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_026440.1 Length=2243109 Score E Sequences producing significant alignments: (Bits) Value seq22 293 3e-73 seq19 223 5e-52 seq228 199 6e-45 seq16 172 8e-37 >seq22 Length=61129363 Score = 293 bits (324), Expect = 3e-73 Identities = 410/562 (73%), Gaps = 16/562 (3%) Strand=Plus/Minus Query 1455716 GAGCCGCTGCTGCGCGATAACCCGAACCGCTT-TGTCCTGTTCCCCATCCGCTACC-AGC 1455773 ||||| |||||| || ||||| |||| || ||| |||| || |||| |||| || Sbjct 6288189 GAGCCACTGCTGGCCGCGAACCCAGACCGATTCTGTA-TGTTTCCGATCCAATACCCAGA 6288131 Query 1455774 GGATATGGGAAATGTACCAAAAAGGCCGAGGCCTCCTTTTGGACCGCCGAGGAGGTCGAC 1455833 | |||||||||||||| | |||| |||| || || ||||||||||| ||||| ||||| Sbjct 6288130 AG-TATGGGAAATGTACAAGAAAG-CCGAAGCGTCGTTTTGGACCGCAGAGGAAGTCGAT 6288073 Query 1455834 CTCGGCGCCGA-CACGGTCCACTGGGTGTCGCTGAGCGACGACGAGCGCCATTTCATCAA 1455892 || | || | ||| |||||| | || | || ||| |||| || ||||| | Sbjct 6288072 CTGTCTTCAGATCTTCGTC-ACTGGGAAACTCTCACCGCCGATGAGCATCACTTCATTAG 6288014 Query 1455893 GCACGTCCTCGCCTTTTTTCGCCGCCAGCGATGGCATCGTGGCCGAGAACCTGGCCGGCC 1455952 ||||| ||||||||||| ||||||| ||||||||| || |||||||| || | | Sbjct 6288013 TCACGTTCTCGCCTTTTT-CGCCGCCTCCGATGGCATAGTCCTTGAGAACCTTGCTGTTC 6287955 Query 1455953 GCTTTATGAAAGAGGTCCAATTGCCAGAGGCACGTTTGTTTTACGGGTTCCAGATCGCCA 1456012 | || |||||||||||||| | | ||||| ||| ||||| || ||||| ||||| | Sbjct 6287954 GGTTCATGAAAGAGGTCCAGATCTCCGAGGCGCGTGCTTTTTATGGTTTCCAAATCGCTA 6287895 Query 1456013 TCGAAAACATCCACTCTGAAACCTACTCGCTCCTGATCGACACCTACGTCAAGGACCCGG 1456072 ||||||| |||||||| || | ||| ||||| |||| || ||| | || || | | Sbjct 6287894 TCGAAAATATCCACTCCGAGATGTACAGTCTCCTTCTCGAGACTTACATAAAAGATTCCG 6287835 Query 1456073 TCGAGAAGGACCACCTCTTTCGCGCCATCGACACGGTGCCGTCGGTGAGGAAAAAGGCCG 1456132 || ||| ||| || || ||||||||||| |||||||||| ||| ||||| |||| Sbjct 6287834 ATGAAAAGAACCGTCTTTTCCGCGCCATCGAGACGGTGCCGTGTGTGGCTAAAAAAGCCG 6287775 Query 1456133 ACTGGGCGATGAAGTGGATCAACAAGGAGGGCCTCGACACTTT-GCCGAGCGGCTCGTCG 1456191 | ||||| ||||| |||||| || ||| || ||||| ||||| ||| | ||| Sbjct 6287774 AGTGGGCTATGAAATGGATC------GACGGCGGAGAAACTTTCGCCGAACGGTTAATCG 6287721 Query 1456192 GCTTTGC-CGCGTCGAGGGCATCTTTTTCTCGGGCAGTTTCTGCGCCATCTTTTGGCTCA 1456250 ||||| |||| || || ||||||||||| || |||||||| ||||| |||||| | | Sbjct 6287720 CTTTTGCTTGCGTAGAAGGGATCTTTTTCTCCGGAAGTTTCTGTGCCATATTTTGGTTAA 6287661 Query 1456251 AGAAGCGCGGCCTCATGCCCGG 1456272 | ||| | || | |||||||| Sbjct 6287660 AAAAGAGGGGGTTAATGCCCGG 6287639 >seq19 Length=70911690 Score = 223 bits (246), Expect = 5e-52 Identities = 295/406 (73%), Gaps = 9/406 (2%) Strand=Plus/Plus Query 1455869 CGACGACGAGCGCCATTTCATCAAGCACGTCCTCGCCTTTTTTCGCCGCCAGCGATGGCA 1455928 || |||||| ||||| ||||||| || ||||| ||||| || |||||| |||||||| Sbjct 44463419 CGCCGACGAACGCCACTTCATCAGTCATGTCCTTGCCTTCTT-CGCCGCATCCGATGGCA 44463477 Query 1455929 TCGTGGCCGAGAACCTGGCCGGCCGCTTTATGAAAGAGGTCCAATTGCCAGAGGCACGTT 1455988 |||| || || || || | ||||| ||||||||||||||| | | ||||| ||| Sbjct 44463478 TCGTTCTAGAAAATCTCGCTGTTCGCTTCATGAAAGAGGTCCAAATCGCGGAGGCGCGTG 44463537 Query 1455989 TGTTTTACGGGTTCCAGATCGCCATCGAAAACATCCACTCTGAAACCTACTCGCTCCTGA 1456048 ||||| || ||||| ||||||||||| || ||||||||||| | || ||||| Sbjct 44463538 CATTTTATGGATTCCAAATCGCCATCGAGAATATCCACTCTGAGATGTATAGTCTCCTCC 44463597 Query 1456049 TCGACACCTACGTCAAGGACCCGGTCGAGAAGGACCACCTCTTTCGCGCCATCGACACGG 1456108 |||| || || | || || | ||| || ||| |||||| | ||| | || |||| Sbjct 44463598 TCGAAACTTATATTAAAGATTCCACCGAAAAAAACCGCCTCTTCCACGCTACTGAAACGG 44463657 Query 1456109 TGCCGTCGGTGAGGAAAAAGGCCGACTGGGCGATGAAGTGGATCAACAAGGAGGGCCTCG 1456168 |||||| ||| ||||| ||||| ||||| |||| |||||| || ||| || Sbjct 44463658 TGCCGTGCGTGGCTAAAAAAGCCGATTGGGCTTTGAAATGGATC------GACGGCGGCG 44463711 Query 1456169 ACAC-TTTGCCGAGCGGCTCGTCGGCTTTGC-CGCGTCGAGGGCATCTTTTTCTCGGGCA 1456226 | | |||||||| ||| | ||| || || |||| || ||||| |||||||| |||| Sbjct 44463712 AAGCTTTTGCCGAACGGTTAATCGCTTTCGCTTGCGTAGAAGGCATATTTTTCTCCGGCA 44463771 Query 1456227 GTTTCTGCGCCATCTTTTGGCTCAAGAAGCGCGGCCTCATGCCCGG 1456272 ||||||| || || |||||| | || |||||||| | ||||| || Sbjct 44463772 GTTTCTGTGCGATATTTTGGTTAAAAAAGCGCGGGTTAATGCCTGG 44463817 Score = 93.3 bits (102), Expect = 6e-13 Identities = 94/121 (78%), Gaps = 1/121 (1%) Strand=Plus/Plus Query 1455716 GAGCCGCTGCTGCGCGATAACCCGAACCGCTTTGTCCTGTTCCCCATCCGCTACCAGCGG 1455775 |||||| |||| | |||||| ||||||| | ||||||| |||| |||| | | Sbjct 44463227 GAGCCGTTGCTAGCCTCCAACCCGGACCGCTTCTGCATGTTCCCAATCCAATACCCACAG 44463286 Query 1455776 ATATGGGAAATGTACCAAAAAGGCCGAGGCCTCCTTTTGGACCGCCGAGGAGGTCGACCT 1455835 |||||||||||||| ||| || ||||| ||||| |||||||| |||||||| || || || Sbjct 44463287 ATATGGGAAATGTA-CAAGAAAGCCGAAGCCTCTTTTTGGACTGCCGAGGAAGTTGATCT 44463345 Query 1455836 C 1455836 | Sbjct 44463346 C 44463346 >seq228 Length=356584 Score = 199 bits (220), Expect = 6e-45 Identities = 234/314 (75%), Gaps = 2/314 (1%) Strand=Plus/Minus Query 1455716 GAGCCGCTGCTGCGCGATAACCCGAACCGCTTTGTCCTGTTCCCCATCCGCTACCAGCGG 1455775 |||||| |||| | |||||| ||||||| | ||||||| |||| |||| | | Sbjct 283654 GAGCCGTTGCTAGCCTCCAACCCGGACCGCTTCTGCATGTTCCCAATCCAATACCCACAG 283595 Query 1455776 ATATGGGAAATGTACCAAAAAGGCCGAGGCCTCCTTTTGGACCGCCGAGGAGGTCGACCT 1455835 ||||||||||||||| | |||| |||| ||||| |||||||| |||||||| || || || Sbjct 283594 ATATGGGAAATGTACAAGAAAG-CCGAAGCCTCTTTTTGGACTGCCGAGGAAGTTGATCT 283536 Query 1455836 CGGCGCCGACACGGTCCACTGGGTGTCGCTGAGCGACGACGAGCGCCATTTCATCAAGCA 1455895 || |||| |||||| || | || |||||| ||||| ||||||| || Sbjct 283535 CGATTCCGATCTTCCACACTGGCAAAATCTTACCGCCGACGAACGCCACTTCATCAGTCA 283476 Query 1455896 CGTCCTCGCCTTTTTTCGCCGCCAGCGATGGCATCGTGGCCGAGAACCTGGCCGGCCGCT 1455955 || || ||||| || |||||| |||||||||||| ||| || || |||| | || Sbjct 283475 TGTTCTTGCCTTCTT-CGCCGCATCCGATGGCATCGTCCTCGAAAATCTCGCCGTTCTCT 283417 Query 1455956 TTATGAAAGAGGTCCAATTGCCAGAGGCACGTTTGTTTTACGGGTTCCAGATCGCCATCG 1456015 | ||||||||||||||| | ||||||| ||| ||||| || ||||| |||||||||| Sbjct 283416 TCATGAAAGAGGTCCAAATCGCAGAGGCGCGTGCATTTTATGGATTCCAAATCGCCATCG 283357 Query 1456016 AAAACATCCACTCT 1456029 | || ||||||||| Sbjct 283356 AGAATATCCACTCT 283343 Score = 113 bits (124), Expect = 6e-19 Identities = 147/201 (73%), Gaps = 8/201 (4%) Strand=Plus/Minus Query 1456074 CGAGAAGGACCACCTCTTTCGCGCCATCGACACGGTGCCGTCGGTGAGGAAAAAGGCCGA 1456133 ||| || ||| |||||| | ||| | || |||||||||| ||| ||||| ||||| Sbjct 282584 CGAAAAAAACCGCCTCTTCCACGCTACTGAAACGGTGCCGTGCGTGGCTAAAAAAGCCGA 282525 Query 1456134 CTGGGCGATGAAGTGGATCAACAAGGAGGGCCTCGACACTTT-GCCGAGCGGCTCGTCGG 1456192 ||||| | || |||||| || |||| ||| |||| ||||| ||| | ||| Sbjct 282524 TTGGGCTTTCAAATGGATCGAC------GGCCGCGAAGCTTTTGCCGAACGGTTAATCGC 282471 Query 1456193 CTTTGCC-GCGTCGAGGGCATCTTTTTCTCGGGCAGTTTCTGCGCCATCTTTTGGCTCAA 1456251 || || |||| || ||||| |||||||| |||||||||||||| || |||||| | || Sbjct 282470 TTTCGCTTGCGTAGAAGGCATATTTTTCTCCGGCAGTTTCTGCGCGATATTTTGGTTAAA 282411 Query 1456252 GAAGCGCGGCCTCATGCCCGG 1456272 |||||||| | ||||| || Sbjct 282410 AAAGCGCGGGTTAATGCCTGG 282390 Score = 105 bits (116), Expect = 1e-16 Identities = 97/123 (79%), Gaps = 0/123 (0%) Strand=Plus/Minus Query 1455907 TTTTTCGCCGCCAGCGATGGCATCGTGGCCGAGAACCTGGCCGGCCGCTTTATGAAAGAG 1455966 || |||||||| |||||||||||| ||| || || |||| | ||| ||||||||| Sbjct 283190 TTCTTCGCCGCATCCGATGGCATCGTCCTCGAAAATCTCGCCGTTCTCTTCATGAAAGAG 283131 Query 1455967 GTCCAATTGCCAGAGGCACGTTTGTTTTACGGGTTCCAGATCGCCATCGAAAACATCCAC 1456026 |||||| | ||||||| ||| ||||| || ||||| ||||||||||| || |||||| Sbjct 283130 GTCCAAATCGCAGAGGCGCGTGCATTTTATGGATTCCAAATCGCCATCGAGAATATCCAC 283071 Query 1456027 TCT 1456029 ||| Sbjct 283070 TCT 283068 >seq16 Length=102030775 Score = 172 bits (190), Expect = 8e-37 Identities = 210/284 (74%), Gaps = 8/284 (3%) Strand=Plus/Plus Query 1455991 TTTTACGGGTTCCAGATCGCCATCGAAAACATCCACTCTGAAACCTACTCGCTCCTGATC 1456050 ||||| || ||||| ||||| |||||||| |||||||| || | ||| ||||| || Sbjct 57862038 TTTTATGGTTTCCAAATCGCTATCGAAAATATCCACTCCGAGATGTACAGTCTCCTTCTC 57862097 Query 1456051 GACACCTACGTCAAGGACCCGGTCGAGAAGGACCACCTCTTTCGCGCCATCGACACGGTG 1456110 || || ||| | || || | | || ||| ||| || || ||||||||||| |||||| Sbjct 57862098 GAGACTTACATAAAAGATTCCGATGAAAAGAACCGTCTTTTCCGCGCCATCGAGACGGTG 57862157 Query 1456111 CCGTCGGTGAGGAAAAAGGCCGACTGGGCGATGAAGTGGATCAACAAGGAGGGCCTCGAC 1456170 |||| ||| ||||| ||||| ||||| ||||| |||||| || ||| || Sbjct 57862158 CCGTGTGTGGCTAAAAAAGCCGAGTGGGCTATGAAATGGATC------GACGGCGGAGAA 57862211 Query 1456171 ACTTT-GCCGAGCGGCTCGTCGGCTTTGC-CGCGTCGAGGGCATCTTTTTCTCGGGCAGT 1456228 ||||| ||||| ||| | ||| ||||| |||| ||||| ||||||||||| || ||| Sbjct 57862212 ACTTTCGCCGAACGGTTAATCGCTTTTGCTTGCGTAGAGGGGATCTTTTTCTCCGGAAGT 57862271 Query 1456229 TTCTGCGCCATCTTTTGGCTCAAGAAGCGCGGCCTCATGCCCGG 1456272 ||||| ||||| |||||| | || ||| | || | |||||||| Sbjct 57862272 TTCTGTGCCATATTTTGGTTAAAAAAGAGGGGGTTAATGCCCGG 57862315 Lambda K H 0.634 0.408 0.912 Gapped Lambda K H 0.625 0.410 0.780 Effective search space used: 7176928858585976