Command line: [exonerate -m p2g --showtargetgff -q selenom_zf.aa.fa.canviat -t genomeselenom_JXSJ01000037.1.fa] Hostname: [ws101151U] C4 Alignment: ------------ Query: SPP00000638_2.0 # Protein # Selenoprotein M (SELENOM) # Zebrafish Target: JXSJ01000037.1:subseq(972323,101357) Miichthys miiuy scaffold37, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 456 Query range: 0 -> 126 Target range: 52545 -> 49999 1 : LeuIlePheThrAlaLeuLeuProSerValIleLeuThrTyrGluValAsnIleGluLys : 20 |||||| ! !||| !|||! !..! ! !! !.!!|||!!:|||:!!:!::!!||| LeuIleValLeuAlaSerLeuLeuGlnCysAlaSerAlaTyrAspValAspLeuLysLys 52545 : CTGATAGTGTTGGCCAGTTTACTTCAGTGCGCCTCGGCCTACGATGTGGATCTGAAGAAA : 52488 21 : LeuSerGlyLeuAlaArgAlaArgValGlu >>>> Target Intron 1 >>>> T : 31 |||..!|||||||||!:!|||||||||||| 750 bp | LeuAspGlyLeuAlaLysAlaArgValGlu++ ++T 52487 : CTGGACGGGCTGGCAAAAGCGAGGGTGGAGgt.........................agA : 51705 32 : hrCysGlyGlyUnkGlnLeuAsnArgMetArgGlu >>>> Target Intron 2 >> : 43 ||||||||||| ||||||||||||:!:|||||| 162 bp hrCysGlyGly***GlnLeuAsnArgLeuArgGlu++ 51704 : CATGCGGTGGATGACAGCTGAACAGGCTCAGAGAGgt....................... : 51667 44 : >> ValLysAlaPheValThrGlnAspIleProLeu{Ty} >>>> Target Intro : 54 |||||||||||||||..!|||||||||||||||{||} 120 bp ++ValLysAlaPheValValGlnAspIleProLeu{Ty}++ 51666 : ..aggtcaAAGCCTTTGTGGTCCAGGACATTCCTCTT{TA}gt................. : 51470 55 : n 3 >>>> {r}HisAsnLeuValMetLysHisIleProGlyAlaAspProGluLeuVa : 70 {|}||||||||||||||||||||||||||||||||||||||||||||||| ++{r}HisAsnLeuValMetLysHisIleProGlyAlaAspProGluLeuVa 51469 : ........ag{C}CATAACCTGGTGATGAAGCATATTCCTGGGGCCGACCCTGAGCTTGT : 51306 71 : lLeuLeuAsnHisTyrTyrGluGluLeuAsp >>>> Target Intron 4 >>>> : 81 ||||||||||||||||||||||||||||||| 1136 bp lLeuLeuAsnHisTyrTyrGluGluLeuAsp++ ++ 51305 : CCTCCTGAACCACTATTACGAAGAGCTGGATgt.........................ag : 50139 82 : ArgIleProLeuSerGluMetThrArgAlaGluIleAsnLysLeuLeuAlaGluLeuGly : 100 |||||| !!||||||!!:|||||||||:!!|||||||||:!!||||||! !:!!|||||| ArgIleAlaLeuSerAspMetThrArgSerGluIleAsnGluLeuLeuGluLysLeuGly 50138 : CGGATCGCCCTGTCCGACATGACCCGCTCTGAGATCAACGAGCTGCTGGAGAAGCTTGGC : 50080 101 : PheTyrLysLysAspHisProGluAspGlnValProGluGluPheArgPheSerProAla : 120 ||||||||||||! !!!. !!||||||:!!|||||||||||||||||||||||||||||| PheTyrLysLysAlaGlnAlaGluAspGluValProGluGluPheArgPheSerProAla 50079 : TTCTACAAGAAGGCTCAAGCTGAGGATGAGGTGCCGGAGGAGTTTCGCTTCTCTCCTGCC : 50020 121 : LysAspSerProPheGlu : 126 |||||||||||||||:!! LysAspSerProPheLys 50019 : AAAGACAGCCCGTTTAAA : 50000 vulgar: SPP00000638_2.0 0 126 . JXSJ01000037.1:subseq(972323,101357) 52545 49999 - 456 M 30 90 5 0 2 I 0 746 3 0 2 M 12 36 5 0 2 I 0 158 3 0 2 M 11 33 S 0 2 5 0 2 I 0 116 3 0 2 S 1 1 M 26 78 5 0 2 I 0 1132 3 0 2 M 46 138 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-17 ##type DNA # # # seqname source feature start end score strand frame attributes # JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local gene 50000 52545 456 - . gene_id 1 ; sequence SPP00000638_2.0 ; gene_orientation + JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local cds 52456 52545 . - . JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local exon 52456 52545 . - . insertions 0 ; deletions 0 JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local splice5 52454 52455 . - . intron_id 1 ; splice_site "GT" JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local intron 51706 52455 . - . intron_id 1 JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local splice3 51706 51707 . - . intron_id 0 ; splice_site "AG" JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local cds 51670 51705 . - . JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local exon 51670 51705 . - . insertions 0 ; deletions 0 JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local splice5 51668 51669 . - . intron_id 2 ; splice_site "GT" JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local intron 51508 51669 . - . intron_id 2 JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local splice3 51508 51509 . - . intron_id 1 ; splice_site "ag" JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local cds 51473 51507 . - . JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local exon 51473 51507 . - . insertions 0 ; deletions 0 JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local splice5 51471 51472 . - . intron_id 3 ; splice_site "GT" JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local intron 51353 51472 . - . intron_id 3 JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local splice3 51353 51354 . - . intron_id 2 ; splice_site "AG" JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local cds 51274 51352 . - . JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local exon 51274 51352 . - . insertions 0 ; deletions 0 JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local splice5 51272 51273 . - . intron_id 4 ; splice_site "GT" JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local intron 50138 51273 . - . intron_id 4 JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local splice3 50138 50139 . - . intron_id 3 ; splice_site "AG" JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local cds 50000 50137 . - . JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local exon 50000 50137 . - . insertions 0 ; deletions 0 JXSJ01000037.1:subseq(972323,101357) exonerate:protein2genome:local similarity 50000 52545 456 - . alignment_id 1 ; Query SPP00000638_2.0 ; Align 52546 1 90 ; Align 51706 31 36 ; Align 51508 43 33 ; Align 51352 55 78 ; Align 50138 81 138 # --- END OF GFF DUMP --- # -- completed exonerate analysis