Command line: [exonerate -m p2g --showtargetgff -q selenos_zf.aa.fa.canviat -t genomeselenos_JXSJ01001008.1.fa] Hostname: [ws101072u] C4 Alignment: ------------ Query: SPP00000648_2.0 # Protein # Selenoprotein S (SELENOS) # Zebrafish Target: JXSJ01001008.1:subseq(27347,63653) Miichthys miiuy scaffold1008, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 433 Query range: 16 -> 190 Target range: 50579 -> 48186 17 : GlnAsnGlnAspLeuSerPheLeuGlnProSerValThrAlaPheMetSerGluTyrGly : 36 :::......:!!:!! !! !|||! ! !!!!!||| !!.!|||:!!|||:!!|||||| LysThrSerAsnMetLeuCysLeuLeuSerThrValGlyGlyPheLeuSerGlnTyrGly 50579 : aaaacaaGTAACATGCTGTGTTTGCTGTCCACAGTAGGAGGGTTTCTGTCCCAGTATGGG : 50522 37 : TrpTyrLeuLeuPheGlyCysValGlyValTyrLeuLeuIleGlnHisLeuArgLysSer : 56 |||||||||:!! !!! ! !!.! !||||||||||||||||||:!!|||!.!|||!!! TrpTyrLeuValValValThrAlaLeuValTyrLeuLeuIleGlnTyrLeuAsnLysArg 50521 : TGGTACCTGGTGGTTGTGACTGCGCTGGTCTACCTGCTTATCCAGTACCTAAACAAGAGG : 50462 57 : ArgSerSerThrGlnThrArgSerSerSerGlySerAlaGluAla{H} >>>> Targe : 72 ! !|||||| !... !||||||||| !! !..!.!! ! !{.} LeuSerSerGlnSerTyrArgSerSerProProGlnThrProGln{G}++ 50461 : CTATCCAGCCAGAGCTATCGCAGCTCACCACCACAAACACCACAA{G}gt.......... : 50411 73 : t Intron 1 >>>> {is}AspValGlySerValValArgArgGlnGluAlaLeuGlu : 85 122 bp {!.}|||!.!! ! !|||!.!|||!.!|||||||||:!!!!: --{lu}AspAlaGluValValAlaArgAsnGlnGluAlaMetAsp 50410 : ...............ta{AA}GATGCTGAGGTCGTGGCGAGAAATCAAGAGGCCATGGAC : 50253 86 : AlaSerArgArgArgMetGlnGluGluGlnAspAlaArgAlaAlaGluPheArgGluLys : 105 |||:!!|||||||||||||||||||||! ||||||!:!|||||| |||||||||||| AlaAlaArgArgArgMetGlnGluGluLeuAspAlaLysAlaAlaIlePheArgGluLys 50252 : GCAGCTCGGAGAAGGATGCAAGAGGAGCTCGATGCTAAAGCAGCCATcttcagagagaaa : 50193 106 : GlnArgMet >>>> Target Intron 2 >>>> LeuGluGluGluLysArgArgG : 116 |||:::... 92 bp ||||||||||||||||||| GlnLysGln++ ++GlnGluGluGluLysArgArgG 50192 : cagaaacaggt.........................agcaagaagaagagaagaggaggc : 50068 117 : lnLysIleGluMetTrpAspSerMetGlnGluGlyLysSerTyrLysGlySerAlaLysV : 136 |||||||||||!!:|||!!:|||||||||:!!||||||||||||||||||:!!|||||| lnLysIleGluIleTrpGluSerMetGlnGlnGlyLysSerTyrLysGlyAlaAlaLysP 50067 : agaaaaTAGAGATATGGGAGAGTATGCAGCAGGGAAAGAGTTACAAAGGAGCTGCAAAAC : 50008 137 : alAlaGln >>>> Target Intron 3 >>>> GlnAsnThrGluGluAlaAlaSe : 146 !.!!||| 540 bp !!.! !|||! ::!.!!|| roThrGln++ ++ThrThrGluGluAlaSerThrSe 50007 : CAACACAGgt.........................agACAACTGAAGAAGCCAGCACGTC : 49438 147 : rSerSerSerLeuArgProLysThrGluLysLysProLeuArgSerSer{G} >>>> T : 163 |!!!!!!:!! !!:!|||||||||!!:|||!:!||||||||||||:!!{!} rThrThrAlaThrLysProLysThrAspLysArgProLeuArgSerAla{A}++ 49437 : AACAACGGCGACAAAACCAAAGACGGACAAGAGGCCACTTCGCAGTGCA{G}gt...... : 49384 164 : arget Intron 4 >>>> {ly}TyrSerProLeuSerGlyAspAlaGlyGlySerCy : 175 1117 bp { !}|||!:!||||||!!!|||.!.!.!||||||!!!|| ++{sp}TyrAsnProLeuThrGlyGlnGlyGlyGlyThrCy 49383 : ...................ag{ac}taCAATCCCCTGACTGGACAGGGAGGAGGCACCTG : 48234 176 : sSerTrpArgProGlyArgArgGlyProSerAlaGlyGlyUnkGly : 190 |||||||||||||||||||||||||||||||:!!|||||| ||| sSerTrpArgProGlyArgArgGlyProSerSerGlyGly***Gly 48233 : CTCCTGGAGACCTGGGAGGAGAGGGCCGTCTTCTGGTGGATGAGGT : 48187 vulgar: SPP00000648_2.0 16 190 . JXSJ01001008.1:subseq(27347,63653) 50579 48186 - 433 M 55 165 S 0 1 5 0 2 I 0 118 3 0 2 S 1 2 M 36 108 5 0 2 I 0 88 3 0 2 M 30 90 5 0 2 I 0 536 3 0 2 M 24 72 S 0 1 5 0 2 I 0 1113 3 0 2 S 1 2 M 27 81 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-21 ##type DNA # # # seqname source feature start end score strand frame attributes # JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local gene 48187 50579 433 - . gene_id 1 ; sequence SPP00000648_2.0 ; gene_orientation + JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local cds 50414 50579 . - . JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local exon 50414 50579 . - . insertions 0 ; deletions 0 JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local splice5 50412 50413 . - . intron_id 1 ; splice_site "GT" JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local intron 50292 50413 . - . intron_id 1 JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local splice3 50292 50293 . - . intron_id 0 ; splice_site "TA" JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local cds 50182 50291 . - . JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local exon 50182 50291 . - . insertions 0 ; deletions 0 JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local splice5 50180 50181 . - . intron_id 2 ; splice_site "gt" JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local intron 50090 50181 . - . intron_id 2 JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local splice3 50090 50091 . - . intron_id 1 ; splice_site "ag" JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local cds 50000 50089 . - . JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local exon 50000 50089 . - . insertions 0 ; deletions 0 JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local splice5 49998 49999 . - . intron_id 3 ; splice_site "GT" JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local intron 49460 49999 . - . intron_id 3 JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local splice3 49460 49461 . - . intron_id 2 ; splice_site "AG" JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local cds 49387 49459 . - . JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local exon 49387 49459 . - . insertions 0 ; deletions 0 JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local splice5 49385 49386 . - . intron_id 4 ; splice_site "GT" JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local intron 48270 49386 . - . intron_id 4 JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local splice3 48270 48271 . - . intron_id 3 ; splice_site "ag" JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local cds 48187 48269 . - . JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local exon 48187 48269 . - . insertions 0 ; deletions 0 JXSJ01001008.1:subseq(27347,63653) exonerate:protein2genome:local similarity 48187 50579 433 - . alignment_id 1 ; Query SPP00000648_2.0 ; Align 50580 17 165 ; Align 50290 73 108 ; Align 50090 109 90 ; Align 49460 139 72 ; Align 48268 164 81 # --- END OF GFF DUMP --- # -- completed exonerate analysis