Alignment viewer

BLASTN 2.6.0+ Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schaffer, 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. Database: Gossypium_20hirsutum_20[refseq_20GCF_5F000987745.1_202015-05-05] 9,148 sequences; 2,189,140,010 total letters Query= NC_004105.1 Length=209771 Score E Sequences producing significant alignments: (Bits) Value seq22 163 4e-35 seq19 136 5e-27 seq16 125 1e-23 seq228 93.3 6e-14 seq4 93.3 6e-14 seq25 91.5 2e-13 seq2 91.5 2e-13 seq7 87.8 2e-12 >seq22 Length=61129363 Score = 163 bits (180), Expect = 4e-35 Identities = 391/587 (67%), Gaps = 6/587 (1%) Strand=Plus/Plus Query 42057 ACATCAAACATGCGAAATCGCAGTGCAGACCCTCATCTCTACTAATTAATTCGTTGGAAA 42116 ||| ||| || |||||||||||||| ||||| ||||||| ||||| ||||| || | Sbjct 6287571 ACAGCAAGCAAGCGAAATCGCAGTGGAGACCTTCATCTCGTGAGATTAACTCGTTTGAGA 6287630 Query 42117 ACGTGAGTCCGGGCATTAGGCCACGCTTTTTAAGCCAAAATATAGACGCA-AATGATCCA 42175 | || | ||||||||||| || | |||||| | ||||||||| | | || || ||| Sbjct 6287631 AAGTTAATCCGGGCATTAACCCCCTCTTTTTTAACCAAAATAT-GGCACAGAAACTTCCG 6287689 Query 42176 GAAAAGAAGATTCCTTCTACTGCCGCAAAGGCAATAAGTCTCTCTCCATAACCGGCACTG 42235 || || ||||| |||||||| ||||| || || | | || | || | | | Sbjct 6287690 GAGAAAAAGATCCCTTCTACGCAAGCAAAAGCGATTAACCGTTCGGCGAAAGTTTCTCCG 6287749 Query 42236 TCATGTATCCACTTTTGAGCCCAATCGGCCTTCTTTTTTACACAAGGCATCGTTTCTATG 42295 | | ||||| || |||||| ||||| || || ||||| |||| ||| || ||| Sbjct 6287750 CCGTCGATCCATTTCATAGCCCACTCGGCTTTTTTAGCCACACACGGCACCGTCTCGATG 6287809 Query 42296 GCATTAAAGAGATAGtttttttCATTACTATCTTTAACATATGTATCGATCAAAAGACTA 42355 || || ||| ||| ||||||| |||||| | || || |||| | ||||| Sbjct 6287810 GCGCGGAAAAGACGGTTCTTTTCATCGGAATCTTTTATGTAAGTCTCGAGAAGGAGACTG 6287869 Query 42356 TACATTTCTGAATGAATGTTTTCAATGGCCATCTGAAATCCGTAGAAACATCTGGCCTCG 42415 ||||| || || || || ||||| || || || || || || || ||| | |||||| Sbjct 6287870 TACATCTCGGAGTGGATATTTTCGATAGCGATTTGGAAACCATAAAAAGCACGCGCCTCG 6287929 Query 42416 GTAACCTGTACTTCTGTACAAAATCGTTCAGCTAAATTTTCGTTCACTATTCCGTCACTG 42475 | | ||| || ||| | || || |||| | || || ||||| || || | Sbjct 6287930 GAGATCTGGACCTCTTTCATGAACCGAACAGCAAGGTTCTCAAGGACTATGCCATCGGAG 6287989 Query 42476 GCTGCAAAAAACGCCAATACATGTTTTATAAAATATTTTTCGTC--CGGTGTTAATTTAT 42533 || || ||||| || | || || | || || | | || || ||||| | || | Sbjct 6287990 GCGGCGAAAAAGGCGAGAACGTGACTAATGAAGTGATGCTCATCGGCGGTGAGAGTT--T 6288047 Query 42534 TCCAATCATTGATATCTTTAGATATATCTACTTCTTCTACCGTCCAAAATGATGCTTCTG 42593 ||| | | | |||| ||| | ||| ||||| ||| | |||||||| || ||||| | Sbjct 6288048 CCCAGTGACGAAGATCTGAAGACAGATCGACTTCCTCTGCGGTCCAAAACGACGCTTCGG 6288107 Query 42594 CCTTTTTATACATATTCCAGATATCATGATATTGAATTGGGAAAATA 42640 | || || ||||| | ||| | || | ||||| || || || ||| Sbjct 6288108 CTTTCTTGTACATTTCCCATACTTCTGGGTATTGGATCGGAAACATA 6288154 >seq19 Length=70911690 Score = 136 bits (150), Expect = 5e-27 Identities = 241/348 (69%), Gaps = 4/348 (1%) Strand=Plus/Minus Query 42057 ACATCAAACATGCGAAATCGCAGTGCAGACCCTCATCTCTACTAATTAATTCGTTGGAAA 42116 ||| ||| || || || ||||| || ||||| ||||||| | || || ||||| || | Sbjct 44463885 ACAGCAAGCAAGCAAAGTCGCAATGGAGACCTTCATCTCGAGAGATCAACTCGTTTGAGA 44463826 Query 42117 ACGTGAGTCCGGGCATTAGGCCACGCTTTTTAAGCCAAAATATAG-ACGCAAA-TGATCC 42174 | || | ||| ||||||| || |||||||| | ||||||||| | || ||| || || Sbjct 44463825 AAGTTAATCCAGGCATTAACCCGCGCTTTTTTAACCAAAATATCGCACAGAAACTG--CC 44463768 Query 42175 AGAAAAGAAGATTCCTTCTACTGCCGCAAAGGCAATAAGTCTCTCTCCATAACCGGCACT 42234 || || || || |||||||| || || || || | | || || || | | | Sbjct 44463767 GGAGAAAAATATGCCTTCTACGCAAGCGAAAGCGATTAACCGTTCGGCAAAAGCTTCGCC 44463708 Query 42235 GTCATGTATCCACTTTTGAGCCCAATCGGCCTTCTTTTTTACACAAGGCATCGTTTCTAT 42294 | | | ||||| || |||||||||||| || || || || |||| |||||| | Sbjct 44463707 GCCGTCGATCCATTTCAAAGCCCAATCGGCTTTTTTAGCCACGCACGGCACCGTTTCAGT 44463648 Query 42295 GGCATTAAAGAGATAGtttttttCATTACTATCTTTAACATATGTATCGATCAAAAGACT 42354 || | ||||| ||||||||| | |||||||| ||| || |||| | ||||| Sbjct 44463647 AGCGTGGAAGAGGCGGTTTTTTTCGGTGGAATCTTTAATATAAGTTTCGAGGAGGAGACT 44463588 Query 42355 ATACATTTCTGAATGAATGTTTTCAATGGCCATCTGAAATCCGTAGAA 42402 |||||| || || || || || || ||||| || || ||||| || || Sbjct 44463587 ATACATCTCAGAGTGGATATTCTCGATGGCGATTTGGAATCCATAAAA 44463540 >seq16 Length=102030775 Score = 125 bits (138), Expect = 1e-23 Identities = 238/348 (68%), Gaps = 2/348 (1%) Strand=Plus/Minus Query 42057 ACATCAAACATGCGAAATCGCAGTGCAGACCCTCATCTCTACTAATTAATTCGTTGGAAA 42116 ||| ||| || |||||||| ||||| ||||| ||||||| ||||| ||||| || | Sbjct 57862383 ACAGCAAGCAAGCGAAATCACAGTGGAGACCTTCATCTCGTGAGATTAACTCGTTTGAGA 57862324 Query 42117 ACGTGAGTCCGGGCATTAGGCCACGCTTTTTAAGCCAAAATATAGACGCA-AATGATCCA 42175 | || | ||||||||||| || | |||||| | ||||||||| | | || || ||| Sbjct 57862323 AAGTTAATCCGGGCATTAACCCCCTCTTTTTTAACCAAAATAT-GGCACAGAAACTTCCG 57862265 Query 42176 GAAAAGAAGATTCCTTCTACTGCCGCAAAGGCAATAAGTCTCTCTCCATAACCGGCACTG 42235 || || ||||| || ||||| ||||| || || | | || | || | | | Sbjct 57862264 GAGAAAAAGATCCCCTCTACGCAAGCAAAAGCGATTAACCGTTCGGCGAAAGTTTCTCCG 57862205 Query 42236 TCATGTATCCACTTTTGAGCCCAATCGGCCTTCTTTTTTACACAAGGCATCGTTTCTATG 42295 | | ||||| || |||||| ||||| || || ||||| |||| ||| || ||| Sbjct 57862204 CCGTCGATCCATTTCATAGCCCACTCGGCTTTTTTAGCCACACACGGCACCGTCTCGATG 57862145 Query 42296 GCATTAAAGAGATAGtttttttCATTACTATCTTTAACATATGTATCGATCAAAAGACTA 42355 || || ||| ||| ||||||| |||||| | || || |||| | ||||| Sbjct 57862144 GCGCGGAAAAGACGGTTCTTTTCATCGGAATCTTTTATGTAAGTCTCGAGAAGGAGACTG 57862085 Query 42356 TACATTTCTGAATGAATGTTTTCAATGGCCATCTGAAATCCGTAGAAA 42403 ||||| || || || || ||||| || || || || || || || ||| Sbjct 57862084 TACATCTCGGAGTGGATATTTTCGATAGCGATTTGGAAACCATAAAAA 57862037 >seq228 Length=356584 Score = 93.3 bits (102), Expect = 6e-14 Identities = 193/285 (68%), Gaps = 2/285 (1%) Strand=Plus/Plus Query 42061 CAAACATGCGAAATCGCAGTGCAGACCCTCATCTCTACTAATTAATTCGTTGGAAAACGT 42120 ||| || || || ||||| || ||||| ||||||| | || || ||||| || || || Sbjct 282326 CAAGCAAGCAAAGTCGCAATGGAGACCTTCATCTCGAGAGATCAACTCGTTTGAGAAAGT 282385 Query 42121 GAGTCCGGGCATTAGGCCACGCTTTTTAAGCCAAAATATAGACGCAAATGAT-CCAGAAA 42179 | ||| ||||||| || |||||||| | ||||||||| | |||| | | || || | Sbjct 282386 TAATCCAGGCATTAACCCGCGCTTTTTTAACCAAAATATCG-CGCAGAAACTGCCGGAGA 282444 Query 42180 AGAAGATTCCTTCTACTGCCGCAAAGGCAATAAGTCTCTCTCCATAACCGGCACTGTCAT 42239 | || || |||||||| || || || || | | || || || | | | | | | Sbjct 282445 AAAATATGCCTTCTACGCAAGCGAAAGCGATTAACCGTTCGGCAAAAGCTTCGCGGCCGT 282504 Query 42240 GTATCCACTTTTGAGCCCAATCGGCCTTCTTTTTTACACAAGGCATCGTTTCTATGGCAT 42299 ||||| || |||||||||||| || || || || |||| |||||| | || | Sbjct 282505 CGATCCATTTGAAAGCCCAATCGGCTTTTTTAGCCACGCACGGCACCGTTTCAGTAGCGT 282564 Query 42300 TAAAGAGATAGtttttttCATTACTATCTTTAACATATGTATCGA 42344 ||||| ||||||||| | |||||| | | | || |||| Sbjct 282565 GGAAGAGGCGGTTTTTTTCGGTGGAATCTTTGATAGAAGTTTCGA 282609 >seq4 Length=78750349 Score = 93.3 bits (102), Expect = 6e-14 Identities = 153/221 (69%), Gaps = 0/221 (0%) Strand=Plus/Minus Query 72178 CCTCCCTGATCTATGTATCTAGCGGTGTTATTATAAACTCTCAACATTGGAATAATACCA 72237 ||||| ||||| | || | ||| |||| ||| | || | || |||||| | ||| ||| Sbjct 13233814 CCTCCTTGATCAACATAACGAGCAGTGTCATTGAACACCCGCAGCATTGGGACAATGCCA 13233755 Query 72238 TTGGATGCACCATTGGTCCCGGAGATATAGCTTCCACTGGCACGAATATTGCTAATTGAT 72297 || |||| |||||| || || || || || | | || ||||||||| || ||| Sbjct 13233754 TTAGATGTACCATTTGTTCCACGAATGTAACTACTTGTAGCCCGAATATTGTGAACTGAG 13233695 Query 72298 AGACCTATTCCCCCTGCCATTTTAGAGATTAATGCGCATCGTTTTAACGTATCATAGATG 72357 | ||| ||||| || || ||| ||||| || || || || || ||||| || Sbjct 13233694 ACACCAATTCCTCCAGCTGATTTGCTGATTATAGCACACTCCTTCAAAGTGTCATATATT 13233635 Query 72358 CCCTCTATACTATCATCCATCATGTTAAGTAGAAAACAGCT 72398 ||||| ||||||||||| |||| |||| ||| ||||| Sbjct 13233634 CCCTCGATACTATCATCTTTCATACACAGTAAAAAGCAGCT 13233594 Score = 87.8 bits (96), Expect = 2e-12 Identities = 156/228 (68%), Gaps = 0/228 (0%) Strand=Plus/Minus Query 72417 AGTTCCCGCATTAAATAAGGTAGGAGAAGCGTGCGTAAACCATTTTTCAGACAGTAGATT 72476 |||||| ||||| || | || |||||||| || ||||||||| ||| ||||| | | Sbjct 13233471 AGTTCCAGCATTGAAAAGTGTGGGAGAAGCATGAGTAAACCATCTTTGAGACATCATGTG 13233412 Query 72477 GTACGTCTCAATAGCTGATTCTATATCCCATTGATGTATTCCTACCGCGACACGCATTAA 72536 || || | ||||| || || || || | ||| ||||| || || || | ||| || Sbjct 13233411 ATAAGTTTTTATAGCAGAATCAATGTCATTCTTATGAATTCCAACTGCAACCCTCATCAA 13233352 Query 72537 CATATGCTGAGGTCTTTCAACGATCTTGTTATTTATTTTCAACAAGTAGGATTTTTCCAA 72596 ||| || || || ||||| | | ||| | | ||| || | |||||| | || | Sbjct 13233351 CATGTGTTGGGGCCTTTCTATAACCTTCCCTTGAACTTTTAAGAGGTAGGACCTCTCAAG 13233292 Query 72597 AGTTTTAAAACCAAAATAGTTGTATGAAAAGTCTCGTTCGTAAATAAT 72644 ||||| ||||||||||| | || |||||| || || || || || Sbjct 13233291 GGTTTTGAAACCAAAATAATCATAGTCAAAGTCCCGATCATATATGAT 13233244 Score = 84.2 bits (92), Expect = 3e-11 Identities = 115/158 (73%), Gaps = 2/158 (1%) Strand=Plus/Minus Query 71164 ACTCTACGAGTGTAAATATTACTGGTATACGGTTCCACTGACTCATTATTTCCCAAAATT 71223 ||||||||| | || ||||| ||||| ||||| | ||||||||||||| | ||| Sbjct 13235774 ACTCTACGACTATAGATATTGGAAGTATATGGTTCAAAGCACTCATTATTTCCAAGAATC 13235715 Query 71224 TGAGCAGTTGATGCAGTCGGCATAGGTGCCACCAATAGACTATTTCTAAGACCATG-TGA 71282 || |||||||||||| ||||||||||| | ||| || |||||| | ||||| | | Sbjct 13235714 TGGCTAGTTGATGCAGTTGGCATAGGTGCTAACAAAAGTGAATTTCTCACTCCATGCTTA 13235655 Query 71283 TCGGATTTTATCTTTTAGAGATTCCCAATTCCAAAGAT 71320 | || || ||| | |||| | ||| | ||| |||| Sbjct 13235654 GC-TATGTTGTCTCTAAGAGCATTCCAGTCCCACAGAT 13235618 >seq25 Length=50193149 Score = 91.5 bits (100), Expect = 2e-13 Identities = 143/205 (70%), Gaps = 0/205 (0%) Strand=Plus/Minus Query 72177 TCCTCCCTGATCTATGTATCTAGCGGTGTTATTATAAACTCTCAACATTGGAATAATACC 72236 |||||| ||||| | |||| ||| || | ||| | || | || |||||| | ||| || Sbjct 26656093 TCCTCCTTGATCAACATATCGAGCAGTATCATTGAACACCCGCAGCATTGGGACAATTCC 26656034 Query 72237 ATTGGATGCACCATTGGTCCCGGAGATATAGCTTCCACTGGCACGAATATTGCTAATTGA 72296 ||| |||| |||||| || || ||||| || || |||| ||||||||| || || Sbjct 26656033 ATTAGATGTACCATTTGTTCCACGAATATAACTACCTGTGGCTCGAATATTGTGAACAGA 26655974 Query 72297 TAGACCTATTCCCCCTGCCATTTTAGAGATTAATGCGCATCGTTTTAACGTATCATAGAT 72356 | ||| ||||| || || ||| ||| | || || || || || ||||| || Sbjct 26655973 AACACCAATTCCTCCAGCTGATTTGCTGATAACAGCACACTCCTTCAAAGTTTCATAAAT 26655914 Query 72357 GCCCTCTATACTATCATCCATCATG 72381 || || ||||||||||| ||||| Sbjct 26655913 TCCTTCAATACTATCATCTTTCATG 26655889 Score = 84.2 bits (92), Expect = 3e-11 Identities = 90/119 (76%), Gaps = 0/119 (0%) Strand=Plus/Minus Query 71160 CAATACTCTACGAGTGTAAATATTACTGGTATACGGTTCCACTGACTCATTATTTCCCAA 71219 ||| ||||||||| | |||||||| |||||| || || | | |||||||| || | Sbjct 26658072 CAAAACTCTACGACTATAAATATTGGAGGTATATGGCTCAAAGCATTCATTATTCCCAAG 26658013 Query 71220 AATTTGAGCAGTTGATGCAGTCGGCATAGGTGCCACCAATAGACTATTTCTAAGACCAT 71278 ||| ||| |||||| ||||| ||||||||||| | |||||| |||||| | |||| Sbjct 26658012 AATCTGACTAGTTGAAGCAGTTGGCATAGGTGCTAACAATAGTGAATTTCTCACTCCAT 26657954 >seq2 Length=106994729 Score = 91.5 bits (100), Expect = 2e-13 Identities = 143/205 (70%), Gaps = 0/205 (0%) Strand=Plus/Minus Query 72177 TCCTCCCTGATCTATGTATCTAGCGGTGTTATTATAAACTCTCAACATTGGAATAATACC 72236 |||||| ||||| | |||| ||| || | ||| | || | || |||||| | ||| || Sbjct 29496030 TCCTCCTTGATCAACATATCGAGCAGTATCATTGAACACCCGCAGCATTGGGACAATTCC 29495971 Query 72237 ATTGGATGCACCATTGGTCCCGGAGATATAGCTTCCACTGGCACGAATATTGCTAATTGA 72296 ||| |||| |||||| || || ||||| || || |||| ||||||||| || || Sbjct 29495970 ATTAGATGTACCATTTGTTCCACGAATATAACTACCTGTGGCTCGAATATTGTGAACAGA 29495911 Query 72297 TAGACCTATTCCCCCTGCCATTTTAGAGATTAATGCGCATCGTTTTAACGTATCATAGAT 72356 | ||| ||||| || || ||| ||| | || || || || || ||||| || Sbjct 29495910 AACACCAATTCCTCCAGCTGATTTGCTGATAACAGCACACTCCTTCAAAGTTTCATATAT 29495851 Query 72357 GCCCTCTATACTATCATCCATCATG 72381 || || ||||||||||| ||||| Sbjct 29495850 TCCTTCAATACTATCATCTTTCATG 29495826 >seq7 Length=42802127 Score = 87.8 bits (96), Expect = 2e-12 Identities = 156/228 (68%), Gaps = 0/228 (0%) Strand=Plus/Minus Query 72417 AGTTCCCGCATTAAATAAGGTAGGAGAAGCGTGCGTAAACCATTTTTCAGACAGTAGATT 72476 |||||| ||||| || | || |||||||| || ||||||||| ||| ||||| | | Sbjct 28741192 AGTTCCAGCATTGAAAAGTGTGGGAGAAGCATGAGTAAACCATCTTTGAGACATCATGTG 28741133 Query 72477 GTACGTCTCAATAGCTGATTCTATATCCCATTGATGTATTCCTACCGCGACACGCATTAA 72536 || || | ||||| || || || || | ||| ||||| || || || | ||| || Sbjct 28741132 ATAAGTTTTTATAGCAGAATCAATGTCATTCTTATGAATTCCAACTGCAACCCTCATCAA 28741073 Query 72537 CATATGCTGAGGTCTTTCAACGATCTTGTTATTTATTTTCAACAAGTAGGATTTTTCCAA 72596 ||| || || || ||||| | | ||| | | ||| || | |||||| | || | Sbjct 28741072 CATGTGTTGGGGCCTTTCTATAACCTTCCCTTGAACTTTTAAGAGGTAGGACCTCTCAAG 28741013 Query 72597 AGTTTTAAAACCAAAATAGTTGTATGAAAAGTCTCGTTCGTAAATAAT 72644 ||||| ||||||||||| | || |||||| || || || || || Sbjct 28741012 GGTTTTGAAACCAAAATAATCATAGTCAAAGTCCCGATCATATATGAT 28740965 Score = 84.2 bits (92), Expect = 3e-11 Identities = 88/116 (76%), Gaps = 0/116 (0%) Strand=Plus/Minus Query 71164 ACTCTACGAGTGTAAATATTACTGGTATACGGTTCCACTGACTCATTATTTCCCAAAATT 71223 ||||||||| | || ||||| ||||| ||||| | ||||||||||||| | ||| Sbjct 28743500 ACTCTACGACTATAGATATTGGATGTATATGGTTCAAAGCACTCATTATTTCCAAGAATC 28743441 Query 71224 TGAGCAGTTGATGCAGTCGGCATAGGTGCCACCAATAGACTATTTCTAAGACCATG 71279 || |||||||||||| ||||||||||| | ||| || |||||| | ||||| Sbjct 28743440 TGGCTAGTTGATGCAGTTGGCATAGGTGCTAACAAAAGTGAATTTCTCACTCCATG 28743385 Lambda K H 0.634 0.408 0.912 Gapped Lambda K H 0.625 0.410 0.780 Effective search space used: 671062455232480