Command line: [exonerate --exhaustive yes -m p2g --showtargetgff -q MSRA.anole.fa -t MSRA.extraccio.KQ745055.1.fa] Hostname: [sitdoc] C4 Alignment: ------------ Query: SPP00000202_2.0 # Protein # Methionine sulfoxide reductase A (MsrA) # Anole lizard Target: KQ745055.1:subseq(1345426,218395) Gekko japonicus isolate JY-2015 unplaced genomic scaffold scaffold7, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 867 Query range: 0 -> 205 Target range: 211634 -> 19999 1 : LysLeuLysArgLeuProSerGlnAlaGluAlaLeuProGlyArgSerArgSer >> : 19 |||:::||| |||||| !::! ! !! !||||||||| ...:::... LysIleLysAlaLeuProValArgIleTrpGluLeuProGlyGlyGlyLysGlu+- 211634 : aaaataaaagcattacCTGTAAGGATATGGGAGCTGCccggaggaggaaaagaaga.. : 211578 20 : >> Target Intron 1 >>>> LeuPheArgIleLeu{A} >>>> Target I : 24 279 bp ||| !:!!|||{!} 1291 ++LysPhePheValLeu{G}++ 211577 : .......................agaaattttTTGTTCTT{G}gt............. : 211283 25 : ntron 2 >>>> {sp}LysHisHisValAsnGlyAsnThrLeuValGluProPheP : 38 8 bp { !}||||||||||||||||||||| !:!!||||||||||||| ++{ly}LysHisHisValAsnGlyAsnCysIleValGluProPheP 211282 : ............ag{GT}AAACACCATGTCAATGGGAACTGTATAGTTGAACCTTTTC : 198326 39 : roGluGlyLeuHisMetAlaMetPhe{G} >>>> Target Intron 3 >>>> : 47 ||||||||:!!|||||||||!!:|||{|} 9859 bp roGluGlyMetHisMetAlaIlePhe{G}++ ++ 198325 : CAGAGGGAATGCACATGGCAATATTT{G}gt.........................ag : 188441 48 : {ly}MetGlyCysPheTrpGlyValGluArgLysPheTrpThrGlnLysGlyValTyr : 65 {||}||||||||||||||||||!.!|||||||||||||||! !||||||||||||||| {ly}MetGlyCysPheTrpGlyAlaGluArgLysPheTrpArgGlnLysGlyValTyr 188440 : {GT}ATGGGCTGTTTCTGGGGAGCAGAAAGAAAATTTTGGAGGCAGAAGGGAGTCTAC : 188386 66 : SerThrGlnValGlyTyrValGlyGlyIleThrProAsnProThrTyrGluGluValC : 85 ||||||||||||||||||!.!|||||| !|||! !|||||||||||||||||||||| SerThrGlnValGlyTyrAlaGlyGlyHisThrLeuAsnProThrTyrGluGluValC 188385 : TCAACTCAAGTGGGCTATGCAGGAGGACATACCCTAAATCCCACCTATGAAGAGGTCT : 188326 86 : ysThr{G} >>>> Target Intron 4 >>>> {ly}ArgThrGlyHisThrGl : 93 ||:!!{|} 48657 bp {||}!:!|||||||||.!!|| ysSer{G}++ ++{ly}LysThrGlyHisAlaGl 188325 : GTTCA{G}gt.........................ag{GA}AAAACTGGCCATGCCGA : 139645 94 : uValValArgValValPheGlnProGluThrIleSerPheGluLysLeuLeuLysVal : 112 |!.!||||||||||||!:!||||||||||||||||||||||||||||||||||||||| uAlaValArgValValTyrGlnProGluThrIleSerPheGluLysLeuLeuLysVal 139644 : AGCTGTGCGAGTGGTATATCAGCCGGAAACCATCAGTTTTGAGAAACTACTCAAGGTC : 139588 113 : PheTrpGluAsnHisAspProThrGln{G} >>>> Target Intron 5 >>>> : 122 |||||||||||||||||||||||||||{|} 14430 bp PheTrpGluAsnHisAspProThrGln{G}++ + 139587 : TTCTGGGAGAATCATGACCCAACGCAA{G}gt.........................a : 125129 123 : {ly}MetArgGlnGlyAsnAspValGlyThrGlnTyrArgSerAlaIleTyrThrTy : 140 {||}||||||||||||||||||||||||||||||||||||||||||||||||||||| +{ly}MetArgGlnGlyAsnAspValGlyThrGlnTyrArgSerAlaIleTyrThrTy 125128 : g{GA}ATGCGGCAGGGGAATGATGTTGGCACACAGTATAGATCTGCTATCTACACATA : 125074 141 : rSerProGlnGlnMetGluAlaAlaLeuArgSerArgAspGluTyrGlnLys >>>> : 158 |||| !!:!!||||||||||||||||||||||||!:!!!:!!:||||||||| rSerSerGluGlnMetGluAlaAlaLeuArgSerLysGluAspTyrGlnLys++ 125073 : CTCCTCAGAACagatggaagctgccctgagatCCAAAGAAGATTACCAGAAGgt.... : 125018 159 : Target Intron 6 >>>> ValLeuThrGluAsnGlyPheGlyProIleThrTh : 169 104877 bp |||||||||! !|||||||||||| !!|||||||| ++ValLeuThrAlaAsnGlyPheGlyAlaIleThrTh 125017 : .....................agGTGTTGACAGCGAATGGCTTTGGTGCGATCACAAC : 20110 170 : rGluIleArgGluAlaProGluPheTyrTyrAlaGluAspTyrHisGlnGlnTyrLeu : 188 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| rGluIleArgGluAlaProGluPheTyrTyrAlaGluAspTyrHisGlnGlnTyrLeu 20109 : TGAAATCCGTGAAGCTCCGGAGTTCTACTATGCTGAAGATTACCACCAGCAGTATCTA : 20053 189 : SerLysAsnProLysGlyTyrCysSerLeuArgGlyThrGlyValCysCys : 205 ||||||:!!|||!..|||||||||.!!||||||||||||||||||! !||| SerLysHisProSerGlyTyrCysGlyLeuArgGlyThrGlyValSerCys 20052 : AGCAAGCACCCCAGTGGGTACTGCGGTCTTCGAGGCACTGGGGTTTCCTGT : 20000 vulgar: SPP00000202_2.0 0 205 . KQ745055.1:subseq(1345426,218395) 211634 19999 - 867 M 18 54 5 0 2 I 0 275 3 0 2 M 5 15 S 0 1 5 0 2 I 0 12914 3 0 2 S 1 2 M 22 66 S 0 1 5 0 2 I 0 9855 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 48653 3 0 2 S 1 2 M 34 102 S 0 1 5 0 2 I 0 14426 3 0 2 S 1 2 M 35 105 5 0 2 I 0 104873 3 0 2 M 48 144 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-10 ##type DNA # # # seqname source feature start end score strand frame attributes # KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local gene 20000 211634 867 - . gene_id 1 ; sequence SPP00000202_2.0 ; gene_orientation + KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local cds 211581 211634 . - . KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local exon 211581 211634 . - . insertions 0 ; deletions 0 KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local splice5 211579 211580 . - . intron_id 1 ; splice_site "ga" KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local intron 211302 211580 . - . intron_id 1 KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local splice3 211302 211303 . - . intron_id 0 ; splice_site "ag" KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local cds 211286 211301 . - . KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local exon 211286 211301 . - . insertions 0 ; deletions 0 KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local splice5 211284 211285 . - . intron_id 2 ; splice_site "GT" KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local intron 198368 211285 . - . intron_id 2 KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local splice3 198368 198369 . - . intron_id 1 ; splice_site "AG" KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local cds 198299 198367 . - . KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local exon 198299 198367 . - . insertions 0 ; deletions 0 KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local splice5 198297 198298 . - . intron_id 3 ; splice_site "GT" KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local intron 188440 198298 . - . intron_id 3 KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local splice3 188440 188441 . - . intron_id 2 ; splice_site "AG" KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local cds 188320 188439 . - . KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local exon 188320 188439 . - . insertions 0 ; deletions 0 KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local splice5 188318 188319 . - . intron_id 4 ; splice_site "GT" KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local intron 139663 188319 . - . intron_id 4 KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local splice3 139663 139664 . - . intron_id 3 ; splice_site "AG" KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local cds 139558 139662 . - . KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local exon 139558 139662 . - . insertions 0 ; deletions 0 KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local splice5 139556 139557 . - . intron_id 5 ; splice_site "GT" KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local intron 125128 139557 . - . intron_id 5 KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local splice3 125128 125129 . - . intron_id 4 ; splice_site "AG" KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local cds 125021 125127 . - . KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local exon 125021 125127 . - . insertions 0 ; deletions 0 KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local splice5 125019 125020 . - . intron_id 6 ; splice_site "GT" KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local intron 20144 125020 . - . intron_id 6 KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local splice3 20144 20145 . - . intron_id 5 ; splice_site "AG" KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local cds 20000 20143 . - . KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local exon 20000 20143 . - . insertions 0 ; deletions 0 KQ745055.1:subseq(1345426,218395) exonerate:protein2genome:local similarity 20000 211634 867 - . alignment_id 1 ; Query SPP00000202_2.0 ; Align 211635 1 54 ; Align 211302 19 15 ; Align 198366 25 66 ; Align 188438 48 117 ; Align 139661 88 102 ; Align 125126 123 105 ; Align 20144 158 144 # --- END OF GFF DUMP --- # -- completed exonerate analysis