Command line: [exonerate -m p2g --showtargetgff -q MsrA.x.fa -t MsrA.extraction.KV884701.1.fa] Hostname: [sitdoc] C4 Alignment: ------------ Query: MsrA Protein # Methionine sulfoxide reductase A (MsrA) # Zebrafish Target: KV884701.1:subseq(3858856,100000) Monopterus albus unplaced genomic scaffold scaffold13.1, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 796 Query range: 8 -> 238 Target range: 77839 -> 49832 9 : PheValLeuGlnLeuGlyLeuCysValValValAlaGlnLeuGluMetAlaAsnLysSer : 28 |||:!!||| |||!.!!!! !:!!! !||| ! !|||||| !...::: PheLeuLeuPheLeuAlaPheValSerLeuAspAlaAlaGluProMetAlaCysAsnAla 77839 : TTTCTGCTATTTCTAGCGTTTGTGTCGCTGGACGCCGCCGAACCGATGGCATGTaatgct : 77782 29 : ValLeuProThrLysGluArgAlaLeuLysGlyArgGluGluLysValValValAla{A} : 48 ||||||:::::!!!:||||||||||||||||||:::||||||:::|||||||||{!} GlnLeuProSerArgAspArgAlaLeuLysGlyArgLysGluLysMetValValAla{A} 77781 : cagctgccaagcagAGACCGCGCTCtgaaaggaagaaaagagaaaatggttGTTGCA{G} : 77722 49 : >>>> Target Intron 1 >>>> {la}LysHisAlaAlaAsnGlyAsnThrThr : 57 5519 bp { !}|||||||||!.!||||||||| !!||| ++ ++{sp}LysHisAlaValAsnGlyAsnProThr 77721 : gt.........................ag{AC}AAGCATGCAGTCAATGGGAATCCCACT : 72176 58 : ValGluProPheProAspGlyMetGluMetIleMetPhe{G} >>>> Target Intr : 71 |||||||||||||||!!:|||||||||! |||||||||{|} 146 bp ValGluProPheProGluGlyMetGluThrIleMetPhe{G}++ 72175 : GTGGAGCCTTTTCCAGAAGGCATGGAGACCATCATGTTT{G}gt................ : 72131 72 : on 2 >>>> {ly}MetGlyCysPheTrpGlyAlaGluArgArgPheTrpLysIleThr : 86 {||}|||||||||||||||||||||||||||! !||||||:!!||| !! ++{ly}MetGlyCysPheTrpGlyAlaGluArgLeuPheTrpGlnIlePro 72130 : .........ag{GT}ATGGGCTGTTTCTGGGGAGCCGAGAGACTTTTCTGGCAGATTCCA : 71943 87 : GlyValPheSerThrGlnValGlyTyrAlaGlyGlyPheThrSerAsnProThrTyrHis : 106 ||||||||||||||||||||||||!:!|||||||||||||||:!!||||||||||||!!. GlyValPheSerThrGlnValGlyPheAlaGlyGlyPheThrAlaAsnProThrTyrGln 71942 : GGGGTCTTCTCCACACAGGTGGGCTTTGCCGGTGGCTTTACAGCCAACCCCACGTACCAG : 71883 107 : GluValCysSer{G} >>>> Target Intron 3 >>>> {ly}LeuThrGlyHis : 115 |||||| !!!!!{|} 3597 bp {||}|||||||||||| GluValArgThr{G}++ ++{ly}LeuThrGlyHis 71882 : GAGGTCCGCACA{G}gt.........................ag{GT}CTGACGGGTCAC : 68259 116 : ThrGluValValArgValValPheSerProLysAspValSerLeuGluLysLeuLeuLys : 135 ||||||||||||||||||||||||||||||||||||:!!|||||||||:!!||||||||| ThrGluValValArgValValPheSerProLysAspIleSerLeuGluGluLeuLeuLys 68258 : ACTGAGGTGGTCAGGGTGGTCTTCTCCCCAAAAGACATCAGCCTTGAGGAACTGCTCAAA : 68199 136 : ValPheTrpGluSerHisAspProThrGln{G} >>>> Target Intron 4 >>>> : 146 !|||||||||||||||||||||||||||{|} 10501 bp HisPheTrpGluSerHisAspProThrGln{G}++ 68198 : CACTTTTGGGAGAGCCATGATCCTACACAA{G}gt......................... : 68163 147 : {ly}MetAlaGlnGlyAsnAspHisGlyThrGlnTyrArgSerAlaIleTyrThrTyr : 164 {||}||| !||| !.!.||||||||||||||||||||||||||||||||||||! ! ++{ly}MetArgGlnGlnGluAspHisGlyThrGlnTyrArgSerAlaIleTyrThrSer 68162 : ag{GT}ATGAGGCAGCAGGAGGACCATGGTACTCAGTATCGTTCAGCCATTTACACATCC : 57611 165 : SerProGluGlnGlnAspLeuAlaMetLysSerLysHisMetTyrGlnGlu >>>> Ta : 182 ||||||! ||||||.!.||||||:!!!!.|||!:!.!. !:!|||:!! SerProAlaGlnGlnGlnLeuAlaLeuAsnSerArgGluAlaPheGlnGln++ 57610 : AGTCCCGCTCAACAGCAGCTTGCACTGAACAGCAGAGAGGCCTTCCAGCAGgt....... : 57555 183 : rget Intron 5 >>>> AlaLeuSerArgLysGlyLeuGlyGluIleThrThrAspI : 195 7554 bp !|||..!!:!||||||! !! ! |||||||||!!:| ++LysLeuAspLysLysGlyTyrAspProIleThrThrGluI 57554 : ..................agAAGCTGGATAAAAAAGGCTATGACCCCATCACCACAGAGA : 49964 196 : leArgGlnLeuThrValPheTyrTyrAlaGluAspTyrHisGlnGlnTyrLeuHisLysV : 215 ||! !:!! ! ! !|||||||||||||||||||||||||||||||||||| ! |||| leLeuGluGlyGlnGlnPheTyrTyrAlaGluAspTyrHisGlnGlnTyrLeuLysLysV 49963 : TCCTGGAGGGGCAGCAGTTCTACTACGCTGAGGACTATCACCAGCAGTACTTGAAGAAGG : 49904 216 : alProLysGlyTyrCysGlyLeuLysGlyThrGlyValThrCysSerIleThrGluGlyA : 235 |||||!!.||||||||||||||||||||||||||||||:!!||| !!||| !! !!! alProAsnGlyTyrCysGlyLeuLysGlyThrGlyValSerCysProIleGlyAlaArgL 49903 : TGCCTAACGGCTACTGTGGGCTCAAAGGCACCGGGGTCTCTTGTCCTATTGGAGCCAGGA : 49844 236 : rgAspGluLeu : 238 :!||||||||| ysAspGluLeu 49843 : AGGATGAACTG : 49833 vulgar: MsrA 8 238 . KV884701.1:subseq(3858856,100000) 77839 49832 - 796 M 39 117 S 0 1 5 0 2 I 0 5515 3 0 2 S 1 2 M 22 66 S 0 1 5 0 2 I 0 142 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 3593 3 0 2 S 1 2 M 34 102 S 0 1 5 0 2 I 0 10497 3 0 2 S 1 2 M 35 105 5 0 2 I 0 7550 3 0 2 M 57 171 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-28 ##type DNA # # # seqname source feature start end score strand frame attributes # KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local gene 49833 77839 796 - . gene_id 1 ; sequence MsrA ; gene_orientation + KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local cds 77722 77839 . - . KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local exon 77722 77839 . - . insertions 0 ; deletions 0 KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local splice5 77720 77721 . - . intron_id 1 ; splice_site "GT" KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local intron 72203 77721 . - . intron_id 1 KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local splice3 72203 72204 . - . intron_id 0 ; splice_site "AG" KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local cds 72134 72202 . - . KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local exon 72134 72202 . - . insertions 0 ; deletions 0 KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local splice5 72132 72133 . - . intron_id 2 ; splice_site "GT" KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local intron 71988 72133 . - . intron_id 2 KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local splice3 71988 71989 . - . intron_id 1 ; splice_site "AG" KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local cds 71868 71987 . - . KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local exon 71868 71987 . - . insertions 0 ; deletions 0 KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local splice5 71866 71867 . - . intron_id 3 ; splice_site "GT" KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local intron 68271 71867 . - . intron_id 3 KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local splice3 68271 68272 . - . intron_id 2 ; splice_site "AG" KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local cds 68166 68270 . - . KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local exon 68166 68270 . - . insertions 0 ; deletions 0 KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local splice5 68164 68165 . - . intron_id 4 ; splice_site "gt" KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local intron 57665 68165 . - . intron_id 4 KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local splice3 57665 57666 . - . intron_id 3 ; splice_site "AG" KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local cds 57558 57664 . - . KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local exon 57558 57664 . - . insertions 0 ; deletions 0 KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local splice5 57556 57557 . - . intron_id 5 ; splice_site "GT" KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local intron 50004 57557 . - . intron_id 5 KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local splice3 50004 50005 . - . intron_id 4 ; splice_site "AG" KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local cds 49833 50003 . - . KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local exon 49833 50003 . - . insertions 0 ; deletions 0 KV884701.1:subseq(3858856,100000) exonerate:protein2genome:local similarity 49833 77839 796 - . alignment_id 1 ; Query MsrA ; Align 77840 9 117 ; Align 72201 49 66 ; Align 71986 72 117 ; Align 68269 112 102 ; Align 57663 147 105 ; Align 50004 182 171 # --- END OF GFF DUMP --- # -- completed exonerate analysis