LOCUS       reference_p1            9060 bp    DNA              UNK 23-SEP-2015
DEFINITION  reference for patient p1, genomewide
ACCESSION   reference_p1
VERSION     reference_p1
KEYWORDS    .
SOURCE      
  ORGANISM  HIV-1
            .
FEATURES             Location/Qualifiers
     fragment        1..1789
                     /note="F1"
     fragment        1482..3334
                     /note="F2"
     fragment        3124..4651
                     /note="F3"
     fragment        4389..6034
                     /note="F4"
     fragment        5449..7473
                     /note="F5"
     fragment        7266..9060
                     /note="F6"
     RNA_structure   7227..7460
                     /note="RRE"
     RNA_structure   1..86
                     /note="LTR5'"
     RNA_structure   8559..9060
                     /note="LTR3'"
     gene            5529..5774
                     /note="vpu"
     gene            join(5296..5510,7837..7927)
                     /note="tat"
     gene            1551..4562
                     /note="pol"
     gene            4507..5085
                     /note="vif"
     gene            5692..8274
                     /note="env"
     gene            5025..5315
                     /note="vpr"
     gene            262..1758
                     /note="gag"
     gene            8276..8890
                     /note="nef"
     gene            join(5435..5510,7837..8132)
                     /note="rev"
     other           5692..5778
                     /note="env peptide"
     other           6160..6285
                     /note="V2"
     other           170..251
                     /note="psi"
     other           6841..6927
                     /note="V4"
     other           7048..7092
                     /note="V5"
     other           6079..6159
                     /note="V1"
     other           6457..6813
                     /note="V3"
     protein         262..657
                     /note="p17"
     protein         658..1350
                     /note="p24"
     protein         1351..1392
                     /note="p2"
     protein         1390..1551
                     /note="p7"
     protein         1552..1599
                     /note="p1"
     protein         1600..1758
                     /note="p6"
     protein         1719..2015
                     /note="PR"
     protein         2016..3335
                     /note="RT"
     protein         3336..3695
                     /note="p15"
     protein         3696..4562
                     /note="IN"
     protein         5779..7215
                     /note="gp120"
     protein         7216..8274
                     /note="gp41"
     other           6067..6297
                     /note="V1V2ext"
     other           6829..6939
                     /note="V4ext"
     other           7030..7107
                     /note="V5ext"
ORIGIN
        1 ttaaagtggt gtgtgcccgt ctgtgatagg actctggtaa ctagagatcc ctcagaccac
       61 tctagactga gtaaaaatct ctagcagtgg cgcccgaaca gggacttgaa agcgaaagtt
      121 aatagggact cgaaagcgaa agttccagag aagttctctc gacgcaggac tcggcttgct
      181 gaggtgcaca cagcaagagg cgagagcggc gactggtgag tacgccaaaa tttttgacta
      241 gcggaggcta gaaggagaga gatgggtgcg agagcgtcag tattaagtgg gggaaaatta
      301 gatgcatggg agaagattcg gttacggcca gggggaaaga aacaatatag aatgaaacat
      361 ttagtatggg caagcagaga gctagaaaga ttcgcactta accctggcct tttagaaaca
      421 gcagaagggt gtcaacaact aatggaacag ttacaatcag ctctcaagac aggatcagaa
      481 gaacttaaat cattatataa tacaatagca accctctggt gcgtacatca aaagatagaa
      541 ataagagaca ccaaggaagc tttagataaa atagaggaag tacaaaataa gaacaagcaa
      601 aagacacagc aagcagcagc tgccacagga agcagcagca aagtcagcca aaattaccct
      661 atagtgcaaa atgcacaagg gcaaatggta catcaggcct tatcacctag aactttgaat
      721 gcatgggtga aagtagtaga agaaaagggt tttaacccag aagttatacc catgttctca
      781 gcattatcag agggagccac cccacaagat ttaaatatga tgctaaacat agtgggggga
      841 caccaggcag caatgcaaat attaaaagat accatcaatg aggaagctgc agaatgggat
      901 agggtacacc cagtacaggc agggcctatt ccaccaggcc agctgagaga accaagggga
      961 agtgacatag caggaactac tagtaccctt caagaacaga taggatggat gacaagcaac
     1021 ccacctatcc cagtaggaga catctataaa aggtggataa tcctaggatt aaataaaata
     1081 gtaagaatgt atagccctgt tagcattttg gacataagac aagggccaaa agaacccttc
     1141 agagactatg tagataggtt ctttaaaaca ctcagagcag aacaagctac acaggaggta
     1201 aaaaactgga tgacagaaac cttgctagtt caaaatgcga atccagactg taagtccatt
     1261 ttaaaggcat taggaacagg ggctacatta gaagaaatga tgacagcatg ccagggagtg
     1321 ggaggacctg gccataaagc aagggttttg gctgaggcaa tgagtcaaat aaaacatcca
     1381 aatataatga tgcagagagg caattttaag ggccagagaa gaattaagtg tttcaactgt
     1441 ggcagagaag gacacctagc cagaaattgc agggccccta gaaaaaaggg ttgttggaaa
     1501 tgtggaaagg aaggacacca aatgaaagat tgcactgaaa gacaggctaa ttttttaggg
     1561 aaaatttggc cttccagcaa ggggaggcca ggaaattttc ctcagagcag accagagcca
     1621 acagccccac cagcagagag ctttgggatg ggggaagaga taacctcctt cccgaagcag
     1681 gagcagaaag acaaagaaca tcctcctccc ttagtctccc tcaaatcact ctttggcaac
     1741 gaccccttgt cacagtaaaa ataggaggac agctgaaaga ggctctatta gatacaggag
     1801 cagatgatac agtattagaa gatataaatt tgccaggaaa atggaaacca aaaatgatag
     1861 ggggaattgg aggttttatc aaagtaagac aatatgatca gatacttata gaaatctgtg
     1921 ggaaaaaggc tataggtaca gtattaatag gacctacacc tgtcaacata attgggcgaa
     1981 atatgttgac tcagcttggt tgtactttaa atttcccaat tagtcctatt gacactgtgc
     2041 cagtagcatt aaagccaggg atggatggac caaaggttaa acaatggcca ttgacagaag
     2101 aaaaaataaa agcattaaca gaaatttgta aagagatgga agcggaagga aaaatctcaa
     2161 aaattgggcc tgaaaatccg tacaatactc cagtatttgc tataaagaaa aaggacagta
     2221 ctaaatggag aaaattagta gatttcagag agctcaacaa aagaactcag gacttttggg
     2281 aagttcaatt aggaataccg catccagcag gtttaaaaaa gaaaaaatca gtaacagtac
     2341 tagatgtggg agacgcatat ttttcagttc ctttatatga aggctttaga aagtatactg
     2401 cattcaccat acctagtata aacaatgaga caccaggaat cagatatcag tacaatgtgc
     2461 tgccacaggg atggaaagga tcaccagcaa tattccagag tagcatgata aaaatcttag
     2521 agccctttag agcaaaaaat ccagaaatag ttatctatca atacatggat gacttgtatg
     2581 taggatctga tttagaaata gggcagcata gaacaaaaat agaggagcta agagctcatc
     2641 tattgagctg gggatttact acaccagaca aaaagcatca gaaggaacct ccattccttt
     2701 ggatgggata tgaactccat cctgacagat ggacagtcca gcctatagaa ctgccagaaa
     2761 aggacagctg gactgtcaat gatatacaga aattagtggg aaaactaaat tgggcaagtc
     2821 aaatttatgc agggattaaa gtaaggcaac tgtgtaaact cctcagagga gctaaagcac
     2881 taacagacat agtaacactg actgaggagg cagaattaga attggcagag aacaaggaga
     2941 ttctaaaaaa ccctgtgcat ggagtatatt atgacccatc aaaagactta gtagcagaaa
     3001 tacagaaaca agggcaagat caatggacat atcaaattta tcaagagcca tttaaaaatc
     3061 tgaaaacagg aaaatatgca agaaaaaggt ctgctcacac taatgatgta agacaattaa
     3121 cagaagtggt gcaaaaagtg accacagaaa gcatagtaat atggggaaag acccctaagt
     3181 ttagattacc catacaaaga gaaacatggg agacatggtg gatggagtat tggcaggcta
     3241 cctggattcc tgaatgggag tttgtcaata cccctcctct agtaaaatta tggtaccaat
     3301 tagaaaaaga ccccatagta ggagcagaga ctttctatgt agatggggca gctagtaggg
     3361 agactaagct aggaaaagca gggtatgtca ctgacagagg aagacaaaag gtagtttccc
     3421 tatctgagac aacaaatcaa aagactgaat tacatgcgat ccatttagcc ttgcaggatt
     3481 caggatcaga agtaaatata gtaacagact cacaatatgc attaggaatc attcaggcac
     3541 agccagacag gagtgaatca gaagtagtca accaaataat agagaagcta atagaaaagg
     3601 aaaaggtcta cctgtcatgg gtgccagcac acaaggggat tggaggtaat gaacaagtag
     3661 ataaattagt cagttctgga attaggaagg tactgttttt agatgggata gataaagctc
     3721 aagaagacca tgaaaaatat cacagcaatt ggagaacaat ggctagtgat tttaatttgc
     3781 cacctatagt agcgaaggaa atagtagcca actgtgataa atgtcaacta aaaggggaag
     3841 ctatgcatgg acaagtggac tgtagtccag ggatatggca attagattgc acgcatctag
     3901 aaggaaaaat catcctggta gcagtccacg tggccagtgg atatatagaa gcagaagtta
     3961 tcccagcaga aacaggacag gagacagcat acttcctgct aaaattagca ggaagatggc
     4021 cagtaaaggt aatacacaca gataatggta gcaatttcac cagcgctgca gttaaagcag
     4081 cctgttggtg ggccaatgtc caacaggaat ttgggattcc ctacaatccc caaagccaag
     4141 gagtagtgga atctatgaat aaggaattaa agaaaatcat agggcaggta agagagcaag
     4201 ctgaacacct taagacagca gtacaaatgg cagtattcat tcacaatttt aaaagaaaag
     4261 gggggattgg ggggtacagt gcaggggaga gaataataga cataatagca acagacatac
     4321 aaactaaaga attacaaaaa caagttacaa aaattcaaaa ttttcgggtt tattacaggg
     4381 acagcagaga cccaatttgg aaaggaccag caaaactgct ctggaaaggt gaaggggcag
     4441 tagtaataca agacaatagt gatataaaag tagtaccaag aagaaaagca aagatcatta
     4501 gggattatgg aaaacagatg gcaggtgatg attgtgtggc aggtagacag gatgaggatt
     4561 agaacatgga acagtttagt aaaacatcat aagtatatct caaagaaagc taataaatgg
     4621 ttttatagac atcattatga aagccaacat ccaaaagtaa gttcagaagt acacatccca
     4681 ctaggggatg ctaaattagt aataagaaca tattggggtc tgcatacagg agaaaaagac
     4741 tggcacttgg gtcatggagt ctccatagaa tggaggcaga aaagatatag cacacaaata
     4801 gatcctgatc tagcagatcg actgattcat ctgcaatatt ttgactgttt ttcagactct
     4861 gccataagga aagccatatt aggacaagta gttagcccta ggtgtgaata tccaacagga
     4921 cataacaagg taggatcgct acaatatttg gcactgagag cattggtaac accaaaaaag
     4981 ataaaaccac ctctgcctag tgttaagaaa ttaacagaag atagatggaa caagccccag
     5041 aagaccaggg gccacagaga gaaccccata atgaatggac attggaactg ttagaggagc
     5101 ttaaacttga agctgttaga cattttccta ggccctggct tcatgactta ggacagcata
     5161 tctataacac ttatggggat acttgggaag gggttgaagc tataataaga actttgcagc
     5221 aactactgtt tgttcatttc agaattgggt gccatcatag cagaataggc atcatacgag
     5281 ggagaagagg caggaatgga gctggtagat cctaacctag agccctggaa tcatccagga
     5341 agccagccta caactccctg tagcaactgt tactgtaaaa aatgctcctg gcattgccaa
     5401 ttatgctttc tgaaaaaagg cttaggaatc tcctatggca ggaagaagcg gaagcaccga
     5461 cgaggaactc ctcgcgacag taaggatcat caaaatcctg taccaaagca gtaagtaaag
     5521 tagatgtaat gacacctttg gacatctctg caatagtagg actgatagta gcgataatct
     5581 tagcaatagt agtgtggact gtagtggcta tagaatataa gaaattacta agacaaagaa
     5641 aaatagacag gttaattgag agaatagaag aaagagcaga agacagtgga aatgaaagtg
     5701 atggggacac aaatgaattg ctcgcactta tggaaatggg gaactttgat ccttggattg
     5761 gtgataattt gtagtgcctc aaacaacttg tgggttacag tttattatgg ggttcctgtg
     5821 tggagagatg cagataccac cctcttttgt gcatcagatg ctaaagcaca taagacagaa
     5881 gtgcataatg tctgggctac acatgcctgt gtacccacag accccaaccc acaagaaata
     5941 cacctgggaa atgtaacaga agattttaac atgtggaaaa ataacatggc agagcagatg
     6001 caagaggatg tcatcagttt atgggatcaa agtctaaaac catgtgtaaa gttaactcct
     6061 ctctgcgtta ctttaaattg tactaatgct aattttaata atgctagttc tactgacctt
     6121 aagaatgaga cagaagaaat gaaacaggaa ataagaaact gttcttttaa tatgaccaca
     6181 gaactaaggg ataagaagca gaaggtctat gcactttttt ataggcctga tatagtacaa
     6241 attaatagta gtgggaatag tagtgagtat agattaataa attgtaatac ttcagtcatt
     6301 acacaggctt gtccaaaggt atcctttgat ccaattccca tacattattg tgctccagct
     6361 ggttatgcga ttttaaagtg taataataaa gctttcaatg gaacagggcc atgtaataat
     6421 gtcagctcag tacaatgcac acatggaatt aagccagtgg tatcaactca attgctgtta
     6481 aatggcagtc tagcagaaga agacataata atcagatctg aaaatatcac aaacaatgct
     6541 aaaaccataa tagtgcacct taaagaacct gtagaaatca attgtacgag accctccaac
     6601 aatacaatag caagtgtaag gataggacca ggacaagtat tctataaaac aggagacata
     6661 ataggagaca taagaagagc attttgtgta attaatggaa caaaatggaa tgaaacttta
     6721 aaacaggtag ctgaaaaatt aagagagcac tttaataaga caatagtctt taaaccacac
     6781 tcaggaggag atctagaaat tacaatgcat cattttaatt gtaaagggga atttttttat
     6841 tgcaatacat cacaactgtt taatagtact tggagtggaa ccgaggggaa gcttaatgac
     6901 actaataaaa atatcacact tccatgcaga ataaagcaaa ttgtaaacat gtggcaggaa
     6961 gtaggacgag caatgtatgc tcctcccatc agtggaatag ttaattgtgt atcaaatatt
     7021 acaggaattc tattgacaag agatgggggt actaataatg atactaataa tgataccgag
     7081 atcttcagac ctggaggagg aaatataaag gacaattgga gaagtgaatt atataaatat
     7141 aaagtagtac aaattgaacc attaggaata gcacccacca gggcaaggag aagagtggtg
     7201 gagagagaaa aaagagcagt gggaatagga gctatgatct ttgggttctt aggagcagca
     7261 ggaagcacta tgggcgcagc gtcaataacg ctgacggtac aggccagaca attattgtct
     7321 ggtatagtgc aacagcaaag caatttgctg agagctatag aggcgcagca gcatctgttg
     7381 caactcacag tctggggcat taaacagctc caggcaagag tcctggctgt ggaaagatac
     7441 ctaaaggatc aaaagttcct aggactttgg ggctgctctg gaaaaatcat ctgcaccact
     7501 tctgtgccct ggaactccag ttggagtaat aaatcttatg aagaaatttg gggcaacatg
     7561 acatggatag aatgggagag agaaattgac acttacacaa accaaatata tgagctactt
     7621 acagaatcgc agaaccagca ggaaaagaat gaacaggatt tgttagcatt agaccagtgg
     7681 gcaagtctgt ggaattggtt taacataaca aaatggctgt ggtatataaa aatattcata
     7741 atgatagtag gaggtttaat aggtttaaga atagtttttg ctgtgctttc aatagtaaaa
     7801 agagctaggc agggatactc acctttatct tttcagaccc ttacccccca gcagagggaa
     7861 cccgacaggc ccgaaggaat cgaagaagga ggtggcgagc aaggcaaaga cagatccatt
     7921 cgattagtga gcggattctt agcacttgtc tgggacgacc tacggagcct gtgccttttc
     7981 agctaccacc gcttgagaga cttcatcttg attgcagcga ggactgtgga acttctggga
     8041 cacagcagtc tcaagggact gagacggggg tgggaaggcc tcaaatatct gtggaatctt
     8101 ctgttatatt ggagtcagga actaaagagt agtgctatta ctttgtttga tgctatagca
     8161 atagcagtag cagggtggac agatagggtt atagaactag cacaaagagc ttgtagagcg
     8221 attctccata tccctacaag aatcagacag ggctttgaaa gagctttgct ataacatggg
     8281 tggcaagtgg tcaaagagta gcatagtggg atggcctcag gtcagggaaa gaatgaagca
     8341 aactcctgca gcagcagaag gagtaggagc aacatctaaa gatctagata aacatggagc
     8401 agtaacaagt agtaatatga ataatgctga taatgtctgg ctagaagcgc aagaggacga
     8461 ggaggtaggc tttccagtca ggccgcaggt acctctaaga ccaatgactt ataagggagc
     8521 ttttgatctt agcttctttt taaaagaaaa ggggggactg gatgggctaa tttactccaa
     8581 gaaaagacaa gagatccttg atttatgggt ccatcacaca caaggcttct tccctgattg
     8641 gcaaaactac acaccaggac caggggtcag atacccactg tgttttggat ggctctacaa
     8701 gctagtgcca gttgatccaa gagaagtaga agaggatacc aaaggagaaa acaactgcct
     8761 gttgcacccc ataagccagc atggaataga tgatgaagaa ggagaagtgc tgaagtggga
     8821 gtttgacagc gccctagcac gaaagcacat agcccgagag ctgcatccgg agtactacaa
     8881 agactgctga caaagaagtt tctaactagg acttccgctg gggactttcc aggggtgtgg
     8941 cctgggcgga gttggggagt ggctaaccct cagatgctgc ataaaagcag ccgcttctcg
     9001 cttgtactgg gtctctcttg ttagaccagg tcgagcccgg gagctctctg gctagcaagg
//
