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_003083.1 Length=118584 Score E Sequences producing significant alignments: (Bits) Value seq14 118 8e-22 seq23 107 1e-18 seq25 104 2e-17 seq13 104 2e-17 seq48 89.7 4e-13 seq19 89.7 4e-13 seq24 87.8 1e-12 seq1 86.0 5e-12 >seq14 Length=44799946 Score = 118 bits (130), Expect = 8e-22 Identities = 168/236 (71%), Gaps = 18/236 (8%) Strand=Plus/Plus Query 18099 CCTCCCCGTAGTCTAAGTACCATGTGAAGTGTTGATTCTTTTTGAATGTTGTAGTCGGCC 18158 || || || || | ||| || | ||||||||| || ||||| |||||||| || || ||| Sbjct 8847904 CCACCACGGAGACGAAGAACAAGGTGAAGTGTAGACTCTTTCTGAATGTTATAATCAGCC 8847963 Query 18159 ATTGTTTTACAATCTTCCAATTGTTTGCCCGCATAGATAAGTCTTTGTTGATCCACGGGC 18218 | || | | |||||||||||||||||| ||| |||| || ||||| ||||| || Sbjct 8847964 AAAGTCCTCCCATCTTCCAATTGTTTGCCGGCAAAGATGAGCCTTTGCTGATCAGGTGGG 8848023 Query 18219 ACGCCTTCCTTATCGGCAATTTGTTGCTTGACCTGTGCAACAGTGTCACCGGGCTCGG-- 18276 | ||||||||||| ||| | |||| | |||| ||||| || |||| Sbjct 8848024 ATTCCTTCCTTATCCTGAATCT-TTGCCT--------TAACATTGTCAATGGTATCGGAG 8848074 Query 18277 -TTTCA------ATGGTGATGCTTTTGCCGGTCAATGTTTTTACAAAAATTTGCAT 18325 ||||| | |||||| ||||||||||||| || || |||||||| ||||| Sbjct 8848075 CTTTCAACCTCCAAGGTGATTGTTTTGCCGGTCAAAGTCTTGACAAAAATCTGCAT 8848130 Score = 95.1 bits (104), Expect = 9e-15 Identities = 157/227 (69%), Gaps = 0/227 (0%) Strand=Plus/Plus Query 18099 CCTCCCCGTAGTCTAAGTACCATGTGAAGTGTTGATTCTTTTTGAATGTTGTAGTCGGCC 18158 ||||| || || || | || | |||||| || ||||| ||||| || || || || ||| Sbjct 8848132 CCTCCACGAAGCCTCAAAACAAGGTGAAGGGTGGATTCCTTTTGGATATTATAATCAGCC 8848191 Query 18159 ATTGTTTTACAATCTTCCAATTGTTTGCCCGCATAGATAAGTCTTTGTTGATCCACGGGC 18218 | || | | |||||||||||||||||| || |||| | | ||||| || || Sbjct 8848192 AAGGTCCTCCCATCTTCCAATTGTTTGCCAGCGAAGATCAAACGCTGTTGGTCAGGTGGG 8848251 Query 18219 ACGCCTTCCTTATCGGCAATTTGTTGCTTGACCTGTGCAACAGTGTCACCGGGCTCGGTT 18278 | ||||||||| || ||| | ||| || | | | ||||| |||| | Sbjct 8848252 ATGCCTTCCTTGTCTTGAATCTTGGCCTTAACGTTGTCGATGGTGTCGGAACTCTCGACT 8848311 Query 18279 TCAATGGTGATGCTTTTGCCGGTCAATGTTTTTACAAAAATTTGCAT 18325 || | ||||||| | |||||||| || ||||| ||||| |||||||| Sbjct 8848312 TCGAGGGTGATGGTCTTGCCGGTTAAGGTTTTGACAAAGATTTGCAT 8848358 >seq23 Length=61753794 Score = 107 bits (118), Expect = 1e-18 Identities = 160/227 (70%), Gaps = 0/227 (0%) Strand=Plus/Plus Query 18099 CCTCCCCGTAGTCTAAGTACCATGTGAAGTGTTGATTCTTTTTGAATGTTGTAGTCGGCC 18158 || || || |||| ||| |||| |||||| || |||||||| ||||||||||||||||| Sbjct 39554441 CCGCCACGAAGTCGAAGAACCAAGTGAAGGGTGGATTCTTTCTGAATGTTGTAGTCGGCT 39554500 Query 18159 ATTGTTTTACAATCTTCCAATTGTTTGCCCGCATAGATAAGTCTTTGTTGATCCACGGGC 18218 | || | ||| || | ||||||||| ||| ||||||| || || |||||| || Sbjct 39554501 AGCGTGCGGCCATCCTCAAGTTGTTTGCCAGCAAAGATAAGCCTCTGCTGATCCGGTGGG 39554560 Query 18219 ACGCCTTCCTTATCGGCAATTTGTTGCTTGACCTGTGCAACAGTGTCACCGGGCTCGGTT 18278 | ||||||||||| || | ||| || | ||| ||||| ||| Sbjct 39554561 ATCCCTTCCTTATCTTGGATCTTAGCCTTCACATTATCAATGGTGTCTGAACTCTCCACC 39554620 Query 18279 TCAATGGTGATGCTTTTGCCGGTCAATGTTTTTACAAAAATTTGCAT 18325 || | ||||||| | ||||| || | ||||| ||||| |||||||| Sbjct 39554621 TCGAGGGTGATGGTCTTGCCAGTGAGGGTTTTAACAAAGATTTGCAT 39554667 Score = 89.7 bits (98), Expect = 4e-13 Identities = 156/227 (69%), Gaps = 0/227 (0%) Strand=Plus/Minus Query 18099 CCTCCCCGTAGTCTAAGTACCATGTGAAGTGTTGATTCTTTTTGAATGTTGTAGTCGGCC 18158 || |||| || | ||| || | ||| || || || |||||||||||||||||||| || Sbjct 11030358 CCACCCCTGAGACGAAGCACAAGGTGGAGGGTAGACTCTTTTTGAATGTTGTAGTCAGCA 11030299 Query 18159 ATTGTTTTACAATCTTCCAATTGTTTGCCCGCATAGATAAGTCTTTGTTGATCCACGGGC 18218 | || || |||||||| ||| || || ||| ||||||| || |||||||| || Sbjct 11030298 AGGGTGCGACCATCTTCCAGTTGCTTACCGGCAAAGATAAGCCTCTGTTGATCAGGAGGG 11030239 Query 18219 ACGCCTTCCTTATCGGCAATTTGTTGCTTGACCTGTGCAACAGTGTCACCGGGCTCGGTT 18278 | ||||||||||| || | |||||| | ||| ||||| | || Sbjct 11030238 ATCCCTTCCTTATCCTGGATCTTAGCCTTGACATTATCAATTGTGTCGGAGCTTTCAACC 11030179 Query 18279 TCAATGGTGATGCTTTTGCCGGTCAATGTTTTTACAAAAATTTGCAT 18325 |||| |||||| | ||||| || | ||||| || || || ||||| Sbjct 11030178 TCAAGGGTGATTGTCTTGCCAGTGAGGGTTTTCACGAAGATCTGCAT 11030132 Score = 84.2 bits (92), Expect = 2e-11 Identities = 148/214 (69%), Gaps = 4/214 (2%) Strand=Plus/Minus Query 18114 AGTACCATGTGAAGTGTTGATTCTTTTTGAATGTTGTAGTCGGCCATTGTTTTACAATCT 18173 || || | ||| || || |||||||| || ||||||||||| |||| || | | |||| Sbjct 10997532 AGGACAAGGTGCAGAGTCGATTCTTTCTGGATGTTGTAGTCTGCCAAGGTCCTTCCATCT 10997473 Query 18174 TCCAATTGTTTGCCCGCATAGATAAGTCTTTGTTGATCCACGGGCACGCCTTCCTTATCG 18233 || | ||| || || ||| |||| | || || || || | ||| | ||||||||||| Sbjct 10997472 TCAAGTTGCTTCCCTGCAAAGATCAACCTCTGCTGGTCTAGGGGGATTCCTTCCTTATCT 10997413 Query 18234 GCAATTTGTTGCTTGACCTGTGCAACAGTGTCACCGGGC--TCGGTTTCAATGGTGATGC 18291 || | ||| || | ||| | ||| ||| || || ||| | ||||| Sbjct 10997412 TGGATCTTGGCCTTCACATTATCAATAATGT--CCGAGCTTTCAACTTCCAAAGTGATAG 10997355 Query 18292 TTTTGCCGGTCAATGTTTTTACAAAAATTTGCAT 18325 | || || |||||||| || |||||||||||||| Sbjct 10997354 TCTTTCCTGTCAATGTCTTCACAAAAATTTGCAT 10997321 >seq25 Length=50193149 Score = 104 bits (114), Expect = 2e-17 Identities = 159/227 (70%), Gaps = 0/227 (0%) Strand=Plus/Minus Query 18099 CCTCCCCGTAGTCTAAGTACCATGTGAAGTGTTGATTCTTTTTGAATGTTGTAGTCGGCC 18158 || || || |||| ||| |||| |||||| || |||||||| ||||||||||||||||| Sbjct 28160033 CCGCCACGAAGTCGAAGAACCAAGTGAAGGGTGGATTCTTTCTGAATGTTGTAGTCGGCT 28159974 Query 18159 ATTGTTTTACAATCTTCCAATTGTTTGCCCGCATAGATAAGTCTTTGTTGATCCACGGGC 18218 | || | ||| || | ||||||||| ||| | ||||| || || |||||| || Sbjct 28159973 AGCGTGCGGCCATCCTCAAGTTGTTTGCCAGCAAATATAAGCCTCTGCTGATCCGGTGGG 28159914 Query 18219 ACGCCTTCCTTATCGGCAATTTGTTGCTTGACCTGTGCAACAGTGTCACCGGGCTCGGTT 18278 | ||||||||||| || | ||| || | ||| ||||| ||| Sbjct 28159913 ATCCCTTCCTTATCTTGGATCTTAGCCTTCACATTATCAATGGTGTCTGAACTCTCCACC 28159854 Query 18279 TCAATGGTGATGCTTTTGCCGGTCAATGTTTTTACAAAAATTTGCAT 18325 || | ||||||| | ||||| || | ||||| ||||| |||||||| Sbjct 28159853 TCGAGGGTGATGGTCTTGCCAGTGAGGGTTTTAACAAAGATTTGCAT 28159807 >seq13 Length=56485995 Score = 104 bits (114), Expect = 2e-17 Identities = 165/236 (70%), Gaps = 18/236 (8%) Strand=Plus/Minus Query 18099 CCTCCCCGTAGTCTAAGTACCATGTGAAGTGTTGATTCTTTTTGAATGTTGTAGTCGGCC 18158 || || || || | ||| || | |||||| || || ||||| |||||||| || || ||| Sbjct 54271230 CCACCACGGAGACGAAGAACAAGGTGAAGGGTAGACTCTTTCTGAATGTTATAATCAGCC 54271171 Query 18159 ATTGTTTTACAATCTTCCAATTGTTTGCCCGCATAGATAAGTCTTTGTTGATCCACGGGC 18218 | || | | |||||||||||||||||| ||| |||| || |||| ||||| || Sbjct 54271170 AAAGTCCTCCCATCTTCCAATTGTTTGCCGGCAGAGATGAGCATTTGCTGATCAGGTGGG 54271111 Query 18219 ACGCCTTCCTTATCGGCAATTTGTTGCTTGACCTGTGCAACAGTGTCACCGGGCTCGG-- 18276 | ||||||||||| ||| | |||| | |||| ||||| || |||| Sbjct 54271110 ATTCCTTCCTTATCCTGAATCT-TTGCCT--------TAACATTGTCAATGGTATCGGAG 54271060 Query 18277 -TTTCA------ATGGTGATGCTTTTGCCGGTCAATGTTTTTACAAAAATTTGCAT 18325 ||||| | |||||| ||||||| ||||| || || |||||||| ||||| Sbjct 54271059 CTTTCAACCTCCAAGGTGATTGTTTTGCCTGTCAAAGTCTTGACAAAAATCTGCAT 54271004 Score = 89.7 bits (98), Expect = 4e-13 Identities = 156/227 (69%), Gaps = 0/227 (0%) Strand=Plus/Minus Query 18099 CCTCCCCGTAGTCTAAGTACCATGTGAAGTGTTGATTCTTTTTGAATGTTGTAGTCGGCC 18158 ||||| || || || | || | |||||| || ||||| ||||| || || || || ||| Sbjct 54271002 CCTCCACGAAGCCTCAAAACAAGGTGAAGGGTGGATTCCTTTTGGATATTATAATCAGCC 54270943 Query 18159 ATTGTTTTACAATCTTCCAATTGTTTGCCCGCATAGATAAGTCTTTGTTGATCCACGGGC 18218 | || | | |||||||||||||||||| || |||| | | ||||| || || Sbjct 54270942 AAGGTCCTCCCATCTTCCAATTGTTTGCCAGCGAAGATCAAACGCTGTTGGTCAGGTGGG 54270883 Query 18219 ACGCCTTCCTTATCGGCAATTTGTTGCTTGACCTGTGCAACAGTGTCACCGGGCTCGGTT 18278 | |||||||| || ||| | ||| || | | | ||||| |||| | Sbjct 54270882 ATTCCTTCCTTGTCTTGAATCTTGGCCTTAACGTTGTCGATGGTGTCGGAACTCTCGACT 54270823 Query 18279 TCAATGGTGATGCTTTTGCCGGTCAATGTTTTTACAAAAATTTGCAT 18325 || | ||||||| | |||||||| || ||||| ||||| |||||||| Sbjct 54270822 TCGAGGGTGATGGTCTTGCCGGTTAAGGTTTTGACAAAGATTTGCAT 54270776 >seq48 Length=1435396 Score = 89.7 bits (98), Expect = 4e-13 Identities = 156/227 (69%), Gaps = 0/227 (0%) Strand=Plus/Minus Query 18099 CCTCCCCGTAGTCTAAGTACCATGTGAAGTGTTGATTCTTTTTGAATGTTGTAGTCGGCC 18158 || |||| || | ||| || | ||| || || || |||||||||||||||||||| || Sbjct 1250065 CCACCCCTGAGACGAAGCACAAGGTGGAGGGTAGACTCTTTTTGAATGTTGTAGTCAGCA 1250006 Query 18159 ATTGTTTTACAATCTTCCAATTGTTTGCCCGCATAGATAAGTCTTTGTTGATCCACGGGC 18218 | || || |||||||| ||| || || ||| ||||||| || ||||| || || Sbjct 1250005 AGGGTGCGACCATCTTCCAGTTGCTTACCGGCAAAGATAAGCCTCTGTTGGTCAGGAGGG 1249946 Query 18219 ACGCCTTCCTTATCGGCAATTTGTTGCTTGACCTGTGCAACAGTGTCACCGGGCTCGGTT 18278 | ||||| ||||| || | |||||| | ||| |||||| | || Sbjct 1249945 ATCCCTTCTTTATCCTGGATCTTAGCCTTGACATTATCAATTGTGTCAGAGCTTTCAACC 1249886 Query 18279 TCAATGGTGATGCTTTTGCCGGTCAATGTTTTTACAAAAATTTGCAT 18325 |||| |||||| | ||||| || | |||||||| || || ||||| Sbjct 1249885 TCAAGGGTGATTGTCTTGCCAGTAAGGGTTTTTACGAAGATCTGCAT 1249839 Score = 84.2 bits (92), Expect = 2e-11 Identities = 148/214 (69%), Gaps = 4/214 (2%) Strand=Plus/Minus Query 18114 AGTACCATGTGAAGTGTTGATTCTTTTTGAATGTTGTAGTCGGCCATTGTTTTACAATCT 18173 || || | ||| || || ||||| || || ||||||||||| |||| || | | |||| Sbjct 1230195 AGGACAAGGTGCAGAGTCGATTCCTTCTGGATGTTGTAGTCTGCCAAGGTCCTTCCATCT 1230136 Query 18174 TCCAATTGTTTGCCCGCATAGATAAGTCTTTGTTGATCCACGGGCACGCCTTCCTTATCG 18233 || | ||| || || || |||| | || || || || ||| | ||||||||||| Sbjct 1230135 TCAAGTTGCTTCCCTGCGAAGATCAACCTCTGCTGGTCTGGGGGGATTCCTTCCTTATCT 1230076 Query 18234 GCAATTTGTTGCTTGACCTGTGCAACAGTGTCACCGGGC--TCGGTTTCAATGGTGATGC 18291 || | |||||| | ||| ||||| ||| || || ||| | |||||| Sbjct 1230075 TGGATCTTGGCCTTGACATTATCAATAGTGT--CCGAGCTTTCAACTTCCAAAGTGATGG 1230018 Query 18292 TTTTGCCGGTCAATGTTTTTACAAAAATTTGCAT 18325 | || || |||||||| || |||||||||||||| Sbjct 1230017 TCTTTCCTGTCAATGTCTTCACAAAAATTTGCAT 1229984 >seq19 Length=70911690 Score = 89.7 bits (98), Expect = 4e-13 Identities = 156/227 (69%), Gaps = 0/227 (0%) Strand=Plus/Plus Query 18099 CCTCCCCGTAGTCTAAGTACCATGTGAAGTGTTGATTCTTTTTGAATGTTGTAGTCGGCC 18158 || |||| ||| | ||| || || || || || || || ||||| |||||||||||||| Sbjct 3138180 CCACCCCTTAGACGAAGGACGATTTGGAGGGTGGACTCCTTTTGGATGTTGTAGTCGGCA 3138239 Query 18159 ATTGTTTTACAATCTTCCAATTGTTTGCCCGCATAGATAAGTCTTTGTTGATCCACGGGC 18218 | ||| | ||| || | |||||| || ||| ||||||| |||||||| || || Sbjct 3138240 AGAGTTCGGCCATCCTCAAGTTGTTTTCCGGCAAAGATAAGCCTTTGTTGGTCTGGAGGA 3138299 Query 18219 ACGCCTTCCTTATCGGCAATTTGTTGCTTGACCTGTGCAACAGTGTCACCGGGCTCGGTT 18278 | ||||| || || |||| |||||| | | | ||| || | ||| Sbjct 3138300 ATCCCTTCTTTGTCTTGGATTTTGGCCTTGACATTATCGATAGTATCGGAGCTCTCCACC 3138359 Query 18279 TCAATGGTGATGCTTTTGCCGGTCAATGTTTTTACAAAAATTTGCAT 18325 |||| ||||||| | || || || | ||||||||||| || ||||| Sbjct 3138360 TCAAGGGTGATGGTCTTACCAGTAAGGGTTTTTACAAAGATCTGCAT 3138406 >seq24 Length=55877068 Score = 87.8 bits (96), Expect = 1e-12 Identities = 156/228 (68%), Gaps = 0/228 (0%) Strand=Plus/Minus Query 18098 TCCTCCCCGTAGTCTAAGTACCATGTGAAGTGTTGATTCTTTTTGAATGTTGTAGTCGGC 18157 |||||| ||||| | ||| |||| ||| ||||| || || || || |||||||| || || Sbjct 24584307 TCCTCCACGTAGGCGAAGCACCAAGTGGAGTGTGGACTCCTTCTGGATGTTGTAATCAGC 24584248 Query 18158 CATTGTTTTACAATCTTCCAATTGTTTGCCCGCATAGATAAGTCTTTGTTGATCCACGGG 18217 || ||| | ||| || | ||| || || || |||| || ||||| || || ||| Sbjct 24584247 CAATGTGCGGCCATCCTCAAGTTGCTTACCAGCGAAGATCAGCCTTTGCTGGTCTGGGGG 24584188 Query 18218 CACGCCTTCCTTATCGGCAATTTGTTGCTTGACCTGTGCAACAGTGTCACCGGGCTCGGT 18277 | ||||||||| || ||| | |||||| | ||| || ||| ||| Sbjct 24584187 GATGCCTTCCTTGTCCTGAATCTTGGCCTTGACATTGTCAATCGTATCAGAACTCTCCAC 24584128 Query 18278 TTCAATGGTGATGCTTTTGCCGGTCAATGTTTTTACAAAAATTTGCAT 18325 || | |||||| | || ||||| | || || |||||||||||||| Sbjct 24584127 CTCCAATGTGATGGTCTTTCCGGTGAGGGTCTTGACAAAAATTTGCAT 24584080 >seq1 Length=92291805 Score = 86.0 bits (94), Expect = 5e-12 Identities = 155/227 (68%), Gaps = 0/227 (0%) Strand=Plus/Plus Query 18099 CCTCCCCGTAGTCTAAGTACCATGTGAAGTGTTGATTCTTTTTGAATGTTGTAGTCGGCC 18158 || |||| ||| | ||| || | ||| || || || || ||||| |||||||||||||| Sbjct 4409801 CCACCCCTTAGACGAAGGACTAGGTGGAGGGTGGACTCCTTTTGGATGTTGTAGTCGGCA 4409860 Query 18159 ATTGTTTTACAATCTTCCAATTGTTTGCCCGCATAGATAAGTCTTTGTTGATCCACGGGC 18218 | ||| | ||| || | |||||| || ||| | ||||| || ||||| || || Sbjct 4409861 AGAGTTCGGCCATCCTCGAGTTGTTTTCCGGCAAAAATAAGCCTCTGTTGGTCTGGAGGA 4409920 Query 18219 ACGCCTTCCTTATCGGCAATTTGTTGCTTGACCTGTGCAACAGTGTCACCGGGCTCGGTT 18278 | |||||| || || |||| |||||| | ||| ||| || | || Sbjct 4409921 ATGCCTTCTTTGTCTTGGATTTTGGCCTTGACATTATCAATAGTATCGGAGCTTTCCACC 4409980 Query 18279 TCAATGGTGATGCTTTTGCCGGTCAATGTTTTTACAAAAATTTGCAT 18325 |||| ||||||| |||| || || | ||||| ||||| || ||||| Sbjct 4409981 TCAAGGGTGATGGTTTTACCAGTAAGGGTTTTCACAAAGATCTGCAT 4410027 Lambda K H 0.634 0.408 0.912 Gapped Lambda K H 0.625 0.410 0.780 Effective search space used: 379301706463260