LOCUS       reference_p11           9011 bp    DNA              UNK 23-SEP-2015
DEFINITION  reference for patient p11, genomewide
ACCESSION   reference_p11
VERSION     reference_p11
KEYWORDS    .
SOURCE      
  ORGANISM  HIV-1
            .
FEATURES             Location/Qualifiers
     fragment        1..1783
                     /note="F1"
     fragment        1466..3328
                     /note="F2"
     fragment        3118..4645
                     /note="F3"
     fragment        4383..6017
                     /note="F4"
     fragment        5443..7420
                     /note="F5"
     fragment        7213..9011
                     /note="F6"
     RNA_structure   7174..7407
                     /note="RRE"
     RNA_structure   1..88
                     /note="LTR5'"
     RNA_structure   8506..9011
                     /note="LTR3'"
     gene            5521..5757
                     /note="vpu"
     gene            join(5290..5504,7784..7874)
                     /note="tat"
     gene            1536..4556
                     /note="pol"
     gene            4501..5079
                     /note="vif"
     gene            5684..8200
                     /note="env"
     gene            5019..5309
                     /note="vpr"
     gene            241..1752
                     /note="gag"
     gene            8202..8837
                     /note="nef"
     gene            join(5429..5504,7784..8058)
                     /note="rev"
     other           5684..5761
                     /note="env peptide"
     other           6122..6235
                     /note="V2"
     other           151..230
                     /note="psi"
     other           6791..6886
                     /note="V4"
     other           7007..7039
                     /note="V5"
     other           6062..6121
                     /note="V1"
     other           6407..6763
                     /note="V3"
     protein         241..636
                     /note="p17"
     protein         637..1329
                     /note="p24"
     protein         1330..1371
                     /note="p2"
     protein         1372..1536
                     /note="p7"
     protein         1537..1584
                     /note="p1"
     protein         1585..1752
                     /note="p6"
     protein         1713..2009
                     /note="PR"
     protein         2010..3329
                     /note="RT"
     protein         3330..3689
                     /note="p15"
     protein         3690..4556
                     /note="IN"
     protein         5762..7162
                     /note="gp120"
     protein         7163..8200
                     /note="gp41"
     other           6050..6247
                     /note="V1V2ext"
     other           6779..6898
                     /note="V4ext"
     other           6989..7054
                     /note="V5ext"
ORIGIN
        1 ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagacctt
       61 tatagtctgt gtagaaaaat ctctagcagt ggcgcccgaa cagggacctg aaaacgaaag
      121 tgagaccaga ggagctctct cgacgcagga ctcggcttgc tgaagcgcgc acggcaagag
      181 gcgaggggcg gcgactggtg agtacgccat ttttgactag cggaggctag aaggagagag
      241 atgggtgcga gagcgtcagt attaagcggg ggaaaattgg atagctggga aaaaattcgg
      301 ttaaggccag ggggaaagaa aaaatatcac ctaaaacatc tagtatgggc aagcagggag
      361 ctagaacgat tcgcggttaa tcctggcctg ttagaaacat caggaggctg tagacaaata
      421 ctgggacagc tacagccatc ccttcagaca ggatcagaag agcttaaatc attatataat
      481 acagtagcag tcctctattg tgtgcatcaa ggggtagata taaaagacac caaggaagct
      541 ttggataaga tagaggaaga gcaaaacaaa agtaagacaa aggcacagca aacaacagct
      601 gacacaggaa atagaggcca ggtcagccaa aattacccta tagtacagaa cctccagggg
      661 caaatggtac atcaggcctt atcacctaga actttaaatg catgggtaaa agtagtagaa
      721 gaaaaggctt ttagcccaga agtaataccc atgtttacag cattatcaga aggagccacc
      781 ccacaagatt taaacaccat gctaaacaca gtggggggac atcaagcagc tatgcagatg
      841 ttaaaagaaa ccatcaatga ggaagctgca gaatgggata gattgcaccc agtacatgca
      901 gggcctgttg caccaggcca gatgagagaa ccaaggggaa gtgacatagc aggaactact
      961 agtacccttc aggaacaaat agcatggatg acaggtaatc cagctatccc agtaggagaa
     1021 atctataaaa gatggataat catggggtta aataaaatag taaggatgta tagccccacc
     1081 agcattctgg acataagaca gggaccaaag gaacccttta gagactatgt agacaggttc
     1141 tataaaactc taagagccga gcaagcttca caggatgtaa aaaattggat gacagaaacc
     1201 ttgttggtcc aaaatgcgaa cccagattgt aagactattt taaaagcatt gggaccagca
     1261 gccacactag aagaaatgat gacagcatgt cagggagtgg gaggacccag ccataaagca
     1321 agaattttgg ctgaagcaat gagccaagta acaaatccaa ctgccataat gatgcagaaa
     1381 ggcaacttta ggagtcaaag aaagattgtt aagtgcttca attgtggcaa agaggggcac
     1441 atagccaaaa attgcagggc ccctagaaaa agaggctgtt ggagatgtgg aaaggaagga
     1501 cacctaatga aagattgtaa tgagagacag gctaattttt tagggaaaat ctggcctgtc
     1561 cacaaggaca ggccagggaa tttttgtcag agcagaccag aaccaacagc cccaccagcc
     1621 ccaccagaag agagcttcag gtttggggta gagacaacga ctccctctca gaagcaggag
     1681 ccgatggaca aggatctgta tcctttagct tccctcaaat cactctttgg caacgacccc
     1741 tcgtcacaat aaagataggg gggcaactga aggaagctct attagataca ggagcagatg
     1801 atacagtatt agaagaaatg aatttgccag gaagatggaa accaaaaatg atagggggaa
     1861 ttggaggttt tatcaaagta agacagtatg atcagatacc catagaaatc tgtggacata
     1921 aagctatagg tacagtatta gtaggaccta cacctgtcaa cataattgga agaaatctgt
     1981 tgactcagat tggttgtact ttaaattttc ccattagtcc tattgaaact gtaccagtaa
     2041 aattaaagcc aggaatggat ggcccaaaag ttaaacaatg gccattgaca gaagaaaaga
     2101 taaaagcatt agtagaaatt tgtacagaaa tggaaaagga agggaaaatt tcaaaaattg
     2161 ggcctgaaaa tccatacaat actccagtat ttgccataaa gaaaaaagac agtactaaat
     2221 ggagaaaatt agtagatttc agagaactta ataaaagaac tcaagacttc tgggaagttc
     2281 aattaggaat accacatccc gcagggttaa aaaagaaaaa atcagtaaca gtactggatg
     2341 taggtgatgc atatttttca gttcccttag ataaagactt caggaagtat actgcattta
     2401 ccatacctag tataaacaat gagacaccag gggttagata tcagtacaat gtgcttccac
     2461 agggatggaa aggatcacca gcaatattcc aaagtagcat gacaagaatc ttagagcctt
     2521 ttagaaaaca aaatccagac atagttatct atcaatacat ggatgatttg tatgtaggat
     2581 ctgacctaga aatagggcag catagaataa aaatagagga actgagacaa catttgttga
     2641 ggtggggatt taccacacca gacaaaaaac atcagaaaga acctccattc ctttggatgg
     2701 gttatgaact ccatcctgat aaatggacag tacagcctat agagctgcca gaaaaagaca
     2761 gctggactgt taatgacata cagaagttag tgggaaaatt gaattgggca agtcagattt
     2821 attcagggat taaagtaagg caattatgta aactccttag gggaaccaaa gcattaacag
     2881 aagtaatatc actaacagaa gaagcagaac tagagctggc agaaaacagg gagattttaa
     2941 aacaaccagt acatggggtg tattatgacc catcaaaaga cttaatcgca gagatacaga
     3001 aacaggggca aggccaatgg acatatcaaa tttatcaaga accatttaaa aatctaaaaa
     3061 caggaaaata tgcaagaatg aggggtgccc acactaatga tgtaaaacaa ttaacagagg
     3121 cagtgcaaaa aatagccaca gaaagcatag taatatgggg aaagactcct aaatttaaac
     3181 tacctataca aaaggaaaca tgggaagcat ggtggacaga gtattggcaa gccacctgga
     3241 ttcccgagtg ggagtttgtc aatacccctc ctttagtaaa actatggtac cagttagaaa
     3301 aagaacccat agtaggagca gaaactttct atgtagatgg ggcagctaac agggagacta
     3361 aattaggaaa agcaggatat gttactaaca aaggaagaca aaaggttgtc tccctaactg
     3421 acacaacaaa tcagaagact gagttacaag caattcatct agctctgcag gattcgggat
     3481 cagaagtaaa catagtaaca gactcgcaat atgcattagg aatcattcaa gcacaaccag
     3541 acaaaagtga atcagagtta gtcaatcaaa taatagagca gctaataaaa aaggaaagga
     3601 tctacctggc atgggtgcca gcacacaaag gaattggagg aaatgaacaa gtagacaaat
     3661 tagtcagtgc tggaatcagg aaggtactat ttttagatgg aatagataag gcccaagaag
     3721 aacatgaaaa atatcacaat aattggagag caatggctag tgattttaac ctgccacctg
     3781 tagtagcaaa agaaatagta gccagctgtg ataaatgtca gctaaaagga gaagccatgc
     3841 atggacaagt agactgtagt ccaggaatat ggcagctaga ttgtacacat ttagaaggaa
     3901 aaattatcct ggtagcagtt catgtagcca gtggatatat agaagcagaa attatcccag
     3961 cagagacagg gcaagaaaca gcatacttta tcttaaaact agcaggaaga tggccagtaa
     4021 acacaataca tacagacaat ggcagcaatt tcaccagtac cgcggttaag gccgcctgtt
     4081 ggtgggcagg gatcaagcag gaatttggta ttccctacaa tccccaaagt caaggggtag
     4141 tagaatctat gaataaagaa ttaaagaaaa ttatagcaca ggtaagagat caggctgaac
     4201 atcttaagac agcagtacaa atggcagtat tcatccacaa ttttaaaaga aaagggggga
     4261 ttggggggta cagtgcaggg gaaagaatag tagacataat agcaacagac atacaaacta
     4321 aagaattaca aaaacaaatt acaaaaattc aaaatttccg ggtttattac agggacagca
     4381 gagatccact ttggaaagga ccagcaaagc ttctctggaa aggtgaaggg gcagtagtaa
     4441 tacaagataa cagtgaaata aaagtagtgc caagaagaaa agcaaagatc attagggatt
     4501 atggaaaaca gatggcaggt gatgattgtg tggcaagtag acaggatgag gattagaaca
     4561 tggaacagct tagtaaaaca ccatatgtat gtttccagga aagctaagga ctgggtttat
     4621 agacatcact atgaaagcac taatccaaga ataaattcag aagtacacat accactaggg
     4681 gatgataaat tggtaataac aacatattgg ggcctgcata caggagaaag agactggcat
     4741 ttgggacagg gagtctccat agaatggagg aaagagagat atagaacaca agtagaccct
     4801 gacacagcag accaactaat tcatctgtat tattttgaat gtttttcagg gtctgctata
     4861 agaaatgcca tattaggacg tttagttagg cctaagtgtg aatatcaagc aggacataac
     4921 aaggtaggat ctctacagta cttggcacta gcagcactaa taacaccaag aaggataaag
     4981 ccacctttgc ctagtgtcag gaaattgaca gaggatagat ggaacaagcc ccagaagacc
     5041 aagggccacc aagggagcca ttcaatgaat ggacactaga acttttagag gaacttaaga
     5101 gtgaagctgt tagacatttt cctaggccat ggcttcatgg cttaggacaa catatctatg
     5161 aaacttatgg agatacttgg gcaggagtgg aagccataat aagaatactg caacaactgc
     5221 tgtttattca tttcagaatt ggatgccaac atagcagaat aggcattatt cgacagagga
     5281 gagcaagaaa tggagccagt agatcctaga ctagagccct ggaagcatcc aggaagtcag
     5341 cctaaaactg cttgtaccaa ttgctattgt aaaaagtgtt gccttcattg ccaagtttgt
     5401 ttcataaaaa aaggcttagg catctcctat ggcaggaaga agcggagaca gcgacgaaga
     5461 gctcctcaag acagtaagac tcatcaagca tctctatcaa agcagtaagt agttaatgtg
     5521 atgcaacctg aagcaatatt agcaatagta gcattagtag tagtagcaat aatagcaata
     5581 gttgtgtgga ccatagtagg cttagaatat aggaaaatat taagacaaag gaaaatagat
     5641 aggttaattg atagaataag agaaagagca gaagacagtg gcaatgagag tgatggagat
     5701 caggaagaat tattggagat ggggcatctt gttccttggg atgttgatga tctgtagtgc
     5761 tgcagaacaa ttgtgggtca cagtctatta tggggtacct gtgtggaaag aagcaaccac
     5821 cactctattt tgtgcatcag atgctaaagg atatgagaca gaggcacata atgtttgggc
     5881 cacacatgcc tgtgtaccca cagaccccaa cccacaagaa ataaatttga aaaatgtgac
     5941 agaaaatttt aacatgtgga aaaataacat ggtagaacag atgcatgagg atataatcag
     6001 tttatgggat caaagcctaa agccatgtgt aaaattaacc ccactctgtg ttactttaaa
     6061 ttgcagtaac aatgttacta gtattaacgg gacaaagata gagggaggag aaatgaaaaa
     6121 ctgctctttc aatatcacaa cagatttaag agataaggtg cagaaacaat acgcgctttt
     6181 ttatgcactt gatgtagtac aaatgaatga taccaactat aggttgataa gttgtaacac
     6241 ctcaattatt acacaagcct gtccaaaggt atcctttcag ccaattccca tacattattg
     6301 tgccccagct ggttttgcaa ttgtaaagtg taatgataaa aagttcaatg gaacaggacc
     6361 atgtacaaat gtcagcacag tacaatgtac acatggcatt aggccaacag tatcaactca
     6421 actgctgtta aatggcagcc tagcagaaga agaagtaata attagatctg aaaatttcac
     6481 aaacaatgca aaaatcataa tagtacagct gaatgaatct gtagaaatta attgtacaag
     6541 acccaataat aatacaagaa gaagtatacc tataggacca gggagagcat tttatacaac
     6601 agaaatagta ggaaatataa gacaagcata ttgtaacgtt agtagagcaa aatggaagaa
     6661 cactttagaa caggtagcaa aaaaattagg tgaacaattt gtgaataaaa caatagtttt
     6721 taagaattcc tcaggagggg acccagaaat tgtaatgcac agttttaatt gtggagggga
     6781 attcttctac tgtaattcaa caccactgtt taatagtact tgggttaatg gtacttggga
     6841 taatactgaa gggtcaaata gcactgaccc aattacactc caatgcaaaa taaaacaaat
     6901 tataaacatg tggcaggaag taggaaaagc aatgtatgcc cctcccatca aaggacaaat
     6961 taactgttca tcaaatatta cagggctgct attaacaaga gatggtggta gcaatgacac
     7021 gaatgagatc ttcagacctg gaggaggaga tatgagggac aattggagaa gtgaattata
     7081 taaatataaa gtagtacaac ttgaaccatt aggaatagca cccaccaagg caaggagaag
     7141 agtggtgcag agagaaaaaa gagcagtggg actaggagct atgttccttg ggttcttggg
     7201 agcagcagga agcactatgg gcgcagcgtc aataacgctg acggtacatg ccagacaatt
     7261 gttgtctggt atagtgcaac agcagaacaa tctgctgaag gctattgagg cgcaacagca
     7321 tctgttgcaa ctcacagtct ggggcatcaa gcagctccag gcaagagtcc tagctgtgga
     7381 aagataccta aaggatcaac agctcctggg aatttggggt tgctctggaa aactcatttg
     7441 taccactagt gtgccttgga accatagttg gagtaagaga aatctgactc agatttggga
     7501 taacatgacc tggatgcagt gggaaagaga gattgacaat tacacagacc taatatactc
     7561 cttaattgaa gaagcgcaag accaacaaga aaagaatgaa ctagacttat taaaattaga
     7621 ttcatgggca agtttgtgga attggtttaa tatatcaaac tggctgtggt atataaaaat
     7681 attcataatg atagtaggag gcttgatagg tttaagaata gtttttgctg tactttctat
     7741 agtaaataga gttaggcagg gatactcacc tttatcattt cagacccgcc tcccaaccca
     7801 gaggggaccc gacaggcccg gaggaatcga aaaagaaggt ggagagcaaa acagaggcag
     7861 atccacacgc ttagtggatg gattattagc acttatctgg gacgacctgc ggagcctgtg
     7921 cctcttcagc taccaccgct tgagcgactt actcttgatt gcaaagagga ttgtggaact
     7981 tctgggacgc agggggtggg aaatcctcaa atattggtgg aatctcctgc aatattggat
     8041 tcaggaacta aagaatagtg ctgttagctt gctcaacgcc actgccatag cagtagctga
     8101 agggacagat agggttatag aattcttaca aagaacattt agagctattc tccacatacc
     8161 tactagaata agacagggct tggaaagggc tttactataa gatgggtggc aaggggtcaa
     8221 aaatggctgg atggtccact gtaagggaaa gaatgaggcg agctgggccc agggaaagac
     8281 cagcagagcc agcagcagct ggggtgggag cagtatctcg agacctggaa aaacatggag
     8341 caatcacaaa tagcaataca gcagctacca atgctgattg tgcctggcta gaagcacagg
     8401 aggaggagga ggttggtttt ccagtcagac ctcaagtacc tttaaggcca atgacttaca
     8461 agggagctct tgatctcagc cactttttaa aagaaaaggg gggactggaa gggctaattt
     8521 actcccaaaa aagacaggat atccttgatc tgtgggtcta ccacacacaa ggctacttcc
     8581 ctgattggca gaactacaca ccagggccag ggaccagata tccactgact tttgggtggt
     8641 gtttcaagct agtaccagtt gatccagaca aggtagaaga ggccaatgca ggagaaaaca
     8701 actgcctgct acaccctata agccagcatg ggatggatga cccagacaga gaagtattag
     8761 tgtggaaatt tgacagccat ctggcatatt atcacatggc ccgagagctg catccggagt
     8821 actacaaaga ctgctgacag cgagctttct acaagggact ttccgctggg gactttccag
     8881 ggaggtgtgg ccggggcggg actggggagt ggcgagccct cagatgctgc atataagcag
     8941 ctgctttctg cctgtactgg gtctctctgg ttagaccaga tcagagcctg ggagctctct
     9001 ggctagctag g
//
