BLAST Basic Local Alignment Search Tool

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### Job Title: Nucleotide Sequence (53 letters)

RID=PACZ05KA014, BLASTN 2.2.19+

    Reference:
    Stephen F. Altschul, Thomas L. Madden, Alejandro A.
    Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David
    J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new
    generation of protein database search programs", Nucleic
    Acids Res. 25:3389-3402.

    RID: PACZ05KA014

    Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
    GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
               7,956,467 sequences; 25,886,828,050 total letters
     If you have any problems or questions with the results of this search
    please refer to the BLAST FAQs
    Taxonomy reports

    Query=
    Length=53

### Distribution of 100 Blast Hits on the Query Sequence

    Distance tree of results

                                                                       Score     E
    Sequences producing significant alignments:                       (Bits)  Value

    gb|M90847.1|HIVFLDD  Human immunodeficiency virus type 1, vira...  96.9    4e-18
    gb|M90853.1|HIVFLD8  Human immunodeficiency virus type 1, vira...  96.9    4e-18
    gb|M90851.1|HIVFLD5  Human immunodeficiency virus type 1, vira...  96.9    4e-18
    emb|Z47539.1|HIVY1V315  HIV-1 RNA V3 region (patient Y, sample...  91.5    2e-16
    emb|AM156916.1|  Human immunodeficiency virus type 1 proviral ...  91.5    2e-16
    emb|AM156915.1|  Human immunodeficiency virus type 1 proviral ...  91.5    2e-16
    gb|U13299.1|HIV1U13299  Human immunodeficiency virus type 1 pa...  91.5    2e-16
    gb|U13294.1|HIV1U13294  Human immunodeficiency virus type 1 pa...  91.5    2e-16
    gb|M92100.1|HIVFLPAR3A  Human immunodeficiency virus type 1, v...  91.5    2e-16
    gb|M90854.1|HIVFLPAD  Human immunodeficiency virus type 1, vir...  91.5    2e-16
    gb|M90855.1|HIVFLPA1  Human immunodeficiency virus type 1, vir...  91.5    2e-16
    gb|EU329964.1|  HIV-1 isolate BRII24 from Italy envelope glyco...  87.8    2e-15
    gb|EF178361.1|  HIV-1 MS2004-37_063 from Australia, genomic se...  87.8    2e-15
    gb|AF188690.1|  HIV-1 isolate IH5346 from Italy envelope glyco...  87.8    2e-15
    gb|S70936.1|  HIV-1 isolate KM-03 gp120 third hypervariable (V...  87.8    2e-15
    gb|AF092652.1|AF092652  HIV-1 patient 1036 clone 2 from USA, e...  87.8    2e-15
    gb|AF105785.1|AF105785  HIV-1 isolate B-RII-24 from Italy, env...  87.8    2e-15
    gb|AF105516.1|AF105516  HIV-1 isolate B-DIII-17 from Italy, en...  87.8    2e-15
    gb|AF105512.1|AF105512  HIV-1 isolate B-DIII-11 from Italy, en...  87.8    2e-15
    gb|AF105499.1|AF105499  HIV-1 isolate B-DII-16 from Italy, env...  87.8    2e-15
    gb|U58426.1|HIVU58426  Human immunodeficiency virus type 1 env...  87.8    2e-15
    gb|U58419.1|HIVU58419  Human immunodeficiency virus type 1 env...  87.8    2e-15
    gb|U58416.1|HIVU58416  Human immunodeficiency virus type 1 env...  87.8    2e-15
    gb|U58404.1|HIVU58404  Human immunodeficiency virus type 1 env...  87.8    2e-15
    gb|EU578073.1|  HIV-1 isolate CRPE_TA4 from USA envelope glyco...  82.4    9e-14
    gb|EU578072.1|  HIV-1 isolate CRPE_TA3 from USA envelope glyco...  82.4    9e-14
    gb|EU578071.1|  HIV-1 isolate CRPE_B35 from USA envelope glyco...  82.4    9e-14
    gb|EU578070.1|  HIV-1 isolate CRPE_B34 from USA envelope glyco...  82.4    9e-14
    gb|EU578069.1|  HIV-1 isolate CRPE_B33 from USA envelope glyco...  82.4    9e-14
    gb|EU578068.1|  HIV-1 isolate CRPE_B32 from USA envelope glyco...  82.4    9e-14
    gb|EU578067.1|  HIV-1 isolate CRPE_B30 from USA envelope glyco...  82.4    9e-14
    gb|EU578066.1|  HIV-1 isolate CRPE_B29 from USA envelope glyco...  82.4    9e-14
    gb|EU578065.1|  HIV-1 isolate CRPE_B28 from USA envelope glyco...  82.4    9e-14
    gb|EU578064.1|  HIV-1 isolate CRPE_B26 from USA envelope glyco...  82.4    9e-14
    gb|EU578063.1|  HIV-1 isolate CRPE_B21 from USA envelope glyco...  82.4    9e-14
    gb|EU578062.1|  HIV-1 isolate CRPE_B14 from USA envelope glyco...  82.4    9e-14
    gb|EU578061.1|  HIV-1 isolate CRPE_B13 from USA envelope glyco...  82.4    9e-14
    gb|EU578060.1|  HIV-1 isolate CRPE_B11 from USA envelope glyco...  82.4    9e-14
    gb|EU578059.1|  HIV-1 isolate CRPE_A8 from USA envelope glycop...  82.4    9e-14
    gb|EU578058.1|  HIV-1 isolate CRPE_A5 from USA envelope glycop...  82.4    9e-14
    gb|EU329974.1|  HIV-1 isolate BRIII08 from Italy envelope glyc...  82.4    9e-14
    gb|EF593221.1|  HIV-1 isolate CRPE_SGA_TA3 from USA envelope g...  82.4    9e-14
    gb|EF457058.1|  HIV-1 isolate 108_m33_c5M2_3 from USA envelope...  82.4    9e-14
    gb|EF457057.1|  HIV-1 isolate 108_m33_c1A_1 from USA envelope ...  82.4    9e-14
    gb|EF457056.1|  HIV-1 isolate 108_m30_c1A_8 from USA envelope ...  82.4    9e-14
    gb|EF457055.1|  HIV-1 isolate 108_m30_c1A_9 from USA envelope ...  82.4    9e-14
    gb|EF457054.1|  HIV-1 isolate 108_m30_c1A_7 from USA envelope ...  82.4    9e-14
    gb|EF457053.1|  HIV-1 isolate 108_m30_c1A_6 from USA envelope ...  82.4    9e-14
    gb|EF457052.1|  HIV-1 isolate 108_m30_c1A_5 from USA envelope ...  82.4    9e-14
    gb|EF457051.1|  HIV-1 isolate 108_m30_c5M8_3 from USA envelope...  82.4    9e-14
    gb|EF457050.1|  HIV-1 isolate 108_m30_c5M6_3 from USA envelope...  82.4    9e-14
    gb|EF457049.1|  HIV-1 isolate 108_m30_c5M6_2 from USA envelope...  82.4    9e-14
    gb|EF457048.1|  HIV-1 isolate 108_m30_c5M6_1 from USA envelope...  82.4    9e-14
    gb|EF457047.1|  HIV-1 isolate 108_m30_c5M2_4 from USA envelope...  82.4    9e-14
    gb|EF457046.1|  HIV-1 isolate 108_m27_c1A-3 from USA envelope ...  82.4    9e-14
    gb|EF457045.1|  HIV-1 isolate 108_m24_c1B_4 from USA envelope ...  82.4    9e-14
    gb|EF457044.1|  HIV-1 isolate 108_m24_c1B_3 from USA envelope ...  82.4    9e-14
    gb|EF457043.1|  HIV-1 isolate 108_m24_c1B_2 from USA envelope ...  82.4    9e-14
    gb|EF457042.1|  HIV-1 isolate 108_m24_c1B_1 from USA envelope ...  82.4    9e-14
    gb|EF457041.1|  HIV-1 isolate 108_m24_c1A_5 from USA envelope ...  82.4    9e-14
    gb|EF457040.1|  HIV-1 isolate 108_m24_c1A_4 from USA envelope ...  82.4    9e-14
    gb|EF457039.1|  HIV-1 isolate 108_m24_c1A_3 from USA envelope ...  82.4    9e-14
    gb|EF457038.1|  HIV-1 isolate 108_m24_c1A_2 from USA envelope ...  82.4    9e-14
    gb|EF457037.1|  HIV-1 isolate 108_m24_c2C_8 from USA envelope ...  82.4    9e-14
    gb|EF457036.1|  HIV-1 isolate 108_m24_c2C_1 from USA envelope ...  82.4    9e-14
    gb|EF457035.1|  HIV-1 isolate 108_p_5_1 from USA envelope glyc...  82.4    9e-14
    gb|EF457034.1|  HIV-1 isolate 108_p_4_2 from USA envelope glyc...  82.4    9e-14
    gb|EF457033.1|  HIV-1 isolate 108_p_4_1 from USA env gene, par...  82.4    9e-14
    gb|EF457032.1|  HIV-1 isolate 108_p_3_1 from USA envelope glyc...  82.4    9e-14
    gb|EF457031.1|  HIV-1 isolate 108_p_2_3 from USA envelope glyc...  82.4    9e-14
    gb|EF457030.1|  HIV-1 isolate 108_p_2_2 from USA envelope glyc...  82.4    9e-14
    gb|EF457029.1|  HIV-1 isolate 108_p_1_3 from USA envelope glyc...  82.4    9e-14
    gb|EF457028.1|  HIV-1 isolate 108_p_1_1 from USA envelope glyc...  82.4    9e-14
    gb|AY348371.1|  HIV-1 isolate p2p158 clone 15 from USA envelop...  82.4    9e-14
    gb|AY348342.1|  HIV-1 isolate p2p138 clone 10 from USA envelop...  82.4    9e-14
    gb|AY253958.1|  HIV-1 isolate Pt16 from Japan envelope glycopr...  82.4    9e-14
    gb|DQ061780.1|  HIV-1 isolate T21_141_539 from Belgium envelop...  82.4    9e-14
    gb|AF200858.1|AF200858  HIV-1 98MX.MC04 from Mexico envelope g...  82.4    9e-14
    gb|AF092653.1|AF092653  HIV-1 patient 1036 clone 3 from USA, e...  82.4    9e-14
    gb|AF111922.1|AF111922  HIV-1 isolate Biol_Gf1 from USA, envel...  82.4    9e-14
    gb|AF105794.1|AF105794  HIV-1 isolate B-RIII-08 from Italy, en...  82.4    9e-14
    gb|AF105513.1|AF105513  HIV-1 isolate B-DIII-12 from Italy, en...  82.4    9e-14
    gb|AF105509.1|AF105509  HIV-1 isolate B-DIII-08 from Italy, en...  82.4    9e-14
    gb|AF105507.1|AF105507  HIV-1 isolate B-DIII-05 from Italy, en...  82.4    9e-14
    gb|AF105502.1|AF105502  HIV-1 isolate B-DII-19 from Italy, env...  82.4    9e-14
    gb|AF105498.1|AF105498  HIV-1 isolate B-DII-15 from Italy, env...  82.4    9e-14
    gb|AF105497.1|AF105497  HIV-1 isolate B-DII-14 from Italy, env...  82.4    9e-14
    gb|AF105496.1|AF105496  HIV-1 isolate B-DII-13 from Italy, env...  82.4    9e-14
    gb|AF105494.1|AF105494  HIV-1 isolate B-DII-11 from Italy, env...  82.4    9e-14
    gb|AF105492.1|AF105492  HIV-1 isolate B-DII-08 from Italy, env...  82.4    9e-14
    gb|AF105491.1|AF105491  HIV-1 isolate B-DII-06 from Italy, env...  82.4    9e-14
    gb|AF100080.1|AF100080  HIV-1 clone p129d84c9 from the Netherl...  82.4    9e-14
    gb|AF100079.1|AF100079  HIV-1 clone p129d84c8 from the Netherl...  82.4    9e-14
    gb|AF100078.1|AF100078  HIV-1 clone p129d84c7 from the Netherl...  82.4    9e-14
    gb|AF100075.1|AF100075  HIV-1 clone p129d84c15 from the Nether...  82.4    9e-14
    gb|AF100074.1|AF100074  HIV-1 clone p129d84c13 from the Nether...  82.4    9e-14
    gb|AF100073.1|AF100073  HIV-1 clone p129d84c12 from the Nether...  82.4    9e-14
    gb|AF100072.1|AF100072  HIV-1 clone p129d84c11 from the Nether...  82.4    9e-14
    gb|EF028250.1|  HIV-1 isolate MC-ACH320.3.1.b_p1 from Netherla...  80.6    3e-13
    gb|AY156762.1|  HIV-1 clone LA24.EN from USA envelope glycopro...  75.2    1e-11

Alignments

    >gb|M90847.1|HIVFLDD  Human immunodeficiency virus type 1, viral sample FLDD, V3 region
    Length=343

     Score = 96.9 bits (106),  Expect = 4e-18
     Identities = 53/53 (100%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                |||||||||||||||||||||||||||||||||||||||||||||||||||||
    Sbjct  98   ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  150

    >gb|M90853.1|HIVFLD8  Human immunodeficiency virus type 1, viral sample FLD8, V3 region
    Length=360

     Score = 96.9 bits (106),  Expect = 4e-18
     Identities = 53/53 (100%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                |||||||||||||||||||||||||||||||||||||||||||||||||||||
    Sbjct  110  ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  162

    >gb|M90851.1|HIVFLD5  Human immunodeficiency virus type 1, viral sample FLD5, V3 region
    Length=360

     Score = 96.9 bits (106),  Expect = 4e-18
     Identities = 53/53 (100%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                |||||||||||||||||||||||||||||||||||||||||||||||||||||
    Sbjct  110  ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  162

    >emb|Z47539.1|HIVY1V315  HIV-1 RNA V3 region (patient Y, sample Y1, clone 15)
    Length=276

     Score = 91.5 bits (100),  Expect = 2e-16
     Identities = 52/53 (98%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                |||||||||||||||||||||||||||||||||||||||| ||||||||||||
    Sbjct  95   ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCCGTTTATGCAGCA  147

    >emb|AM156916.1|  Human immunodeficiency virus type 1 proviral partial env gene
    for envelope glycoprotein precursor gp160, clone VI943-2
    Length=672

     Score = 91.5 bits (100),  Expect = 2e-16
     Identities = 52/53 (98%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                ||||||||||||||||||||||||||||||||||||||||||| |||||||||
    Sbjct  215  ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTCTATGCAGCA  267

    >emb|AM156915.1|  Human immunodeficiency virus type 1 proviral partial env gene
    for envelope glycoprotein precursor gp160, clone VI943-1
    Length=675

     Score = 91.5 bits (100),  Expect = 2e-16
     Identities = 52/53 (98%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                ||||||||||||||||||||||||||||||||||||||||||| |||||||||
    Sbjct  215  ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTCTATGCAGCA  267

    >gb|U13299.1|HIV1U13299  Human immunodeficiency virus type 1 patient HIVAms199, clone
    A9, envelope glycoprotein (env) gene, V3 region, partial cds
    Length=105

     Score = 91.5 bits (100),  Expect = 2e-16
     Identities = 52/53 (98%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1   ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
               |||||||||||||||||||||||||||||||||||||||| ||||||||||||
    Sbjct  17  ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCCGTTTATGCAGCA  69

    >gb|U13294.1|HIV1U13294  Human immunodeficiency virus type 1 patient ACH9012, clone E6,
    envelope glycoprotein (env) gene, V3 region, partial cds
    Length=105

     Score = 91.5 bits (100),  Expect = 2e-16
     Identities = 52/53 (98%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1   ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
               |||||||||||||||||||||||||||||||||||||||| ||||||||||||
    Sbjct  17  ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCCGTTTATGCAGCA  69

    >gb|M92100.1|HIVFLPAR3A  Human immunodeficiency virus type 1, viral sample FLPAR3A (Florida
    patient A), partial env cds, V3 region
    Length=105

     Score = 91.5 bits (100),  Expect = 2e-16
     Identities = 52/53 (98%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1   ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
               || ||||||||||||||||||||||||||||||||||||||||||||||||||
    Sbjct  17  ACAATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  69

    >gb|M90854.1|HIVFLPAD  Human immunodeficiency virus type 1, viral sample FLPAD, V3 region
    Length=337

     Score = 91.5 bits (100),  Expect = 2e-16
     Identities = 52/53 (98%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||||||||||||||||||||||
    Sbjct  92   ACAATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  144

    >gb|M90855.1|HIVFLPA1  Human immunodeficiency virus type 1, viral sample FLPA1, V3 region
    Length=351

     Score = 91.5 bits (100),  Expect = 2e-16
     Identities = 52/53 (98%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||||||||||||||||||||||
    Sbjct  110  ACAATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  162

    >gb|EU329964.1|  HIV-1 isolate BRII24 from Italy envelope glycoprotein (env) gene,
    partial cds
    Length=792

     Score = 87.8 bits (96),  Expect = 2e-15
     Identities = 51/53 (96%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||| ||||||||||||||||||
    Sbjct  149  ACAATACAAGAAAAGGTATACGTATAGGACCAGGCAGAGCAGTTTATGCAGCA  201

    >gb|EF178361.1|  HIV-1 MS2004-37_063 from Australia, genomic sequence
    Length=7951

     Score = 87.8 bits (96),  Expect = 2e-15
     Identities = 51/53 (96%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1     ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                 || ||||||||||||||||||||||||||||||||||||||||||||||| ||
    Sbjct  6409  ACAATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAACA  6461

    >gb|AF188690.1|  HIV-1 isolate IH5346 from Italy envelope glycoprotein C2-V3-C3
    region (env) gene, partial cds
    Length=171

     Score = 87.8 bits (96),  Expect = 2e-15
     Identities = 51/53 (96%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||||||||||||||||||| ||
    Sbjct  56   ACAATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAACA  108

    >gb|S70936.1|  HIV-1 isolate KM-03 gp120 third hypervariable (V3) region gene,
    partial cds
    Length=368

     Score = 87.8 bits (96),  Expect = 2e-15
     Identities = 48/48 (100%), Gaps = 0/48 (0%)
     Strand=Plus/Plus

    Query  6    ACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                ||||||||||||||||||||||||||||||||||||||||||||||||
    Sbjct  169  ACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  216

    >gb|AF092652.1|AF092652  HIV-1 patient 1036 clone 2 from USA, envelope glycoprotein V3
    region (env) gene, partial cds
    Length=81

     Score = 87.8 bits (96),  Expect = 2e-15
     Identities = 51/53 (96%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1   ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
               ||||||||||||||||||||||| ||||||||||||||||||||||| |||||
    Sbjct  5   ACTATACAAGAAAAGGTATACGTGTAGGACCAGGGAGAGCAGTTTATACAGCA  57

    >gb|AF105785.1|AF105785  HIV-1 isolate B-RII-24 from Italy, envelope glycoprotein, C2-V5
    region (env) gene, partial cds
    Length=792

     Score = 87.8 bits (96),  Expect = 2e-15
     Identities = 51/53 (96%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||| ||||||||||||||||||
    Sbjct  149  ACAATACAAGAAAAGGTATACGTATAGGACCAGGCAGAGCAGTTTATGCAGCA  201

    >gb|AF105516.1|AF105516  HIV-1 isolate B-DIII-17 from Italy, envelope glycoprotein, C2-V5
    region (env) gene, partial cds
    Length=789

     Score = 87.8 bits (96),  Expect = 2e-15
     Identities = 51/53 (96%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||| ||||||||||||||||||
    Sbjct  149  ACAATACAAGAAAAGGTATACGTATAGGACCAGGCAGAGCAGTTTATGCAGCA  201

    >gb|AF105512.1|AF105512  HIV-1 isolate B-DIII-11 from Italy, envelope glycoprotein, C2-V5
    region (env) gene, partial cds
    Length=789

     Score = 87.8 bits (96),  Expect = 2e-15
     Identities = 51/53 (96%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||| ||||||||||||||||||
    Sbjct  149  ACAATACAAGAAAAGGTATACGTATAGGACCAGGCAGAGCAGTTTATGCAGCA  201

    >gb|AF105499.1|AF105499  HIV-1 isolate B-DII-16 from Italy, envelope glycoprotein, C2-V5
    region (env) gene, partial cds
    Length=789

     Score = 87.8 bits (96),  Expect = 2e-15
     Identities = 51/53 (96%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||| ||||||||||||||||||
    Sbjct  149  ACAATACAAGAAAAGGTATACGTATAGGACCAGGCAGAGCAGTTTATGCAGCA  201

    >gb|U58426.1|HIVU58426  Human immunodeficiency virus type 1 envelope glycoprotein, V3
    region (env) gene, partial cds
    Length=252

     Score = 87.8 bits (96),  Expect = 2e-15
     Identities = 51/53 (96%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                |||||||||||| |||||||||||||||||| |||||||||||||||||||||
    Sbjct  110  ACTATACAAGAAGAGGTATACGTATAGGACCGGGGAGAGCAGTTTATGCAGCA  162

    >gb|U58419.1|HIVU58419  Human immunodeficiency virus type 1 envelope glycoprotein, V3
    region (env) gene, partial cds
    Length=252

     Score = 87.8 bits (96),  Expect = 2e-15
     Identities = 51/53 (96%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                |||||||||||| |||||||||||||||||| |||||||||||||||||||||
    Sbjct  110  ACTATACAAGAAGAGGTATACGTATAGGACCGGGGAGAGCAGTTTATGCAGCA  162

    >gb|U58416.1|HIVU58416  Human immunodeficiency virus type 1 envelope glycoprotein, V3
    region (env) gene, partial cds
    Length=249

     Score = 87.8 bits (96),  Expect = 2e-15
     Identities = 51/53 (96%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                |||||||||||| |||||||||||||||||| |||||||||||||||||||||
    Sbjct  110  ACTATACAAGAAGAGGTATACGTATAGGACCGGGGAGAGCAGTTTATGCAGCA  162

    >gb|U58404.1|HIVU58404  Human immunodeficiency virus type 1 envelope glycoprotein, V3
    region (env) gene, partial cds
    Length=252

     Score = 87.8 bits (96),  Expect = 2e-15
     Identities = 51/53 (96%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                |||||||||||| |||||||||||||||||| |||||||||||||||||||||
    Sbjct  110  ACTATACAAGAAGAGGTATACGTATAGGACCGGGGAGAGCAGTTTATGCAGCA  162

    >gb|EU578073.1|  HIV-1 isolate CRPE_TA4 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578072.1|  HIV-1 isolate CRPE_TA3 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578071.1|  HIV-1 isolate CRPE_B35 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578070.1|  HIV-1 isolate CRPE_B34 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578069.1|  HIV-1 isolate CRPE_B33 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578068.1|  HIV-1 isolate CRPE_B32 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578067.1|  HIV-1 isolate CRPE_B30 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578066.1|  HIV-1 isolate CRPE_B29 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578065.1|  HIV-1 isolate CRPE_B28 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578064.1|  HIV-1 isolate CRPE_B26 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578063.1|  HIV-1 isolate CRPE_B21 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578062.1|  HIV-1 isolate CRPE_B14 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2575

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578061.1|  HIV-1 isolate CRPE_B13 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2577

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578060.1|  HIV-1 isolate CRPE_B11 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578059.1|  HIV-1 isolate CRPE_A8 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU578058.1|  HIV-1 isolate CRPE_A5 from USA envelope glycoprotein (env) gene,
    complete cds; and vpu protein (vpu), rev protein (rev),
    and tat protein (tat) genes, partial cds
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EU329974.1|  HIV-1 isolate BRIII08 from Italy envelope glycoprotein (env)
    gene, partial cds
    Length=801

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||| ||| ||||||||||||||
    Sbjct  149  ACAATACAAGAAAAGGTATACGTATAGGACCAGGCAGAACAGTTTATGCAGCA  201

    >gb|EF593221.1|  HIV-1 isolate CRPE_SGA_TA3 from USA envelope glycoprotein (env)
    gene, complete cds; and vpu protein (vpu) pseudogene, partial
    sequence
    Length=2574

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || |||||||||||||||||| |||||||||||||||||||||||||||| ||
    Sbjct  899  ACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCAGTTTATGCAACA  951

    >gb|EF457058.1|  HIV-1 isolate 108_m33_c5M2_3 from USA envelope glycoprotein (env)
    gene, partial cds
    Length=1218

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||| ||||||||||||||| ||
    Sbjct  818  ACAATACAAGAAAAGGTATACGTATAGGACCAGGCAGAGCAGTTTATGCAACA  870

    >gb|EF457057.1|  HIV-1 isolate 108_m33_c1A_1 from USA envelope glycoprotein (env)
    gene, partial cds
    Length=1218

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||| ||||||||||||||| ||
    Sbjct  818  ACAATACAAGAAAAGGTATACGTATAGGACCAGGCAGAGCAGTTTATGCAACA  870

    >gb|EF457056.1|  HIV-1 isolate 108_m30_c1A_8 from USA envelope glycoprotein (env)
    gene, partial cds
    Length=1218

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||| ||||||||||||||| ||
    Sbjct  818  ACAATACAAGAAAAGGTATACGTATAGGACCAGGCAGAGCAGTTTATGCAACA  870

    >gb|EF457055.1|  HIV-1 isolate 108_m30_c1A_9 from USA envelope glycoprotein (env)
    gene, partial cds
    Length=1218

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||| ||||||||||||||| ||
    Sbjct  818  ACAATACAAGAAAAGGTATACGTATAGGACCAGGCAGAGCAGTTTATGCAACA  870

    >gb|EF457054.1|  HIV-1 isolate 108_m30_c1A_7 from USA envelope glycoprotein (env)
    gene, partial cds
    Length=1218

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||| ||||||||||||||| ||
    Sbjct  818  ACAATACAAGAAAAGGTATACGTATAGGACCAGGCAGAGCAGTTTATGCAACA  870

    >gb|EF457053.1|  HIV-1 isolate 108_m30_c1A_6 from USA envelope glycoprotein (env)
    gene, partial cds
    Length=1218

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||| ||||||||||||||| ||
    Sbjct  818  ACAATACAAGAAAAGGTATACGTATAGGACCAGGCAGAGCAGTTTATGCAACA  870

    >gb|EF457052.1|  HIV-1 isolate 108_m30_c1A_5 from USA envelope glycoprotein (env)
    gene, partial cds
    Length=1218

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||| ||||||||||||||| ||
    Sbjct  818  ACAATACAAGAAAAGGTATACGTATAGGACCAGGCAGAGCAGTTTATGCAACA  870

    >gb|EF457051.1|  HIV-1 isolate 108_m30_c5M8_3 from USA envelope glycoprotein (env)
    gene, partial cds
    Length=1218

     Score = 82.4 bits (90),  Expect = 9e-14
     Identities = 50/53 (94%), Gaps = 0/53 (0%)
     Strand=Plus/Plus

    Query  1    ACTATACAAGAAAAGGTATACGTATAGGACCAGGGAGAGCAGTTTATGCAGCA  53
                || ||||||||||||||||||||||||||||||| ||||||||||||||| ||
    Sbjct  818  ACAATACAAGAAAAGGTATACGTATAGGACCAGGCAGAGCAGTTTATGCAACA  870

      Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
    GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
        Posted date:  Jan 6, 2009  5:48 PM
      Number of letters in database: 117,024,274
      Number of sequences in database:  7,956,467

    Lambda     K      H
       0.634    0.408    0.912
    Gapped
    Lambda     K      H
       0.625    0.410    0.780
    Matrix: blastn matrix:2 -3
    Gap Penalties: Existence: 5, Extension: 2
    Number of Sequences: 7956467
    Number of Hits to DB: 1272186
    Number of extensions: 66335
    Number of successful extensions: 19676
    Number of sequences better than 10: 2685
    Number of HSP's better than 10 without gapping: 0
    Number of HSP's gapped: 19653
    Number of HSP's successfully gapped: 2685
    Length of query: 53
    Length of database: 25886828050
    Length adjustment: 31
    Effective length of query: 22
    Effective length of database: 25640177573
    Effective search space: 564083906606
    Effective search space used: 564083906606
    A: 0
    X1: 22 (20.1 bits)
    X2: 33 (29.8 bits)
    X3: 110 (99.2 bits)
    S1: 24 (22.9 bits)
    S2: 39 (36.5 bits)