Command line: [exonerate -m p2g --showtargetgff -q ../MSRB3-human.fa -t MSRB3-NIVO01040223.1.subseq] Hostname: [sitdoc] C4 Alignment: ------------ Query: SPP00000270_2.0 # Protein # Methionine-R-sufoxide reductase 3 (MSRB3) # Cow Target: NIVO01040223.1:subseq(1447076,279199) Ammotragus lervia isolate NAZ scaffold2320_len1942639_cov71, whole genome shotgun sequence Model: protein2genome:local Raw score: 987 Query range: 0 -> 191 Target range: 49999 -> 229292 1 : MetSerProArgArgThrLeuProArgProPheLeuLeuCysLeuCysLeuSerLeuC : 20 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MetSerProArgArgThrLeuProArgProPheLeuLeuCysLeuCysLeuSerLeuS 50000 : ATGAGCCCGCGGCGGACCCTCCCGCGCCCCTTCTTGCTCTGCCTCTGCCTCAGCCTCA : 50057 21 : ysLeuAlaAlaAlaAlaAlaArgGlyAlaValGlnSer{G} >>>> Target Int : 33 !!||||||||||||||||||||||||||||||||||||{|} 57431 erLeuAlaAlaAlaAlaAlaArgGlyAlaValGlnSer{G}++ 50058 : GCCTGGCCGCGGCCGCGGCCCGCGGAGCAGTGCAGTCC{G}gt............... : 50099 34 : ron 1 >>>> {ly}SerCysArgAspLysLysAsnCysLysValValPheSerGln : 47 bp {||}|||||||||||||||||||||||||||||||||||||||||| ++{ly}SerCysArgAspLysLysAsnCysLysValValPheSerGln 50100 : ..........ag{GG}TCATGTAGGGATAAAAAGAACTGTAAGGTGGTCTTTTCCCAG : 107569 48 : GlnGluLeuArgLysArgLeuThrProLeuGlnTyrHisValThrGlnGluLysGlyT : 67 :!!||||||||||||||||||||||||||||||||||||||||||||||||||||||| GluGluLeuArgLysArgLeuThrProLeuGlnTyrHisValThrGlnGluLysGlyT 107570 : GAGGAACTGAGGAAGCGGCTAACACCCCTGCAATACCATGTCACTCAGGAGAAAGGGA : 107629 68 : hrGlu{Se} >>>> Target Intron 2 >>>> {r}AlaPheGluGlyGluTy : 75 |||||{||} 1614 bp {|}||||||||||||||||| hrGlu{Se}++ ++{r}AlaPheGluGlyGluTy 107630 : CCGAA{AG}gt.........................ag{T}GCCTTCGAAGGAGAATA : 109267 76 : rThrHisHisLysAspProGlyIleTyrLysCysValValCysGlyThrProLeuPhe : 94 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| rThrHisHisLysAspProGlyIleTyrLysCysValValCysGlyThrProLeuPhe 109268 : TACACATCACAAAGATCCTGGAATATACAAATGTGTTGTTTGTGGAACTCCATTGTTT : 109324 95 : {Ly} >>>> Target Intron 3 >>>> {s}SerGluThrLysPheAspSerG : 103 {||} 44702 bp {|}|||||||||||||||||||||| {Ly}++ ++{s}SerGluThrLysPheAspSerG 109325 : {AA}gt.........................ag{G}TCAGAAACCAAATTTGACTCCG : 154053 104 : lySer{G} >>>> Target Intron 4 >>>> {ly}TrpProSerPheHisAs : 111 |||||{|} 65162 bp {||}||||||||||||||||| lySer{G}++ ++{ly}TrpProSerPheHisAs 154054 : GTTCA{G}gt.........................ag{GC}TGGCCTTCATTCCACGA : 219239 112 : pValIleAsnSerAspAlaIleThrPheThrAspAspPheSerTyrGlyMetHisArg : 130 |||||||||||||||||||:!:|||||||||||||||||||||||||||||||||||| pValIleAsnSerAspAlaValThrPheThrAspAspPheSerTyrGlyMetHisArg 219240 : CGTGATCAATTCTGATGCGGTGACATTCACAGATGACTTTTCCTATGGGATGCACAGG : 219296 131 : ValGluThrSerCysSerGln >>>> Target Intron 5 >>>> CysGlyAl : 140 ||||||||||||||||||||| 9811 bp |||||||| ValGluThrSerCysSerGln++ ++CysGlyAl 219297 : GTGGAGACCAGCTGCTCTCAGgt.........................agTGCGGTGC : 229137 141 : aHisLeuGlyHisIlePheAspAspGlyProArgProThrGlyLysArgTyrCysIle : 159 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| aHisLeuGlyHisIlePheAspAspGlyProArgProThrGlyLysArgTyrCysIle 229138 : TCACCTCGGGCACATTTTCGACGACGGACCTCGTCCAACCGGCAAAAGATACTGCATA : 229194 160 : AsnSerAlaSerLeuSerPheSerProAlaGluSerSerGlyAlaGlnGlyAspSerA : 179 |||||||||||||||||||||!!! !!||||||||||||||| !!||||||||||||| AsnSerAlaSerLeuSerPheThrAlaAlaGluSerSerGlyProGlnGlyAspSerA 229195 : AACTCGGCATCCTTGTCTTTCACCGCTGCAGAGAGCAGTGGCCCCCAGGGGGACAGTG : 229254 180 : laGlyGlySerProAlaProGlyAspLysThrGluLeu : 191 |||||||||||||||||||||||||||||||||||||| laGlyGlySerProAlaProGlyAspLysThrGluLeu 229255 : CGGGGGGCAGCCCGGCCCCTGGTGACAAGACGGAGCTG : 229292 vulgar: SPP00000270_2.0 0 191 . NIVO01040223.1:subseq(1447076,279199) 49999 229292 + 987 M 32 96 S 0 1 5 0 2 I 0 57427 3 0 2 S 1 2 M 35 105 S 0 2 5 0 2 I 0 1610 3 0 2 S 1 1 M 25 75 S 0 2 5 0 2 I 0 44698 3 0 2 S 1 1 M 9 27 S 0 1 5 0 2 I 0 65158 3 0 2 S 1 2 M 32 96 5 0 2 I 0 9807 3 0 2 M 54 162 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-24 ##type DNA # # # seqname source feature start end score strand frame attributes # NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local gene 50000 229292 987 + . gene_id 1 ; sequence SPP00000270_2.0 ; gene_orientation + NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local cds 50000 50096 . + . NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local exon 50000 50096 . + . insertions 0 ; deletions 0 NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local splice5 50097 50098 . + . intron_id 1 ; splice_site "GT" NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local intron 50097 107527 . + . intron_id 1 NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local splice3 107526 107527 . + . intron_id 0 ; splice_site "AG" NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local cds 107528 107636 . + . NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local exon 107528 107636 . + . insertions 0 ; deletions 0 NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local splice5 107637 107638 . + . intron_id 2 ; splice_site "GT" NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local intron 107637 109250 . + . intron_id 2 NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local splice3 109249 109250 . + . intron_id 1 ; splice_site "AG" NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local cds 109251 109328 . + . NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local exon 109251 109328 . + . insertions 0 ; deletions 0 NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local splice5 109329 109330 . + . intron_id 3 ; splice_site "GT" NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local intron 109329 154030 . + . intron_id 3 NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local splice3 154029 154030 . + . intron_id 2 ; splice_site "AG" NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local cds 154031 154059 . + . NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local exon 154031 154059 . + . insertions 0 ; deletions 0 NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local splice5 154060 154061 . + . intron_id 4 ; splice_site "Gt" NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local intron 154060 219221 . + . intron_id 4 NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local splice3 219220 219221 . + . intron_id 3 ; splice_site "AG" NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local cds 219222 219319 . + . NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local exon 219222 219319 . + . insertions 0 ; deletions 0 NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local splice5 219320 219321 . + . intron_id 5 ; splice_site "GT" NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local intron 219320 229130 . + . intron_id 5 NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local splice3 229129 229130 . + . intron_id 4 ; splice_site "AG" NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local cds 229131 229292 . + . NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local exon 229131 229292 . + . insertions 0 ; deletions 0 NIVO01040223.1:subseq(1447076,279199) exonerate:protein2genome:local similarity 50000 229292 987 + . alignment_id 1 ; Query SPP00000270_2.0 ; Align 50000 1 96 ; Align 107530 34 105 ; Align 109252 70 75 ; Align 154032 96 27 ; Align 219224 106 96 ; Align 229131 138 162 # --- END OF GFF DUMP --- # -- completed exonerate analysis