LOCUS       reference_p5            8991 bp    DNA              UNK 23-SEP-2015
DEFINITION  reference for patient p5, genomewide
ACCESSION   reference_p5
VERSION     reference_p5
KEYWORDS    .
SOURCE      
  ORGANISM  HIV-1
            .
FEATURES             Location/Qualifiers
     fragment        1..1776
                     /note="F1"
     fragment        1469..3321
                     /note="F2"
     fragment        3111..4638
                     /note="F3"
     fragment        4376..6013
                     /note="F4"
     fragment        5424..7425
                     /note="F5"
     fragment        7218..8991
                     /note="F6"
     RNA_structure   7179..7412
                     /note="RRE"
     RNA_structure   1..87
                     /note="LTR5'"
     RNA_structure   8487..8991
                     /note="LTR3'"
     gene            5502..5747
                     /note="vpu"
     gene            join(5271..5485,7789..7879)
                     /note="tat"
     gene            1538..4549
                     /note="pol"
     gene            4494..5060
                     /note="vif"
     gene            5665..8181
                     /note="env"
     gene            5012..5290
                     /note="vpr"
     gene            243..1745
                     /note="gag"
     gene            8183..8818
                     /note="nef"
     gene            join(5410..5485,7789..8063)
                     /note="rev"
     other           5665..5751
                     /note="env peptide"
     other           6130..6243
                     /note="V2"
     other           150..232
                     /note="psi"
     other           6802..6882
                     /note="V4"
     other           7003..7044
                     /note="V5"
     other           6058..6129
                     /note="V1"
     other           6415..6774
                     /note="V3"
     protein         243..638
                     /note="p17"
     protein         639..1331
                     /note="p24"
     protein         1332..1373
                     /note="p2"
     protein         1374..1538
                     /note="p7"
     protein         1539..1586
                     /note="p1"
     protein         1587..1745
                     /note="p6"
     protein         1706..2002
                     /note="PR"
     protein         2003..3322
                     /note="RT"
     protein         3323..3682
                     /note="p15"
     protein         3683..4549
                     /note="IN"
     protein         5758..7167
                     /note="gp120"
     protein         7168..8181
                     /note="gp41"
     other           6046..6255
                     /note="V1V2ext"
     other           6790..6894
                     /note="V4ext"
     other           6985..7059
                     /note="V5ext"
ORIGIN
        1 ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagaccac
       61 ttaagtcagt gtggaaaatc tctagcagtg gcgcccgaac agggacttga aagcgaaaga
      121 gaaaccagag gagctctctc gacgcaggac tcggcttgct gaagcgcgca cagcaagagg
      181 cgaggggcgg cgactggtga gtacgccaat aattttgact agcggaggct agaaggagag
      241 agatgggtgc gagagcgtca atattaagcg ggggagaatt agataggtgg gaaaaaattc
      301 ggttaaggcc agggggaaag aaaaaatata gattaaaaca tatagtatgg gcaagcaggg
      361 agctagaacg attcgcggtt aaccctggcc tgttagaaac atcagaaggc tgtagacaaa
      421 tactggctca gctacaacca agccttcaga caggatcaga agaacttaaa tcattgtata
      481 atacagtagc aaccctctat tgtgtgcatc aaaagataga ggtaagagac accaaggaag
      541 cgttagagaa ggtagaggag gagcaaaaca aaagtaagaa aaaagcacag caagcagcag
      601 ctgccacagg aaacagcagt gtgggcagcc aaaattaccc tatagtgcag aacctacagg
      661 ggcaaatggt acatcagccc atatccccta gaactttaaa tgcatgggta aaagtaatag
      721 aagagaaggc tttcagccca gaagtaatac ccatgttttc agcactagca gaaggagcca
      781 ccccacaaga tttaaacacc atgctaaaca cagtgggggg acaccaagca gcaatgcaaa
      841 tgttaaaaga aaccatcaat gaggaagctg cagaatggga tagattgcat ccagtacaag
      901 cagggcctgt tgcaccaggc cagatgagag aaccaagggg aagtgacata gcaggaacta
      961 ctagtaacct ccaggagcaa ataggatgga tgacaagtaa tccatctatc ccagtaggag
     1021 aaatctataa aagatggata atcatgggat taaataaaat agtaaggatg tatagtccta
     1081 tcagcatttt ggacataaaa caaggaccaa aagaaccctt tagagactat gtagaccggt
     1141 tctataaaac tctaagagcc gagcaagcta cacaagaagt aaaaaattgg atgacagaaa
     1201 ccttgttggt ccaaaatgcg aacccagatt gtaaaactat tttaaaagca ttaggaccag
     1261 cagctacact agaagaaatg atgacagcat gtcagggagt gggaggaccc agccataaag
     1321 caagagtttt ggctgaagca atgagccaag taacaggttc agccaccata atgatgcaga
     1381 aaggcaattt taggaaccaa agaaaaggtg ttaagtgctt caattgtggc agagaagggc
     1441 acatagccaa acattgtagg gcccctagaa aaaagggctg ttggaaatgt ggaagggaag
     1501 gacaccaaat gaaagattgt actgagagac aggctaattt tttagggaaa atctggcctt
     1561 cccacaaggg gaggccagga aacttccttc agaacagacc agagccatca gccccaccag
     1621 aggagagctt caggtttggg gaagagacag caactccctc tcagaagcag gagcagaaag
     1681 acaaggaact gtatccttca acttccctca gatcactctt tggcaacgac ccctcgtcac
     1741 aataaggata ggggggcaac taaaggaagc tctattagat acaggagcag atgatacagt
     1801 attagaagac atggagttgc caggaagatg gaaaccaaaa atgatagggg gaattggagg
     1861 ttttatcaaa gtaaaacagt atgagcagat actcgtagaa atctgtggac ataaagctat
     1921 aggtacagta ttagtaggac ctacacctgt caacataatt ggaagaaatc tgttgactca
     1981 gattggttgc actttaaatt ttcccattag tcctattgaa actgtaccag taaaattaaa
     2041 gccaggaatg gatggcccaa aagttaaaca atggccattg acagaagaaa aaataaaagc
     2101 attaatagaa atttgtacag aaatggaaaa ggaagggaaa atttcaaaaa ttgggcctga
     2161 aaatccatac aatactccag tatttgccat aaagaaaaaa gacagtacta aatggagaaa
     2221 attagtagat ttcagagaac ttaataagaa aactcaagac ttctgggaag ttcaattggg
     2281 aataccacat cccgcagggt taaaaaagaa gaaatcagta acagtgctgg atgtgggtga
     2341 tgcatatttt tcagttccct tagataaaga cttcaggaag tatactgcat ttaccatacc
     2401 tagtacaaac aatgagacac cagggattag atatcagtac aatgtgctgc cacagggatg
     2461 gaaaggatca ccagcaatat tccaaagtag catgacaaaa atcttagagc cttttagaaa
     2521 acaaaaccca gacatagtta tctaccaata catggatgat ttgtatgtag ggtctgactt
     2581 agaaataggg cagcatagaa caaaagtaga ggaactgaga gaacatttgt tgaagtgggg
     2641 atttaccaca ccagacaaaa aacatcagaa agaacctcca ttcctttgga tgggttatga
     2701 actccatcct gataaatgga cagtacagcc tataatacta ccagaaaaag acagctggac
     2761 tgtcaatgac atacagaaat tagtaggaaa attaaattgg gcaagtcaga tttatgcagg
     2821 gattaaagta aagcaattat gcaaactcct taggggagcc aaagcattaa cagaggtgat
     2881 acctctaaca gaagaagcag agctagaatt agcagaaaac agggaaattc taagagagcc
     2941 agtacatgga gtgtattatg acccatcaaa agacttaata gcagaagtac agaagcaggg
     3001 gcaaggccag tggacatatc aaatttatca agagccattt aaaaatctga aaacaggaaa
     3061 atatgcaaga atgaggggag cccacactaa tgatgtaaaa caattaacag aggtagtaca
     3121 aaaaatagcc acagaaagca tagtaatatg gggaaagatt cctaaattta gactacccat
     3181 acaaaaagag acatgggacg catggtggac agagtattgg caggctacct ggattcctga
     3241 gtgggagttt gtcaataccc ctcccttagt gaaattatgg taccagttag agacagaacc
     3301 catagtagga gcagaaactt tctatgtaga tggagcagct aacagggaga ctaaactagg
     3361 aaaagcagga tatgttactg acaaaggaag gcaaaaaatt atctccctaa ctgacacaac
     3421 aaatcagaaa actgagttac aagcaattta tctagctttg caggattcgg gattagaagt
     3481 aaacatagta acagactcac aatatgcatt aggaatcatt caagcaaaac cagataaaag
     3541 tgaatcagag ttagtcagtc aaataataga gcagttaata aaaaaggaaa aggtctacct
     3601 ggcatgggta ccagcacaca aaggaattgg gggaaatgaa caagtagata aattagtcag
     3661 tagtggaatc aggaaagtac tatttttaga tggaatagat aaggcccaag aagaccatga
     3721 gaaatatcac agcaattgga aagcaatggc tagtgatttt aacttgccac ctgtggtagc
     3781 aaaagaaata gtagccagct gtgataaatg tcagctaaaa ggagaagcca tgcatggaca
     3841 agtagactgt agtccaggaa tatggcaact agattgtaca catttagaag gaaaaattat
     3901 cctggtagca gttcatgtag ccagtggata tatagaagca gaagttattc cagcagagac
     3961 aggacaggaa acagcatatt ttatcttaag gctagcagga agatggccag taaaaacaat
     4021 acatacagac aatggcccaa acttcatcag tgccacggtt aaggccgctt gttggtgggc
     4081 ggggatcaaa caggaatttg gcattcccta caatccccaa agtcaaggag tagtagaatc
     4141 tatgaataaa gaattaaaga aaattatagg acaggtaaga gatcaggctg aacatcttaa
     4201 gacagcagta caaatggcag tattcattca caattttaaa agaaaagggg ggattgggga
     4261 ctacagtgca ggggaaagaa taatagacat aatagcaaca gacatacaaa ctaaagaatt
     4321 acaaaaacaa gttacaaaaa ttcaaaattt tcgggtttat tacagggaca gcagagatcc
     4381 actgtggaaa ggaccagcaa aacttctttg gaaaggtgaa ggggcagtag taatacaaga
     4441 taatagtgac ataaaagtag tgccaagaag aaaagcaaag atcattaggg attatggaaa
     4501 acagatggca ggtgatggtt gtgtggcaag tagacaggat gaggattaaa acatggaaaa
     4561 gtttagtaaa acaccatatg tatatttcag ggaaagctaa gggatgggct tataaacatc
     4621 actatgaaag cattaatcca agaataagtt cagaagtaca catcccacta ggggaagcta
     4681 aattagtaat aacaacatat tggggtctac agacaggaga gagagactgg catttgggtc
     4741 aaggagtctc catagaatgg aggaaaaaga gatatagcac acaagtagac cctgaactag
     4801 cagaccgact aattcatctg tattactttg attgtttttc agaaactgct ataagaaatg
     4861 ccatattagg acatatagtt agtcctaggt gtgactatca agcaggacat aacaaggtag
     4921 gatctctaca gtacttggca ctagcagcat taacaacacc aaaaaggagc aagccacctc
     4981 tgcctagtgt tgcgaaactg acagaggata gatggaacaa gccccagaaa accaagggcc
     5041 acagagggag tggacactag agcttttaga ggagcttaag agtgaagctg ttaaacattt
     5101 tcctaggcca tggcttcaca atttagggca atatatctat gaaacttatg gggatacttg
     5161 gacaggagtg gaagccataa taagaatact gcaacaactg ctgtttattc atttcagaat
     5221 tgggtgccac cacagcagaa taggcattgt tcgacaggcg agagcaagaa atggagccag
     5281 tagatcctag actagagccc tggcagcatc caggaagtca gcctaaaact gcttgcacca
     5341 attgctattg taaaaagtgt tgctttcatt gccaagtttg tttcataaca aaaggcttag
     5401 gcatctccta tggcaggaag aagcggagac agcgacgaag agctcctcaa gacagtcaga
     5461 ctaatcaagc tcctctatca aagcagtaag taatatatgt aatgcaatct atacaaatat
     5521 tagcaatagt agcattagta gtaggagcaa tattagcaat agttgtgtgg tctatagtat
     5581 tcatagaata taggaaaata ttaagacaaa gaaaaataga caggttaatt gatagaataa
     5641 gagaaagagc agaagacagt ggcaatgaga gtgaggggga tcaggaagaa ttgtcagagc
     5701 tggtggagag ggggcatctt gctccttggg atgttgatga cctgtagtgc tgaagaaaag
     5761 gaacaaacgt gggtcacagt ctattatggg gtacctgtgt ggaaagaagc aaccaccact
     5821 ctattttgtg cctcagatgc taaagcatat aatacagagg cacataatgt ttgggccact
     5881 catgcctgcg tacccacaga ccccaaccca caagaagtag tattggaaaa tgtgacagaa
     5941 aattttaata tgtggaaaaa tgacatggta gaacagatgc aggaggatgt aatcaattta
     6001 tgggatcaaa gcctaaagcc atgtgtaaaa ttaaccccac tctgtgttac tttaaattgc
     6061 actgattatg tgggaaatac tactaacacc actaacaata gcactatgga gaaaggggaa
     6121 ataaagaact gctctttcta tgtcaccaca agcatgaaag ataaaaaaca gagagaatat
     6181 gccctctttt ataagcttga tgtagtacca atagagaata acagctatag gttgataagt
     6241 tgtaacacct cagtcattac acaggcctgt ccaaagacat cctttgaacc aattcctata
     6301 cattattgtg ccccggctgg ttttgcgatt ataaagtgta atgataagaa gttcaatgga
     6361 acaggaccat gtaaaaatgt cagcacagta caatgcacac atggaattag gccagtagtg
     6421 tcaactcaac tgttgttaaa tggcagccta gcagaagaag agatagtaat tagatctgaa
     6481 aatttcacaa acaatgctaa aaccataata gtgcagctga acgagactgt acaaattcat
     6541 tgtgtaagac ccaacaacaa tacaagaaag agtatacata tagcaccagg gagagcattt
     6601 tatgcaacag gagcaataat aggagatata agacaggcac attgtaacat tagtaaagca
     6661 aactggacta acactttaag aaagataaag gataaattaa aagaacaatt taataataca
     6721 aaaattgtct ttaatcactc ctcaggaggg gacccagaaa ttgtaatgca cagttttaat
     6781 tgtggagggg aatttttcta ctgtaataca acacaactgt ttaatagtac ttggaatgaa
     6841 actgaaagtt ataataacaa tgacactatc acactcccat gtagaataaa gcagattata
     6901 aacatgtggc aggaagtagg aaaagcaatg tatgcccctc ccatcagagg aaacattagc
     6961 tgtaaatcaa atattacagg actaatatta acaagagatg gtggtaatgg caatagcagc
     7021 aatggcagcg aaatcttcag acctggagga ggagatatga gggacaattg gagaagtgaa
     7081 ttatataaat ataaagtagt aaaaattgaa ccattaggga tagcacccac caaggcaaag
     7141 aggagagtgg tgcaaagaga aaaaagagca gtgggaatag gagctttgtt ccttgggttc
     7201 ttgggagcag caggaagcac tatgggcgca gcgtcaatga cgctgacggt acaggccaga
     7261 ctattattgt ctggtatagt gcaacagcag aacaatttgc tgagggctat tgaggcgcaa
     7321 caacatctgt tgcaactcac agtctggggc atcaagcagc tccaggcaag agtcctggct
     7381 gtggaaagat acctaaagga tcaacagctc ctgggaattt ggggttgctc tggaaaactc
     7441 atttgcacca ctgctgtacc ttggaatact agttggagta ataaatctct acatcagatt
     7501 tgggataaca tgacctggat ggagtgggat agagaaatta acaattacac aagcttaata
     7561 tacactttaa ttgaagaatc gcaaaaccaa caagaaaaga atgaacaaga attattggaa
     7621 ttagataaat gggcaagttt gtggaattgg tttgacataa caaaatggct gtggtatata
     7681 aaaatattca taatgatagt aggaggctta ataggtttaa gaatagtttt tgctgtactt
     7741 actatagtga atagagttag gcagggatat tcaccattat cgtttcagac ccactaccca
     7801 gccccacggg gacccgacag gcccgaagga accgaagaag aaggtggaga gaaagacaga
     7861 ggcagatcca cacgcttagt ggatggattc ttagcactga tctgggacga tctgcgaagc
     7921 ctgtgcctct tcagctacca ccgcttgaga gacttactct tgattctagc gaggattgtg
     7981 gaacttctgg gacgcagggg gtgggaagcc ctcaagtatt ggtggaatct tctacagtat
     8041 tggagacagg aactgaagaa tagtgccatt agtttgttca atgatacagc tatagcagta
     8101 gctgagggaa cagatagggt tagagctatt cgccacatac ctagaagaat aagacagggc
     8161 ttggaaaggg ctttgcaata agatgggtgg caaattttca aaacgggaat ggcctgctgt
     8221 aagggaaaaa atgaggcgag ctaagccagc agctgagcca gcagctgagc cagcagcagt
     8281 tggggtggga gcagtatctc gagacctgga aaaacatgga gcaatcacaa gtaacaatac
     8341 agcagctacc aatgctgatt gtgccagggt agaagcacaa gaggaagagg aggtgggttt
     8401 tcctgtcacg cctcaggtac ctttacgacc aatgacttac caggcagctg tagatcttag
     8461 ccacttttta aaagaaaagg ggggactgga agggctagtt tactcaacaa agagacaaga
     8521 aatccttgat ctgtgggtct accacacaca aggctacttc cctgattggc agaactacac
     8581 accagggcca ggggtcagat atccactgac ctttggatgg tgctttaagc tagtaccagt
     8641 tgacccagat acggtagaag aggccaatga aggagaaaac aactgcttgc tacaccctat
     8701 gagccagcat gggatggatg acccagagag agaagtgtta gtgtggaagt ttgacagcct
     8761 cttagcattt catcacaagg cccgagagct gcatccggac tactacaaga actgctgaca
     8821 gcgtacttct acaagggact ttccgctggg gactttccag ggaggcgtgg ccggggcggg
     8881 actggggagt ggcgagccct cagatgctgc atataagcag ccgctttttg cctgtactgg
     8941 gtctctctag ttagaccaga tctgagcctg ggagctctct ggctgactag g
//
