AACTTAGAATAAAATTTGCA
7183 SEQ ID N0:7418 -0.2 -14.4 48 -14.2 0 -5.2
CCTAAATTAAATATAGAGCT
7207 SEQ TD N0:7419 -0.2 -16.3 51.9 -16.1 0 -5.3
AAGATGGCAAAGCAATACTG
7318 SEQ ID N0:7420 -0.2 -18.8 56.6 -17.7 -0.7 -4.3
TACATAACATAGGGTATTTA
7371 SEQ ID N0:7421 -0.2 -17.4 55.4 -17.2 0 -3.1
TATTTACATAACATAGGGTA
7375 SEQ ID N0:7422 -0.2 -17.4 55.4 -17.2 0 -3.2
343
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mol kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
TATCACCAATATGTGACATT
7623 SEQ ID N0:7423 -0.2 -19.5 59.1 -17.8 -1.4 -6.5
GTGTTTCCTTGAAATCCAGA
7754 SEQ ID N0:7424 -0.2 -22.9 67 -21.9 -0.6 -4.3
AATTATCCATTGAAAAATCT
7991 SEQ ID N0:7425 -0.2 -15.4 49.8 -14.5 -0.5 -3.4
TGCTTATAGCCAAGGGAGTT
8774 SEQ ID N0:7426 -0.2 -24.3 70.7 -22.8 -1.2 -4.9
GAGATAGCATCAATTATATT
8813 SEQ ID N0:7427 -0.2 -17.4 55.5 -16.3 -0.7 -5,7
AAGTTAATATAAATTCTCAA
8928 SEQ ID N0:7428 -0.2 -13.4 46.6 -13.2 0 -3.1
TGAAATACATATTTAGATCC
9044 SEQ ID N0:7429 -0.2 -16.4 52.6 -15.6 -0.3 -5.8
CAAAGCCCAGCATCCAAGAT
172 SEQ ID N0:7430 -0.1 -25.3 68.6 -24.3 -0.7 -4.1
TTGATGTGGCTTGGCTTCAG
244 SEQ ID N0:7431 -0.1 -25 73.6 -24.2 -0.4 -6
GCAATTTTCCTAACAGGGTT
814 SEQ ID N0:7432 -0.1 -23 67 -22 -0.7 -4.6
AAATGAGCCCAAGAAAATGA
1691 SEQ ID N0:7433 -0.1 -18.1 53.8 -18 0 -3.2
GGATCAAATTCACCAAATAA
1710 SEQ ID N0:7434 -0.1 -17.2 53 -17.1 0 -5.3
CCTCTTTTTGTTCTGCTTCT
1779 SEQ ID N0:7435 -0.1 -25.3 75.9 -25.2 0 -3.6
ACTGAAATCTCTTGAAGCAG
1871 SEQ ID N0:7436 -0.1 -19.4 59.3 -18.8 -0.2 -4.1
GGAAAGCTGTCTCTCTCTCC
2023 SEQ ID N0:7437 -0.1 -25.9 76.5 -25.8 0 -6.4
TCTGTCTAGATTCTTCAAGT
2625 5EQ ID N0:7438 -0.1 -21.2 66.9 -20.6 -0.2 -6
AATTAAATTCACAAGATGTT
2720 SEQ ID N0:7439 -0.1 -15 49.6 -14.9 0 -3
CATAACAATTAAATTCACAA
2726 SEQ ID N0:7440 -0.1 -13.7 46.4 -13.6 0 -3.1
AGCGTACAGTCATCATTGAT
3214 SEQ ID N0:7441 -0.1 -22.5 67.2 -21.7 -0.5 -5.7
CCATGACCAACATGAAAACA
3357 SEQ ID N0:7442 -0.1 -19.8 56.9 -17.4 -2.3 -5.9
ATAATAAGGCCAGAAAGAGG
3402 SEQ TD N0:7443 -0.1 -18.7 56.5 -18.1 0 -7.7
GCAATCTGCAGATTATTCAT '
3472 SEQ ID N0:7444 -0.1 -21.2 63.9 -18.2 -1.7 -14
GCAATTGGCACTGTGACGGT
3769 SEQ ID N0:7445 -0.1 -25.9 72.3 -24.9 -0.7 -7
TCACTGCTGAACTCTTCAGT
3820 SEQ ID N0:7446 -0.1 -23.6 70.7 -20.8 -2.7 -7,6
TTCTAGTTCTGACTCACTGC
3833 SEQ ID N0:7447 -0.1 -23.4 71.8 -22.6 -0.4 -4
CAAGCTTCCGGTTTAAAGTC
3955 SEQ ID N0:7448 -0.1 -22.5 65.4 -22.4 0 -6.6
ACAGAATGGAAACTTTTTAA
3992 SEQ ID N0:7449 -0.1 -15.7 50.8 -14.9 -0.4 -2.7
CACCAGGCATTAGTGAAATA
4270 SEQ ID N0:7450 -0.1 -21.2 62.2 -21.1 0 -4.2
GCACCAGGCATTAGTGAAAT
4271 SEQ ID N0:7451 -0.1 -23.3 66,7 -22.3 -0.7 -4.6
344
CA 02495398 2005-02-10
WO 2004/016754 PCT/US2003/025465
kcal/
mot kcal/moldeg kcal/molkcal/molkcal/mol
C
Intra- Inter-
total duplex Tm target molecularmolecular
of
Positionoligo bindingformationDuplexstructureoligo oligo
GTTACAAAATCAAAGACCAT
5023 SEQ ID N0:7452 -0.1 -17 52.8 -16.9 0 -2.8
CAAGGTAGGGGACACAGAAT
5309 SEQ ID N0:7453 -0.1 -22 64.3 -21.3 -0.3 -2.8
ATTTGGAACAAGCAGATCAT
5566 SEQ ID N0:7454 -0.1 -19.7 59.6 -18 -1.6 -8.6
TCATAGGCTGTAAACAATTG
6502 SEQ ID N0:7455 -0.1 -18.5 57 -18.4 0 -6.7
CCTCAGCAGTGTCAGCTGGT
6690 SEQ ID N0:7456 -O.l -29.1 84.9 -26.2 -2.8 -9.2
GTAAACCTCATTTACAAAAA
6903 SEQ ID NO:7457 -0.1 -15.7 50.2 -13.4 -2.2 -5.9
AACTGAAACTGTAGCCATTA
7023 SEQ ID N0:7458 -O.l -19.9 59.4 -19.8 0 -3.3
GACTAAAATACTTTCAAAAT
7067 SEQ ID N0:7459 -O.l -13.3 45.9 -13.2 0 -2
TTACATTATTTATATTTAAA
7838 SEQ ID N0:7460 -0.1 -12.6 45.2 -12 -O.l -4.6
GATTCAAAAGTTTGGAATTG
7967 SEQ ID N0:7461 -0.1 -16.3 52.3 -15.3 -0.8 -7.1
AAATAGTTTTGTAAAAAGAA
8360 SEQ ID N0:7462 -O.l -11.8 43.1 -10.3 -1.3 -4.2
AAAGTTCACAAAGCTGCTTT
8664 SEQ ID N0:7463 -0.1 -20.1 60.5 -18.7 -0.1 -10.6
AAAACAAAGAGACCTTTCCA
32 SEQ ID N0:7464 0 -19 56.3 -18.1 -0.8 -4.4
CAGAGGTTTACAAATTAGTT
85 5EQ ID N0:7465 0 -18.2 57.4 -18.2 0 -3.3
TGAATGTGTACTCTACATTC
936 SEQ TD N0:7466 0 -19.5 61.1 -16.4 -3.1 -11
TGGAATGACTGAAATTGTTT
1145 SEQ ID N0:7467 0 -17.5 54.7 -17.5 0 -3.2
CTGGAATGACTGAAATTGTT
1146 SEQ ID N0:7468 0 -18.3 56.2 -18.3 0 -3.2
AACACGCTCAGACAGAACAC
1234 SEQ ID N0:7469 0 -21.5 62.2 -21.5 0 -3.4
AGATTGCCCATGAACAGCTG
1270 SEQ ID N0:7470 0 -24.7 69.2 -24.2 0.5 -8.6
GACAGGAAAGCCCAGCTAAA
1576 SEQ ID N0:7471 0 -23.4 65.1 -22.4 -0.9 -6
AGCCAGGATCAAATTCACCA
1715 SEQ ID N0:7472 0 -24.1 67.9 -24.1 0.5 -5.3
CATCAGCAAAGTCATTTTCA
2238 SEQ ID N0:7473 0 -20.6 62.6 -20.6 0 -3.3
AAGCCCTGGCACCATCCTGG
2366 SEQ ID N0:7474 0 -31.1 81.2 -30 -0.8 -9.6
AAGGAAACCACACCATTGCA
2419 SEQ ID N0:7475 0 -23 63.8 -22.3 -0.5 -5.3
CAGTCAACACACTACTGAAT
2832 SEQ ID N0:7476 0 -19.9 60 -l9 -0.8 -4.2
TTGACAGAATGGAAACTTTT
3995 SEQ ID N0:7477 0 -17.3 54.2 -16.6 -0.4 -3.2
AATATGTTTGAAATCCATAA
4254 SEQ ID N0:7478 0 -15.7 50.6 -15.7 0 -3.5
TTAATGTCCGTAATGATTTG
4371 SEQ ID N0:7479 0 -18.5 56.6 -18.5 0 -2.6
TTGAAGCAGTGCAAGATAGC
4688 SEQ ID N0:7480 0 -21.6 64.6 -20.9 0.1 -8.8
345
DEMANDE OU BREVET VOLUMINEUX
LA PRESENTE PARTIE DE CETTE DEMANDE OU CE BREVET COMPREND
PLUS D'UN TOME.
CECI EST LE TOME 1 DE 2
CONTENANT LES PAGES 1 A 345
NOTE : Pour les tomes additionels, veuillez contacter le Bureau canadien des
brevets
JUMBO APPLICATIONS/PATENTS
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VOLUME
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CONTAINING PAGES 1 TO 345
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