LOCUS       reference_p2            9095 bp    DNA              UNK 23-SEP-2015
DEFINITION  reference for patient p2, genomewide
ACCESSION   reference_p2
VERSION     reference_p2
KEYWORDS    .
SOURCE      
  ORGANISM  HIV-1
            .
FEATURES             Location/Qualifiers
     fragment        1..1784
                     /note="F1"
     fragment        1477..3329
                     /note="F2"
     fragment        3119..4646
                     /note="F3"
     fragment        4384..6024
                     /note="F4"
     fragment        5441..7487
                     /note="F5"
     fragment        7280..9095
                     /note="F6"
     RNA_structure   7241..7474
                     /note="RRE"
     RNA_structure   1..87
                     /note="LTR5'"
     RNA_structure   8591..9095
                     /note="LTR3'"
     gene            5519..5764
                     /note="vpu"
     gene            join(5288..5502,7851..7941)
                     /note="tat"
     gene            1546..4557
                     /note="pol"
     gene            4502..5080
                     /note="vif"
     gene            5682..8267
                     /note="env"
     gene            5020..5307
                     /note="vpr"
     gene            242..1753
                     /note="gag"
     gene            8269..8922
                     /note="nef"
     gene            join(5427..5502,7851..8125)
                     /note="rev"
     other           5682..5768
                     /note="env peptide"
     other           6159..6299
                     /note="V2"
     other           150..231
                     /note="psi"
     other           6855..6950
                     /note="V4"
     other           7071..7106
                     /note="V5"
     other           6069..6158
                     /note="V1"
     other           6471..6827
                     /note="V3"
     protein         242..649
                     /note="p17"
     protein         650..1342
                     /note="p24"
     protein         1343..1384
                     /note="p2"
     protein         1382..1546
                     /note="p7"
     protein         1547..1594
                     /note="p1"
     protein         1595..1753
                     /note="p6"
     protein         1714..2010
                     /note="PR"
     protein         2011..3330
                     /note="RT"
     protein         3331..3690
                     /note="p15"
     protein         3691..4557
                     /note="IN"
     protein         5769..7229
                     /note="gp120"
     protein         7230..8267
                     /note="gp41"
     other           6057..6311
                     /note="V1V2ext"
     other           6843..6962
                     /note="V4ext"
     other           7053..7121
                     /note="V5ext"
ORIGIN
        1 tttaagtagt gtgtgcccgt ctgttgtgtg actctggtaa ctagagatcc ctcagaccca
       61 tttagtcagt gtggaaaatc tctagcagtg gcgcccgaac agggacctga aagcgaaagg
      121 gaaaccagag aagttctctc gacgcaggac tcggcttgct gaagtgcgca cggcaagagg
      181 cgaggggcgg cggtaggtaa gtacgccaac tttttgacta gcggaggcta gaaggagaga
      241 gatgggtgcg agagcgtcaa tattaagcgg gggaaaatta gataggtggg agaaaattcg
      301 gttaaggcca gggggaaaga aacaatataa attaaaacat atagtatggg caagcaggga
      361 gctagaacga ttcgcagtta accctggcct gttagaaaca gcagaaggat gtagacaaat
      421 actgggacag ctacaaccgt cccttcagac aggatcagaa gaacttaaat cattgtataa
      481 tacaatagca accctctatt gtgtgcatca aaggatagat gttaaagaca ccaaggaagc
      541 cttagatcag atagaggaag agcaaaataa aagtaagaaa aaagcacagc aagcagcagc
      601 tgcagcagct gacacaggaa acagcagcgg tcaggtcagc caaaattacc ccatagtgca
      661 gaacctccag gggcaaatgg tacaccaagc cctatcacct agaactttaa atgcatgggt
      721 aaaagtagta gaagagaagg ctttcagtcc agaagtaata cccatgttta cagcattatc
      781 agaaggagcc accccacaag atttaaacac catgctaaac acagtggggg gacatcaagc
      841 agccatgcaa atgttaaaag agactatcaa tgaggaagct gcagaatggg atagactgca
      901 cccagtgcat gcagggccta ttgcaccagg ccagatgaga gaaccaaggg gaagtgacat
      961 agcaggaact accagtaccc ttcaggaaca aataggatgg atgacaaata atccacctat
     1021 cccagtagga gaaatttata aaagatggat aatcctggga ttaaataaaa tagtaagaat
     1081 gtatagccct accagcattc tggacataaa acaaggtcca aaggaaccct ttagagacta
     1141 tgtagatcgg ttctataaaa ctctaagagc cgagcaagcc tcacaggagg taaaaaattg
     1201 gatgacagaa accttgttgg tccaaaatgc gaacccagac tgtaagacta ttctaaaagc
     1261 attgggacca gcagctacac tagaagaaat gatgacagca tgtcagggag tgggaggacc
     1321 tggccataaa gcaagagttt tggctgaagc aatgagccag gtaacaaatc caaccgtaat
     1381 gatgcagaga ggcaatttta agaaccaaag aaagagtgtt aagtgtttca attgtggcaa
     1441 agaagggcac atagccagaa attgcagggc ccctaggaaa aagggctgtt ggaaatgtgg
     1501 aaaggaagga catcaaatga aagattgtac tgagagacag gctaattttt tagggaaaat
     1561 ctggccttcc cacaagggga ggccagggaa tttccttcag agcaggccag agccaacagc
     1621 cccaccagaa gagagcttca ggtttgggga agggacaaca accccctctc agaagcagga
     1681 gccgatagac aaggaaacgt accctttaac ttccctcaga tcactctttg gcaacgaccc
     1741 ctcgtcacaa taaaaatagg ggggcaacta aaggaagctc tattagatac aggagcagat
     1801 gatacagtat tagaagacat gcagttgcca ggaagatgga aaccaaaaat gataggggga
     1861 attggaggtt ttatcaaggt aaaacagtat gatcagatat ccatggaaat ttgtggacat
     1921 aaagttatag gtacagtatt aataggacct acacctgtca acataattgg aagaaatctg
     1981 ttgactcagc ttgggtgcac tttaaatttt cccattagcc ctattgaaac tgtaccagtg
     2041 aaattaaagc caggaatgga tggcccaaga attaaacaat ggccattgac agaagaaaaa
     2101 ataaaagcat taacagaaat ctgtgcagac atggaaaagg aaggaaaaat ttcaagaatt
     2161 gggcctgaaa atccatacaa tactccagta tttgccataa agaagaaaga cagtactaaa
     2221 tggagaaagt tagtagattt cagagaactt aataaaagaa ctcaagactt ctgggaagtt
     2281 caattaggaa taccacatcc cgcagggtta aaaaagaaaa aatcagtaac agtactggat
     2341 gtgggtgatg catatttttc agtcccttta gataaagaat tcaggaagta tactgcattt
     2401 accataccta gtacaaacaa tgagacacca gggattagat atcagtacaa tgtgcttcca
     2461 cagggatgga aaggatcacc agcaatattc caatgtagca tgacaaaaat cttagagcct
     2521 tacagaaaac aaaatacaga catagttatc tatcaataca tggatgattt gtatgtagga
     2581 tctgacctag aaatagagca gcatagaaca aaagtagaag aactgagaca acatctgttg
     2641 gggtggggat ttaccacacc agacaaaaaa catcagaaag aacctccatt cctttggatg
     2701 ggttatgaac tccatcctga taaatggaca gtacagccta taaagctgcc agaaaaagac
     2761 agctggactg tcaatgacat acagaagtta gtgggaaaat tgaattgggc aagtcagatt
     2821 tatgcaggaa ttaaagtaag acaattatgt aaacttctta gaggaaccaa agcactaaca
     2881 gatgtaatac cactaacaga ggaagcagag ctagaactgg cagaaaacag ggagattcta
     2941 aaagaaccag tacatggggt atattatgac ccatcaaaag acttaatagc agagctacaa
     3001 aagcaggggc aaggccaatg gacatatcaa atttatcaag aaccatttaa gaatctgaaa
     3061 acaggaaaat atgcaagaac gaggggcgcc cacaccaatg atgtaagaca attaacggag
     3121 gcagtgcaaa aaatagccac agaaagcata gtaatctggg gaaagacccc taaatttaag
     3181 ttacccatac aaaaagaaac gtgggaagca tggtggacag attattggca agccacctgg
     3241 atccctgagt gggagtttgt caatacccct cccttagtaa aattatggta ccagttagag
     3301 aaagaaccca tagtaggagc agaaactttc tatgtagatg gggcagctaa cagggagact
     3361 aaactaggaa aagcaggata tgttactaac agaggaagac aaaaagttgt ctccctaact
     3421 gacacaacaa atcagaagac tgagttacaa gcaattcatt tggctttgca ggattcggga
     3481 ttagaagtga atatagtaac agactcacaa tatgcattag gaatcattca agcacaacca
     3541 gataaaagtg aatcagagtt agtcaatcaa ataatagagc aattaataaa gaaggaaaag
     3601 gtctacctgg catgggtacc agcacacaaa ggaattggag gaaatgaaca catagataaa
     3661 ttagtcagtg ctggaatcag gaaagtgcta tttttagatg gaatagataa ggcccaagag
     3721 gaccatgaga aatatcatag taattggaga gcaatggcta gtgattttaa cctgccacct
     3781 gtggtagcaa aagaaatagt agccagctgt gataaatgtc agctaaaagg agaggccatg
     3841 catggacaag tagactgtag tccaggaata tggcaactag attgtacaca cttagaagga
     3901 aaaataatcc tggtagcagt tcatgtagcc agtggatata tagaagcaga agttattcca
     3961 gcagagacag ggcaggaaac agcatacttc ctcttaaaat tagcaggaag atggccagta
     4021 acaacaatac atacagacaa tggcagcaat ttcaccagca ctgcacttaa ggccgcctgt
     4081 tggtgggcgg ggatcaagca ggaatttggc attccctaca atcctcaaag tcaaggagta
     4141 gtagaatcta tgaataaaga attaaagaaa attataggac aggtaagaga tcaggctgaa
     4201 catcttaaga cagcagtaca aatggcagta ttcatccaca attttaaaag aaaagggggg
     4261 attggggggt acagtgcagg agaaagaata gtagacatag tagcaacaga catacaaact
     4321 aaagaactac aaaaacaaat tacaaaaatt caaaattttc gggtttatta cagggacagc
     4381 agagatccac tctggaaagg accagcaaag ctcctctgga aaggtgaagg ggcagtagta
     4441 atacaagata atagtgacat aaaagtagtg ccaagaagaa aagcaaagat cattagggat
     4501 tatggaaaac agatggcagg tgatgattgt gtggcaggta gacaggatga ggattagaac
     4561 atggaacagt ttagtaaaac accatatgta tatttcaaag aaagctaagg gatgggttta
     4621 tagacatcac tatgaaagca ctaatccaag gacaagttca gaagtacaca tcccactagg
     4681 ggatgctaaa atggtaataa caacatattg gggtctgcat gcaggagaaa gagactggca
     4741 cttgggtcag ggagtctcca tagaatggaa gaaaaaagga tacagcacac aagtagaccc
     4801 tgacctagca gaccatctaa ttcatctgta ttactttgat tgtttttcag aatctgctat
     4861 aagaaacgcc atattaggac atagagttag tcctaggtgt gaatatcaag caggacataa
     4921 ccaggtagga tctctacagt acttggcact agcagcatta ataacaccaa aaaagataaa
     4981 gccacctttg cctagtgtta ggaaactgac agaagacaga tggaacaagc cccagaagac
     5041 caaggaccac agagggagcc atacaatgaa tggacactag agcttttaga ggagcttaag
     5101 aatgaagctg ttaggcactt tcctagagtg tggctccatg gcttagggca atacatctat
     5161 gaaacttatg gggatacttg ggcaggggtg gaagccctaa taagaactct gcaacaactg
     5221 ctgtttactc atttcaggat tgggtgtcaa catagcagaa taggcattcg acagagaaga
     5281 gcaagaaatg gagccaatag atcctagact agagccctgg aagcacccag gaagtcagcc
     5341 taggactcct tgtacctctt gctactgtaa aaagtgttgc tttcattgcc aagcttgctt
     5401 cttaagaaaa ggcttaggta tctcctatgg caggaagaag cggagacagc gacgacgagc
     5461 tcatcaagac agtcaaactc atcaagcgca tctaccagag cagtaagtag tacatgtaat
     5521 gcaaccctta gtaatactag taatagtagc attagtagta gtagcaataa tagcaatagt
     5581 tgtgtggtcc atagtactca tagaatatag gaaaatatta agacaaagaa aaatagacag
     5641 attaattgat agaatagcag aaagagcaga agacagtggc aatgagagcg aaggggatca
     5701 ggaggagtta tcagcacttg tggagagggg gcatcttgct ccttgggatg ttaatgatct
     5761 gtagtgcggg ggaacagtta tgggtcacag tctattatgg ggtacctgtg tggaaagaag
     5821 caaccaccac tctattttgt gcatcagatg ctaagggaca tgacacagag gtacataatg
     5881 tttgggctac acatgcctgt gtacccacag accccaaccc acaagaagta gtattggaaa
     5941 atgtgacaga aaattttaac atgtggaaaa ataacatggt agaacagatg catgaggata
     6001 taatcagttt atgggatcaa agcctaaagc catgtgtaaa attaacccca ctctgtgtta
     6061 ctttacattg cactgatttg gggaatgcta ctaatggtgg taacaatact accaatagta
     6121 gcagctgggg aatggaggag aaaggagaaa taaaaaactg ttctttcaat atcaccacaa
     6181 gcataagaga taaggtgcaa aaagaatatg cagcttttta taaacttgat atagtaccaa
     6241 tagaaaatga taatgctaat aataccagca attatactag ctataggttg ataagttgta
     6301 atacctcagt cattacacaa gcctgtccaa aggtgtcctt tgagccaatt ccaatacatt
     6361 attgtgcccc ggctggtttt gcgattctaa agtgtagaga taagaagttt aatgggacag
     6421 gaacatgtac aaatgtcagc acagtacaat gtacacatgg aattaggcca gtagtatcaa
     6481 ctcaactgct gttaaatggc agtctagcag aagaagatgt agtgattaaa tctgccaatt
     6541 tctcagacaa tactaaaacc ataatagtac agctgaacaa atctatagta attaattgta
     6601 caagacccaa caacaataca agaaaaggta tacatatagg accagggaga gcattttttg
     6661 ccacagaaat aataggagac ataagacaag cacattgtaa ccttagtaga acagactggg
     6721 ttaacacttt aaaacagata gccataaaat taagagaaca atttaagaat aaaacaatag
     6781 cctttaatcg atcctcagga ggggacccag aaattgtaat gcacagtttt aattgtggag
     6841 gggaattttt ctattgtaat tcaacacaac tgtttaataa tacttggaat agtactactg
     6901 acctgtttaa tagaactgaa gagtcaaatg acactatcat actcccatgc aaaataaaac
     6961 aaattataaa catgtggcag ggagtaggaa aagcaatgta tgcccctccc atcagaggac
     7021 aaattagatg ttcatcaaat attacaggac tgatattaac aagagatggg ggtaaaaacg
     7081 acagcgagac tgagaccttc agacctggag ggggagatat gagggacaat tggagaagtg
     7141 aattatataa atataaagta gtaaaaattg aaccattagg agtagcaccc accaaggcaa
     7201 agagaagagt ggtgcagaga gaaaaaagag caataggaat aggagctgtg ttccttgggt
     7261 tcttgggagc agcaggaagc actatgggcg cagcgtcatt gacgctgacg gtacaggcca
     7321 ggcaattact gtctggtata gtgcaacagc agaacaatct gctgagggct attgaggcgc
     7381 aacagcatct gttgcaactc acagtctggg gcatcaagca gctccaggca agagtcctgg
     7441 ctgtggaaag atacctacgg gatcaacagc tcctgggaat ttggggttgc tctggaaaac
     7501 tcatttgcac cactactgtg ccttggaata ctagttggag taataaatct ctggatgtaa
     7561 tttggggtaa catgacctgg atgcagtggg aaagagaaat tgacaattac acaggcataa
     7621 tatacaactt aattgaagaa tcgcagaacc aacaagaaaa gaatgaacaa gacttattgg
     7681 cactagacaa atgggcaagt ttgtggaatt ggtttgacat atcaaaatgg ctgtggtata
     7741 taaaaatatt cataatgata gtaggaggct taataggttt aagaatagtt tttactgtac
     7801 tttctatagt aaatagagtt aggcagggat actcaccatt atcgttacag acccgcctcc
     7861 caacccagag gggacccgac aggcccgaag gaatcgaaga agaaggtgga gagagagaca
     7921 gagacagatc cgaaccatta gcgggtggat tcttaacact tatctggatc gacctgagga
     7981 gcctgtgcat cttcagctac caccgcttga gagacttact cttgattgta acgaggattg
     8041 tggaacttct gggacacagg gggtgggcaa tcctcaaata ttggtggaat ctcctacagt
     8101 attggagtca ggagctaaag aatagtgctg ttagcttgtt taatgccata gctatagcag
     8161 tagctgaggg gacagatagg gttatagaag tagcacaaag agcttttaga gctattcttc
     8221 acatacctag aagaataaga cagggcttcg aaagggcttt actataaaat gggtggcaaa
     8281 tggtcaaaaa gtaggatgct tggatggcct gctgtaaggg aaagaatgag gcgaactgag
     8341 ccagagccag cagcagcaag ttcgccagag ccagcagcag ctggggtggg agcagtatct
     8401 cgagatctgg aaaaacatgg ggcaatcaca agtagcaata caccagctac caatgctgat
     8461 tgtgcctggt tagaagcaca acaagaggac gaggaggtag gttttccagt cagacctcag
     8521 gtacctttaa gaccaatgac ttacaaggga gctttagatc ttagccattt tttaaaagaa
     8581 aaggggggac tggaagggtt agtccactcc caaagaagac aagatatcct tgatctgtgg
     8641 gtctacaaca cacaaggcta cttccctgat tggcagaact acacaccagg gccagggacc
     8701 agatttccac tgacctttgg atggtgcttc aagctagtac cggttgagcc agagcaggta
     8761 gaaaaggcca atgagggaga gaacaacagc ttgctacacc ctatgagtca acatgggatg
     8821 gatgacccag agagagaagt gctcgtgtgg aagtttgaca gccgcttagc atttcatcat
     8881 gtggcccgag agatgcatcc ggagtactac aagaactgat gacaccgact ttctacaagg
     8941 gactttccgc tggggacttt ccagggaagg cgtggcctgg gcgggactgg ggagtggcga
     9001 gccctccgat gctgcatata agcagctgct tttgcctgta ctgggtctct ctggttagac
     9061 cagatcagag cctgggagct ctctggctag ctagg
//
