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: Trifolium_20pratense_20[genbank_20GCA_5F900079335.1_202016-04-15] 39,051 sequences; 345,990,850 total letters Query= NC_013797.1 Length=108592 Score E Sequences producing significant alignments: (Bits) Value seq28803 100 2e-16 seq4 98.7 7e-16 seq28626 95.1 8e-15 seq1 89.7 4e-13 seq3 87.8 1e-12 >seq28803 Length=52646 Score = 100 bits (110), Expect = 2e-16 Identities = 117/158 (74%), Gaps = 0/158 (0%) Strand=Plus/Minus Query 39563 CATCGTCCAATTGTTTCCCGCCAAAAATTAAACGCTGCTGATCCGAGGGTACGCCTTCTT 39622 |||| |||||||| ||||| |||| || || | ||||||||| | || | ||||| | Sbjct 8819 CATCCTCCAATTGCTTCCCAGCAAAGATCAACCTCTGCTGATCTGGTGGGATTCCTTCCT 8760 Query 39623 TGTCGCATATTTTTTGTTTAATCGTCGCTACTGTGTCTGCGCTTTCCACGTCCAAAGTAA 39682 |||| ||||||| |||| | | | ||| |||| ||||| || |||||||||| Sbjct 8759 TGTCCTGTATTTTTGCCTTAACATTATCGATTGTATCTGAACTTTCTACCTCCAAAGTAA 8700 Query 39683 TTGTTTTACCCGTTAAAGTTTTTACGAAGATCTGCATG 39720 | || || || || ||||| || || |||||||||||| Sbjct 8699 TGGTCTTCCCTGTCAAAGTCTTCACAAAGATCTGCATG 8662 Score = 87.8 bits (96), Expect = 1e-12 Identities = 114/158 (72%), Gaps = 0/158 (0%) Strand=Plus/Plus Query 39563 CATCGTCCAATTGTTTCCCGCCAAAAATTAAACGCTGCTGATCCGAGGGTACGCCTTCTT 39622 |||| |||||||| ||||| |||| || || | ||||||||| | || | ||||| | Sbjct 32603 CATCCTCCAATTGCTTCCCAGCAAAGATCAACCTCTGCTGATCTGGTGGGATTCCTTCCT 32662 Query 39623 TGTCGCATATTTTTTGTTTAATCGTCGCTACTGTGTCTGCGCTTTCCACGTCCAAAGTAA 39682 |||| ||||||| || | | | | ||| || | ||||| || |||||||||| Sbjct 32663 TGTCCTGTATTTTTGCCTTGACATTATCGATTGTATCAGAACTTTCTACCTCCAAAGTAA 32722 Query 39683 TTGTTTTACCCGTTAAAGTTTTTACGAAGATCTGCATG 39720 | || || || || || || || || |||||||||||| Sbjct 32723 TGGTCTTCCCTGTCAAGGTCTTCACAAAGATCTGCATG 32760 Score = 82.4 bits (90), Expect = 5e-11 Identities = 113/158 (72%), Gaps = 0/158 (0%) Strand=Plus/Plus Query 39563 CATCGTCCAATTGTTTCCCGCCAAAAATTAAACGCTGCTGATCCGAGGGTACGCCTTCTT 39622 |||| |||||||| ||||| |||| || || | ||||||||| | || | ||||| | Sbjct 38816 CATCCTCCAATTGCTTCCCAGCAAAGATCAACCTCTGCTGATCTGGTGGGATTCCTTCCT 38875 Query 39623 TGTCGCATATTTTTTGTTTAATCGTCGCTACTGTGTCTGCGCTTTCCACGTCCAAAGTAA 39682 |||| ||||||| || | | | | ||| || | ||||| || ||||| |||| Sbjct 38876 TGTCCTGTATTTTTGCCTTGACATTATCGATTGTATCAGAACTTTCTACCTCCAATGTAA 38935 Query 39683 TTGTTTTACCCGTTAAAGTTTTTACGAAGATCTGCATG 39720 | || || || || || || || || |||||||||||| Sbjct 38936 TGGTCTTCCCTGTCAACGTCTTCACAAAGATCTGCATG 38973 >seq4 Length=28907061 Score = 98.7 bits (108), Expect = 7e-16 Identities = 158/227 (70%), Gaps = 0/227 (0%) Strand=Plus/Minus Query 39493 CCGCCTCGCAAACGCAGTACCAAATGCAAAGTGCTTTCTTTTTGTATATTATAATCGGCC 39552 || || | || ||| || || | ||| | ||| ||| || || || || ||||||||| Sbjct 27565909 CCTCCCCTCAGACGAAGGACAAGATGAAGGGTGGATTCCTTCTGGATGTTGTAATCGGCC 27565850 Query 39553 AAAACGCGTTCATCGTCCAATTGTTTCCCGCCAAAAATTAAACGCTGCTGATCCGAGGGT 39612 || || |||| || | || || || ||||||| || | |||||||||| ||| Sbjct 27565849 AAGGTTCGGCCATCTTCGAGCTGCTTTCCAGCAAAAATCAACCTTTGCTGATCCGGGGGA 27565790 Query 39613 ACGCCTTCTTTGTCGCATATTTTTTGTTTAATCGTCGCTACTGTGTCTGCGCTTTCCACG 39672 | ||| || ||||| ||| || || | | | | |||||||| ||| || || Sbjct 27565789 ATGCCCTCCTTGTCCTGTATCTTAGCCTTCACATTGTCAATTGTGTCTGAGCTCTCAACC 27565730 Query 39673 TCCAAAGTAATTGTTTTACCCGTTAAAGTTTTTACGAAGATCTGCAT 39719 |||||||| ||||| ||||| || | |||||| || || |||||||| Sbjct 27565729 TCCAAAGTTATTGTCTTACCAGTAAGAGTTTTCACAAAAATCTGCAT 27565683 >seq28626 Length=87040 Score = 95.1 bits (104), Expect = 8e-15 Identities = 160/229 (70%), Gaps = 2/229 (1%) Strand=Plus/Plus Query 39493 CCGCCTCGCAAACGCAGTACCAAATGCAAAGTGCTTTCTTTTTGTATATTATAATCGGCC 39552 || || ||||| | || |||||||| | || ||||| || ||||||||||| || Sbjct 42365 CCACCGCGCAACCTAAGAACCAAATGTAGCGTAGACTCTTTCTGGATATTATAATCCGCA 42424 Query 39553 AAAACGCGTTCATCGTCCAATTGTTTCCCGCCAAAAATTAAACGCTGCTGATCCGAGGGT 39612 | | | |||| |||||||| ||||| |||| || || ||||||||||| | || Sbjct 42425 AGAGTCCTCCCATCTTCCAATTGCTTCCCTGCAAAGATCAATCGCTGCTGATCAGGAGGA 42484 Query 39613 ACGCCTTCTTTGTCGCATATTTTTTGTTTAATCGTCG-CTACTGTGTCTGCGCTTTCCAC 39671 | ||||| ||||| ||||| ||| | ||| | | | || || | | ||| || Sbjct 42485 ATTCCTTCCTTGTCTTGGATTTTGGCTTTGA-CGTTGTCGATGGTATCGGAGGATTCTAC 42543 Query 39672 GTCCAAAGTAATTGTTTTACCCGTTAAAGTTTTTACGAAGATCTGCATG 39720 || | || || ||||| || |||| ||||| ||||||||||||||| Sbjct 42544 CTCTAGGGTTATGGTTTTGCCGGTTAGGGTTTTCACGAAGATCTGCATG 42592 >seq1 Length=28142018 Score = 89.7 bits (98), Expect = 4e-13 Identities = 156/227 (69%), Gaps = 0/227 (0%) Strand=Plus/Plus Query 39493 CCGCCTCGCAAACGCAGTACCAAATGCAAAGTGCTTTCTTTTTGTATATTATAATCGGCC 39552 || || | ||||||||| || | || | |||| || || || ||||| ||||| || Sbjct 1586411 CCACCCCTCAAACGCAGCACAAGGTGAAGAGTGGACTCCTTCTGGATATTGTAATCCGCA 1586470 Query 39553 AAAACGCGTTCATCGTCCAATTGTTTCCCGCCAAAAATTAAACGCTGCTGATCCGAGGGT 39612 | | | |||| ||||||||||| || |||| || || | ||||||||| | ||| Sbjct 1586471 AGGGTCCTTCCATCTTCCAATTGTTTGCCTGCAAAGATCAACCTCTGCTGATCTGGGGGA 1586530 Query 39613 ACGCCTTCTTTGTCGCATATTTTTTGTTTAATCGTCGCTACTGTGTCTGCGCTTTCCACG 39672 | ||||| || || || || || | | | | ||||||| ||| ||||| Sbjct 1586531 ATACCTTCCTTATCCTGGATCTTAGCCTTGACATTGTCAATGGTGTCTGAGCTCTCCACC 1586590 Query 39673 TCCAAAGTAATTGTTTTACCCGTTAAAGTTTTTACGAAGATCTGCAT 39719 ||||| || || || ||||| || ||||| || || || |||||||| Sbjct 1586591 TCCAAGGTTATGGTCTTACCGGTCAAAGTCTTGACAAATATCTGCAT 1586637 >seq3 Length=31061273 Score = 87.8 bits (96), Expect = 1e-12 Identities = 156/228 (68%), Gaps = 0/228 (0%) Strand=Plus/Minus Query 39492 GCCGCCTCGCAAACGCAGTACCAAATGCAAAGTGCTTTCTTTTTGTATATTATAATCGGC 39551 ||| || | |||||| || || | ||| | ||| ||| || || || || |||||||| Sbjct 12366859 GCCTCCCCTCAAACGAAGGACAAGATGAAGGGTGGATTCCTTCTGGATGTTGTAATCGGC 12366800 Query 39552 CAAAACGCGTTCATCGTCCAATTGTTTCCCGCCAAAAATTAAACGCTGCTGATCCGAGGG 39611 ||| || |||| |||| || || ||| ||||||| || | ||||| || | || Sbjct 12366799 CAAGGTTCGGCCATCTTCCAGCTGCTTTCCGGCAAAAATCAACCTTTGCTGGTCTGGAGG 12366740 Query 39612 TACGCCTTCTTTGTCGCATATTTTTTGTTTAATCGTCGCTACTGTGTCTGCGCTTTCCAC 39671 | || || ||||| ||| || || | | | | |||||||| |||||| || Sbjct 12366739 AATACCCTCCTTGTCTTGTATCTTGGCCTTCACATTGTCAATTGTGTCTGAGCTTTCTAC 12366680 Query 39672 GTCCAAAGTAATTGTTTTACCCGTTAAAGTTTTTACGAAGATCTGCAT 39719 ||||||||||| || || || || | || || || || |||||||| Sbjct 12366679 CTCCAAAGTAATGGTCTTGCCTGTAAGCGTCTTAACAAAAATCTGCAT 12366632 Score = 86.0 bits (94), Expect = 4e-12 Identities = 137/193 (71%), Gaps = 4/193 (2%) Strand=Plus/Minus Query 39529 TCTTTTTGTATATTATAATCGGCCAAAACGCGTTCATCGTCCAATTGTTTCCCGCCAAAA 39588 ||||| || || |||||||| |||||| || |||| || | || || || |||| Sbjct 12367278 TCTTTCTGAATGTTATAATCAGCCAAAGTCCGGCCATCTTCAAGCTGCTTTCCAGCAAAT 12367219 Query 39589 ATTAAACGCTGCTGATCCGAGGGTACGCCTTCTTTGTCGCATAT-TTTTTGTTTA-ATCG 39646 || || | ||||| || | ||| | ||||||||||| ||| || | || | || | Sbjct 12367218 ATCAACCTTTGCTGGTCTGGGGGAATACCTTCTTTGTCCTGTATCTTGGTCTTCACATTG 12367159 Query 39647 TCGCTACTGTGTCTGCGCTTTCCACGTCCAAAGTAATTGTTTTACCCGTTAAAGTTTTTA 39706 || || ||||||| ||| || || ||||| ||||| || || || || | ||| || | Sbjct 12367158 TCAATA--GTGTCTGAGCTCTCTACCTCCAAGGTAATAGTCTTTCCGGTAAGAGTCTTCA 12367101 Query 39707 CGAAGATCTGCAT 39719 |||| |||||||| Sbjct 12367100 CGAAAATCTGCAT 12367088 Lambda K H 0.634 0.408 0.912 Gapped Lambda K H 0.625 0.410 0.780 Effective search space used: 347204274975083