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Added tests for amrfinder integration options
Additional tests for --amrfinder and --amrfinder --print_node Also updated test_amrfinder.sh script to be slightly more sophisticated and report which tests failed at the end.
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| #Protein identifier Contig id Start Stop Strand Element symbol Element name Scope Element type Element subtype Class Subclass Method Target length Reference sequence length % Coverage of reference sequence % Identity to reference sequence Alignment length Accession of closest sequence Name of closest sequence HMM id HMM description | ||
| na partial 27 1048 + stx2_operon Partial stx2 operon plus VIRULENCE STX_TYPE STX2 STX2 PARTIAL 1022 99.41 337 AAA16362.1, AAS07607.1 Shiga toxin stx2 na na | ||
| na partial_contig_end 3 661 - stx2_operon Partial stx2 operon plus VIRULENCE STX_TYPE STX2 STX2 PARTIAL_CONTIG_END 659 100.00 216 AAM70046.1, AAA16362.1 Shiga toxin stx2 na na | ||
| na stx1a 218 1444 + stx1a_operon stx1a operon plus VIRULENCE STX_TYPE STX1 STX1A COMPLETE 1227 100.00 406 AAA98347.1, AAA71894.1 Shiga toxin stx1a na na | ||
| na stx2_fs 2165 3232 + stx2_operon stx2 operon with frameshift plus VIRULENCE STX_TYPE STX2 STX2 FRAMESHIFT 1068 99.15 355 AAG01033.1, AAA16363.1 Shiga toxin stx2c na na | ||
| na stx2_novel 216 1456 + stx2_operon Novel stx2 operon plus VIRULENCE STX_TYPE STX2 STX2 COMPLETE_NOVEL 1241 99.76 410 AAA19623.1, AAA16363.1 Shiga toxin stx2c na na | ||
| na stx2_stop 694 1653 + stx2_operon stx2 operon with internal stop plus VIRULENCE STX_TYPE STX2 STX2 INTERNAL_STOP 960 91.25 320 AUM09788.1 Shiga toxin stx2h subunit A na na | ||
| na stx2c 1298 2538 - stx2c_operon stx2c operon plus VIRULENCE STX_TYPE STX2 STX2C COMPLETE 1241 100.00 410 AAA16363.1, AAS07596.1 Shiga toxin stx2c na na |
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| >stx2_stop gb|AARRMG010000054.1| Escherichia coli strain PNUSAE017474 SAMN09934175-rid9288223.guided.45, whole genome shotgun sequence | ||
| CGACGGAGGCATTTAATGCCATACGCAAAGTGACGAGTGCTATCACGCTTGATACGTGGAAAAAATCAGT | ||
| GAAACGCTTTTACGATACCCTGGTGGTTCGGTTTGACATTGAAGAGGCATGGGCGGAGCGGCAGTTAAAG | ||
| AGGGTGACGCGATAGTGTTGTTGATTTTTCCCGAATCTGTGGTAAATTTACCCTAACGATGGGCGTTTTA | ||
| TGCCTGACGTTAGAGGAATTTTTACAACCCGCCGCCGAGCGGGTTTTATCATTTCTGGGGCTCGCTACGG | ||
| CGGGCCTTTTTCATATCCGCGCCACGTCCGGCACACATCACTTCAGATAACACCACACAAAAGGCATCTG | ||
| CGGGTGCCGTTGACGGGGTGTTTTTTACGGGTCGCTGGTGGCCCTTTTTTATTTACAGGAGAAAAAGTAT | ||
| GTCTGAACCCTTATACGGTTCTGGTACAGTTGCGGCGCTCGGGGGTGCGACGGTATTCGGGCTGTTTACC | ||
| GGGACGGATTTCGGGATTGTGTTTGGTGCATCTGCTGGTATCGTTTACCGTCGGTGTGCCAAAAGCTCGT | ||
| GGGCTGTCAGATTGGGTTGCGGTTCATTTCCCCCACTATGTAGCGCTATCAATAAAGCCTCACTTCGGTG | ||
| AGACTTTTTCATATCTGCGCCATGTCTGATGCCGGGGTAATCTAGTTAAAAGGAATATCATAGATGAAGT | ||
| GTATATTCTTGAAGTGGTTGCTGTGTCTTTTATTAAATTTCTCTGCTATATCTTATGCCCGTGAGTTTAC | ||
| AATAGACTTTTCGTCTCAACAAAGTTATGTATCTTCGTTAAATAGTATACGCACAGCGATATCGACACCC | ||
| CTTGAAAATATATCTCAGGGGGGTACATCGGTATCGGTTATTAATCATACGCCACCAGGAAGTTATATTG | ||
| CCGTAGATATACGAGGGCTTGATGTTTATCAGGCGCGTTTTGACCACCTTCGTCTGATTGTTGAGCAAAA | ||
| TAATTTATATGTGGCTGGATTTGTTAATACGGCAACAAATACTTTCTACAGATTTTCAGATTTTTCACAT | ||
| ATATCAGTGCCCGGTGTGACAACGGTTTCCATGACAACAGACAGCAGTTATACCACTCTGCAACGTGTCG | ||
| CAGCGCTGGAACGTTCTGGGATGCAAATCAGTCGTCACTCACTGGTTTCATCATATCTGGCGTTAATGGA | ||
| GTTTAGTGGTAATGCCATGAACAGTGAGGCCTCCAGAGCAATCCTGCGTTTTGTCACTGTCACAGCCGAA | ||
| GCTTTACGCTTCAGGCAAATACAGAGAGAATTTCGTAAGGCACTATCTGAAGCAGCTCCGGTTTATACGA | ||
| TGACATCGGAAGATGTGGACCTTACTCTGAACTGGGGAAGAATAAGCAATGTTCTTCCTGAATACAGAGG | ||
| AGAAGAGGGCGTCAGGGTGGGGCGAATATCCTTCAATAGTCTTCCGGCAATACTAGGGAGTGTGGCGGTT | ||
| ATATTGAATTGCCATCATCAGGGGGCACGTTCTGTTCGCTCCGTTAATCAAGAGAAGCAACCGGAATGTC | ||
| AAATAACTGGCGACAGGCCAGTTATAAAAATAAACAATATCTTATGGGAAAGTAATACAGCAGCAGCTTT | ||
| TCTGAACCGGAAATCTCAGTCTTGATATGCAACTGGTAAATGACAGGAGT | ||
|
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||
| >stx2_fs gb|AAAFFU020000197.1| Escherichia coli strain 599478 SAMN10075572-rid9463843.guided.094, whole genome shotgun sequence | ||
| ATGCAATTCTGAGGGAATTACTGGATCAATCCACAGGAGTAATTATGACAAAACGTCGTAAGAAATACCA | ||
| GGAAAAAGAAGAGATTCGACACCCTGATTCACCTGAGGGATTAGTGGTAGCCGCAGCAAATAACAGGGCG | ||
| TTCGCAGAGCGCCTTGTTGGTGTTTACAGACTAGCCAAAGCAGGAGTGAAACATGGGCGTCGTTAAGTTA | ||
| GCTGATTACAGGCCTCAACTGGAGGTCGTGGAGCATCGCGTGGCAGATACCGAAGATGGTTTCATGCGCG | ||
| TTGCTAACGAGATTACCGACAGTCTGCTGATGGCTGATTTAACCGTCCGGCAGTTGAAGGTGATGCTCGC | ||
| TATCATGCGCAAGACATACGGATTCAATAAGCCGATGGATCGACTCACAAACACGCAGATAGCAGCCATG | ||
| ACAGGTATTCATCACACTCATGTTTGCGCTGCCAAGCGCCAGCTTATTGAGCGTAAATTCCTCATTGCTG | ||
| ATGGCGTGAAAATCGGAGTGAACAAGGTGGTTTCTCAGTGGATTAGCCAGGACAGCTTAACATTAGCTAA | ||
| AACAGCTAATAAAACATTAGCCAAGTCGGCTAATGGGTATAAGCCAAGTCAGCTAAACACAAAAGACAAT | ||
| ATACAAAAGACAATAAATACAAATACCCCCTTACCCCCTAACGGGGATGGCGATGGGCAGGTTAAACCTG | ||
| AACGTCGCAAGGCAGAACGAATCGACTACGAATCCTTCCTGAACGCCTACAACACCGAAGTCGGTGACAG | ||
| ACTTCCACACGCTGTTGCGGTCAACGAGAAACGAAAACGCCGCCTGAAGAAAATTATCCCGCAACTGAAA | ||
| ACGCCAAACGTGGACGGTTTCAGAGCGTATGTCAGGGCGTTTGTGCATCAGGCCAAGCCGTTTTACTTCG | ||
| GAGACAACGACACGGGCTGGACGGCAGATTTTGATTACCTGCTGAGGGAAGATTCGTTAACGGGAGTTCG | ||
| GGAAGGGAAGTTTGCAGACAGGGGGATTGCATGAGACAGGATATCGAAGCTAGCGTTATCGGTGGCCTGC | ||
| TGATTGGTGGATTAACTCCAACCGCCAGTGACGTTCTGGCAACGCTGGAGCCGGAAGCGTTTTCAATTCC | ||
| GCTCTACCGGAAAGCCTTCGAGGTTATTCGCAAGCAGGCGAGAAACAGAAACCTAATCGATGCGCTGATG | ||
| GTTGCCGAGGCGTGCGGAGAGGAGCATTTCACGTCAATCCTGATGACCAGCAAAAACTGCCCGAGTGCCG | ||
| CAAACCTGAAGGGATATGCCGGAATGGTCGCGGATAACTATCACCGCCGTCTGGTGCTGGAAATCATGGA | ||
| TGAAATGCGTGAACCAATCCAAAGCGGAACCATCGACGCATCGAGTCAGGCGATGGATGAACTTGTAAAG | ||
| CGTCTTTCAGCCATCAGAAAGCCCCGTGACGAGGTTAAACCTGTACGGTTAGGGGAAATCATCACTGACT | ||
| ACACTGACACGCTTGACAGGCGTCTGAGGAACGGAGAAGAGTCAGATACCCTGAAGACCGGAATCGAAGA | ||
| GCTTGACGCTATCACCGGAGGGATGAACGCAGAAGACCTGGTGATTATCGCCGCTCGTCCTGGTATGGGG | ||
| AAAACCGAACTGGCGCTGAAGATTGCCGAAGGTGTGGCAAGCCGCGTTATTCCTGGTTCTGACGTCCGGC | ||
| GCGGGGTATTGATTTTCTCAATGGAAATGAGCGCATTGCAGATTGCAGAGCGAAGCATTGCCAACGCCGG | ||
| GAGGATGTCGGTTAGCGTACTGCGAAATCCTGCATCGATGGATGACGAGGGCTGGGCACGTGTTGCTAAC | ||
| GGCATGAGTCAGCTTGCAGATTTGGATGTATGGGTAGTCGATGCTTCGCGGTTATCGGTCGAAGAAATAC | ||
| GCTCAATCGCAGAACGGCATAAGCAGGAAAATCCAAACCTGTCACTCATCATGGCGGATTATCTTGGCCT | ||
| GATTGAGAAGCCGAAAGCAGACCGCAACGACCTCGCAATTGCTCACATCTCCGGAAGCCTGAAGGCGATG | ||
| GCGAAAGACCTGAAAACACCGGTTATCTCCCTGAGTCAGCTTTCGCGCGATGTTGAGAAGCGACCAAACA | ||
| AACGCCCGACAAACGCAGATTTGCGTGATTCAGGAAGCATTGAACAGGACGCAGACTCAATCACACATCG | ||
| GTGTCTGTTATTAACCACACCCCACCGGGCAGTTATTTTGCTGTGGATATACGAGGGCTTGATGTCTATC | ||
| AGGCGCGTTTTGACCATCTTCGTCTGATTATTGAGCAAAATAATTTATATGTGGCCGGGTTCGTTAATAC | ||
| GGCAACAAATACTTTCTACCGTTTTTCAGATTTTACACATATATCAGTGCCCGGTGTGACAACGGTTTCC | ||
| ATGACAACGGACAGCAGTTATACCACTCTGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCA | ||
| GTCGTCACTCACTGGTTTCATCATATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGATGC | ||
| ATCCAGAGCAGTTCTGCGTTTTGTCAGTCACAGCAGAAGCCTTACGCTTCAGGCAGATACAGAGAGAATT | ||
| TCGTCAGGCACTGTCTGAAACTGCTCCTGTGTATACGATGACGCCGGGAGACGTGGACCTCACTCTGAAC | ||
| TGGGGGCGAATCAGCAATGTGCTTCCGGAGTATCGGGGAGAGGATGGTGTCAGAGTGGGGAGAATATCCT | ||
| TTAATAATATATCGGCGATACTGGGCACTGTGGCCGTTATACTGAATTGTCATCATCAGGGGGCGCGTTC | ||
| TGTTCGCGCCGTGAATGAAGATAGTCAACCAGAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATA | ||
| AACAATACATTATGGGAAAGTAATACAGCTGCAGCGTTTCTGAACAGAAAGTCACAGTTTTTATATACAA | ||
| CGGGTAAATAAAGGAGTTAAGTATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTAGTTTCTGTTAAT | ||
| GCAATGGCGGCGGATTGCGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGAATGATACATTCACAG | ||
| TAAAAGTGGCCGGAAAAGAGTACTGGACCAGTCGCTGGAATCTGCAACCGTTACTGCAAAGTGCTCAGTT | ||
| GACAGGAATGACTGTCACAATCAAATCCAGTACCTGTGAATCAGGCTCCGGATTTGCTGAAGTGCAGTTT | ||
| AATAATGACTGAGGCATAACCTGATTCGTGGTATGTGGGTAACAAGTGTAATCTGTGTCACAATTCAGTC | ||
| AGTTGACAGTTGCCTGTCAGACTGAGCATTTGTTAAAAAAATTCGCATGGTGAATCCCCCTGTGCGGAGG | ||
| GGCGACTGGTGTATAAGGTGTCATCTCTGACGACAACCTGGATCGAGATACGCGGGTTCAGGGACACCGG | ||
| ACTGAACTCACCGGGAGGCACCCGGCACCATGTACATGATGATACAGATACGCAGTGTCAGCCCCTCTCC | ||
| GGAGGGGCTTTTTATCTGAATGATTCTGTTATTTTCGCCCGTATGGGCATATTTCCAGAATGCAGCGATG | ||
| ATTAAAACACTTATCTGTGATATTTCCTGTGTTTGCAGGGCACTCCTGGCTGTTTTTAATTAAATTCCAG | ||
| ACGTTTTTATTAAATGGGGCCACGTTGTAAATGGTGACGGGGAGCTCTTTATTATTGAGTATTACGCCTG | ||
| TCCGGGTTGGTGTAAAAATACAGCCCGGAGGGAGGAAGGTATCTGACTGATACCATAATATTAATTTTAT | ||
| GTTACACCATATGGCTGAAAATGATATGCCACATGCTGGCTGGATTACCGTGTCAATCACTATCCAGTTC | ||
| ATTTGCTTTCCTTATTTTCTTAAGGTTTTAAATGATGCCATAAATTATAGGTGATGTTTTGAAAGCAATC | ||
| TGTCAGGCTGAGTTGTTTTTCTGGTGTCGTTTATTCTTTGTTTAAAATAAGAGGGCATTTTAAATTGTCG | ||
| GCGTTTTTTTGTTATATAAGAGACATGGTTTTTTTATAGCGTGTTTTTTATGTGTTACATGATTGTGTGT | ||
| TCCGGATAATTACTTTGCTGGCGGCAGGAGAGGTTATGACATTTAAACACTACGATGTGGTCAGGGCGGC | ||
| ATCGCCGTCAGACCTTGCTGAACGACTGACACAAAAACTGA | ||
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||
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||
| >stx2_novel gb|AARSJU010000054.1| Escherichia coli strain PNUSAE016060 SAMN09787738-rid9281453.guided.46, whole genome shotgun sequence | ||
| GGCTGCGCGGGGTTCGAGTCCTCGATGGCGGTCCATTATCGGTATTCAGCGTTGTTAGCTCAGCCGGACA | ||
| GAGCAATTGCCTTCTAAGCAATCGGTCACTGGTTCGAATCCAGTACAACGCGCCATATTTATTTACCAGG | ||
| CTCGCTTTTGCGGGCCTTTTTTATATCTGCGCCGGGTCTGGTGCTGATTACTTCAGCCAAAAGGAACACC | ||
| TGTATATGAAGTGTATATTATTTAAATGGGTACTGTGCCTGTTACTGGGTTTTTCTTCGGTATCCTATTC | ||
| CCGGGAATTTACGATAGACTTTTCGACTCAACAAAGTTATGTCTCTTCGTTAAATAGTATACGGACAGAG | ||
| ATATCGACCCCTCTTGAACATATATCTCAGGGGACCACATCGGTGTCTGTTATTAACCACACCCCGCCGG | ||
| GCAGTTATTTTGCTGTGGATATACGAGGGCTTGATGTCTATCAGGCGCGTTTTGACCATCTTCGTCTGAT | ||
| TATTGAGCAAAATAATTTATATGTGGCCGGGTTCGTTAATACGGCAACAAATACTTTCTACCGTTTTTCA | ||
| GATTTTACACATATATCAGTGCCCGGTGTGACAACGGTTTCCATGACAACGGACAGCAGTTATACCACTC | ||
| TGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGTCGTCACTCACTGGTTTCATCATATCT | ||
| GGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGATGCATCCAGAGCAGTTCTGCGTTTTGTCACT | ||
| GTCACAGCAGAAGCCTTACGCTTCAGGCAGATACAGAGAGAATTTCGTCAGGCACTGTCTGAAACTGCTC | ||
| CTGTGTATACGATGACGCCGGGAGACGTGGACCTCACTCTGAACTGGGGGCGAATCAGCAATGTGCTTCC | ||
| GGAGTATCGGGGAGAGGATGGTGTCAGAGTGGGGAGAATATCCTTTAATAATATATCGGCGATACTGGGT | ||
| ACTGTGGCCGTTATACTGAATTGCCATCATCAGGGGGCGCGTTCTGTTCGCGCCGTGAATGAAGAGAGTC | ||
| AACCAGAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATAAACAATACATTATGGGAAAGTAATAC | ||
| AGCAGCAGCGTTTCTGAACAGAAAATCACAGTCTTTATATACAACGGGTAAATAAAGGAGTTAAGTATGA | ||
| AGAAGATGTTTATGGCGGTTTTATTTGCATTAGTTTCTGTTAATGCAATGGCGGCGGATTGCGCTAAAGG | ||
| TAAAATTGAGTTTTCCAAGTATAATGAGAATGATACATTCACAGTAAAAGTGGCCGGGAAAGAATACTGG | ||
| ACCAGTCGCTGGAATCTGCAACCGTTACTGCAAAGTGCTCAGCTGACAGGAATGACTGTCACAATCAAAT | ||
| CCAGTACCTGTGAATCAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACTGAGGCATAACCTGATT | ||
| CGTGGTATGTGGGTAACAAGTGTAATCTGTGTCACAATTCAGTCAGTTGACAGTTGCCTGTCAGACTGAG | ||
| CATTTGTTAAAAAA | ||
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| >stx1a gb|AAXXHU010000093.1| Escherichia coli strain PNUSAE065727 SAMN17086846-rid11246123.denovo.095, whole genome shotgun sequence | ||
| CATCCTGTGTATCAATAAATGTTGTTATCTACGTACGTCAAGTAGTCGCATGAGATCTGACCAGATATGT | ||
| TAAGGTTGCAGCTCTCTTTGAATATGATTATCATTTTCATTACGTTATTGTTACGTTTATCCGGTGCGCC | ||
| GTAAAACGCCGTCCTTCAGGGCGTGGAGGATGTCAAGAATATAGTTATCGTATGGTGCTCAAGGAGTATT | ||
| GTGTAATATGAAAATAATTATTTTTAGAGTGCTAACTTTTTTCTTTGTTATCTTTTCAGTTAATGTGGTG | ||
| GCGAAGGAATTTACCTTAGACTTCTCGACTGCAAAGACGTATGTAGATTCGCTGAATGTCATTCGCTCTG | ||
| CAATAGGTACTCCATTACAGACTATTTCATCAGGAGGTACGTCTTTACTGATGATTGATAGTGGCACAGG | ||
| GGATAATTTGTTTGCAGTTGATGTCAGAGGGATAGATCCAGAGGAAGGGCGGTTTAATAATCTACGGCTT | ||
| ATTGTTGAACGAAATAATTTATATGTGACAGGATTTGTTAACAGGACAAATAATGTTTTTTATCGCTTTG | ||
| CTGATTTTTCACATGTTACCTTTCCAGGTACAACAGCGGTTACATTGTCTGGTGACAGTAGCTATACCAC | ||
| GTTACAGCGTGTTGCAGGGATCAGTCGTACGGGGATGCAGATAAATCGCCATTCGTTGACTACTTCTTAT | ||
| CTGGATTTAATGTCGCATAGTGGAACCTCACTGACGCAGTCTGTGGCAAGAGCGATGTTACGGTTTGTTA | ||
| CTGTGACAGCTGAAGCTTTACGTTTTCGGCAAATACAGAGGGGATTTCGTACAACACTGGATGATCTCAG | ||
| TGGGCGTTCTTATGTAATGACTGCTGAAGATGTTGATCTTACATTGAACTGGGGAAGGTTGAGTAGCGTC | ||
| CTGCCTGACTATCATGGACAAGACTCTGTTCGTGTAGGAAGAATTTCTTTTGGAAGCATTAATGCAATTC | ||
| TGGGAAGCGTGGCATTAATACTGAATTGTCATCATCATGCATCGCGAGTTGCCAGAATGGCATCTGATGA | ||
| GTTTCCTTCTATGTGTCCGGCAGATGGAAGAGTCCGTGGGATTACGCACAATAAAATATTGTGGGATTCA | ||
| TCCACTCTGGGGGCAATTCTGATGCGCAGAACTATTAGCAGTTGAGGGGGTAAAATGAAAAAAACATTAT | ||
| TAATAGCTGCATCGCTTTCATTTTTTTCAGCAAGTGCGCTGGCGACGCCTGATTGTGTAACTGGAAAGGT | ||
| GGAGTATACAAAATATAATGATGACGATACCTTTACAGTTAAAGTGGGTGATAAAGAATTATTTACCAAC | ||
| AGATGGAATCTTCAGTCTCTTCTTCTCAGTGCGCAAATTACGGGGATGACTGTAACCATTAAAACTAATG | ||
| CCTGTCATAATGGAGGGGGATTCAGCGAAGTTATTTTTCGTTGACTCAGAATAGCTCAGTGAAAATAGCA | ||
| GGCGGAGATTCATAAATGTTAAATACATCTCAATTCAGTCAGTTGTTGCCGGTCTGATAATAGATGTGTT | ||
| AGAAAATTTCTGCATGGTGAATCCCCCTGTGCGGAGGGGCGACTGGTGAACGGTATGATCTCTTTGATGA | ||
| TCGTAAGCGAGAATACGCGGGTTTGGTGGCACCAGGCCGAACTCACCGGGAGGCACCCGGCATCATGCTG | ||
| TATACAGAGATTAGGCATATATCCAGGCTCCTCATCGCAGGAGCCTTTTTACATGCAAAAAAAAGCCCGA | ||
| GTGGGTTCGGGCAACAGCATGAGATACTTGCATTGTCATTTTTATCGTGCGGATTTTAACCAGGATTCAT | ||
| AAGGCTGCGCAACTGCGCGGCCTTTTTCGTATTTCGGGCTGTAGTCCCCGTGTGTCATTCAGGCTTCCGG | ||
| ACTACAGCCCACTCCATATCTGATTTAATACACTATCCCGGCCGGGAGGAATAATGACA | ||
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| >stx2c gb|AAASXN010000098.1| Listeria monocytogenes strain 104657 SAMN11191667-rid7376543.denovo.100, whole genome shotgun sequence | ||
| CGGCTCATGTCCTGCACATCATGCAGACAATGGTCCGCCGGAATGATGTCGTTATATCTGCATGCTGCAC | ||
| CACCCGGTGTCACCGTACTGCGACGCGCCAGTTGCTTAATACGCGGCTCCGGACGGTCATATGTCTCCGG | ||
| CAGCGGAAGACCTTCACCATACGACATGCCGTTTGACTGCCCTGCCAGAACCACAACAAAGTAATACTCC | ||
| GGGGCTCTGGTGGCACTGACAGCCACCGCCTTACCCTCATTACCGGTCACCGCCACTGGTGTGGTGACAT | ||
| CACCTTCCGCCGCAATGGCCTGCATCAGGGTGTAAGGCGTGATGGCCACCGGACTGCCAAATGGCTGCCA | ||
| GCCCTCCTTCAGTTTTTGTGTCAGTCGTTCAGCAAGGTCTGACGGCGATGCCGCCCTGACCACATCGTAG | ||
| TGTTTAAATGTCATAACCTCTCCTGCCGCCAGCAAAGTAATTATCCGGAACACACAATCATGTAACACAT | ||
| AAAAAACACGCTATAAAAAAACCATGTCTCTTATATAACAAAAAAACGCCGACAATTTAAAATGCCCTCT | ||
| TATTTTAAACAAAGAATAAACGACACCAGAAAAACAACTCAGCCTGACAGATTGCTTTCAAAACATCACC | ||
| TATAATTTATGGCATCATTTAAAACCTTAAGAAAATAAGGAAAGCAAATGAACTGGATAGTGATTGACAC | ||
| GGTAATCCAGCCAGCATGTGGCATATCATTTTCAGCCATATGGTGTAACATAAAATTAATATTATGGTAT | ||
| CAGTCAGATACCTTCCTCCCTCCGGGCTGTATTTTTACACCAACCCGGACAGGCGTAATACTCAATAATA | ||
| AAGAGCTCCCCGTCACCATTTACAACGTGGCCCCATTTAATAAAAACGTCTGGAATTTAATTAAAAACAG | ||
| CCAGGAGTGCCCTGCAAACACAGGAAATATCACAGATAAGTGTTTTAATCATCGCTGCATTCTGGAAATA | ||
| TGCCCATACGGGCGAAAATAACAGAATCATTCAGATAAAAAGCCCCTCCGGAGAGGGGCTGACACTGCGT | ||
| ATCTGTATCATCATGTACATGGTGCCGGGTGCCTCCCGGTGAGTTCAGTCCGGTGTCCCTGAACCCGCGT | ||
| ATCTCGCTCCAGGTTGTCGTCAGAGATGACACCTTATACACCAGTCGCCCCTCCGCACAGGGGGATTCAC | ||
| CATGCGAATTTTTTTAACGAATGCTCAGTCTGACAGGCAACTGTCAACTGACTGAATTGTGACACAGATT | ||
| ACACTTGTTACCCACATACCACGAATCAGGTTATGCCTCAGTCATTATTAAACTGCACTTCAGCAAATCC | ||
| GGAGCCTGATTCACAGGTACTGGATTTGATTGTGACAGTCATTCCTGTCAACTGAGCACTTTGCAGTAAC | ||
| GGTTGCAGATTCCAGCGACTGGTCCAGTACTCTTTTCCGGCCACTTTTACTGTGAATGTATCATTCTCAT | ||
| TATACTTGGAAAACTCAATTTTACCTTTAGCGCAATCCGCCGCCATTGCATTAACAGAAACTAATGCAAA | ||
| TAAAACCGCCATAAACATCTTCTTCATACTTAACTCCTTTATTTACCCGTTGTATATAAAAACTGTGACT | ||
| TTCTGTTCAGAAACGCTGCAGCTGTATTACTTTCCCATAATGTATTGTTTATTTTTATAACGGGCCTGTC | ||
| GCCAGTTATCTGACATTCTGGTTGACTATCTTCATTCACGGCGCGAACAGAACGCGCCCCCTGATGATGA | ||
| CAATTCAGTATAACGGCCACAGTGCCCAGTATCGCCGATATATTATTAAAGGATATTCTCCCCACTCTGA | ||
| CACCATCCTCTCCCCGATACTCCGGAAGCACATTGCTGATTCGCCCCCAGTTCAGAGTGAGGTCCACGTC | ||
| TCCCGGCGTCATCGTATACACAGGAGCAGTTTCAGACAGTGCCTGACGAAATTCTCTCTGTATCTGCCTG | ||
| AAGCGTAAGGCTTCTGCTGTGACAGTGACAAAACGCAGAACTGCTCTGGATGCATCTCTGGTCATTGTAT | ||
| TACCACTGAACTCCATTAACGCCAGATATGATGAAACCAGTGAGTGACGACTGATTTGCATTCCGGAACG | ||
| TTCCAGCGCTGCGACACGTTGCAGAGTGGTATAACTGCTGTCCGTTGTCATGGAAACCGTTGTCACACCG | ||
| GGCACTGATATATGTGTAAAATCTGAAAAACGGTAGAAAGTATTTGTTGCCGTATTAACGAACCCGGCCA | ||
| CATATAAATTATTTTGCTCAATAATCAGACGAAGATGGTCAAAACGCGCCTGATAGACATCAAGCCCTCG | ||
| TATATCCACAGCAAAATAACTGCCCGGTGGGGTGTGGTTAATAACAGACACCGATGTGGTCCCCTGAGAT | ||
| ATATGTTCAAGAGGGGTCGATATCTCTGTCCGTATACTATTTAACGAAGATACATAACTTTGTTGAGTCG | ||
| AAAAGTCTATCGTAAATTCCCGGGAATAGGATACCGAAGAAAAGCCCAGTAACAGGCACAGTACCCATTT | ||
| AAATAATATACACTTCATATACAAGGTGTTCCTTTTGGCTGAAGTAATCAGCACCAGACCCGGCGCAGAT | ||
| ATAAAAAAGGCCCGCAAAAGCGAGCCAGGGAAAATAAGTGTGGCGCGTTGTACTGGATTCGAACCAGTGA | ||
| CCGATTGCTTAGAAGGCAATTGCTCTGTCCTGCTGAGCTAACAACGCAGAATACCGATAATGGACCACCA | ||
| CCGGGGACTCGAACCTCGCGCAACCAGCTTCGAAGGCTGACGCTCTATCCCGATGAGCTAATGGCGGTTG | ||
| GTGGCCCTTGCTGGATTTGAACCAGCGACCTGGCGATTATGAGTCGCTCGCTCTCACCACTGAGCTAAAG | ||
| GGCC | ||
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| >partial_contig_end gb|AAMEYR010000123.1| Salmonella enterica subsp. enterica serovar Senftenberg strain 2017K-0250 SAMN06761671-rid5489163.denovo.123, whole genome shotgun sequence | ||
| GAAAACTCAATTTTACCTTTAGCACAATCCGCCGCCATTGCATTAACAGAAGCTAATGCAAATAAAACCG | ||
| CCATAAACATCTTCTTCATGCTTAACTCCTTTATTTACCCGTTGTATATAAAAACTGTGACTTTCTGTTC | ||
| AGAAACGCTGCAGCTGTATTACTTTCCCATAATGTATTGTTTATTTTTATAACAGGCCTGTCGCCAGTTA | ||
| TCTGACATTCTGGTTGACTCTCTTCATTCACGGCGCGAACAGAACGCGCCCCCTGATGATGGCAATTCAG | ||
| TATAACGGCCACAGTCCCCAGTATCGCTGATATATTATTAAAGGATATTCTCCCCACTCTGACACCATCC | ||
| TCTCCCCGATACTCCGGAAGCACATTGCTGATTCGCCCCCAGTTCAGAGTGAGGTCCACGTCTCCCGGCG | ||
| TCATCGTATACACAGGAGCAGTTTCAGACAGTGCCTGACGAAATTCTCTCTGTATCTGCCTGAAGCGTAA | ||
| GGCTTCTGCTGTGACAGTGACAAAACGCAGAACTGCTCTGGATGCATCTCTGGTCATTGTATTACCACTG | ||
| AACTCCATTAACGCCAGATATGATGAAACCAGTGAGTGACGACTGATTTGCATTCCGGAACGTTCCAGCG | ||
| CTGCGACACGTTGCAGAGTGGTATAACTGCT | ||
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| >partial gb|AATDDC010000166.1| Escherichia coli strain 2014C-3076 SAMN04502368-rid9102293.guided.129, whole genome shotgun sequence | ||
| ACAAATGGTAGTGTCCGCTATTGCCAGTACACCTCAGAGGGCTTGATGTCTATCAGGCGCGTTTTGACCA | ||
| TCTTCGTCTGATTATTGAGCAAAATAATTTATATGTGGCCGGGTTCGTTAATACGGCAACAAATACTTTC | ||
| TACCGTTTTTCAGATTTTACACATATATCAGTGCCCGGTGTGACAACGGTTTCCATGACAACGGACAGCA | ||
| GTTATACCACTCTGCAACGTGTCGCAGCGCTGGAACGTTCCGGAATGCAAATCAGTCGTCACTCACTGGT | ||
| TTCATCATATCTGGCGTTAATGGAGTTCAGTGGTAATACAATGACCAGAGATGCATCCAGAGCAGTTCTG | ||
| CGTTTTGTCACTGTCACAGCAGAAGCCTTACGCTTCAGGCAGATACAGAGAGAATTTCGTCAGGCACTGT | ||
| CTGAAACTGCTCCTGTGTATACGATGACGCCGGGAGACGTGGACCTCACTCTGAACTGGGGGCGAATCAG | ||
| CAATGTGCTTCCGGAGTATCGGGGAGAGGATGGTGTCAGAGTGGGGAGAATATCCTTTAATAATATATCA | ||
| GCGATACTGGGGACTGTGGCCGTTATACTGAATTGCCATCATCAGGGGGCGCGTTCTGTTCGCGCCGTGA | ||
| ATGAAGAGAGTCAACCAGAATGTCAGATAACTGGCGACAGGCCCGTTATAAAAATAAACAATACATTATG | ||
| GGAAAGTAATACAGCTGCAGCGTTTCTGAACAGAAAGTCACAGTTTTTATATACAACGGGTAAATAAAGG | ||
| AGTTAAGCATGAAGAAGATGTTTATGGCGGTTTTATTTGCATTAGCTTCTGTTAATGCAATGGCGGCGGA | ||
| TTGTGCTAAAGGTAAAATTGAGTTTTCCAAGTATAATGAGGATGACACATTTACAGTGAAGGTTGACGGG | ||
| AAAGAATACTGGACCAGTCGCTGGAATCTGCAACCGTTACTGCAAAGTGCTCAGTTGACAGGAATGACTG | ||
| TCACAATCAAATCCAGTACCTGTGAATCAGGCTCCGGATTTGCTGAAGTGCAGTTTAATAATGACTGAGG | ||
| CATAACCTGATTCGTGGTATGTGGGTAACAAGTGTAATCTGTGTCACAATTCAGTCAGTTGACAGTTGCC | ||
| TGTCAGACTGAGCATTTGTTAAAAAAATTTCGCATGGTGAATCCCCCTGTGTGGAGGGGCGACTGGTGAA | ||
| AAATCCTTGCTTGTGATTCATTATCGACACGGGTTCGGTGGTACCAAGCCGAACTCACCGGGAGGCACCC | ||
| GGCACCATGCAGTATACAGAGATTAGGCATATACCAAGGCCTCTCATAGCAGGGGCCTTTTTACATGTAA | ||
| AAAAAGCCCGAGTGGGTTCGGGCAATTGCATGAGATACTCGTTTTAATAATCGAAAGCATTTTAACCAGG | ||
| ATTCATAAGGCTGCGCAACTGCGCGGCCTTTTTCGTATTTCGGGCTGTAGTCTTCCTTCTGCCATTGTCC | ||
| TGTAACTTCCGGACTTCAGCCCGCT | ||
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| #Protein identifier Contig id Start Stop Strand Element symbol Element name Scope Element type Element subtype Class Subclass Method Target length Reference sequence length % Coverage of reference sequence % Identity to reference sequence Alignment length Accession of closest sequence Name of closest sequence HMM id HMM description Hierarchy node | ||
| na partial 27 1048 + stx2_operon Partial stx2 operon plus VIRULENCE STX_TYPE STX2 STX2 PARTIAL 1022 99.41 337 AAA16362.1, AAS07607.1 Shiga toxin stx2 na na stxA2c, stxB2a | ||
| na partial_contig_end 3 661 - stx2_operon Partial stx2 operon plus VIRULENCE STX_TYPE STX2 STX2 PARTIAL_CONTIG_END 659 100.00 216 AAM70046.1, AAA16362.1 Shiga toxin stx2 na na stxB2a, stxA2c | ||
| na stx1a 218 1444 + stx1a_operon stx1a operon plus VIRULENCE STX_TYPE STX1 STX1A COMPLETE 1227 100.00 406 AAA98347.1, AAA71894.1 Shiga toxin stx1a na na stxA1a, stxB1a | ||
| na stx2_fs 2165 3232 + stx2_operon stx2 operon with frameshift plus VIRULENCE STX_TYPE STX2 STX2 FRAMESHIFT 1068 99.15 355 AAG01033.1, AAA16363.1 Shiga toxin stx2c na na stxA2c, stxB2c | ||
| na stx2_novel 216 1456 + stx2_operon Novel stx2 operon plus VIRULENCE STX_TYPE STX2 STX2 COMPLETE_NOVEL 1241 99.76 410 AAA19623.1, AAA16363.1 Shiga toxin stx2c na na stxA2c, stxB2c | ||
| na stx2_stop 694 1653 + stx2_operon stx2 operon with internal stop plus VIRULENCE STX_TYPE STX2 STX2 INTERNAL_STOP 960 91.25 320 AUM09788.1 Shiga toxin stx2h subunit A na na stxA2h | ||
| na stx2c 1298 2538 - stx2c_operon stx2c operon plus VIRULENCE STX_TYPE STX2 STX2C COMPLETE 1241 100.00 410 AAA16363.1, AAS07596.1 Shiga toxin stx2c na na stxB2c, stxA2a |
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