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Primer Name Origin Protein Direction Start End Length Box Loc
CCACACACAAGGCTACTTCC SQ16F HIV(CLADEC) F 56 75 20
CACCATCCAAAGGTCAGTGG SQ2R HIV(CLADEC) R 136 117 20
AGACCAGATCTGAGCCYGGGAGCTCT 5'UTR1 HIV(CLADEC) GAG F 468 493 26
ATCTGAGCCTGGGAGCTCTCTGGCT 5'UTR1 HIV 5UTR F 475 499 25 1 1
CTAGGGAACCCACTGCTTAAGCCT 5'UTR2 HIV 5UTR F 502 525 24 1 2
CACTGCTTAAGCCTCAATAAAGCTTGCC 5'UTR2 HIV(CLADEC) GAG F 512 539 28
TAGAGCACTCAAGGCAAGCTTTATTGAGGCTTA 2.3'3'p1Cb HIV(CLADEC) R 551 519 33
AGTAGTGTGTGCCCGTCTGTTGTGTGACTC U5Cd HIV(CLADEC) F 552 581 30
AAATCTCTAGCAGTGGCGCCCGAACAG 623-Fi(gag) HIV GAG F 623 649 27 1 3
GAGGAGATCTCTCGACGCAGGAC Gag+1 HIV GAG F 675 697 23 1 4
GATCTCTCGACGCAGGACTCGGCT Gag+2 HIV GAG F 680 703 24 1 5
GACGCAGGACTCGGCTTGCTGA GS1F HIV GAG F 688 709 22 1 6
GCAGGACTCGGCTTGCTGAA G1(gag) HIV GAG F 691 710 20 1 7
GCGCGCACAGCAAGAGGCGA LA8 HIV 5'LTR F 711 730 20 1 8
GCGGCGACTGGTGAGTA G2(gag) HIV GAG F 734 750 17 1 9
GCGGCGACTGGTGAGTACGC Gag+3 HIV GAG F 734 753 20 1 10
TTGACTAGCGGAGGCTAGAAGG GA783F HIV GAG F 762 783 22 1 11
TGACTAGCGGAGGCTAGAA GF763 HIV(CLADEC) GAG F 763 781 19
AGAGATGGGTGCGAGAGCGTC GA806F HIV GAG F 786 806 21 1 12
ACCGAATTTTTTCCCATCGAT GA850R HIV GAG R 850 830 21 1 13
TAGTATGGGCAAGCAGGGAGCT GS1A HIV GAG F 890 911 22 1 14
TAGTATGGGCAAGCAGGGARCTRGA GA890F HIV GAG F 890 914 25 1 15
TCTAGCTCCCTGCTTGCCCATACTA GA889R HIV GAG R 914 890 25 1 16
TTCTAGCTCCCTGCTTGCCCATACTA GS889R HIV GAG R 915 890 26 1 17
GATTCGCAGTTAATCCTGGCCT GA917F HIV GAG F 917 938 22 1 18
GGATTAACTGCGAATCGTTCTAGCTCC GA932R HIV GAG R 932 906 27 1 19
CCCTYCAGACAGGATCAGAAG 1cFx HIV GAG F 989 1009 21 1 20
CTTCAGACAGGAACAGAGGA SQ2FC HIV(CLADEC) F 991 1010 20
GCAACCCTCTATTGTGTRCATC t1cF HIV GAG F 1036 1057 22 1 21
GAKRTAAAAGACACCAAGGAAGCTTTAGA GA1074F HIV GAG F 1066 1094 29 1 22
TTAGACAAGATAGAGGAAGA GAS1F HIV GAG F 1090 1109 20 1 23
TTATCTAAAGCTTCCTTGGTGTCT GS1R HIV GAG R 1097 1074 24 1 24
CTTGTCTAGGGCTTCCTTGGT SQ16RC HIV(CLADEC) R 1098 1078 21
GAGGAAGAACAAAACAAAAGTCAG SQ2FC(2) HIV(CLADEC) F 1102 1125 24
CTGACCTGATTGCTGTGTCC GAS2R HIV GAG R 1175 1156 20 1 25
GCCTATAGTGCAGAACATG T7JFp24-F HIV GAG F 1185 1203 19 1 26
CTGATGTACCATTTGCCC t1bR HIV GAG R 1224 1207 18 1 27
ACCTAGAACTTTAAATGCATGGG pan1dFx HIV GAG F 1233 1255 23 1 28
ACCCATGCATTTAAAGTTC pan1bR HIV GAG R 1256 1238 19 1 29
AGAAGARAAGGCTTTYAGCCC 1dFx HIV GAG F 1266 1286 21 1 30
GGTATTACTTCTGGGCTRAAAGC 1bRx HIV GAG R 1298 1276 23 1 31
CCATGTTTTCAGCATTATCA t1dF HIV GAG F 1298 1317 20 1 32
CAGCATTATCAGAAGGAGCCAC GS2F HIV GAG F 1307 1328 22 1 33
AATCTTGTGGGGTGGCTCCTTCTG GS1B HIV GAG R 1339 1316 24 1 34
AAAAGAGACCATCAATGAGGAAGC FNL43 HIV GAG F 1392 1415 24 1 35
CATCAATGAGGAAGCTGCAG GAS3F HIV GAG F 1401 1420 20 1 36
CATCAATGAGGAAGCTGCAGATGGGA GS3F HIV GAG F 1401 1427 27 1 37
TGGTGCAATAGGCCCTGC RNL43 HIV GAG R 1464 1447 18 1 38
GGTTCTCTCATCTGGCCTGG GAS4R HIV GAG R 1481 1462 20 1 39
GGTTCTCTCATCTGGCCTGGT GS2R HIV GAG R 1481 1461 21 1 40
TTCCTGCTATGTCACTTCC pan1cRx HIV GAG R 1504 1486 19 1 41
TGTCATCCATSCTATTTGTTCC t1cR HIV GAG R 1542 1521 22 1 42
TAATCCACCTATCCCAGTAGG 1eFx HIV GAG F 1545 1565 21 1 43
CCACCTATCCCAGTAGGAG pan1eFx HIV GAG F 1549 1567 19 1 44
GGGAGACATCTATAAAAGATGGATAA SQ3FC(2) HIV(CLADEC) F 1563 1588 26
TATAAAAGATGGATAATC seq1eF HIV GAG F 1573 1590 18 1 45
ATAGTAAGAATGTATAGCCCT GS4F HIV GAG F 1606 1626 21 1 46
TTTGGTCCTTGTCTTATGTCCAGAATGC SQ15R HIV(CLADEC) R 1658 1631 28
CTCTAAGAGCCGAGCAAGCT GAS5F HIV GAG F 1697 1716 20 1 47
CAGAAACCTTGTTGGTCCAAAATGCG ProD+ HIV GAG F 1742 1767 26 1 48
CAACAAGGTTTCTGTCATCC pan1dRx HIV GAG R 1755 1736 20 1 49
AAAATAGTCTTACAATCTGG GAS6R HIV GAG R 1790 1771 20 1 50
CACTAGAAGAAATGATGACAGC GS5F HIV GAG F 1814 1835 22 1 51
AGAAATGATGACAGCATGTC pan1fFx HIV GAG F 1821 1840 20 1 52
GCTGTCATCATTTCTTCTAGTG t1dR HIV GAG R 1835 1814 22 1 53
TGTCAGGGAGTGGGAGGACC t2bF HIV GAG F 1837 1856 20 1 54
TGACATGCTGTCATCATTTCTTCTA GS3R HIV GAG R 1841 1817 25 1 55
GTTAAGTGTTTCAATTGTGG HPR1977F HIV PR F 1957 1977 21 1 56
GAAGGGCACACAGCCAGAAATTGCAGGG 5'CP1 HIV RT F 1981 2008 28 1 57
GCCCCTAGGAAAAAGGGCTGTTGG PRTO5 HIV RT F 2008 2031 24 1 58
CCCTGCAATTTYTGGCTRTGTGCCCT GA2008R HIV GAG R 2008 1983 26 1 59
CCTAGGAAAAAGGGCTGTTGGAAATGTGG 2.5 HIV RT F 2011 2039 29 1 60
CATTTCCAACAGCCCTTTTTCCTAGG GA2036R HIV GAG R 2036 2011 26 1 61
TGTCCTTCCTTTCCACATTTCCAACAGCC GS4R HIV GAG R 2051 2023 29 1 62
TCTTTCATTTGGTGTCCTTC t1eR HIV GAG R 2063 2044 20 1 63
TCAGTACAATCTTTCATTTG GAS7R HIV GAG R 2072 2053 20 1 64
ACAGGCTAATTTTTTAGGGA SQ4F HIV(CLADEC) F 2076 2095 20
GGGAAGATCTGGCCTTCCTACAAGGG 5'RVP HIV PR F 2092 2117 26 1 65
TTCCCTAAAAAATTAGCCTG pan1efRx HIV GAG R 2096 2077 20 1 66
TGTRGGAAGGCCAGATCTTCC 1eRx HIV GAG R 2113 2093 21 1 67
AGACCAGAGCCAACAGCCCC p2c-F HIV GAG F 2143 2162 20 1 68
GAGAGCTTCAGGTTTGGGGA 5PR.1 HIV PR F 2170 2189 20 1 69
GAGAGCTTCAGGTTTGGGG SEQ1FOR HIV RT F 2170 2188 19 1 70
TGAAGCTCTCTTCTGGTGGG HPR2160R HIV PR R 2179 2160 20 1 71
TCGAATCTGAAGCTCTCTGCTGGTG 14R(3)C HIV(CLADEC) R 2186 2162 25
GGAGCCGATAGACAAGG 5'INPROT HIV PR F 2217 2233 17 1 72
CCAAAGAGTGACCTGAGGGAAG GA2249R HIV GAG R 2270 2249 22 1 73
TCTTTATTGTGACGAGGGGTCG GA2274R HIV GAG R 2295 2274 22 1 74
CCTTTAGTTGCCCCCCTATC G9(gag) HIV GAG R 2313 2294 20 1 75
TATCATCTGCTCCTGTATC G10(gag) HIV GAG R 2343 2325 19 1 76
CTAATACTGTATCATCTGCTCCTGT HIP202 HIV(CLADEC) R 2353 2328 26
CAAATTCATTTCTTCTAAT seq2bR HIV GAG R 2366 2348 19 1 77
GGAAACCAAAAATGATAGGGGGAATTGGAGG PR2377F HIV PR F 2377 2407 31 1 78
GGGAATTGGAGGTTTTATCAAAGTAAGACAGTA PR2396F HIV PR F 2396 2428 33 1 79
ATTCCCCCTATCATTTTTGG t2bR HIV GAG R 2401 2382 20 1 80
TTACTTTGATAAAACCTCC HPR2403R HIV PR R 2421 2403 19 1 81
TCTTACTTTGATAAAACCTC pan2bRx HIV GAG R 2423 2404 20 2 1
GGACCTACACCTGTCAACATAATTGGAAGAA PR2484F HIV PR F 2484 2514 31 2 2
CCAATTATGTTGACAGGTGTAGGTCCTA SCafR HIV RT R 2509 2482 28 2 3
CCTGGCTTTAATTTTACTGGTACAG 3'INPROT HIV RT R 2593 2569 25 2 4
AAACAATGGCCATTAACAGAAGAGA SQ5F HIV(CLADEC) F 2613 2637 25
TCTTCTGTCAATGGCCATTGTTTAAC CP2 HIV RT R 2635 2610 26 2 5
TCTTCTGTCAATGGCCATTG GR2635 HIV(CLADEC) GAG R 2635 2616 20
GTGTTATATGGATTTTCAGGCCC 13R(2)C(2) HIV(CLADEC) R 2722 2700 23
GAGTATTGTATGGATTTTCAGGCCCAAT ProC- HIV GAG R 2724 2697 28 2 6
GAGTATTRTATGGATTTTCAGGCCC PR.R2 HIV GAG R 2724 2700 25 2 7
GGAGTGTTATATGGATTTTCAGGCCCAATT 3'rvp HIV(CLADEC) GAG R 2725 2696 30
GGCAAATACTGGAGTATTGTATGG 3'RVP HIV RT R 2735 2712 24 2 8
GGCAAATACTGGAGTATTGTATG ProA- HIV GAG R 2735 2713 23 2 9
CTGAAATCTACTAATTTYCTCCA PR.R1 HIV GAG R 2782 2760 23 2 10
CTTCCCAGAAGTCTTGAGTTC SEQ6R HIV RT R 2817 2797 21 2 11
TAACCCTGCGGGATGTGGTATTCC 2cRx(nt2850) HIV RT R 2849 2826 24 2 12
TTTAACCCTGCTGGGTGTGGTATYCCT 2cRx HIV(CLADEC) GAG R 2851 2825 27
TACTGCATTTACCATACCTAGTATAAAC RH14 HIV RT F 2930 2957 28 2 13
GGTGATCCTTTCCATCC BR HIV RT R 3019 3003 17 2 14
GGATGATTTGTATGTAGG SEQ6A HIV RT F 3101 3118 18 2 15
AACATCAGAAAGAACCTCCATT RT3208F HIV RT F 3208 3229 22 2 16
CTTTGGATGGGTTATGAACT SQ6F HIV(CLADEC) F 3231 3250 20
CATTTGTCAGGATGGAGTTCATA RTC HIV(CLADEC) R 3265 3243 23
ATAGGCTGTACTGTCCATTTATCAGG COMB3 HIV RT R 3280 3255 26 2 17
TGTATGTCATTGACAGTCC SQ12R HIV(CLADEC) R 3322 3304 19
CCACTAACTTCTGTATGTCATTGACAGTCCAGC NE1 HIV RT R 3333 3301 33 2 18
GCAGAGTTAGAATTAGCAGAGAACAG SQ6.5FC HIV(CLADEC) F 3444 3469 26
TATTATGACCCATCAAAAGACT RT3501F HIV RT F 3501 3522 22 2 19
AGCAGGGGCAAGGCCAATGG RT3560F HIV RT F 3541 3560 20 2 20
ATTTGATATGTCCATTGGCC RT3571R HIV RT R 3571 3552 20 2 21
TAAATGGCTCTTGATAAATTTG RT3588R HIV RT R 3588 3567 22 2 22
CCATTTAAAAATCTGAAAACAG RT3582F HIV RT R 3603 3582 22 2 23
GCATAGTAATATGGGGAAAGA INS1F HIV RT F 3685 3705 21 2 24
ACAGAAAGCATAGTAATATGGG RT3678F HIV RT R 3699 3678 22 2 25
TTTAGGAGTCTTTCCCCATATTACTAT SQ11RC(3) HIV(CLADEC) R 3713 3687 27
CAAACTCCCACTCAGGAATCCA RT3798R HIV RT R 3798 3777 22 2 26
TTAATACCCCTCCCTTAGTG RT3818F HIV RT F 3799 3818 20 2 27
CTAACTGGTACCATAATTTCACTAAGGGAG 2.3 HIV RT R 3837 3808 30 2 28
AAGAACCCATAGTAGGAGC RT3860F HIV RT F 3841 3859 19 2 29
AGGAGCAGAAACTTTCTATGTAGATGG SQ7F(2) HIV(CLADEC) F 3854 3880 27
GCTCCTACTATGGGTTCTTTCTCTAACTGG RT3.1 HIV RT R 3859 3830 30 2 30
CTTTCTATGTAGATGGGGCAGC 3fFx HIV POL F 3865 3886 22 2 31
GCTTGTAATTCAGTCTTCTGATTTGTTG SQ11RC(4) HIV(CLADEC) R 3991 3964 28
CTAAKCCYGAATCCTGCAAAGC 3eRx HIV POL R 4023 4002 22 2 32
AGTAAACATAGTAACAGACTCACA RT4025F HIV RT F 4025 4048 24 2 33
GTAACAGACTCACAGTATGCATTAGG RT4035F HIV RT F 4035 4060 26 2 34
TGCTCTATTATTTGATTGAC RT4101R HIV RT R 4120 4101 20 2 35
TCTACCTGTCATGGGTACCAGCACA IN4141F HIV INT F 4141 4165 25 2 36
TGGCATGGGTACCAGCACAC RT4166F HIV RT F 4147 4166 20 2 37
CACAAAGGAATTGGAGGAAATGAACA IN4164F HIV INT F 4164 4189 26 2 38
TCTACTTGTTCATTTCCTCCAAT IN4195R HIV INT R 4195 4173 23 2 39
CTGTGATATTTCTCATGTTC RT4260R HIV RT R 4279 4260 20 2 40
CATTGCTCTCCAATTACTGTGATATTTCTCATG OUT3 HIV RT R 4295 4263 33 2 41
AGGTTAAAATCACTAGCCATTGCTCTCC RT22R HIV RT R 4312 4285 28 2 42
GGTGGCAGGTTAAAATCACYAGCC 3g/fRx HIV POL R 4318 4295 24 2 43
GYATGGCTTCTCCTTTTAGCTGRCA IN4380R HIV INT R 4380 4356 25 2 44
CTAGYTGCCATATTCCTGGACTACAGTC IN4419R HIV INT R 4419 4392 28 2 45
GTGTACAATCTAGTTGCCA HIN4410R HIV RT R 4428 4410 19 2 46
ATGTGTACAATCTAGTTGCCATAT IN4430R HIV INT R 4430 4407 24 2 47
AAGTTATCCTGGTAGCAGTT HIN4460F HIV RT F 4441 4460 20 2 48
CCTGGTAGCAGTCCATGTAGC SQ8FC HIV(CLADEC) F 4448 4468 21
GTAGCAGTCCATGTAGCCAGTGG IN4452F HIV INT F 4452 4474 23 2 49
CTTCTGCTTCTATATATCCACTGGCTACATG IN4491R HIV INT R 4491 4461 31 2 50
CAGCAGARACAGGGCARGAAACAGC 4cFx HIV POL F 4498 4522 25 2 51
TAAAATTAGCAGGAAGATGGCCAGT IN4534F HIV INT F 4534 4558 25 2 52
GCCATTGTCTGTATGTATTACTTTGACTG SQ10RC HIV(CLADEC) R 4583 4555 29
ACTCCTTGACTTTGGGGATTGTAGG IN4678R HIV INT R 4678 4654 25 2 53
TTCTACTACTCCCTGACTTTGGGGAT SQ8RC HIV(CLADEC) R 4685 4660 26
TCTCTTACCTGTCCTATAAT HIN4710R HIV RT R 4729 4710 20 2 54
CAGCCTGATCTCTTACCTGTCC 4bRx HIV POL R 4737 4716 22 2 55
ATCTTAAGACAGCAGTACAA HIN4760F HIV RT F 4741 4760 20 2 56
CTTAAGACAGCAGTACAAATGGCAGT IN4743F HIV INT F 4743 4768 26 2 57
ATCCCCCCTTTTCTTTTAAAATTGTG IN4801R HIV INT R 4801 4776 26 2 58
TTCAAAATTTTCGGGTTTATTACAG VIF4888F HIV VIF F 4888 4912 25 2 59
CTCTGGAAAGGTGAAGGGGCAGT VIF4952F HIV VIF F 4953 4975 23 2 60
TGTATTACTACTGCCCCTTC LA89 HIV INT R 4984 4965 20 2 61
AGATAATAGTGACATAAAAGTAGTGCCAAGAAG VVVc HIV VIF F 4985 5017 33 2 62
CATCACCTGCCATCTGTTTTCC 4cRx HIV POL R 5064 5043 22 2 63
CAGGTAGACAGGATGAAGATCAGAAC SQ9FC(3) HIV(CLADEC) F 5074 5099 26
TTGGATGTCTGCTTTCATAATGAT SQ9RC(3) HIV(CLADEC) F 5165 5188 24
GGATGAGTGCTTTCATAGTGA P16 HIV R 5186 5166 21 2 64
TGGGATGTGTACTTCTGAACTTA IN5214R HIV INT R 5214 5192 23 2 65
CCCCTAGTGGGATGTGTACTTCTG P17 HIV R 5221 5198 24 2 66
AACATATTGGGGTCTGCATA HIN5260F HIV INT F 5241 5260 20 2 67
CTGCATACAGGAGAAAGAGACTGG 4eFx HIV VIF F 5254 5277 24 2 68
TCTCCTGTATGCARACCCCAATATGT IN5267R HIV INT R 5267 5242 26 2 69
CCCAAATGCCAGTCTCTTTCTCCTG IN5285R HIV INT R 5285 5261 25 2 70
ATATGAATTAGTTGGTCTGCCAGGCC SQ9'RC HIV(CLADEC) R 5366 5341 26
GCAGCATTAATAACACCAAA HIN5510F HIV INT F 5491 5510 20 2 71
TTGGTCTTCTGGGGCTTGTTCC 4eRx HIV R 5582 5561 22 2 72
GATACTTGGGCAGGAGTGGAAGC 5cFx-2 HIV F 5712 5734 23 2 73
GGAGCCAGTAGATCCTAACCTAGAG SQ10FC HIV(CLADEC) F 5833 5857 25
CCTGGAAICATCCAGGAAGTCAGCCTA SC04F HIV TAT F 5859 5885 27 2 74
TAGGCTGACTTCCTGGATGCTTC SC04R HIV TAT R 5885 5863 23 2 75
AGTRTTAGGCTGACTTCCTGGATGC 5bRx-1 HIV R 5890 5866 25 2 76
AGICTTAGGCATCTCCTATGGCAGGAA SC02F HIV TAT F 5952 5979 28 2 77
GAAGAAGCGGAGACAGCGACGAAGAICTC SC05F HIV TAT F 5977 6005 29 2 78
CTTCCTGCCATAGGAGATGCCTA SC02R HIV TAT R 5980 5958 23 2 79
CTCCGCTTCTTCCTGCCATAGGAGAT SQ8R HIV(CLADEC) R 5988 5963 26
AGCTCTTCGTCGCTGTCTCCGCTT SC05R HIV TAT R 6004 5981 24 2 80
AAAGAGCAGAAGACAGTGGCAATG EIF HIV F 6204 6227 24 2 81
CACTCTCATTGCCACTGTCTTCTGC 5cRx HIV R 6233 6209 25 3 1
CAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCT MK603 HIV ENV F 6316 6353 38 3 2
CCATAATAGACTGTGACCCACAA VVd HIV ENV R 6346 6324 23 3 3
AGGTACCCCATAATAGACTGTGA VPU-R HIV ENV R 6353 6331 23 3 4
ACTCTATTTTGTGCATCAGA SQ11F HIV(CLADEC) F 6375 6394 20
TCTATTCTGTGCATCAGGTGCTAAAGCATA SQ11FC HIV(CLADEC) F 6377 6406 30
ACACATGCCTGTGTACCCACAGA SQV2F1 HIV ENV F 6435 6457 23 3 5
ACACATGCCTGTGTACCCACAGA SQV2F1 HIV ENV F 6435 6457 23 3 6
CCTGTGTACCCACARACC F6c-F HIV F 6442 6459 18 3 7
GGTCTGTGGGTACACAGGCATGT ENV6437R HIV ENV R 6459 6437 23 3 8
TCTACCATGTTATTTTTCCACAT ENV6507R HIV ENV R 6529 6507 23 3 9
GCATGAGGATATAATCAGTTTATGGGAT V2IF HIV ENV F 6536 6563 28 3 10
GATATAATCAGTTTATGGGATC SQV2F2 HIV ENV F 6543 6564 22 3 11
GTTTATGGGATCAAAGCCTAAA V2I2F HIV ENV F 6553 6574 22 3 12
CAATTTAAAGAAACACAGAGTGG p6b-R HIV ENV R 6616 6594 23 3 13
ARATAAAAAACTGCTCTTTCAA p6d-F HIV ENV F 6682 6703 22 3 14
CCTCAGCCATTACACAGGCCTGTCCAAAG SQ12F HIV(CLADEC) F 6817 6845 29
GCCTGTCCAAAGGTATCCTTTGAGCCA V2IRF HIV ENV F 6834 6860 27 3 15
TGGCTCAAAGGATACCTTTGGACAGGC V2IR HIV ENV R 6860 6834 27 3 16
CTGTGGGTACACAGGCATGTGTAGC SQ7R(2)C HIV(CLADEC) R 6864 6839 26
GAATTGGGTCAAAAGAGACCTTTGGA SQ6RC(2) HIV(CLADEC) R 6864 6839 26
ATAATGTATAGGAATCGGGT SQ6RC HIV(CLADEC) R 6875 6856 20
AATGTCAGYACAGTACAATGTACAC V302F HIV ENV F 6945 6969 25 3 17
AATGTCAGYACAGTACAATGTACAC V3O2F HIV ENV F 6945 6969 25 3 18
GTGTACATTGTACTGTGCTGACAT SQV2R1 HIV ENV R 6969 6946 24 3 19
ATTCCATGTGTACATTGTACTGT VVVb HIV ENV R 6976 6954 23 3 20
TCAACTCAACTACTGTTAAATGGTAGCCTAGC DR7C HIV(CLADEC) F 6990 7021 32
TAAATGGCAGTYTAGCAGAAGAAG V3I2F HIV ENV F 7006 7029 24 3 21
TAAATGGCAGTYTAGCAGAAGAAG V3I2F HIV V3 F 7006 7029 24 3 22
TTCTTCTGCTAGACTGCCATTTAA V3IFR(new) HIV V3 R 7028 7005 24 3 23
TACAATATGCTTGTCTTAT 6d-R HIV ENV R 7219 7200 20 3 24
ACAATYTCTGGGTCCCCTCCTGAGGA V3I2R HIV V3 R 7339 7314 26 3 25
GTTTTAWTTGTGGAGGGG F6f-F HIV ENV F 7348 7365 18 3 26
GTGGAGGGGAATTTTTCTACTGTA SQV4FI HIV V3 F 7357 7380 24 3 27
ATTACAGTAGAAAAATTCCCCTCCAC V3O2R HIV V3 R 7382 7357 26 3 28
CATTGCTCGTCCTACCCCCTGCCAC 5R(3)C HIV(CLADEC) R 7526 7502 25
GGGAGGGGCATACATTGC F6e-R HIV ENV R 7538 7521 18 3 29
GGACAATTGGAGAAGTGAATTAT GP41FI HIV ENV F 7652 7674 23 3 30
TCCAATTGTCCCTCATATCTCCTCCTCCA CO601 HIV ENV R 7662 7634 29 3 31
GAATTATATAAATATAAAGTAGTA GP41FI2 HIV ENV F 7668 7691 24 3 32
TATATAAATATAAAGTGGTAGAAATTAAGC SQ13F(2)C HIV(CLADEC) F 7672 7701 30
TATAATTCACTTCTCCAATTGTCC CD4R HIV ENV R 7675 7652 24 3 33
TATAATTCACTTCTCCAATTGTCC CD4R HIV ENV R 7675 7652 24 3 34
CCATTAGGAGTAGCACCCACC GP41.1A HIV ENV F 7701 7721 21 3 35
CCCATAGTGCTTCCTGC p6f-R HIV ENV R 7816 7800 17 3 36
GCCCATAGTGCTTCCTGCTGCTCCCAAGAACC CO602 HIV ENV R 7817 7786 32 3 37
TTGCAACTCACAGTCTGGGG p7d-F HIV ENV F 7920 7939 20 3 38
ACTCACGGTCTGGGGCATTA SQ14FC HIV(CLADEC) F 7925 7944 20
ATCAAGCAGCTCCAGGCAAGA GP41.2A HIV ENV F 7941 7961 21 3 39
TGCCTGGAGCTGCTTGATGCCCCAGAC ENVR HIV ENV R 7958 7931 28 3 40
GTTGATCCCTTAGGTATCTTTCTA 4R(2)C HIV(CLADEC) R 7995 7972 24
CTAGGAGCTGTTGATCCTTTAGGTAT SQ5.5RC HIV(CLADEC) R 8004 7979 26
TTGTTCATTCTTTTCTTGCTG GP41.1B HIV ENV R 8198 8178 21 3 41
TTTGTGGAATTGGTTTRACATAA SQGP41F HIV ENV F 8228 8250 23 3 42
GCCTCCTACTATCATTATGAATA SQGP41R HIV ENV R 8297 8275 23 3 43
AARCCTAYYAAGCCTCC F7c-R HIV ENV R 8308 8292 17 3 44
AATAGAGTTAGGCAGGGATACTCACC ENV8340F HIV ENV F 8340 8365 26 3 45
AGTTAGGMAGGGATAYTCACC 7eFx3 HIV ENV F 8345 8365 21 3 46
TGGAGAGAGAGACAGAGACAGATCC ENV8435F HIV ENV F 8435 8459 25 3 47
GGATCTGTCTCTGTCTCTCTCTCCA SC90R HIV ENV R 8459 8435 25 3 48
CAGCTACCACCGCTTGAGAGACTTA ENV8522F HIV ENV F 8522 8546 25 3 49
TAAGTCTCTCAAGCGGTGGTAGCTGAA SC52R HIV ENV R 8546 8520 27 3 50
GAGAGCGGTGGAACTTCTGG SQ15FC HIV(CLADEC) F 8561 8580 20
TTTAGTTCCAGACCCCAATA SQ3RC HIV(CLADEC) R 8647 8628 20
GCTATGGTATCAAGCAGACTAATAGCACTC SQ3R(2)C HIV(CLADEC) R 8680 8651 30
TAGCAGTAGCTGAGGGGACAGATAG NEF8683F HIV NEF F 8683 8707 25 3 51
GTAGCTGAGGGGACAGATAGGGTTAT NefOF HIV NEF F 8688 8713 26 3 52
GAGGGGACAGATAGGGTTATAGAAGTAGTAC NEF8694F HIV NEF F 8694 8724 31 3 53
CACATACCTAGAAGAATAAGACAGGGCT NEF8748F HIV NEF F 8748 8775 28 3 54
ACATACCTASAAGAATAAGACAGG NefIF HIV NEF F 8749 8772 24 3 55
CTGTCTTATTCTTCTAGGTATGT GP41RI HIV ENV R 8771 8749 23 3 56
TTGCTATAARATGGGTGGCAAGTGGTC NEF1F HIV NEF F 8787 8813 27 3 57
CTTTTTGACCACTTGCCACCCAT GP41RO HIV ENV R 8819 8797 23 3 58
GGATGGCCTACTGTAAGGGAAAGAATG NEF2F HIV NEF F 8830 8856 27 3 59
GGGGTGGGAGCAGYATCTCG NEF5F HIV NEF F 8881 8900 20 3 60
CCTTGTAAGTCATTGGTCTTAAAGGTACC EIR HIV R 9043 9015 29 3 61
GGGAGTRAAYTAGCCCTTCCAG NEF6R HIV NEF R 9106 9085 22 3 62
AGACAAGATATCCTTGATCTGTGG NEF9112F HIV NEF F 9112 9135 24 3 63
TGTGTAGTTCTGCTAATCAGGGAAGTAGCCTTGTG EOR HIV R 9180 9145 36 3 64
TATCTGGCTCAACTGGTACTAGC NEF9249R HIV NEF R 9250 9228 23 3 65
CAGCGGAAAGTCCCTTGTAGCAA NEF9448R HIV NEF L 9448 9426 23 3 66
GTCCCCAGCGGAAAGTCCCTTGTA NEFIR HIV NEF/3'LTR R 9453 9430 24 3 67
CTTATATGCAGGATCTGAGGGCTC NEF4R HIV NEF R 9517 9494 24 3 68
AAGCAGCTGCTTATATGCAGGATCTGA NEF3R HIV NEF R 9526 9500 27 3 69
GGTCTAACYAGAGAGACCCAGTACAG FB13 HIV NEF/3'LTR R 9557 9532 26 3 70
TCCCTAGTTAGCCAGAGAGCT NEF9593R HIV NEF R 9593 9573 21 3 71
TCAAGGCAAGCTTTATTGAGGCTTAA 3LTRi HIV 3LTR R 9628 9603 26 3 72
GCACTCAAGGCAAGCTTTATTGAGGCTTAA NefOR/FB12 HIV NEF/3'LTR R 9632 9607 26 3 73
ACCGGGACTCAGATTCTCCCCAGAC HLA-Apre1F HUMAN HLA
CACACATYAGGYCCTCCAAGCTCTCAC HLA-Ain7R HUMAN HLA
GAAACSGCCTCTGYGGGGAGAAGCAA HLA-AF HUMAN HLA
TGTTGGTCCCAATTGTCTCCCCTC HLA-AR HUMAN HLA
AGCCGCGCCKGGASGAGGGTC HLA-AS1F HUMAN HLA
GGCCCGTCCGTGGGGGATGAG HLA-AS2R HUMAN HLA
GTTTCATTTTGRGTTKAGGCCA HLA-AS3F HUMAN HLA
TGTGGGAGGCCAGCCCGGGAGA HLA-AS4R HUMAN HLA
CTACGTGGACGACACGCAGTT HLA-AS5F HUMAN HLA
ACAGTCTCCGGGTCCGAGAT HLA-AS6F HUMAN HLA
TTTGGCCTMAACYSAAAATGAAAC HLA-AS7R HUMAN HLA
TTCCCGTTCTCCAGGTRTCTGC HLA-AS8R HUMAN HLA
CTCATCCCCCACGGACGGGCC HLA-AS9F HUMAN HLA
CGACGTGGGGYCGGACKGGC HLA-AS10F HUMAN HLA 37.5
CGGGAGAYCTAYAGGCGATCAG HLA-AS11R HUMAN HLA 37.5
GGGAGGAGMGAGGGGACCSCAG HLA-BF HUMAN HLA 52
GGAGGCCATCCCCGGCGACCTAT HLA-BR HUMAN HLA 127
GCAGGCGGGGGCGCAGGACC HLA-BnewF HUMAN HLA
GGAGATGGGGAAGGCTCCCCACT HLA-BS4R HUMAN HLA
GGAGCCGCGCCGGGAGGAGGGTC HLA-BS1F HUMAN HLA
GGATGGGGAGTCGTGACCT HLA-BS2R HUMAN HLA
GGCGGGTYTCAGCYCCTCCT HLA-BS10F HUMAN HLA
CGGGGTCACTCACCGKCCTC HLA-BS11R HUMAN HLA
ACKGKGCTGACCGCGGGG HLA-BS3F HUMAN HLA
ACTGCCCCTGGTACCMGCGC HLA-BS13R HUMAN HLA
GGSCKGGGCCAGGGTCTCAC HLA-BS12F HUMAN HLA
ARCGAGGKGCCCKCCCGGCGA HLA-CF HUMAN HLA
GGAGATRGGGAAGGCTCCCCACT HLA-CR HUMAN HLA
GGAGCCGCGCAGGGAGGWGGGTC HLA-CS1F HUMAN HLA
GGCTCCCCACTGCCCYTGGTAC HLA-CS7R HUMAN HLA
CGGGTCTCAGCCMCTCCTC HLA-CS8F HUMAN HLA
TGGATCTCAGACSGGGAGACT HLA-CS9R HUMAN HLA
GGAGGGGTCGKGACCTGCGC HLA-CS2R HUMAN HLA
GGGCTGACCRCGGGGGCG HLA-CS10F HUMAN HLA
CGGGGCCAGGKTCTCACAYC HLA-CS11F HUMAN HLA
TGGTACCYGCGCGCTGCAGC HLA-CS4R HUMAN HLA
GGGAGGAGMRAGGGGACCSCAG HLA-BF_mod HUMAN HLA
GGAGGCCATCCCSGGCGAYCTAT HLA_BR_mod HUMAN HLA
TCTCASCCACTSCTCGYCCCCA HLA_AEXON2F HUMAN HLA F
CSGGGSYGGGGTCACTCAC HLA_AEXON2R HUMAN HLA R
TCSGGGCCAGGTTCTCACACC HLA_AEXON3F HUMAN HLA F
CYGGTACCCGTGCGCTGCAG HLA_AEXON3R HUMAN HLA R
CCCAGGCTCCCACTCCATGAGG HLA_BEXON2F HUMAN HLA F
CCRGGCCGGGGTCACTCAC HLA_BEXON2R HUMAN HLA R
SCKRGGCCAGGGTCTCACA HLA_BEXON3F HUMAN HLA F
GCTCCCCACTGCCCCTGGTA HLA_BEXON3R HUMAN HLA R
CCCAGGCTCCCACTCCATGARG HLA_CEXON2F HUMAN HLA F
CCGGGCYGGGGTCACTCAC HLA_CEXON2R HUMAN HLA R
SCGGGGCCAGGKTCTCACA HLA_CEXON3F HUMAN HLA F
CTTTACCAGATCTCAAAAAGAAGGTC CCR5OUTF HUMAN CCR5
AGGTCTTCATTACACCTGCAGC CCR5F HUMAN CCR5
CTTCTCATTTCGACACYGAAGC POLYCCR5R HUMAN CCR5
ATGATGGTGAAGATAAGCCTCACAG CCR5OUTR HUMAN CCR5
GTAAAACGACGGCCAG M13F PLASMID F
CAGGAAACAGCTATGAC M13R PLASMID R
AGAGGAATTCTCCACATACCTASAAGAATAAGACAGG Nef1F_ECORI HIV NEF (construct) F 3 74
GCCTCCGCGGAAAGTCCCCAGCGGAAAGTCCCTTGTA NefIR_SACII HIV NEF (construct) R 3 75