LOCUS       reference_p4            9059 bp    DNA              UNK 23-SEP-2015
DEFINITION  reference for patient p4, genomewide
ACCESSION   reference_p4
VERSION     reference_p4
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..6019
                     /note="F4"
     fragment        5436..7482
                     /note="F5"
     fragment        7275..9059
                     /note="F6"
     RNA_structure   7236..7469
                     /note="RRE"
     RNA_structure   1..87
                     /note="LTR5'"
     RNA_structure   8553..9059
                     /note="LTR3'"
     gene            5514..5759
                     /note="vpu"
     gene            join(5283..5497,7846..7936)
                     /note="tat"
     gene            1538..4549
                     /note="pol"
     gene            4494..5072
                     /note="vif"
     gene            5677..8262
                     /note="env"
     gene            5012..5302
                     /note="vpr"
     gene            243..1745
                     /note="gag"
     gene            8264..8884
                     /note="nef"
     gene            join(5422..5497,7846..8120)
                     /note="rev"
     other           5677..5763
                     /note="env peptide"
     other           6154..6273
                     /note="V2"
     other           150..232
                     /note="psi"
     other           6832..6942
                     /note="V4"
     other           7063..7104
                     /note="V5"
     other           6064..6153
                     /note="V1"
     other           6445..6804
                     /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         5764..7227
                     /note="gp120"
     protein         7225..8262
                     /note="gp41"
     other           6052..6285
                     /note="V1V2ext"
     other           6820..6954
                     /note="V4ext"
     other           7045..7119
                     /note="V5ext"
ORIGIN
        1 ttcaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagaccct
       61 tttagtcagt gtggaaaatc tctagcagtg gcgcccgaac agggacccga aagcgaaagg
      121 gaaaccagag gagctctctc gacgcaggac tcggcttgct gaagcgcgca cagcaagagg
      181 cgagaggcgg cgactggtga gtacgccaaa atttttgact agcggaggct agaaggagag
      241 agatgggtgc gagagcgtca gtattaagcg ggggagaatt agatagatgg gaaaaaattc
      301 ggttaaggcc aggaggaaag aaaaaatata agttaaaaca tatagtatgg gcaagcaggg
      361 agctagagcg attcgcagtt aatcctggcc tgttagaaac atcagaaggc tgtagacaaa
      421 tattggaaca gctacaacca tcccttcaga caggatcaga agaacttaga tcattattta
      481 atacaatagc aaccctctat tgtgtgcatc agaggataga tgtaaaagac accaaggaag
      541 ctttagagaa gatagaggaa gagcaaaaca aatgtaagaa aaaagcacag ccagtagcag
      601 ctgacacagg aaacagcagc aaggtcagcc aaaattaccc tatagtgcag aacctacagg
      661 ggcaaatggt acatcaggcc atatcgccta gaacgttaaa tgcctgggta aaagtagtag
      721 aagagaaggc tttcagccca gaagtaatac ccatgttttc agcattatca gaaggagcca
      781 ccccacaaga tttaaacacc atgctaaaca cggtgggggg acatcaagca gctatgcaaa
      841 tgttaaaaga gaccattaat gaggaagctg cagaatggga tagattgcat ccagtgcatg
      901 cagggcctat tgcaccaggc cagatgagag aaccaagggg aagtgacata gcaggaacta
      961 ctagtaccct tcaggaacaa ataggatgga tgacaaacaa tccacctatc ccagtaggag
     1021 aaatctataa aagatggata atcctgggat taaataaaat agtaaggatg tatagcccta
     1081 ccagcatcct ggacataagg cagggaccaa aggaatcctt tagagattat gtggaccggt
     1141 tctataaaac tctaagagcc gagcaagctt cacaggaggt aaaaaattgg atgacagaaa
     1201 ccttgttggt ccaaaatgcg aacccagatt gtaagaccat tttaaaagca ttgggaccag
     1261 cagctacact agaagaaatg atgacagcat gtcagggagt gggaggaccc ggccacaaag
     1321 caagagtttt ggctgaagca atgagccaag taacaaatac agctaccgca atgatgcaga
     1381 ggggcaattt taggaaccaa agaaagatta ttaagtgttt caactgtggc aaagaagggc
     1441 acctagccaa aaattgcagg gcccctagga aaaagggctg ttggaaatgt ggaaaggaag
     1501 gacaccaaat gaaagattgt actgagagac aggctaattt tttagggaaa atctggcctt
     1561 cccacaaggg aaggccaggg aattttcttc agaacagacc agagccaaca gccccaccag
     1621 cagagagctt caggtttggg gaagagacaa caactccctc tcagaagcag gagacgatag
     1681 acaaggaact atatccttta gcttccctca gatcactctt tggcaacgac ccctcgtcac
     1741 aataaaagta ggggggcaac aaaaggaagc tctattagat acaggagcag atgatacagt
     1801 attagaagac ataaatttgc caggaagatg gaaaccaaaa atgatagggg gaattggagg
     1861 ttttatcaaa gtaagacagt atgatcagat actcatagaa atttgtggac ataaagctat
     1921 aggtacagta ctagtaggac ctacacctgt caacataatt ggaagaaatc tgttgactca
     1981 gattggttgc actttaaatt ttcccattag tcctattgaa actgtaccag taaaattaaa
     2041 gccaggaatg gatggcccaa aggttaaaca atggccattg acagaagaaa aaataaaagc
     2101 attagtagaa atttgtacag aaatggaaaa ggaagggaaa atttcaagaa ttgggcctga
     2161 aaatccatac aatactccag tatttgccat aaagaaaaaa gacagtacta aatggagaaa
     2221 attagtagat tttagagaac ttaataagaa aactcaagac ttctgggaag ttcaattagg
     2281 aataccacat ccagcagggt taaaaaagaa aaaatcagta acagtgctgg atgtgggtga
     2341 tgcatatttt tcagttccct tagataaaga cttcaggaag tatactgcat tcaccatacc
     2401 tagtgtaaac aatgagacac cagggatcag atatcagtac aatgtgcttc cacagggatg
     2461 gaaaggatca ccagcaatat tccaaagtag catgataaaa atcttagagc cttttagaaa
     2521 acaaaatcca gacatagtca tctatcaata catggatgat ttgtatgtag gatctgactt
     2581 agaaataggg cagcatagaa caaaaataga ggaactgaga cagcatctgt tgaagtgggg
     2641 atttaccaca ccagacaaga aacatcagaa agaacctcca ttcctttgga tgggttatga
     2701 actccatcct gacaaatgga cagtacagcc tatagtgctg ccagaaaaag acagctggac
     2761 tgtcaatgac atacagaagt tagtgggaaa attgaattgg gcaagtcaga tctatgcagg
     2821 gattaaagta aagcaattat gtaaactcct taggggagct aaagcactaa cagaagtaat
     2881 accactaaca gaagaagcag agctagaact agcagaaaac agggagattc tgaaagaacc
     2941 agtacatgga gtgtattatg acccatcaaa agacttaata gcagaaatac agaagcaggg
     3001 gcaaggacaa tggacatatc aaatttatca agagccattt aaaaatctga aaacaggaaa
     3061 atatgcaaga atgaggggtg cccattctaa tgatgtaaaa caattaacag aggcagtgca
     3121 aaaaataacc acagaaagta tagtaatatg gggaaagact cctaaattta aattacccat
     3181 acaaagagaa acatgggata catggtggac agagtattgg caagccacct ggattcctga
     3241 gtgggagttt gtcaataccc ctcccttagt gaaattatgg taccggttag agaaagaacc
     3301 catagtagga gcagaaactt tctatgtaga tggggcagct aacagggaga ctaaattagg
     3361 aaaagcagga tatgttacta acagaggaag acaaaaagtg gtccccctaa ctgacacaac
     3421 aaatcagaag actgagctac aagcaattca tctagctttg caggattcgg gatcagaagt
     3481 aaacatagta acagactcac aatatgcatt aggaattatt caagcacaac cagataaaag
     3541 tgaatcagag ttagtcagtc aaataataga gcagttaata aaaaaggaaa aggtctacct
     3601 ggcatgggta ccagcacaca aaggaattgg aggaaatgaa caagtagata aattagtcag
     3661 tgctggaatc aggaaagtac tatttttaga tggaatagat aaggcccaag aagatcatga
     3721 aaaatatcac agtaattgga gagcaatggc tagtgatttt aacctgccac ctgtagtagc
     3781 aaaagaaata gtagccagct gtgataaatg tcagctaaaa ggagaagcca tgcatggaca
     3841 agtagactgt agtccaggaa tatggcaact agattgtaca catttagaag gaaaaattat
     3901 cctggtagca gttcatgtag ccagtggata tatagaagca gaagttattc cagcagaaac
     3961 agggcaggaa acagcatact ttatcttaaa attagcaggg agatggccag taaaaataat
     4021 acatacagac aatggcagca atttcaccag cactacggtt aaggccgcct gttggtgggc
     4081 gggggtcaag caggaatttg gcattcccta caatccccaa agtcaaggag tagtggaatc
     4141 tatgaataaa gaattaaaga aaattatagg acaggtaaga gatcaggctg aacatcttaa
     4201 gacagcagta caaatggcag tactcatcca caattttaaa agaaaagggg ggattggggg
     4261 gtacagtgca ggggaaagaa tagtagacat aatagcaaca gacatacaaa ctaaagaatt
     4321 acaaaaacaa attacaaaaa ttcaaaattt tcgggtttat tacagggaca gcagagatcc
     4381 actttggaaa ggaccagcaa agcttctctg gaaaggtgaa ggggcagtag taatacaaga
     4441 taatagtgac ataaaagtag tgccaagaag aaaagcaaag atcattaggg attatggaaa
     4501 acagatggca ggtgatgatt gtgtggcaag tagacaggat gaggattaaa acatggaaca
     4561 gtttagtaaa acaccatatg tataggtcag ggaaagctaa gggatgggtt tacaaacatc
     4621 actatgaaag cattaatcca agaataagtt cagaagtaca catcccacta ggggatgcta
     4681 aattggtaat aacaacatat tggggtctgc acacaggaga aagagactgg catttgggtc
     4741 agggagtctc catagaatgg aggaaaaaga gatatagcac acaagtagac cctggcctag
     4801 cagaccaact aattcatctg tattactttg attgtttttc agaatctgct ataagaaatg
     4861 ccatattaga acatagagtt agtcctagtt gtgaatatca agcaggacat aacaaggtag
     4921 gatctctaca gtacttggca ctagcagcat taataacacc aaaaaggata aagccacctt
     4981 tgcctagtgt tacgaaactg acagaggata gatggaacaa gccccggaag accaaggacc
     5041 acaaagggaa ccatacaatg aatgggcact agagctttta gaggagctta agaatgaagc
     5101 tgttaggcat ttccctaggg tgtggctcca tggcttaggg cagcatatct atgaaactta
     5161 tggggatact tgggcaggag tggaagccat aataagaatt ctgcaacaac tgctgtttat
     5221 tcatttcaga attgggtgtc aacatagcag aataggcatc actccacaga ggagagcaag
     5281 aaatggagcc cgtagatcct agactagagc cctggaagca tccaggaagt cagcctagga
     5341 ctgcgtgtac cccttgctat tgtaaaagtt gctgctttca ttgccaagtt tgtttcataa
     5401 caaaagcctt aggcatctcc tatggcagga agaagcggag acagcgacga agatctcctc
     5461 aagacagtaa gactcatcaa gcttctatat caaagcagta agtagtacat gtaatgcacc
     5521 ctttacaaat agtagcaata gtagcattag tagtagcagc aataatagca atagttgtgt
     5581 ggaccttagt attcatagaa tataggaaaa tattaagaca aagaaaaata gacaggttaa
     5641 ttgatagaat aagagaaaga gcagaggaca gtggcaatga aagtgaaggc gatcaggaag
     5701 aattatcagc tcttgtggag atggggcatc atgctccttg ggatattgat gatctgtaat
     5761 gctacaaaac cattgtgggt tacagtctat tatggggtac ctgtgtggaa agaagcaaac
     5821 accactctat tttgtgcatc agatgctaaa gcatatagtg cagaggtaca taatgtctgg
     5881 gccacacatg cctgtgtacc cacagacccc aacccacaag aagtagtatt gggaaatgtg
     5941 acagaaaaat ttaacatgtg gaaaaatgac atggtagaac agatgcatga ggatataatt
     6001 agcttatggg atcaaagcct aaagccatgt gtaaaattaa ccccactctg tgttacttta
     6061 aattgtactg attggactaa tggtactgcc actaatagta ctgctaccaa taggagtagc
     6121 gagggaacgc tggagggagg agaagtaaaa gaatgctctt tcaatgtcac cacaagcatg
     6181 agagataagg tgcagcgaga atatgcactt ttttataaat ctgatgtagt atcaacaaat
     6241 gagagtagta ccagctatag gttgataagt tgtaacacct cagtcgtcac ccaggcctgt
     6301 ccaaagatat cctttgagcc aattcccata cattattgtg ccccagctgg ttttgcgatt
     6361 ctaaagtgta acaataagac gttcgaagga aaaggagact gtaaaaatgt cagcacagta
     6421 ctatgtacac atggaattaa gccagtagta tcaacccaac tgttgttaaa tggcagccta
     6481 gcagaagaag gggtagtagt tagatctgac aatttctcaa acaatgctaa aaccatcata
     6541 gtacagttgc acaaagctgt agaaattaat tgcacaagac ccagcaacaa tacaagcaaa
     6601 ggtatacata tgggaccagg gaaagcattt tatacaacag aaaaaataat aggagatata
     6661 agacaagcac attgtaacat tagtaaagag aaatggaacg acactttaag acagatagct
     6721 ataaaattaa gagcacaatt tccgagtaaa acaataatct ttgataaatc ctcaggaggg
     6781 gacctagaaa ttgtaacaca cagttttaat tgtggagggg aatttttcta ctgcaataca
     6841 acaaaactgt ttaatagtac ttggaatgat acacaactgc ttaatagtac tgggaatagt
     6901 actgaaggga taaatggcac tgaaattatc acactcccat gtagaataaa acaaattata
     6961 aacctgtggc aggaagtagg aaaagccatg tatgcccctc ctatcagagg acaaattaga
     7021 tgtgaatcaa atattacagg gctgctatta acaagagatg gtggtggtgc tgatcagaac
     7081 aggaccaacg agaccttcag acctggagga ggagatatga gggacaattg gagaagtgaa
     7141 ttatataaat acaaagtagt aaaaattgaa ccattaggag tagcacctac cgaggcaaag
     7201 agaagagtgg tgcagagaga aaaaagagca gcaataggag ctttgttcct tgggttcttg
     7261 gcaacagcag gaagcgctat gggcgcagcg tcaatggcgc tgacggtaca ggccagacta
     7321 ttattgtctg gtatagtgca acagcaaaac aatttgctga gggctattga ggcgcaacag
     7381 catctgttgc aactcacagt ctggggcatc aagcagctcc aggcaagagt cctggctgtg
     7441 gaaagatacc tgagggatca acagctcctg ggaatttggg gttgctctgg aaaactcatt
     7501 tgcaccactg ctgtgccttg gaatactagt tggagtaata aatctctgga ttatatttgg
     7561 cagaacatga cctggatgca gtgggaaaaa gaaattgaca attacacaga tttaatatac
     7621 tccctacttg aaaaatcgca aaatcaacaa gaaaagaatg aacaggaatt attggaattg
     7681 gataaatggg caagtttgtg gaattggttc gacatatcaa actggctgtg gtatataaaa
     7741 atagtcataa tgatagtagg aggcttggta ggtttaagaa tagtctttat tgtattctct
     7801 atagtggata gagttaggca gggatactca ccattatcgt ttcagatccg ccccccagtc
     7861 ccgaggggac ccgacaggcc cgaaggaatc gaagaaggag gtggagagag agacagagac
     7921 agatccggtc gattagtgaa cggattctta gcacttttct gggacgatct gcagaacctg
     7981 tgcctcttca gctaccaccg cttgagagac ttactcttga ttgtaacgag gattgtggaa
     8041 cttctgggac gcagggggtg ggaagtcctc aaatattggt ggaatctcct acagtattgg
     8101 agtcaggaac taaagaatag tgctgttagc ctgctcaatg tcacagccat agtagtagct
     8161 gaggggacgg atagggttat agaagtattc caaagagctc ttagagctat tctccacata
     8221 cctactagaa taagacaagg cttcgaaagg gctttgctat aagatgggtg gcaagtggtc
     8281 aaaaagtagt atagttggat ggccttctgt aagggaaaga atgaaacgag ctgagccagc
     8341 agcagatggg gtgggagcag tatctcgaga cctggaaaaa catggagcaa tcacaagcag
     8401 caatacagca gctaccaatg ctgactgtgc atggctagaa gcacaagagc aggaggaggt
     8461 gggttttcca gtcacacctc aggtaccttt aagaccaatg acttacaagg cagctgtaga
     8521 tcttagccac tttttaaaag aaaagggggg actggaaggg ctaatttact cccagaaaag
     8581 gcaagatatc cttgatctgt ggatctacca cacacaaggc tacttccctg attggcagaa
     8641 ctacacacca gggccaggga ttagatatcc actgaccttt ggatggtgct tcaaactagt
     8701 gccagttgag ccagagaaga tagaagaggc caatgaagga gagaacaaca gcctgctaca
     8761 ccctatgagc ctgcatggga tggatgaccc agagaaagaa gtgttagagt ggaagtttga
     8821 cagccgcctg gcatttcatc acatggcccg agagaaacat ccggagtact ataagaactg
     8881 ctgacattga gctttctaca agggactttc cgctggggac tttccagggg aggcgtggcc
     8941 tgggcgggac tggggagtgg cgagccctca gatgctgcat ataagcagct gctttctgct
     9001 tgtactgggt ctctctggtt agaccagatc tgagcctggg agctctctgg ctagctagg
//
