Command line: [exonerate -m p2g --showtargetgff -q ../MsrA-human.fa -t MsrA-NIVO01055729.1.subseq] Hostname: [sitdoc] C4 Alignment: ------------ Query: SPP00000012_1.0 # Protein # Methionine sulfoxide reductase A (MsrA) # Homo sapiens # Complete Target: NIVO01055729.1:subseq(13555,320826) Ammotragus lervia isolate NAZ scaffold1138_len1806233_cov71, whole genome shotgun sequence Model: protein2genome:local Raw score: 645 Query range: 47 -> 182 Target range: 49999 -> 158027 48 : AlaLysHisHisValAsnGlyAsnArgThrValGluProPheProGluGlyThrGlnM : 67 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| AlaLysHisHisValAsnGlyAsnArgThrValGluProPheProGluGlyThrGlnM 50000 : gccaAACATCATGTCAATGGCAACAGAACAGTTGAACCTTTCCCAGAGGGAACACAGA : 50057 68 : etAlaValPhe{G} >>>> Target Intron 1 >>>> {ly}MetGlyCysPh : 75 |||||:!!|||{|} 23573 bp {||}||||||||||| etAlaLeuPhe{G}++ ++{ly}MetGlyCysPh 50058 : TGGCTCTATTT{G}gt.........................ag{GA}ATGGGCTGTTT : 73654 76 : eTrpGlyAlaGluArgLysPheTrpValLeuLysGlyValTyrSerThrGlnValGly : 94 |||||||||||||||||||||||||..!|||||||||||||||||||||||||||||| eTrpGlyAlaGluArgLysPheTrpThrLeuLysGlyValTyrSerThrGlnValGly 73655 : CTGGGGAGCTGAAAGGAAATTCTGGACCCTGAAAGGTGTATATTCAACTCAAGTTGGT : 73711 95 : PheAlaGlyGlyTyrThrSerAsnProThrTyrLysGluValCysSer{G} >>>> : 111 !:!||||||||||||||| !!|||||||||||||||||||||||||||{!} TyrAlaGlyGlyTyrThrProAsnProThrTyrLysGluValCysSer{G}++ 73712 : TATGCAGGAGGCTATACTCCCAATCCTACTTATAAAGAAGTCTGCTCA{G}gt..... : 73765 112 : Target Intron 2 >>>> {lu}LysThrGlyHisAlaGluValValArgValVa : 122 54922 bp { !}|||||||||||||||||||||||||||||||| ++{ly}LysThrGlyHisAlaGluValValArgValVa 73766 : ....................ag{GA}AAAACTGGCCACGCAGAAGTAGTCCGGGTGGT : 128717 123 : lTyrGlnProGluHisMetSerPheGluGluLeuLeuLysValPheTrpGluAsnHis : 141 |||||||||||||!.!!!:||||||||||||||||||||||||||||||||||||||| lTyrGlnProGluArgIleSerPheGluGluLeuLeuLysValPheTrpGluAsnHis 128718 : GTACCAGCCAGAACGCATCAGCTTTGAGGAACTGCTCAAGGTCTTCTGGGAGAATCAT : 128774 142 : AspProThrGln{G} >>>> Target Intron 3 >>>> {ly}MetArgGlnG : 150 ||||||||||||{|} 29128 bp {||}|||||||||| AspProThrGln{G}++ ++{ly}MetArgGlnG 128775 : GACCCGACCCAA{G}gt.........................ag{GC}ATGCGCCAAG : 157929 151 : lyAsnAspHisGlyThrGlnTyrArgSerAlaIleTyrProThrSerAlaLysGlnMe : 169 ||||||||||||||:!!|||||||||||||||||||||||||||||||||:!!!!.|| lyAsnAspHisGlySerGlnTyrArgSerAlaIleTyrProThrSerAlaGluHisMe 157930 : GCAACGACCACGGCTCTCAGTACCGCTCCGCCATCTACCCGACCTCTGCTGAGCACAT : 157986 170 : tGluAlaAlaLeuSerSerLysGluAsnTyrGlnLysVal : 182 |! !|||||||||!!!|||:!!|||:!!|||||||||||| tGlyAlaAlaLeuArgSerGlnGluAspTyrGlnLysVal 157987 : GGGGGCAGCCCTGAGGTCCCAGGAGGACTACCAGAAGGTA : 158027 vulgar: SPP00000012_1.0 47 182 . NIVO01055729.1:subseq(13555,320826) 49999 158027 + 645 M 23 69 S 0 1 5 0 2 I 0 23569 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 54918 3 0 2 S 1 2 M 34 102 S 0 1 5 0 2 I 0 29124 3 0 2 S 1 2 M 36 108 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-21 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local gene 50000 158027 645 + . gene_id 1 ; sequence SPP00000012_1.0 ; gene_orientation + NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local cds 50000 50069 . + . NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local exon 50000 50069 . + . insertions 0 ; deletions 0 NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local splice5 50070 50071 . + . intron_id 1 ; splice_site "GT" NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local intron 50070 73642 . + . intron_id 1 NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local splice3 73641 73642 . + . intron_id 0 ; splice_site "AG" NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local cds 73643 73762 . + . NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local exon 73643 73762 . + . insertions 0 ; deletions 0 NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local splice5 73763 73764 . + . intron_id 2 ; splice_site "GT" NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local intron 73763 128684 . + . intron_id 2 NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local splice3 128683 128684 . + . intron_id 1 ; splice_site "AG" NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local cds 128685 128789 . + . NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local exon 128685 128789 . + . insertions 0 ; deletions 0 NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local splice5 128790 128791 . + . intron_id 3 ; splice_site "GT" NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local intron 128790 157917 . + . intron_id 3 NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local splice3 157916 157917 . + . intron_id 2 ; splice_site "AG" NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local cds 157918 158027 . + . NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local exon 157918 158027 . + . insertions 0 ; deletions 0 NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local similarity 50000 158027 645 + . alignment_id 1 ; Query SPP00000012_1.0 ; Align 50000 48 69 ; Align 73645 72 117 ; Align 128687 112 102 ; Align 157920 147 108 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000012_1.0 # Protein # Methionine sulfoxide reductase A (MsrA) # Homo sapiens # Complete Target: NIVO01055729.1:subseq(13555,320826) Ammotragus lervia isolate NAZ scaffold1138_len1806233_cov71, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 223 Query range: 182 -> 230 Target range: 270826 -> 270682 183 : LeuSerGluHisGlyPheGlyProIleThrThrAspIleArgGluGlyGlnThrPheT : 202 |||||||||||||||||||||! !||||||||||||||||||||||||||||||! !: LeuSerGluHisGlyPheGlyLeuIleThrThrAspIleArgGluGlyGlnThrSerH 270826 : TTGTCGGAGCATGGTTTCGGCCTGATCACCACGGACATCCGGGAGGGACAGACCTCTC : 270769 203 : yrTyrAlaGluAspTyrHisGlnGlnTyrLeuSerLysAsnProAsnGlyTyrCysGl : 221 !!||| !||||||||||||:!!|||||||||.!!|||||||||:!!|||!:!|||! isTyrMetGluAspTyrHisGluGlnTyrLeuGlyLysAsnProAspGlyPheCysAs 270768 : ACTACATGGAGGATTACCACGAGCAGTACCTAGGCAAGAACCCCGATGGGTTCTGTGA : 270712 222 : yLeuGlyGlyThrGlyValSerCysPro : 230 !||||||||||||||||||||||||||| pLeuGlyGlyThrGlyValSerCysPro 270711 : CCTCGGGGGCACCGGAGTGTCCTGTCCC : 270683 vulgar: SPP00000012_1.0 182 230 . NIVO01055729.1:subseq(13555,320826) 270826 270682 - 223 M 48 144 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-21 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local gene 270683 270826 223 - . gene_id 1 ; sequence SPP00000012_1.0 ; gene_orientation . NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local cds 270683 270826 . - . NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local exon 270683 270826 . - . insertions 0 ; deletions 0 NIVO01055729.1:subseq(13555,320826) exonerate:protein2genome:local similarity 270683 270826 223 - . alignment_id 1 ; Query SPP00000012_1.0 ; Align 270827 183 144 # --- END OF GFF DUMP --- # -- completed exonerate analysis