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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


Distance tree of resultsNew  
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)