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_015398.1 Length=101487 Score E Sequences producing significant alignments: (Bits) Value seq9364 107 1e-18 seq3 107 1e-18 seq28803 98.7 6e-16 seq28674 93.3 3e-14 seq28626 93.3 3e-14 seq1 93.3 3e-14 seq4 89.7 3e-13 seq28613 82.4 5e-11 >seq9364 Length=1264 Score = 107 bits (118), Expect = 1e-18 Identities = 150/209 (72%), Gaps = 1/209 (0%) Strand=Plus/Plus Query 34775 CAAG-TGAATTGTGCTTTCTTTCTGAATGTTATAGTCCGAAAGGCTTCGTTCATCATCCA 34833 |||| |||| ||| ||||||||| ||||| || || | | | | | |||| || | Sbjct 303 CAAGATGAAGAGTGGATTCTTTCTGGATGTTGTAATCAGCTAAGGTCCTGCCATCTTCGA 362 Query 34834 GCTGTTTTCCGGCAAATATTAGTCGTTGCTGGTCTTGCGGCACCCCCTCCTTGTCGCTAA 34893 |||| ||||| ||||| || | | |||||||||| | || | ||||| ||||| || Sbjct 363 GCTGCTTTCCAGCAAAAATCAACCTTTGCTGGTCTGGTGGGATTCCCTCTTTGTCTTGAA 422 Query 34894 TCTTCTGTTTGACGGATGCTATCGATTCACCGGCCTCAACATCGACGGTTATGGTTTTTC 34953 |||| ||||| |||| | ||| ||| || |||| ||| ||||| |||| Sbjct 423 TCTTGGCCTTGACATTGTCTATGGTGTCAGAACTCTCCACCTCGAGGGTGATGGTCTTTC 482 Query 34954 CCGTGAGAGTCTTCACAAAGATCTGCATA 34982 | |||||||||||||||||||| |||||| Sbjct 483 CAGTGAGAGTCTTCACAAAGATTTGCATA 511 Score = 95.1 bits (104), Expect = 8e-15 Identities = 160/230 (70%), Gaps = 4/230 (2%) Strand=Plus/Plus Query 34755 CCTCCCCTCAACCTCAAAACCAAGTGAATTGTGCTTTCTTTCTGAATGTTATAGTC--CG 34812 ||||||||||| | | || | |||| ||| ||| ||||| ||||| || || | Sbjct 56 CCTCCCCTCAAACGAAGGACAAGATGAAGGGTGGATTCCTTCTGGATGTTGTAATCGGCC 115 Query 34813 AAAGGCTTCGTTCATCATCCAGCTGTTTTCCGGCAAATATTAGTCGTTGCTGGTCTTGCG 34872 |||| |||| |||| || ||||| ||||| ||||| || | | |||||||||| | | Sbjct 116 AAAG--TTCGCCCATCTTCGAGCTGCTTTCCAGCAAAGATCAACCTTTGCTGGTCTGGGG 173 Query 34873 GCACCCCCTCCTTGTCGCTAATCTTCTGTTTGACGGATGCTATCGATTCACCGGCCTCAA 34932 | | ||||||||||| |||||| ||| || | || | || | ||||| Sbjct 174 GGATACCCTCCTTGTCCTGAATCTTAGCTTTCACATTGTCAATAGTGTCTGAGCTCTCAA 233 Query 34933 CATCGACGGTTATGGTTTTTCCCGTGAGAGTCTTCACAAAGATCTGCATA 34982 | || | || || || || || || || ||||||||||| ||||||||| Sbjct 234 CCTCCAAAGTAATAGTCTTGCCAGTAAGGGTCTTCACAAAAATCTGCATA 283 >seq3 Length=31061273 Score = 107 bits (118), Expect = 1e-18 Identities = 150/209 (72%), Gaps = 1/209 (0%) Strand=Plus/Minus Query 34775 CAAG-TGAATTGTGCTTTCTTTCTGAATGTTATAGTCCGAAAGGCTTCGTTCATCATCCA 34833 |||| |||| ||| ||| ||||| ||||| || || | | | | |||| || | Sbjct 12366383 CAAGATGAAGGGTGGATTCCTTCTGGATGTTGTAATCAGCTAATGTCCTGCCATCCTCAA 12366324 Query 34834 GCTGTTTTCCGGCAAATATTAGTCGTTGCTGGTCTTGCGGCACCCCCTCCTTGTCGCTAA 34893 |||||||||| ||||| || || | |||||||||| | || | || |||||||| || Sbjct 12366323 GCTGTTTTCCAGCAAAAATCAGCCTTTGCTGGTCTGGTGGAATACCTTCCTTGTCTTGAA 12366264 Query 34894 TCTTCTGTTTGACGGATGCTATCGATTCACCGGCCTCAACATCGACGGTTATGGTTTTTC 34953 |||| ||||| | |||||| || |||||| || | ||| | ||| |||| Sbjct 12366263 TCTTGACCTTGACATTTTCTATCGTATCCGAACTCTCAACCTCAAGGGTGACGGTCTTTC 12366204 Query 34954 CCGTGAGAGTCTTCACAAAGATCTGCATA 34982 | |||||||||||||||||||| |||||| Sbjct 12366203 CGGTGAGAGTCTTCACAAAGATTTGCATA 12366175 Score = 105 bits (116), Expect = 4e-18 Identities = 151/213 (71%), Gaps = 0/213 (0%) Strand=Plus/Minus Query 34772 AACCAAGTGAATTGTGCTTTCTTTCTGAATGTTATAGTCCGAAAGGCTTCGTTCATCATC 34831 ||| | ||||| || ||||||||| ||||| ||||| | || | || |||| || Sbjct 8017652 AACAAGGTGAAGAGTTGATTCTTTCTGGATGTTGTAGTCGGCGAGAGTGCGGCCATCTTC 8017593 Query 34832 CAGCTGTTTTCCGGCAAATATTAGTCGTTGCTGGTCTTGCGGCACCCCCTCCTTGTCGCT 34891 || ||| |||||||| || || || ||||||||||| | || | || |||||||| Sbjct 8017592 CAACTGCTTTCCGGCGAAGATGAGACGTTGCTGGTCAGGTGGAATTCCTTCCTTGTCTTG 8017533 Query 34892 AATCTTCTGTTTGACGGATGCTATCGATTCACCGGCCTCAACATCGACGGTTATGGTTTT 34951 ||||| ||||||| | || | || | |||||| |||| |||||| || || Sbjct 8017532 GATCTTGGCTTTGACGTTGTCGATTGTGTCTGAAGACTCAACCTCGAGGGTTATCGTCTT 8017473 Query 34952 TCCCGTGAGAGTCTTCACAAAGATCTGCATATT 34984 || || || || ||||| ||||||||||| || Sbjct 8017472 CCCTGTTAGGGTTTTCACGAAGATCTGCATCTT 8017440 Score = 87.8 bits (96), Expect = 1e-12 Identities = 156/228 (68%), Gaps = 0/228 (0%) Strand=Plus/Minus Query 34755 CCTCCCCTCAACCTCAAAACCAAGTGAATTGTGCTTTCTTTCTGAATGTTATAGTCCGAA 34814 ||||||||||| | | || | |||| ||| ||| ||||| ||||| || || | Sbjct 12366858 CCTCCCCTCAAACGAAGGACAAGATGAAGGGTGGATTCCTTCTGGATGTTGTAATCGGCC 12366799 Query 34815 AGGCTTCGTTCATCATCCAGCTGTTTTCCGGCAAATATTAGTCGTTGCTGGTCTTGCGGC 34874 | | |||| |||| |||||||| ||||||||||| || | | |||||||||| | || Sbjct 12366798 AAGGTTCGGCCATCTTCCAGCTGCTTTCCGGCAAAAATCAACCTTTGCTGGTCTGGAGGA 12366739 Query 34875 ACCCCCTCCTTGTCGCTAATCTTCTGTTTGACGGATGCTATCGATTCACCGGCCTCAACA 34934 | ||||||||||| ||||| || || | || | || | || || Sbjct 12366738 ATACCCTCCTTGTCTTGTATCTTGGCCTTCACATTGTCAATTGTGTCTGAGCTTTCTACC 12366679 Query 34935 TCGACGGTTATGGTTTTTCCCGTGAGAGTCTTCACAAAGATCTGCATA 34982 || | || ||||| || || || || ||||| ||||| ||||||||| Sbjct 12366678 TCCAAAGTAATGGTCTTGCCTGTAAGCGTCTTAACAAAAATCTGCATA 12366631 >seq28803 Length=52646 Score = 98.7 bits (108), Expect = 6e-16 Identities = 158/227 (70%), Gaps = 0/227 (0%) Strand=Plus/Plus Query 34756 CTCCCCTCAACCTCAAAACCAAGTGAATTGTGCTTTCTTTCTGAATGTTATAGTCCGAAA 34815 |||||||||| | | || | |||| ||| ||| ||||| |||||||| || | | Sbjct 33086 CTCCCCTCAAACGAAGGACAAGATGAAGGGTGGATTCCTTCTGGATGTTATAATCAGCCA 33145 Query 34816 GGCTTCGTTCATCATCCAGCTGTTTTCCGGCAAATATTAGTCGTTGCTGGTCTTGCGGCA 34875 | ||| |||| || ||||| ||||| ||||| || | | |||||||||| | || | Sbjct 33146 AGGTTCTGCCATCTTCAAGCTGCTTTCCAGCAAAAATCAACCTTTGCTGGTCTGGAGGAA 33205 Query 34876 CCCCCTCCTTGTCGCTAATCTTCTGTTTGACGGATGCTATCGATTCACCGGCCTCAACAT 34935 ||||||||||| |||||| ||| || | || | || | |||||| | Sbjct 33206 TGCCCTCCTTGTCCTGAATCTTAGCTTTTACATTGTCAATGGTGTCTGAGCTCTCAACCT 33265 Query 34936 CGACGGTTATGGTTTTTCCCGTGAGAGTCTTCACAAAGATCTGCATA 34982 | | || ||||| || || || | ||||||||||||||||||||| Sbjct 33266 CCAAAGTAATGGTCTTCCCTGTCAATGTCTTCACAAAGATCTGCATA 33312 Score = 98.7 bits (108), Expect = 6e-16 Identities = 148/209 (71%), Gaps = 1/209 (0%) Strand=Plus/Plus Query 34775 CAAG-TGAATTGTGCTTTCTTTCTGAATGTTATAGTCCGAAAGGCTTCGTTCATCATCCA 34833 |||| |||| ||| ||||||||| ||||| || || | | | | | |||| || | Sbjct 33560 CAAGATGAAGAGTGGATTCTTTCTGGATGTTGTAATCAGCTAAGGTCCTGCCATCTTCGA 33619 Query 34834 GCTGTTTTCCGGCAAATATTAGTCGTTGCTGGTCTTGCGGCACCCCCTCCTTGTCGCTAA 34893 |||| ||||| ||||| || | | |||||||||| | || | ||||| ||||| || Sbjct 33620 GCTGCTTTCCAGCAAAAATCAACCTTTGCTGGTCTGGTGGGATTCCCTCTTTGTCTTGAA 33679 Query 34894 TCTTCTGTTTGACGGATGCTATCGATTCACCGGCCTCAACATCGACGGTTATGGTTTTTC 34953 |||| ||||| |||| | ||| ||| || || | ||| ||||| |||| Sbjct 33680 TCTTGGCCTTGACATTGTCTATGGTGTCAGAACTCTCCACCTCAAGGGTGATGGTCTTTC 33739 Query 34954 CCGTGAGAGTCTTCACAAAGATCTGCATA 34982 | ||||| ||||| ||||||||||||||| Sbjct 33740 CGGTGAGGGTCTTAACAAAGATCTGCATA 33768 >seq28674 Length=75340 Score = 93.3 bits (102), Expect = 3e-14 Identities = 154/220 (70%), Gaps = 8/220 (4%) Strand=Plus/Minus Query 34766 CCTCAAAACCAAGTGAATTGTGCTTTCTTTCTGAATGTTATAGTCCGAAAGGCTTCGTTC 34825 ||| | ||| | ||||| || |||||||||||| ||||| || | ||| | | | | Sbjct 21259 CCTGAGAACAAGGTGAAGCGTAGATTCTTTCTGAATATTATAATCAGCAAGAGTCCTTCC 21200 Query 34826 ATCATCCAGCTGTTTTCCGGCAAATATTAGTCGTTGCTGGTCTTGCGGCACCCCCTCCTT 34885 ||| || |||||||| || ||||| || | ||| ||||| || | || | ||||||||| Sbjct 21199 ATCTTCAAGCTGTTTACCAGCAAAGATCAATCGCTGCTGATCAGGTGGAATCCCCTCCTT 21140 Query 34886 GTCGCTAATCTTCTGTTTGACGGATGCTATCGAT----TCACCGGCCTCAACATCGACGG 34941 || ||||||| || || || |||| || ||| ||| || || | | Sbjct 21139 ATCCTGAATCTTCGCCTTCAC--AT--TATCAATAGTATCAGAACTCTCCACCTCCAAAG 21084 Query 34942 TTATGGTTTTTCCCGTGAGAGTCTTCACAAAGATCTGCAT 34981 | || || |||||||| | ||||||||||| |||||||| Sbjct 21083 TAATCGTCTTTCCCGTCAACGTCTTCACAAAAATCTGCAT 21044 >seq28626 Length=87040 Score = 93.3 bits (102), Expect = 3e-14 Identities = 154/220 (70%), Gaps = 8/220 (4%) Strand=Plus/Plus Query 34766 CCTCAAAACCAAGTGAATTGTGCTTTCTTTCTGAATGTTATAGTCCGAAAGGCTTCGTTC 34825 ||| | ||| | ||||| ||| |||||||||||| ||||| || | ||| ||| | | Sbjct 42148 CCTGAGAACAAGGTGAAGTGTAGATTCTTTCTGAATATTATAATCAGCAAGAGTTCATCC 42207 Query 34826 ATCATCCAGCTGTTTTCCGGCAAATATTAGTCGTTGCTGGTCTTGCGGCACCCCCTCCTT 34885 ||| || |||||||| |||||||| || | ||| || || || | || | ||||||||| Sbjct 42208 ATCCTCAAGCTGTTTACCGGCAAAGATCAATCGCTGTTGATCAGGTGGAATCCCCTCCTT 42267 Query 34886 GTCGCTAATCTTCTGTTTGACGGATGCTATCGAT----TCACCGGCCTCAACATCGACGG 34941 || |||||| || || || |||| || ||| ||| || || | | Sbjct 42268 ATCCTGAATCTTGGCCTTCAC--AT--TATCAATAGTATCAGAACTCTCCACCTCAAGAG 42323 Query 34942 TTATGGTTTTTCCCGTGAGAGTCTTCACAAAGATCTGCAT 34981 | || || || ||||| | ||||||||||| |||||||| Sbjct 42324 TAATCGTCTTCCCCGTCAACGTCTTCACAAAAATCTGCAT 42363 Score = 89.7 bits (98), Expect = 3e-13 Identities = 157/229 (69%), Gaps = 0/229 (0%) Strand=Plus/Plus Query 34753 TTCCTCCCCTCAACCTCAAAACCAAGTGAATTGTGCTTTCTTTCTGAATGTTATAGTCCG 34812 |||| || | |||||| | |||||| || | || |||||||| || ||||| |||| Sbjct 42363 TTCCACCGCGCAACCTAAGAACCAAATGTAGCGTAGACTCTTTCTGGATATTATAATCCG 42422 Query 34813 AAAGGCTTCGTTCATCATCCAGCTGTTTTCCGGCAAATATTAGTCGTTGCTGGTCTTGCG 34872 ||| | | |||| |||| || || || ||||| || | ||| ||||| || | | Sbjct 42423 CAAGAGTCCTCCCATCTTCCAATTGCTTCCCTGCAAAGATCAATCGCTGCTGATCAGGAG 42482 Query 34873 GCACCCCCTCCTTGTCGCTAATCTTCTGTTTGACGGATGCTATCGATTCACCGGCCTCAA 34932 | | || |||||||| || || ||||||| | || | || || || | Sbjct 42483 GAATTCCTTCCTTGTCTTGGATTTTGGCTTTGACGTTGTCGATGGTATCGGAGGATTCTA 42542 Query 34933 CATCGACGGTTATGGTTTTTCCCGTGAGAGTCTTCACAAAGATCTGCAT 34981 | || | |||||||||||| || || || || ||||| ||||||||||| Sbjct 42543 CCTCTAGGGTTATGGTTTTGCCGGTTAGGGTTTTCACGAAGATCTGCAT 42591 >seq1 Length=28142018 Score = 93.3 bits (102), Expect = 3e-14 Identities = 135/191 (71%), Gaps = 0/191 (0%) Strand=Plus/Plus Query 34791 TCTTTCTGAATGTTATAGTCCGAAAGGCTTCGTTCATCATCCAGCTGTTTTCCGGCAAAT 34850 || |||||||| || || || | ||| | | | | || |||| ||| |||||||| || Sbjct 1587197 TCCTTCTGAATATTGTAATCAGCAAGAGTCCTTCCGTCTTCCAACTGCTTTCCGGCGAAG 1587256 Query 34851 ATTAGTCGTTGCTGGTCTTGCGGCACCCCCTCCTTGTCGCTAATCTTCTGTTTGACGGAT 34910 || || ||||||||||| | || | || |||||||| ||||| ||||||| Sbjct 1587257 ATGAGACGTTGCTGGTCCGGAGGAATTCCTTCCTTGTCCTGGATCTTGGCTTTGACGTTG 1587316 Query 34911 GCTATCGATTCACCGGCCTCAACATCGACGGTTATGGTTTTTCCCGTGAGAGTCTTCACA 34970 | || | ||| | ||| || || | ||| ||||| ||||| ||||| || ||||| Sbjct 1587317 TCGATGGTGTCAGAGCTCTCCACCTCAAGGGTGATGGTCTTTCCGGTGAGTGTTTTCACG 1587376 Query 34971 AAGATCTGCAT 34981 ||||| ||||| Sbjct 1587377 AAGATTTGCAT 1587387 Score = 84.2 bits (92), Expect = 1e-11 Identities = 112/156 (72%), Gaps = 0/156 (0%) Strand=Plus/Plus Query 34827 TCATCCAGCTGTTTTCCGGCAAATATTAGTCGTTGCTGGTCTTGCGGCACCCCCTCCTTG 34886 || || ||||| ||||||||||| || | | ||||||||| | || | || |||||| Sbjct 1587005 TCCTCAAGCTGCTTTCCGGCAAAGATCAACCTCTGCTGGTCTGGGGGGATTCCTTCCTTG 1587064 Query 34887 TCGCTAATCTTCTGTTTGACGGATGCTATCGATTCACCGGCCTCAACATCGACGGTTATG 34946 || ||||| |||||| | || | ||| | ||||| || | ||| ||| Sbjct 1587065 TCCTGGATCTTGGCCTTGACGTTGTCGATGGTGTCAGAGCTTTCAACCTCAAGGGTGATG 1587124 Query 34947 GTTTTTCCCGTGAGAGTCTTCACAAAGATCTGCATA 34982 || ||||| ||||||||||| || |||||||||||| Sbjct 1587125 GTCTTTCCTGTGAGAGTCTTGACGAAGATCTGCATA 1587160 >seq4 Length=28907061 Score = 89.7 bits (98), Expect = 3e-13 Identities = 135/192 (70%), Gaps = 0/192 (0%) Strand=Plus/Minus Query 34791 TCTTTCTGAATGTTATAGTCCGAAAGGCTTCGTTCATCATCCAGCTGTTTTCCGGCAAAT 34850 |||||||| |||||||| || | ||| ||| |||| || ||||| ||||||||||| Sbjct 27565645 TCTTTCTGGATGTTATAATCAGCCAGGGTTCTGCCATCTTCGAGCTGCTTTCCGGCAAAA 27565586 Query 34851 ATTAGTCGTTGCTGGTCTTGCGGCACCCCCTCCTTGTCGCTAATCTTCTGTTTGACGGAT 34910 || | | ||||| ||| | || | || || || || ||||| ||||| Sbjct 27565585 ATCAACCTCTGCTGATCTGGGGGAATACCTTCTTTATCTTGTATCTTGGCCTTGACATTG 27565526 Query 34911 GCTATCGATTCACCGGCCTCAACATCGACGGTTATGGTTTTTCCCGTGAGAGTCTTCACA 34970 |||| | ||| ||| || || | ||| ||||| ||||| ||||| ||||| ||| Sbjct 27565525 TCTATGGTGTCAGAACTCTCCACCTCAAGGGTGATGGTCTTTCCAGTGAGGGTCTTAACA 27565466 Query 34971 AAGATCTGCATA 34982 |||||||||||| Sbjct 27565465 AAGATCTGCATA 27565454 >seq28613 Length=6376 Score = 82.4 bits (90), Expect = 5e-11 Identities = 105/144 (73%), Gaps = 2/144 (1%) Strand=Plus/Minus Query 34747 AATCAT--TTCCTCCCCTCAACCTCAAAACCAAGTGAATTGTGCTTTCTTTCTGAATGTT 34804 |||||| |||||||||| | ||| | |||||||||| || ||| || |||||||| Sbjct 5611 AATCATGGTTCCTCCCCTGAGCCTTAGGACCAAGTGAAGCGTTGATTCCTTTTGAATGTT 5552 Query 34805 ATAGTCCGAAAGGCTTCGTTCATCATCCAGCTGTTTTCCGGCAAATATTAGTCGTTGCTG 34864 ||| || | ||| | || |||| |||||||| || || ||||| || | | ||||| Sbjct 5551 ATAATCAGCAAGAGTGCGGCCATCTTCCAGCTGCTTACCAGCAAAAATCAACCTCTGCTG 5492 Query 34865 GTCTTGCGGCACCCCCTCCTTGTC 34888 ||| | || | || |||||||| Sbjct 5491 GTCAGGAGGGATACCTTCCTTGTC 5468 Lambda K H 0.634 0.408 0.912 Gapped Lambda K H 0.625 0.410 0.780 Effective search space used: 324479095811928