                               SEQUENCE LISTING

<110> ILLUMINA, INC.
 
<120> COMPOSITIONS AND METHODS FOR POLYNUCLEOTIDE SEQUENCING

<130> 12957-139-228

<140>
<141>

<150> 61/909,316
<151> 2013-11-26

<160> 90    

<170> PatentIn version 3.5

<210> 1
<211> 184
<212> PRT
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      polypeptide"

<400> 1
Gly Leu Asp Asn Glu Leu Ser Leu Val Asp Gly Gln Asp Arg Thr Leu 
1               5                   10                  15      


Thr Val Gln Gln Trp Asp Thr Phe Leu Asn Gly Val Phe Pro Leu Asp 
            20                  25                  30          


Arg Asn Arg Leu Thr Arg Glu Trp Phe His Ser Gly Arg Ala Lys Tyr 
        35                  40                  45              


Ile Val Ala Gly Pro Gly Ala Asp Glu Phe Glu Gly Thr Leu Glu Leu 
    50                  55                  60                  


Gly Tyr Gln Ile Gly Phe Pro Trp Ser Leu Gly Val Gly Ile Asn Phe 
65                  70                  75                  80  


Ser Tyr Thr Thr Pro Asn Ile Leu Ile Asn Asn Gly Asn Ile Thr Ala 
                85                  90                  95      


Pro Pro Phe Gly Leu Asn Ser Val Ile Thr Pro Asn Leu Phe Pro Gly 
            100                 105                 110         


Val Ser Ile Ser Ala Arg Leu Gly Asn Gly Pro Gly Ile Gln Glu Val 
        115                 120                 125             


Ala Thr Phe Ser Val Arg Val Ser Gly Ala Lys Gly Gly Val Ala Val 
    130                 135                 140                 


Ser Asn Ala His Gly Thr Val Thr Gly Ala Ala Gly Gly Val Leu Leu 
145                 150                 155                 160 


Arg Pro Phe Ala Arg Leu Ile Ala Ser Thr Gly Asp Ser Val Thr Thr 
                165                 170                 175     


Tyr Gly Glu Pro Trp Asn Met Asn 
            180                 


<210> 2
<211> 4
<212> PRT
<213> Unknown

<220>
<221> source
<223> /note="Description of Unknown: 'DEAD' box motif
      sequence"

<400> 2
Asp Glu Ala Asp 
1               


<210> 3
<211> 4
<212> PRT
<213> Unknown

<220>
<221> source
<223> /note="Description of Unknown: 'DEAH' box motif 
      sequence"

<400> 3
Asp Glu Ala His 
1               


<210> 4
<211> 8
<212> PRT
<213> Methanococcoides burtonii

<400> 4
Gln Met Ala Gly Arg Ala Gly Arg 
1               5               


<210> 5
<211> 9
<212> PRT
<213> Methanococcoides burtonii

<400> 5
Gln Met Ala Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 6
<211> 8
<212> PRT
<213> Pyrococcus furiosus

<400> 6
Gln Met Leu Gly Arg Ala Gly Arg 
1               5               


<210> 7
<211> 9
<212> PRT
<213> Pyrococcus furiosus

<400> 7
Gln Met Leu Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 8
<211> 8
<212> PRT
<213> Haloferax volcanii

<400> 8
Gln Met Met Gly Arg Ala Gly Arg 
1               5               


<210> 9
<211> 9
<212> PRT
<213> Haloferax volcanii

<400> 9
Gln Met Met Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 10
<211> 8
<212> PRT
<213> Halorubrum lacusprofundi

<400> 10
Gln Met Cys Gly Arg Ala Gly Arg 
1               5               


<210> 11
<211> 8
<212> PRT
<213> Halorubrum lacusprofundi

<400> 11
Gln Met Gly Arg Ala Gly Arg Pro 
1               5               


<210> 12
<211> 8
<212> PRT
<213> Cenarchaeum symbiosum

<400> 12
Gln Leu Cys Gly Arg Ala Gly Arg 
1               5               


<210> 13
<211> 9
<212> PRT
<213> Cenarchaeum symbiosum

<400> 13
Gln Leu Cys Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 14
<211> 8
<212> PRT
<213> Sulfolobus solfataricus

<400> 14
Gln Met Ser Gly Arg Ala Gly Arg 
1               5               


<210> 15
<211> 9
<212> PRT
<213> Sulfolobus solfataricus

<400> 15
Gln Met Ser Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 16
<211> 8
<212> PRT
<213> Methanogenium frigidum

<400> 16
Gln Met Ala Gly Arg Ala Gly Arg 
1               5               


<210> 17
<211> 9
<212> PRT
<213> Methanogenium frigidum

<400> 17
Gln Met Ala Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 18
<211> 8
<212> PRT
<213> Methanothermococcus okinawensis

<400> 18
Gln Cys Ile Gly Arg Ala Gly Arg 
1               5               


<210> 19
<211> 9
<212> PRT
<213> Methanothermococcus okinawensis

<400> 19
Gln Cys Ile Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 20
<211> 8
<212> PRT
<213> Methanotorris igneus

<400> 20
Gln Cys Ile Gly Arg Ala Gly Arg 
1               5               


<210> 21
<211> 9
<212> PRT
<213> Methanotorris igneus

<400> 21
Gln Cys Ile Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 22
<211> 8
<212> PRT
<213> Thermococcus gammatolerans

<400> 22
Gln Met Met Gly Arg Ala Gly Arg 
1               5               


<210> 23
<211> 9
<212> PRT
<213> Thermococcus gammatolerans

<400> 23
Gln Met Met Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 24
<211> 8
<212> PRT
<213> Thermococcus barophilus

<400> 24
Gln Met Ile Gly Arg Ala Gly Arg 
1               5               


<210> 25
<211> 9
<212> PRT
<213> Thermococcus barophilus

<400> 25
Gln Met Ile Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 26
<211> 8
<212> PRT
<213> Thermococcus sibiricus

<400> 26
Gln Met Met Gly Arg Ala Gly Arg 
1               5               


<210> 27
<211> 9
<212> PRT
<213> Thermococcus sibiricus

<400> 27
Gln Met Met Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 28
<211> 8
<212> PRT
<213> Methanosarcina barkeri

<400> 28
Gln Met Ala Gly Arg Ala Gly Arg 
1               5               


<210> 29
<211> 9
<212> PRT
<213> Methanosarcina barkeri

<400> 29
Gln Met Ala Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 30
<211> 8
<212> PRT
<213> Methanosarcina acetivorans

<400> 30
Gln Met Ala Gly Arg Ala Gly Arg 
1               5               


<210> 31
<211> 9
<212> PRT
<213> Methanosarcina acetivorans

<400> 31
Gln Met Ala Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 32
<211> 8
<212> PRT
<213> Methanohalophilus mahii

<400> 32
Gln Met Ala Gly Arg Ala Gly Arg 
1               5               


<210> 33
<211> 9
<212> PRT
<213> Methanohalophilus mahii

<400> 33
Gln Met Ala Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 34
<211> 8
<212> PRT
<213> Methanosarcina mazei

<400> 34
Gln Met Ala Gly Arg Ala Gly Arg 
1               5               


<210> 35
<211> 9
<212> PRT
<213> Methanosarcina mazei

<400> 35
Gln Met Ala Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 36
<211> 8
<212> PRT
<213> Methanosaeta thermophila

<400> 36
Gln Met Ala Gly Arg Ala Gly Arg 
1               5               


<210> 37
<211> 9
<212> PRT
<213> Methanosaeta thermophila

<400> 37
Gln Met Ala Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 38
<211> 8
<212> PRT
<213> Methanosalsum zhilinae

<400> 38
Gln Met Ala Gly Arg Ala Gly Arg 
1               5               


<210> 39
<211> 9
<212> PRT
<213> Methanosalsum zhilinae

<400> 39
Gln Met Ala Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 40
<211> 8
<212> PRT
<213> Methanohalobium evestigatum

<400> 40
Gln Met Ala Gly Arg Ala Gly Arg 
1               5               


<210> 41
<211> 9
<212> PRT
<213> Methanohalobium evestigatum

<400> 41
Gln Met Ala Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 42
<211> 8
<212> PRT
<213> Methanococcus maripaludis

<400> 42
Gln Cys Ile Gly Arg Ala Gly Arg 
1               5               


<210> 43
<211> 9
<212> PRT
<213> Methanococcus maripaludis

<400> 43
Gln Cys Ile Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 44
<211> 8
<212> PRT
<213> Natrialba magadii

<400> 44
Gln Met Met Gly Arg Ala Gly Arg 
1               5               


<210> 45
<211> 9
<212> PRT
<213> Natrialba magadii

<400> 45
Gln Met Met Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 46
<211> 8
<212> PRT
<213> Methanoregula boonci

<400> 46
Gln Met Ala Gly Arg Ala Gly Arg 
1               5               


<210> 47
<211> 9
<212> PRT
<213> Methanoregula boonci

<400> 47
Gln Met Ala Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 48
<211> 8
<212> PRT
<213> Ferroplasma acidarmanus

<400> 48
Gln Met Ile Gly Arg Ala Gly Arg 
1               5               


<210> 49
<211> 9
<212> PRT
<213> Ferroplasma acidarmanus

<400> 49
Gln Met Ile Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 50
<211> 8
<212> PRT
<213> Methanocaldococcus fervens

<400> 50
Gln Cys Ile Gly Arg Ala Gly Arg 
1               5               


<210> 51
<211> 9
<212> PRT
<213> Methanocaldococcus fervens

<400> 51
Gln Cys Ile Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 52
<211> 8
<212> PRT
<213> Methanocaldococcus jannaschii

<400> 52
Gln Cys Ile Gly Arg Ala Gly Arg 
1               5               


<210> 53
<211> 9
<212> PRT
<213> Methanocaldococcus jannaschii

<400> 53
Gln Cys Ile Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 54
<211> 8
<212> PRT
<213> Methanocaldococcus infernus

<400> 54
Gln Cys Ile Gly Arg Ala Gly Arg 
1               5               


<210> 55
<211> 9
<212> PRT
<213> Methanocaldococcus infernus

<400> 55
Gln Cys Ile Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 56
<211> 8
<212> PRT
<213> Methanospirillum hungatei

<400> 56
Gln Met Ala Gly Arg Ala Gly Arg 
1               5               


<210> 57
<211> 9
<212> PRT
<213> Methanospirillum hungatei

<400> 57
Gln Met Ala Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 58
<211> 8
<212> PRT
<213> Archaeoglobus fulgidus

<400> 58
Gln Met Ala Gly Arg Ala Gly Arg 
1               5               


<210> 59
<211> 9
<212> PRT
<213> Archaeoglobus fulgidus

<400> 59
Gln Met Ala Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 60
<211> 8
<212> PRT
<213> Haloterrigena turkmenica

<400> 60
Gln Met Ala Gly Arg Ala Gly Arg 
1               5               


<210> 61
<211> 9
<212> PRT
<213> Haloterrigena turkmenica

<400> 61
Gln Met Ala Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 62
<211> 8
<212> PRT
<213> Haladaptatus paucihalophilus

<400> 62
Gln Met Phe Gly Arg Ala Gly Arg 
1               5               


<210> 63
<211> 9
<212> PRT
<213> Haladaptatus paucihalophilus

<400> 63
Gln Met Phe Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 64
<211> 8
<212> PRT
<213> Halobacterium sp.

<400> 64
Gln Met Phe Gly Arg Ala Gly Arg 
1               5               


<210> 65
<211> 9
<212> PRT
<213> Halobacterium sp.

<400> 65
Gln Met Phe Gly Arg Ala Gly Arg Pro 
1               5                   


<210> 66
<211> 8
<212> PRT
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      peptide"


<220>
<221> VARIANT
<222> (2)..(2)
<223> /replace="Met" or "Leu"

<220>
<221> MOD_RES
<222> (3)..(3)
<223> Any amino acid

<220> 
<221> source
<223> /note="See specification as filed for detailed description of
      substitutions and preferred embodiments"
   
<220>
<221> misc_feature
<222> (1)..(8)
<223> /note="Variant residues given in the sequence have no 
      preference with respect to those in the annotations
      for variant positions"

<400> 66
Gln Cys Xaa Gly Arg Ala Gly Arg 
1               5               


<210> 67
<211> 87
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      oligonucleotide"


<220>
<221> modified_base
<222> (10)..(10)
<223> abasic nucleotide

<400> 67
aaaccttccn cccgtaccgt gccgtaccgt tccgttccgt accgtatttt tttttctcac       60

tatcgcattc tcatgcaggt cgtagcc                                           87


<210> 68
<211> 45
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      oligonucleotide"

<400> 68
cctgcatgag aatgcgatag tgagattttt tttttttttt ttttt                       45


<210> 69
<211> 102
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      polynucleotide"


<220>
<221> modified_base
<222> (19)..(20)
<223> abasic nucleotide

<400> 69
ctcacctatc cttccactnn ccccctttgg gtttaaattt tttcagatct cactatcttt       60

ttaaagtttt ctcactatcg cattctcatg caggtcgtag cc                         102


<210> 70
<211> 91
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      oligonucleotide"


<220>
<221> modified_base
<222> (19)..(20)
<223> abasic nucleotide

<400> 70
catcatcatc atcatcatnn ccccctaaac aagaatacca cgactagcat ttttcagatc       60

tcactatcgc attctcatgc aggtcgtagc c                                      91


<210> 71
<211> 91
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      oligonucleotide"


<220>
<221> modified_base
<222> (19)..(20)
<223> abasic nucleotide

<400> 71
catcatcatc atcatcatnn ccccctaaac aagaatacca cgactagcat ttttcagatc       60

tcactatcgc attctcatgc aggtcgtagc c                                      91


<210> 72
<211> 87
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      oligonucleotide"


<220>
<221> modified_base
<222> (10)..(10)
<223> abasic nucleotide

<400> 72
aaaccttccn cccgtaccgt gccgtaccgt tccgttccgt accgtatttt tttttctcac       60

tatcgcattc tcatgcaggt cgtagcc                                           87


<210> 73
<211> 60
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      oligonucleotide"

<400> 73
aaaaaaaata cggtacggaa cggaacggta cggcacggta cgggtttttt tttttttttt       60


<210> 74
<211> 14
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      oligonucleotide"

<400> 74
atcatcatca tcat                                                         14


<210> 75
<211> 9
<212> PRT
<213> Unknown

<220>
<221> source
<223> /note="Description of Unknown: 'SF2' family motif 
      sequence"

<400> 75
Gly Phe Cys Cys Pro Gln Ser Ile Gln 
1               5                   


<210> 76
<211> 8
<212> PRT
<213> Unknown

<220>
<221> source
<223> /note="Description of Unknown: 'SF2' family motif 
      sequence"


<220>
<221> MOD_RES
<222> (2)..(3)
<223> Any amino acid

<220>
<221> MOD_RES
<222> (5)..(5)
<223> Any amino acid

<400> 76
Ala Xaa Xaa Gly Xaa Gly Lys Thr 
1               5               


<210> 77
<211> 6
<212> PRT
<213> Unknown

<220>
<221> source
<223> /note="Description of Unknown: 'SF2' family motif 
      sequence"

<400> 77
Pro Thr Arg Glu Leu Ala 
1               5       


<210> 78
<211> 4
<212> PRT
<213> Unknown

<220>
<221> source
<223> /note="Description of Unknown: 'SF2' family motif 
      sequence"

<400> 78
Thr Pro Gly Arg 
1               


<210> 79
<211> 6
<212> PRT
<213> Unknown

<220>
<221> source
<223> /note="Description of Unknown: 'SF2' family motif 
      sequence"

<400> 79
Val Leu Asp Glu Ala Asp 
1               5       


<210> 80
<211> 4
<212> PRT
<213> Unknown

<220>
<221> source
<223> /note="Description of Unknown: 'SF2' family motif 
      sequence"

<400> 80
Phe Val Asn Thr 
1               


<210> 81
<211> 8
<212> PRT
<213> Unknown

<220>
<221> source
<223> /note="Description of Unknown: 'SF2' family motif 
      sequence"


<220>
<221> MOD_RES
<222> (6)..(7)
<223> Any amino acid

<400> 81
His Arg Ile Gly Arg Xaa Xaa Arg 
1               5               


<210> 82
<211> 18
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      primer"

<400> 82
tctcgtcgct catcaact                                                     18


<210> 83
<211> 18
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      primer"

<400> 83
gagtcgaggt catatcgt                                                     18


<210> 84
<211> 18
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      primer"

<400> 84
gtctgcctat agtgagtc                                                     18


<210> 85
<211> 65
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      primer"


<220>
<221> modified_base
<222> (22)..(23)
<223> abasic nucleotide

<400> 85
tttttttttt tttttccttc cnnttttctt cttcttcaag aagaagatct cgtcgctcat       60

caact                                                                   65


<210> 86
<211> 65
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      primer"


<220>
<221> modified_base
<222> (22)..(23)
<223> abasic nucleotide

<400> 86
tttttttttt tttttccttc cnntttttta attaattttg ttgttgtgag tcgaggtcat       60

atcgt                                                                   65


<210> 87
<211> 41
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      primer"

<220>
<221> source
<223> /note="Description of Combined DNA/RNA Molecule: Synthetic
      primer"


<220>
<221> modified_base
<222> (9)..(9)
<223> deoxyuracil

<220>
<221> modified_base
<222> (19)..(19)
<223> deoxyuracil

<220>
<221> modified_base
<222> (27)..(27)
<223> deoxyuracil

<220>
<221> modified_base
<222> (36)..(36)
<223> deoxyuracil

<400> 87
atacggcgnc caccgaccnc agcgtcngcc tatagngagt c                           41


<210> 88
<211> 29
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      oligonucleotide"

<400> 88
accgacactg cgtctgccta tagtgagtc                                         29


<210> 89
<211> 20
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      oligonucleotide"

<400> 89
ttaattaatt ttgttgttgt                                                   20


<210> 90
<211> 20
<212> DNA
<213> Artificial Sequence

<220>
<221> source
<223> /note="Description of Artificial Sequence: Synthetic
      oligonucleotide"

<400> 90
cttcttcttc aagaagaaga                                                   20
