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: Neotoma_20lepida_20[genbank_20GCA_5F001675575.1_202016-06-23] 119,373 sequences; 2,353,855,022 total letters Query= NC_020104.1 Length=1021348 Score E Sequences producing significant alignments: (Bits) Value seq27438 192 4e-43 seq104799 132 3e-25 seq76224 123 2e-22 seq87143 109 4e-18 seq97228 100 2e-15 seq7954 89.7 3e-12 seq117227 87.8 1e-11 seq55092 86.0 4e-11 >seq27438 Length=395273 Score = 192 bits (212), Expect = 4e-43 Identities = 379/555 (68%), Gaps = 8/555 (1%) Strand=Plus/Plus Query 474328 TGCAATTGGTATTGATTTAGGAACTACTTACAGTTGTGTAGCTGTTTGGCAAAATGGTAA 474387 |||| |||| |||||| | || || |||||| ||||| | ||||| || |||| || Sbjct 214074 TGCAGTTGGCATTGATCTTGGCACCACTTACTCCTGTGTGGGTGTTTTTCAGCATGGAAA 214133 Query 474388 AGTAGAAATAATTGCCAATGACCAAGGTAATAGAACAACACCATCATATGTTTCTTTTAC 474447 || || ||||||||||||||||| | || |||| |||||| |||||| ||||||| Sbjct 214134 GGTGGAGATAATTGCCAATGACCAGGCGAACCGAACCACACCAAGCTATGTTGCTTTTAC 214193 Query 474448 TGAAACTGAACATCTTATTGGAGATGCTGCTAAATATCAAGCTGCATCTAATCCTGTTAA 474507 ||| | ||| || ||||| ||| | | || |||| | |||| || || || Sbjct 214194 TGACAAAGAATGACTAATTGGGGATACCTCGAAGAATCAGGTTGCAATGAACCCCACCAA 214253 Query 474508 TACTATTTTTGATGCTAAAAGATTGATTGGTCGTAATTTTGATGATACCACTGTCCAATC 474567 || |||||||||| ||| ||||||| ||| ||||||||| | ||| || || Sbjct 214254 CACAGTTTTTGATGCCAAACATCTGATTGGATGTAGGTTTGATGATTCTGTTGTTCAGTC 214313 Query 474568 TGATATGCGTCATTGGCCTTTTAAGGTGATAAATGTTGGTGGTAAACCA----TATATAG 474623 ||||||| || ||||| |||| |||| | |||| || | | ||| | | Sbjct 214314 TGATATGTAGCACTGGCCCTTTATGGTGGTGAATGATGCAGACAGGCCAGGCCAAGGTCC 214373 Query 474624 AAGCAATACACGCAGGTGAAACTAAACAATTTTCA-CCGGAACAAATTTCTTCAATGGTT 474682 ||| | || ||| || || ||| | ||| || ||||| | | || || ||||| Sbjct 214374 AAGTAGAGTACAAAGGAGAGAC-AAAAAGTTTCCACCCGGAGGAGGTGTCCTCTGTGGTT 214432 Query 474683 TTAGCCAAAATGAAACAAACCGCGAGCTCATATCTTGGACAAGA-AGTAACTGATGCAGT 474741 || || ||| | ||| || | |||||||| |||| || || |||| || Sbjct 214433 CTAATAAAGATGGAGGAAATTGCAGAAGCCTATCTTGG-GAAGACGGTTACCAATGCTGT 214491 Query 474742 AATTACTGTTCCAGCATATTTTAATGATTCTCAACGTCAAGCAACTAAAGATGCGGGAAG 474801 | || || |||| | || | ||||||||| | |||||||| |||||||| |||| Sbjct 214492 GGTCACAGTGTCAGCTTGCTTCAGTGATTCTCAGTGGCAAGCAACAAAAGATGCTGGAAC 214551 Query 474802 AATTGCAGGTCTTAATGTTTTACGTATTATTAATGAACCAACAGCAGCCGCACTTGCTTA 474861 ||||| || || ||||| | | ||||| ||||||||||| || || || ||||||| Sbjct 214552 TATTGCTGGCCTCAATGTGCTTTGAATTATCAATGAACCAACTGCTGCTGCTATTGCTTA 214611 Query 474862 TGGTCTTGATAAGAA 474876 ||| | |||||||| Sbjct 214612 TGGGTTAGATAAGAA 214626 Score = 136 bits (150), Expect = 3e-26 Identities = 441/679 (65%), Gaps = 18/679 (3%) Strand=Plus/Plus Query 475497 CTGCTTGTGAACGTGCTAAGCGAGCTCTTTCTTCTGCTACTCAAACTACTGTTGAAGTTG 475556 |||| |||||||| |||||| | | || || ||| || || | | | |||| ||| Sbjct 214857 CTGCCTGTGAACGGGCTAAGTGCACCCTCTCCTCTAGCACCCAGGCCAGTATTGAGATTG 214916 Query 475557 ATTCTCTTTTTGAAGGAATTGATTATAATACTCTTATTACAAGGGCTAAATTTGAAGATA 475616 ||||||| | ||| ||||| || | ||||| ||||| || ||| ||||||||| Sbjct 214917 ATTCTCTGTATGAGGGAATCGACTTCTATACTTCCATTACCAGTGCTCGATTTGAAGAAT 214976 Query 475617 TTTGTTCTGATCTCTTTAGAAAAACAATTGAACCCGTTGAACAAGTTCTCAGAGATTCTA 475676 | | |||| || || || || | || | || ||| | | || ||||| | Sbjct 214977 TAAATGCTGACCTGTTCCGAGGCACTCTGGACCATGTGGAAAAGGCCCTTTGAGATGTCA 215036 Query 475677 AACTTGACAAATCACAAGTCCATGAAATTGTTCTTGTAGGAGGTTCAACAAGAATTC-CA 475735 |||| ||||| ||||| ||| | || || ||||| || ||||| | || Sbjct 215037 AACTAGACAAGTCACAGATCC------------TGGTGGGTGGTTCTACCAGAATCCTCA 215084 Query 475736 AAAATAAGAGAAATGCTTTCATCATATTTTAATGGTAAAAAGTTAAATGAAAGTGTAAAT 475795 | | | ||| | | || | | || ||||| ||| | | ||| | || | || Sbjct 215085 AGATTCAGA-AGCTTCTGCAAGACTTCTTCAATGGAAAAGAACTGAATAAGAGCATTAAC 215143 Query 475796 CCTGATGAAGCTGTTGCATATGGAGCTGCTGTCCAAGCAGCTATTTTATCAGGTCAATCA 475855 || ||||||||||||| ||||| || |||||||| ||||| ||| |||| || | | Sbjct 215144 CCCAATGAAGCTGTTGCTTATGGTGCAGCTGTCCAGGCAGCCATTCTATCTGGAGACA-A 215202 Query 475856 GAC-GAGAAACTAAATAATATTGTACTTGTTGACGTAACTCCACTTTCATTAGGTCTTGA 475914 | | ||||| | | || | | || | || || ||||| || || | ||| ||| Sbjct 215203 GTCTGAGAACATTCAGGATTTGCTGCTCTTGGATGTCACTCCTCTCTCCCTTGGTACTGA 215262 Query 475915 AACAGTTGGAGGGATTATGACTAATCTTATTGACAGAAATACTCCTATCCCATGCAAAAA 475974 | | | ||| || | |||||| || || | ||||| | ||||| ||| | Sbjct 215263 AGCTGCTGGTGGAGTCATGACTGTCCTCATCAGGCGCAATACCACCATCCCTACCAAGCA 215322 Query 475975 ATCAAAAGTATTTTCCACTTATTCTGATAATCAAACAACTGTAACCATCCAAATCTTTGA 476034 || | || ||| || ||||| || | | ||| | || || | | ||| Sbjct 215323 GACACAGACTTTCACCATATACTCTGACAACTAGCCTGGTGTCTC-ATTCAGGTGTATGA 215381 Query 476035 AGGTGAAAGAAAATTCACTAAAGATAATAACAAACTTGGAACTTTTAATCTTGAAGGTAT 476094 ||||||||| | || || ||||| ||| ||||||| ||| | ||| ||| || Sbjct 215382 AGGTGAAAGGGCCATGACCAA-GATAACAACCTGCTTGGAAAGTTTGACCTTACAGGCAT 215440 Query 476095 TCCTCCTGCTCCCAGAGGAGTTCCTCAAATTGAAGTTACTTTTGATATTGATGCAAATGG 476154 |||| ||| | | | || |||||||| |||||||| |||||||| ||||||||||| || Sbjct 215441 ACCTCTTGCACACCGTGGTGTTCCTCAGATTGAAGTCACTTTTGACATTGATGCAAAAGG 215500 Query 476155 TATTCTTAATGTTACTGCT 476173 || || |||||| ||||| Sbjct 215501 CATCCTCAATGTTTCTGCT 215519 >seq104799 Length=2130 Score = 132 bits (146), Expect = 3e-25 Identities = 261/383 (68%), Gaps = 4/383 (1%) Strand=Plus/Minus Query 475793 AATCCTGATGAAGCTGTTGCATATGGAGCTGCTGTCCAAGCAGCTATTTTATCAGGTCAA 475852 || ||||||||||||||||| ||||| || |||||||| ||||| || | || | || Sbjct 2057 AACCCTGATGAAGCTGTTGCTTATGGTGCAGCTGTCCAGGCAGCCATACTGTCTG--CAG 2000 Query 475853 TCA-GAC-GAGAAACTAAATAATATTGTACTTGTTGACGTAACTCCACTTTCATTAGGTC 475910 || | | ||||| | | || | | || | | || ||||| || || | ||| Sbjct 1999 ACAAGTCTGAGAATGTTCAGGATTTGCTGCTCTTGAATGTCACTCCTCTCTCCCTTGGTA 1940 Query 475911 TTGAAACAGTTGGAGGGATTATGACTAATCTTATTGACAGAAATACTCCTATCCCATGCA 475970 ||||| | | ||| || | ||||||| || || | | ||||| | ||||| || Sbjct 1939 TTGAAGCTGCTGGTGGAGTCATGACTATCCTCATCAAGCGCAATACCACCATCCCTACCA 1880 Query 475971 AAAAATCAAAAGTATTTTCCACTTATTCTGATAATCAAACAACTGTAACCATCCAAATCT 476030 | | || | || |||| |||||||| || || | ||| || || | | Sbjct 1879 AGCAGACACAGACGTTCACCACCTATTCTGACAACCAGCCTGGTGTGCTNATTCAGGTGT 1820 Query 476031 TTGAAGGTGAAAGAAAATTCACTAAAGATAATAACAAACTTGGAACTTTTAATCTTGAAG 476090 |||||||||||| | ||||| ||||| ||| ||||||| ||| ||| || Sbjct 1819 ATGAAGGTGAAAGGGCCATGACTAAGGATAACAACCTGCTTGGAAACTTTGTACTTACAG 1760 Query 476091 GTATTCCTCCTGCTCCCAGAGGAGTTCCTCAAATTGAAGTTACTTTTGATATTGATGCAA 476150 | || ||||| || ||| || |||||||| |||||||| |||||||| |||||||| | Sbjct 1759 GCATACCTCCAGCACCCCATGGTGTTCCTCAGATTGAAGTCACTTTTGACATTGATGCCA 1700 Query 476151 ATGGTATTCTTAATGTTACTGCT 476173 |||| || || |||||| ||||| Sbjct 1699 ATGGCATCCTCAATGTTTCTGCT 1677 >seq76224 Length=91619 Score = 123 bits (136), Expect = 2e-22 Identities = 322/483 (67%), Gaps = 13/483 (3%) Strand=Plus/Minus Query 474401 GCCAATGACCAAGGTAATAGAACAACACCATCATATGTTTCTTTTACTGAAACTGAACAT 474460 ||||||||||| || || |||| |||||| |||||| |||||||||| || ||||| Sbjct 6489 GCCAATGACCAGGGGAACTGAACCACACCAAGCTATGTTGCTTTTACTGACACGGAACAA 6430 Query 474461 CTTATTGGAGATGCTGCTAAATATCAAGCTGCATCTAATCCTGTTAATACTATTTTTGAT 474520 | ||||| |||| ||| || |||| | |||| || || | || | | ||||||| Sbjct 6429 TTAATTGGGGATGNTGCCAAGAATCAGGTTGCAATGAACCCCATCAACAGT--TTTTGAT 6372 Query 474521 GCTAAAAGAT-TGATTGGTCGTAATTTTGATGATACCACTGTCCAATCTGATATGCGTCA 474579 | | ||| || |||| || |||| || |||||| | | || | ||||||||| || Sbjct 6371 G-TCAAACATCTGATCGGACGTACGTTGGATGATGCTGTTTTC-AGTCTGATATGAAGCA 6314 Query 474580 TTGGCCTTTT-----AAGGTGATAAATGTTGGTGGTAAACCATATATAGAAGCAATACAC 474634 | || | | | |||| | |||| || || | || | | ||| | | Sbjct 6313 CTAGCTTGGTGGTGAATGGTGGTGAATGATGCAGGCAGGCCCAAGGTCCAAGTAGAGTAA 6254 Query 474635 GCAGGTGAAACTAAACAATTTTCACCGGAACAAATTTCTTCAATGGTTTTAGCCAAAATG 474694 ||| || || ||| || | || || | | ||||| |||||| | || ||| Sbjct 6253 AAAGGAGAGACAAAAGT-TTCTANCCAGAGGAGGTGTCTTCTATGGTTCTGATGAAGATG 6195 Query 474695 AAACAAACCGCGAGCTCATATCTTGGACAAGAAG-TAACTGATGCAGTAATTACTGTTCC 474753 || ||| || | |||||||| |||| | | || |||| || | || || || Sbjct 6194 AAGGAAATTGCAGAAGCCTATCTTGGG-AAGATGGTTACCAATGCTGTGGTCACAGTGCC 6136 Query 474754 AGCATATTTTAATGATTCTCAACGTCAAGCAACTAAAGATGCGGGAAGAATTGCAGGTCT 474813 ||| || || ||| | ||||| || || ||||| |||| ||| |||| ||||| || Sbjct 6135 AGCTTACTTCAATAAGTCTCAGCGACAGGCAACAAAAGTTGCTGGAACTATTGCTAACCT 6076 Query 474814 TAATGTTTTACGTATTATTAATGAACCAACAGCAGCCGCACTTGCTTATGGTCTTGATAA 474873 ||||| | || ||||| ||||||||||| || || || ||||||||| | ||||| Sbjct 6075 CAATGTGCTTCGAATTATCAATGAACCAACTGCTGCTGCTATTGCTTATGTGTTAGATAA 6016 Query 474874 GAA 474876 ||| Sbjct 6015 GAA 6013 >seq87143 Length=1077445 Score = 109 bits (120), Expect = 4e-18 Identities = 114/150 (76%), Gaps = 0/150 (0%) Strand=Plus/Plus Query 476032 TGAAGGTGAAAGAAAATTCACTAAAGATAATAACAAACTTGGAACTTTTAATCTTGAAGG 476091 |||||||||||| | ||||| ||||| ||| ||||| | ||| | ||| ||| Sbjct 613069 TGAAGGTGAAAGGGCCATGACTAAGGATAACAACCTGCTTGGGAAGTTTGAACTTACAGG 613128 Query 476092 TATTCCTCCTGCTCCCAGAGGAGTTCCTCAAATTGAAGTTACTTTTGATATTGATGCAAA 476151 || ||||| || ||| | || |||||||| |||||||| |||||||| |||||||| || Sbjct 613129 CATACCTCCAGCACCCCGTGGTGTTCCTCAGATTGAAGTCACTTTTGACATTGATGCCAA 613188 Query 476152 TGGTATTCTTAATGTTACTGCTTGTGATAA 476181 ||| || || |||||| ||||| ||||| Sbjct 613189 TGGCATCCTCAATGTTTCTGCTGTAGATAA 613218 Score = 107 bits (118), Expect = 1e-17 Identities = 109/142 (77%), Gaps = 0/142 (0%) Strand=Plus/Plus Query 474735 ATGCAGTAATTACTGTTCCAGCATATTTTAATGATTCTCAACGTCAAGCAACTAAAGATG 474794 |||| || | || || ||||| || || ||||||||||| || || ||||| ||||||| Sbjct 611620 ATGCTGTGGTCACAGTGCCAGCTTACTTCAATGATTCTCAGCGACAGGCAACAAAAGATG 611679 Query 474795 CGGGAAGAATTGCAGGTCTTAATGTTTTACGTATTATTAATGAACCAACAGCAGCCGCAC 474854 | |||| ||||| || || ||||| | || ||||| ||||| ||||| || || || Sbjct 611680 CTGGAACTATTGCTGGCCTCAATGTGCTTCGAATTATCAATGAGCCAACTGCTGCTGCTA 611739 Query 474855 TTGCTTATGGTCTTGATAAGAA 474876 |||||||||| | |||||||| Sbjct 611740 TTGCTTATGGGTTAGATAAGAA 611761 Score = 93.3 bits (102), Expect = 3e-13 Identities = 120/166 (72%), Gaps = 0/166 (0%) Strand=Plus/Plus Query 474328 TGCAATTGGTATTGATTTAGGAACTACTTACAGTTGTGTAGCTGTTTGGCAAAATGGTAA 474387 |||| |||| |||||| | || || || ||| ||||| | ||| | || |||| || Sbjct 610847 TGCAGTTGGCATTGATCTTGGCACCACCTACTCCTGTGTGGGTGTCTTCCAGCATGGGAA 610906 Query 474388 AGTAGAAATAATTGCCAATGACCAAGGTAATAGAACAACACCATCATATGTTTCTTTTAC 474447 || || || |||||||||||||| || || |||| || || |||||| ||||||| Sbjct 610907 GGTGGAGATCATTGCCAATGACCAGGGGAACCGAACCACCCCCAGCTATGTTGCTTTTAC 610966 Query 474448 TGAAACTGAACATCTTATTGGAGATGCTGCTAAATATCAAGCTGCA 474493 ||| || |||| | ||||| ||||| || || |||| | |||| Sbjct 610967 TGACACGGAACGATTAATTGGGGATGCCGCGAAGAATCAGGTTGCA 611012 >seq97228 Length=228612 Score = 100 bits (110), Expect = 2e-15 Identities = 157/221 (71%), Gaps = 4/221 (2%) Strand=Plus/Minus Query 480551 ACGAAGACGGAGTACAAGATGAAGTGT--ACTTTCTTTAGAAACATTATAATCAGCTAGA 480608 |||||| | | ||||||||||| || ||| |||| ||| || || |||| | | Sbjct 211787 ACGAAGTCTCAACACAAGATGAAGGGTGGACTC-CTTTTGAATG-TTGTAGTCAGACAAA 211730 Query 480609 GTTCTGTTATCTTCAAGTTGCTTTCCAGCAAAAATAAGACGTTGTTGATCAGGAGGAATT 480668 || | | |||||| || ||||| ||||| || || || | ||| ||||||||||||||| Sbjct 211729 GTACGGCCATCTTCCAGCTGCTTACCAGCGAAGATCAGCCTTTGCTGATCAGGAGGAATT 211670 Query 480669 CCTTCCTTGTCTTGAATCTTTTGTTTGACAGCTTCAATAGTATCAGTGTGTGAAGTTTCA 480728 ||||| || || || ||||| || ||| ||| ||||| || | | || | || Sbjct 211669 CCTTCTTTATCCTGGATCTTGGCCTTTACATTTTCTATAGTGTCCGAGGGTTCAACCTCG 211610 Query 480729 AGGGTAATAGTTTTACCGGTGAGAGTCTTAACGAAAATTTG 480769 || || || ||||| || | || ||||| |||||||| || Sbjct 211609 AGCGTGATGGTTTTCCCCATAAGGGTCTTCACGAAAATCTG 211569 >seq7954 Length=808569 Score = 89.7 bits (98), Expect = 3e-12 Identities = 145/205 (71%), Gaps = 4/205 (2%) Strand=Plus/Minus Query 480564 ACAAGATGAAGTGT--ACTTTCTTTAGAAACATTATAATCAGCTAGAGTTCTGTTATCTT 480621 ||||||||||| || ||| |||| ||| | || |||| | ||| | | ||||| Sbjct 793850 ACAAGATGAAGGGTGGACTC-CTTTTGAATGCTG-TAGTCAGACAAAGTACGGCCATCTT 793793 Query 480622 CAAGTTGCTTTCCAGCAAAAATAAGACGTTGTTGATCAGGAGGAATTCCTTCCTTGTCTT 480681 | || ||||| ||||| || || || | ||| ||||||||||||||||||||||| || | Sbjct 793792 CCAGCTGCTTACCAGCGAAGATCAGCCTTTGCTGATCAGGAGGAATTCCTTCCTTATCCT 793733 Query 480682 GAATCTTTTGTTTGACAGCTTCAATAGTATCAGTGTGTGAAGTTTCAAGGGTAATAGTTT 480741 | ||||| || | | ||| ||||| || | | || | || || || || |||| Sbjct 793732 GGATCTTGGCCTTCAAATTTTCTATAGTGTCTGAGGGTTCAACCTCGAGCGTGATGGTTT 793673 Query 480742 TACCGGTGAGAGTCTTAACGAAAAT 480766 | || || | ||||| || ||||| Sbjct 793672 TCCCTGTAAAGGTCTTCACAAAAAT 793648 >seq117227 Length=121535 Score = 87.8 bits (96), Expect = 1e-11 Identities = 147/208 (71%), Gaps = 5/208 (2%) Strand=Plus/Minus Query 480564 ACAAGATGAAGTGT--ACTTTCTTTAGAAACATTATAATCAGCTAGAGTTCTGTTATCTT 480621 ||||||||||| || ||| |||| ||| || || |||| | ||| | | ||||| Sbjct 79494 ACAAGATGAAGGGTGGACTC-CTTTTGAATG-TTGTAGTCAGACAAAGTACAGCCATCTT 79437 Query 480622 CAAGTTGCTTTCCAGCAAAAATAAGACGTTGTTGATCAGGAGGAATTCCTTCCTTGTCTT 480681 | || ||||| ||||||| || || | || | ||||||||||||||||||||| || | Sbjct 79436 CCAGCTGCTTAGCAGCAAAGATCAGCCTCTGCTCATCAGGAGGAATTCCTTCCTTATCCT 79377 Query 480682 GAATCTTTTGTTTGACAGCTTCAATAGTATCAGTGTGTGAAGTTTCAAGGGTAATAGTTT 480741 | ||||| || ||| ||| ||||| || | | || | | || || || |||| Sbjct 79376 GGATCTTGGCCTTTACATTTTCTATAGTGTCCGAGGGTTCAACCTTGAGCGTGATGGTTT 79317 Query 480742 TACCGGTGAGAGTCTTAACGAAAATTTG 480769 | || || || ||| | |||||||| || Sbjct 79316 TCCCTGTAAG-GTCCTCACGAAAATCTG 79290 >seq55092 Length=657151 Score = 86.0 bits (94), Expect = 4e-11 Identities = 116/162 (72%), Gaps = 0/162 (0%) Strand=Plus/Plus Query 475877 GTACTTGTTGACGTAACTCCACTTTCATTAGGTCTTGAAACAGTTGGAGGGATTATGACT 475936 ||||| |||||||| ||| ||| || | ||| ||||||| || ||||| | ||||| Sbjct 238283 GTACTGCTTGACGTATGTCCCCTTACACTTGGTATTGAAACTGTGGGAGGTGTCATGACC 238342 Query 475937 AATCTTATTGACAGAAATACTCCTATCCCATGCAAAAAATCAAAAGTATTTTCCACTTAT 475996 || || ||| || || ||| | || ||| || || | | |||||||| | Sbjct 238343 AAACTGATTCCAAGGAACACTGTGGTACCCACCAAGAAGTCTCAGATCTTTTCCACAGCT 238402 Query 475997 TCTGATAATCAAACAACTGTAACCATCCAAATCTTTGAAGGT 476038 ||||||||||| |||||||||| ||| || ||| ||||||| Sbjct 238403 TCTGATAATCAGCCAACTGTAACAATCAAAGTCTATGAAGGT 238444 Lambda K H 0.634 0.408 0.912 Gapped Lambda K H 0.625 0.410 0.780 Effective search space used: 3263058712832204