LOCUS       reference_p9            9017 bp    DNA              UNK 23-SEP-2015
DEFINITION  reference for patient p9, genomewide
ACCESSION   reference_p9
VERSION     reference_p9
KEYWORDS    .
SOURCE      
  ORGANISM  HIV-1
            .
FEATURES             Location/Qualifiers
     fragment        1..1768
                     /note="F1"
     fragment        1461..3313
                     /note="F2"
     fragment        3103..4627
                     /note="F3"
     fragment        4368..6008
                     /note="F4"
     fragment        5425..7441
                     /note="F5"
     fragment        7234..9017
                     /note="F6"
     RNA_structure   7195..7428
                     /note="RRE"
     RNA_structure   1..87
                     /note="LTR5'"
     RNA_structure   8512..9017
                     /note="LTR3'"
     gene            5503..5748
                     /note="vpu"
     gene            join(5272..5486,7805..7895)
                     /note="tat"
     gene            1530..4538
                     /note="pol"
     gene            4486..5061
                     /note="vif"
     gene            5666..8221
                     /note="env"
     gene            5001..5291
                     /note="vpr"
     gene            244..1737
                     /note="gag"
     gene            8223..8843
                     /note="nef"
     gene            join(5411..5486,7805..8079)
                     /note="rev"
     other           5666..5752
                     /note="env peptide"
     other           6125..6244
                     /note="V2"
     other           150..233
                     /note="psi"
     other           6803..6898
                     /note="V4"
     other           7019..7060
                     /note="V5"
     other           6053..6124
                     /note="V1"
     other           6416..6775
                     /note="V3"
     protein         244..639
                     /note="p17"
     protein         640..1332
                     /note="p24"
     protein         1333..1374
                     /note="p2"
     protein         1375..1530
                     /note="p7"
     protein         1531..1578
                     /note="p1"
     protein         1579..1737
                     /note="p6"
     protein         1698..1994
                     /note="PR"
     protein         1995..3314
                     /note="RT"
     protein         3315..3674
                     /note="p15"
     protein         3675..4538
                     /note="IN"
     protein         5753..7183
                     /note="gp120"
     protein         7184..8221
                     /note="gp41"
     other           6041..6256
                     /note="V1V2ext"
     other           6791..6910
                     /note="V4ext"
     other           7001..7075
                     /note="V5ext"
ORIGIN
        1 ttcaagtagt gtgtgcccat ctgttgtgtg actctggtag ctagagatcc ctcagactct
       61 tttagtcagt acagaaaatc tctagcagtg gcgcccgaac agggacctga aagcgaaagt
      121 aaaaccagag gagctctctc gacgcaggac tcggcttgct gaagcgcgca cagcaagagg
      181 cgaggggcgg cgactggtga gtacgccaaa actttttgac tagcggaggc tagaaggaga
      241 gagatgggtg cgagagcgtc agtattaagc gggggagaat tagataaatg ggaaaaaatt
      301 cggttaaggc cagggggaaa gaaaaaatat aaattaaaac atatagtatg ggcaagcagg
      361 gagctagagc gattcgcagt taatcctggc ctgttagaaa catcagaagg ctgtagacaa
      421 atactgggac aactacaacc agcccttcag acaggatcag aagaacttag atcattatat
      481 aatacagtag ccaccctcta ttgtgtgcat caaaagatag aggtaaaaga caccaaggaa
      541 gctttagaaa agatagagga agagcaaaac aaaagtaaga aaaaggcaca gcaagaagca
      601 gctggcacag gaaacagcag ccaggtcagc caaaattacc ctatagtaca gaacatgcag
      661 gggcaaatgg tacatcaggc catgtcacct agaactttaa atgcatgggt aaaagtaata
      721 gaagagaagg ctttcagccc agaagtaata cccatgtttt cagcattatc agaaggagcc
      781 accccacaag atttaaacac catgctaaac acagtggggg gacatcaagc agctatgcaa
      841 atgttaaaag agaccatcaa tgaagaagct gcagaatggg atagactgca tccagtgcat
      901 gcagggccta ctgcaccagg ccagatgaga gaaccaaggg gaagtgacat agcaggaact
      961 actagtaccc ttcaggagca aatagcatgg atgacaaata atccacctat cccagtagga
     1021 gaaatctata aaagatggat aattctggga ttaaataaaa tagtaagaat gtatagccct
     1081 accagcattc tggacataag acaaggacca aaggaaccct ttagagatta tgtagatcgg
     1141 ttctataaaa ctctaagagc cgagcaagct tcacaggagg taaaaaattg gatgacagaa
     1201 accttgttgg ttcaaaatgc gaacccagat tgtaagacta ttttaaaagc attgggacca
     1261 gcagccacat tagaagaaat gatgacagca tgtcagggag tgggaggacc cggccataaa
     1321 gcaagagtct tggctgaagc aatgagtcaa gcaacaactt cagctaacat aatgatgcag
     1381 agaggcaatt ttaggaagat tgttaagtgc ttcaattgtg gcagagaagg acacatagcc
     1441 aaaaattgca gggcccctag gaaaaagggc tgttggaagt gtggaaaaga aggacaccaa
     1501 atgaaagatt gtactgagag acaggctaat tttttaggga aaatctggtc ttcccacaag
     1561 ggaaggccag ggaattttct tcagagcaga ccagagccaa cagccccacc agcagagagc
     1621 ttcaggtttg gggaagagac attgactccc tctcagaagc aggagccgat ggacaaggat
     1681 ctatatcctt tagcctccct cagatcactc tttggcaacg acccctcgtc acaataaaga
     1741 taggggggca actaaaggaa gctctattag atacaggagc agatgataca gtattagaag
     1801 aaatgagttt gccaggaaga tggaaaccaa aaatgatagg gggaattgga ggttttatca
     1861 aagtaagaca gtatgatcag atacccatag aaatctgtgg acataaagct ataggtacag
     1921 tattaatagg acctacacct gtcaacataa ttggaagaaa tctgttgact cagcttggtt
     1981 gcactttaaa ttttcccatt agtcctattg aaactgtacc agtaaaatta aagccaggaa
     2041 tggatggccc aaaagttaaa caatggccat tgacagagga aaaaataaaa gcattaatag
     2101 agatttgtac agaaatggaa aaggaaggga aaatttcaaa aattgggcct gaaaacccat
     2161 acaatactcc agtatttgcc ataaagaaaa aagacagtac taaatggaga aaattagtag
     2221 atttcagaga acttaataag aaaactcaag acttctggga agttcaacta ggaataccac
     2281 atcccgcagg gttaaaaaag aaaaaatcag taacagtact ggatgtgggt gatgcatatt
     2341 tttcagttcc cttagataaa gatttcagga agtatactgc atttaccata cctagtacaa
     2401 acaatgagac accagggatt agatatcagt acaatgtact tccacaggga tggaaaggat
     2461 caccagcaat atttcaaagt agcatgacaa aaatcttaga gccttataga aagcaaaatc
     2521 cagacatagt tatctatcaa tacatggatg atttgtacgt aggatctgac ttagaaatag
     2581 agcagcatag aacaaaaata gaggaactga gacaacatct gttgaagtgg ggattaacca
     2641 caccagacaa aaaacatcag aaagagcccc cattcctttg gatgggttat gaactccatc
     2701 ctgataaatg gacagtgcag cctatagagc tgccagaaaa ggacagctgg actgtcaatg
     2761 acatacagaa attagtggga aaattaaact gggcaagtca gatttaccca gggattaaag
     2821 taaggcaatt atgtaaactc ctaaggggaa ccaaagcact aacagaagta gtacctctaa
     2881 caacagaagc agaactagaa ctggcagaaa acagggaaat tctaaaagaa ccagtacatg
     2941 gagtgtatta tgacccaaca aaagacttaa tagcagaaat acagaagcag gggcaaggcc
     3001 aatggacata tcaaatttat caagaaccat ttaaaaatct gaaaacagga aaatatgcaa
     3061 aaatgagggg tgcccacact aatgatgtaa aacaattaac agaggcagtg caaaaaataa
     3121 ccacagaaag catagtaata tggggaaaga ctcctaaatt tagactgccc atacaaaaag
     3181 aaacatggga aacatggtgg acagaatatt ggcaagccac ctggattcct gagtgggagt
     3241 ttgtcaatac ccctccctta gtgaaattat ggtaccagtt agagaaagag cccatagtag
     3301 gagcagaaac cttttatgta gatggggcag ctaacagaga gactaaattg ggaaaagcag
     3361 gatatgttac caacagagga agacaaaagg ttgtctccct aactgacaca acaaatcaga
     3421 agactgagtt acaagccatt catctagctt tgcaggattc aggagtagaa gtaaacatag
     3481 taacagactc acaatatgca ttaggaatta ttcaagcaca accagataaa agtgaatcag
     3541 agttagtcag tcaaataata gagcagttaa taaaaaagga aaaggtctac ctggcatggg
     3601 taccagcaca caaaggaatt ggaggaaatg aacaggtaga taaattagtt agcgctggaa
     3661 tcaggaaagt attattttta gatggaatag ataaggccca agacgaacat gaaaaatatc
     3721 acagtaattg gagagcaatg gccagtgatt ttaacctgcc acctgtagta gcaaaagaaa
     3781 tagtagcctg ctgtgataaa tgtcagttaa aaggagaagc catgcatgga caagtagact
     3841 gtagtccagg aatctggcaa ctagactgta cacatttaga aggaaaagtc atcctggtag
     3901 cagttcatgt agccagtgga tatctagaag cagaagttat tccagcagaa acagggcagg
     3961 aaacagcata ctttctctta aagttagcag gaagatggcc agtaaaaaca atacacacag
     4021 acaatggccc caatttcatc agtactacgg ttaaggccgc ctgttggtgg gcgggaatca
     4081 agcacgaatt tggcattcct tacaatcccc aaagtcaagg agtagtagaa tctatgaata
     4141 aagaattaaa gaaaattata ggacaggtaa gagatcaagc tgaacatctt aagacagcag
     4201 tacaaatggc agtattcatc cacaatttta aaagaaaagg ggggattggg gagtacagtg
     4261 caggggaaag aataatagac ataatagcaa cagacataca aactaaagaa ttacaaaaac
     4321 aaattacaaa aattcaaaat tttcgggttt attacaggga caacagagat ccactttgga
     4381 aaggaccagc aaagcttctc tggaaaggtg aaggggcagt agtaatacaa gataatagtg
     4441 acataaaagt agtgccaaga agaaaagcaa agatcattag ggattatgga aagcagatgg
     4501 ccggtgattg tgtggcaagt agacaggatg aggattagaa catggaaaag tttagtaaaa
     4561 caccatatgt atatttcaag gaaagctaag ggatgggttt atagacatca ctatgaaaac
     4621 actcatccaa aaataagttc agaagtacac atcccactag gggatgctag attggcaata
     4681 acaacatatt ggggtctgca gacaggagaa agagactggc acttgggtca aggagtctcc
     4741 atagagtgga ggcaaaagag atatagcaca caagtagacc ctgacctagc agaccgacta
     4801 attcatctgt attactttga ttgtttttca gaatccgcta taagaaatgc catattagga
     4861 catagagtta gccctagttg tgaatatcaa gcaggacata acaaggtagg atctttacag
     4921 tacttggcac tagtagcatt aacaacacca aaaaagaaaa agccaccttt gcctagtgtt
     4981 gcgaaactga cagaggatag atggaacaag ccccagaaga ccaagggcca cagagggagc
     5041 catacaatga atggacacta gagcttttag aagagcttaa acaagaagct gttaggcatt
     5101 ttcctagggt gtggctccat agcttagggc aatatatcta tgaaacctat ggagatactt
     5161 gggcaggagt ggaagccata ataagaattc tgcagcaact gctgtttatt catttcagga
     5221 ttgggtgtcg acatagcaga ataggtattg atcgacaaag gagagcaaga aatggagcca
     5281 gtagacccta gactagagcc ctggaagcat ccaggaagtc agcctaagac tgcttgtacc
     5341 aattgctatt gtaaaaagtg ttgctatcat tgccaagttt gtttcctgaa aaaagcctta
     5401 ggcctctcct atggcaggaa gaagcggaga cagcgacgaa gagctcctca agatagtaag
     5461 gatcatcaga gctctctatc aaagcagtaa gtagtacatg tgatgcaatc cttagaaata
     5521 ttagcaatag tagcattagt agtagcatta ataatagtaa tagttgtgtg gtccatagta
     5581 ctcatagaat atagaaaaat attaagacaa agaaaaatag acaggttaat tgctagaata
     5641 agagaaagag cagaagacag tggcaatgac agtgaaggtg atcaggagga attatcagcg
     5701 cttgtggaaa gggagcacct tgctccttgg gatattgatg atctgtagtg ctacaggaaa
     5761 cttgtgggtc acagtctatt atggggtgcc tgtgtggaaa gaagcaacca ccactctatt
     5821 ttgtgcatca gatgctaaag catatgacac agaggtccat aatgtttggg ccacacatgc
     5881 ctgtgtaccc acagacccca acccacaaga aatagtatta gaaaatgtga cagaaaattt
     5941 taacatggga aaaaataaca tggtagaaca gatgcatgag gatataatca gtttatggga
     6001 acaaagctta aagccatgtg taaaattaac cccactctgt gttactttaa attgcactga
     6061 tttgaagaat gctactaata ccactagtgg tagtgggagg atggagggag gagagatgaa
     6121 aaactgctca ttcaatatca ccacaagcat aagaaataag atgcagagag aatatgcact
     6181 tttttataaa cttgatatag tacagataga tggtgataat accagttata gattgataaa
     6241 ttgtaacacc tcaatcatta cacaggcctg tccaaaggta tcttttgagc caattcccat
     6301 acattattgt gccccagctg gttttgcgat tctaaagtgt agagataaga agttcaatgg
     6361 aacaggacca tgtaaaaatg tcagcacagt acagtgtaca catggaatta ggccagtagt
     6421 atcaactcaa ctgctgttaa atggcagtct agcagaaaaa gaggtagtaa ttagatctga
     6481 caatttctca gacaatgcta aaaccataat agtacaactg aaaaaatctg taaaaattaa
     6541 ttgtacaaga cccaacaaca atacaagaag aagtatacct ataggaccag ggagagcatt
     6601 ttatgcaaca ggagatataa taggaaatat aagacaagca cactgtaacc ttagtaggtc
     6661 aaaatggaat gacactttaa gacagatagt tatagaatta agaaaacaat ttgggaataa
     6721 aacaatagtc tttaagcgct cctcaggagg ggacccagaa attacaatgc acagttttaa
     6781 ttgtggaggg gaatttttct actgtaatac aacacaactg tttaatagta cttggaataa
     6841 tgctacaggg tcaaatgaca ctgcaggaaa agacaatagc acaatcacac tctcatgtaa
     6901 aataagacaa attataaaca ggtggcagga agtaggaaaa gcaatgtatg ccccccccat
     6961 ccaaggacga attagttgtt catcaaatat tacagggcta ctattagtaa gagatggtgg
     7021 tagcaccacc aacagcagcg agaccgaaat cttcagacct ggaggagaaa atataaagga
     7081 taattggaga agtaaattat ataaatataa agtagtaaaa attgaaccat taggattagc
     7141 acccaccaag gcaaagagaa gagtggtgca gagagaaaaa agagcagtgg gaataggagc
     7201 tgtgttcctt gggttcttag gagcagcagg aagcactatg ggcgcagcgt caatgacgct
     7261 gacggtacaa gccagacaat tattgtctgg tatagtgcaa cagcagaata atttgctgag
     7321 agctattgag gcgcaacagc acctgttgca actcacagtc tggggcatca agcaactcca
     7381 ggcaagagtt ctggctgtgg aaagatacct aaaggatcaa cagctcctgg ggatttgggg
     7441 ttgctctgga aaactcattt gcaccactgc tgtgccttgg aatgctagtt ggagtaataa
     7501 atctctagag acgatttggg gtaacatgac ctggatggag tgggaaaagg aaattgacaa
     7561 ttacacaagc ttaatataca ctttaattga agaatcgcag aaccaacaag aaaagaatga
     7621 acaagaatta ttggaattgg acaagtgggc aagtttgtgg aattggtttg acataacaaa
     7681 atggctgtgg tatataaaaa tattcataat gatagtagga ggcttgatag gtttaaggat
     7741 aatttttgct gtactttcta tagtaaatag agttaggaag ggatactcac cattatcgtt
     7801 gcagacccgt ctcccaacac caaggggacc cgacaggccc gaagaaaccg aagaaggagg
     7861 tggagaaaga gacagcaaca gatccaggag attagtggac ggattcttag cgcttatctg
     7921 ggacgatctg cggagcctgt gcctcttcag ctaccaccac ttgagagact tactcttgat
     7981 tgcaacgagg gttgtggaac ttctgggacg cagggggtgg gaactcctca aatattggtg
     8041 gaatctccta caatattgga gtcaggaact aaagaatagt gctgttagct tgctcaacgc
     8101 cacagccata gcagtagctg aggggacaga tagggttata gaagcattac aaagaattgg
     8161 tagagctatt ctcaatatac ctaaaagaat aagacagggc ttggaaaggg ctttgctata
     8221 agatgggtgg caagtggtca aaacgtagta gggactggtc tactgtaagg gaaaaaatga
     8281 gcagaactga gccagcagca gagggggtgg gagcagtatc tcgagacctg gaaaagcatg
     8341 gagcaatcac aagtagcaat acagcagcta ccaatgctga ttgtgcctgg ctagaagcac
     8401 aagaggagga ggaggaggtg ggttttccag tcagacctca ggtaccttta agaccaatga
     8461 cttacaaagg agctctagat cttagccact ttttaaaaga aaagggggga ctggaagggc
     8521 taatttactc ccaaagaaga caagatatcc ttgatctgtg gatctacaac acacaaggct
     8581 acttccctga ttggcagagc tacacaccag ggccagggat cagatatcca ctgacctttg
     8641 gctggtgctt caagctagta ccagttgagc cagagaagat cgaagaggcc aatgcaggag
     8701 agaacatcgg cttgttacac cctatgagtc tgcatgggat ggaggacccg gagaaagaag
     8761 tgttacagtg gaagtttgac agcaccctag catttcatca cagggccaaa gagatgtttc
     8821 cggattacta caagaactgc tgacaccgag cttctacaag ggactttccg ctggggactt
     8881 tccaggggag gcgtggcctg ggcgggacag gggagtggcg agccctcaga tgctgcatat
     8941 aagcagccgc tttttgcctg tacgtggtct ctctggttag accagatccg agcctgggag
     9001 ctctctggct aactagg
//
