Command line: [exonerate -m p2g --showtargetgff -q SELENOM.fa -t genomic.fa] Hostname: [ws101087U] C4 Alignment: ------------ Query: sp|Q802G7|SELM_DANRE Selenoprotein M OS=Danio rerio GN=selm PE=2 SV=2 Target: CM004435.1:subseq(14750000,150000) Ictalurus punctatus breed USDA103 chromosome 22, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 509 Query range: 1 -> 129 Target range: 9539 -> 4817 2 : TrpProLeuIlePheThrAlaLeuLeuProSerValIleLeuThrTyrGluValAsnIleGl : 22 |||||||||:!!!::.!!|||!!!||||||!!!:!!! !|||.!!|||||||||:!! :! TrpProLeuLeuTrpAlaAlaPheLeuProCysIleSerLeuAlaTyrGluValAspTrpLy 9539 : TGGCCGCTGTTATGGGCTGCGTTTCTCCCATGCATCAGCTTGGCTTATGAAGTGGACTGGAA : 9479 23 : uLysLeuSerGlyLeuAlaArgAlaArgValGlu >>>> Target Intron 1 >>>> : 34 !||||||..!|||||||||||||||!:!|||||| 1491 bp sLysLeuAspGlyLeuAlaArgAlaLysValGlu++ + 9478 : GAAGCTGGATGGTCTCGCCAGAGCAAAAGTGGAGgt.........................a : 7954 35 : ThrCysGlyGlyUnkGlnLeuAsnArgMetArgGlu >>>> Target Intron 2 >> : 46 !:!||||||||| ||||||||||||:!!|||||| 285 bp +SerCysGlyGly***GlnLeuAsnArgLeuArgGlu++ 7953 : gAGCTGTGGAGGATGACAGCTGAATAGACTGAGGGAGgt....................... : 7914 47 : >> ValLysAlaPheValThrGlnAspIleProLeu{Ty} >>>> Target Intron : 57 |||||||||||||||||||||||||||||||||{||} 426 bp ++ValLysAlaPheValThrGlnAspIleProLeu{Ty}++ 7913 : ..agGTCAAGGCCTTCGTGACCCAAGACATCCCTCTC{TA}gt................... : 7594 58 : 3 >>>> {r}HisAsnLeuValMetLysHisIleProGlyAlaAspProGluLeuValLeu : 74 {|}||||||||||||||||||||||||||||||||||||||||||||||||||| ++{r}HisAsnLeuValMetLysHisIleProGlyAlaAspProGluLeuValLeu 7593 : ......ag{T}CATAACTTGGTGATGAAACACATCCCTGGTGCAGACCCTGAGCTCGTCCTC : 7121 75 : LeuAsnHisTyrTyrGluGluLeuAsp >>>> Target Intron 4 >>>> ArgIle : 85 ||||||||||||||||||||||||||| 2136 bp |||||| LeuAsnHisTyrTyrGluGluLeuAsp++ ++ArgIle 7120 : CTGAACCATTACTATGAGGAGCTGGATgt.........................agCGCATC : 4952 86 : ProLeuSerGluMetThrArgAlaGluIleAsnLysLeuLeuAlaGluLeuGlyPheTyrLy : 106 |||||||||.!.|||||||||.!!!!:|||||| ||||||! !||||||||||||||||| ProLeuSerHisMetThrArgThrAspIleAsnGlyLeuLeuGluGluLeuGlyPheTyrLy 4951 : CCGCTGTCCCACATGACCCGTACCGACATCAATGGTCTTCTGGAGGAGTTGGGCTTCTATAA : 4889 107 : sLysGlyHisProGluAspGlnValProGluGluPheArgPheSerProAlaLysAspSerP : 127 ||||!.!!.. !!||||||.!.|||||||||||||||||||||||||||||||||||||||| sLysAlaArgAlaGluAspAspValProGluGluPheArgPheSerProAlaLysAspSerP 4888 : AAAAGCACGAGCCGAAGATGACGTGCCGGAGGAGTTTCGCTTCTCGCCAGCTAAAGACAGCC : 4826 128 : roPheGlu : 129 |||||:!! roPheLys 4825 : CCTTCAAA : 4818 vulgar: sp|Q802G7|SELM_DANRE 1 129 . CM004435.1:subseq(14750000,150000) 9539 4817 - 509 M 32 96 5 0 2 I 0 1487 3 0 2 M 12 36 5 0 2 I 0 281 3 0 2 M 11 33 S 0 2 5 0 2 I 0 422 3 0 2 S 1 1 M 26 78 5 0 2 I 0 2132 3 0 2 M 46 138 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-23 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local gene 4818 9539 509 - . gene_id 1 ; sequence sp|Q802G7|SELM_DANRE ; gene_orientation + CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local cds 9444 9539 . - . CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local exon 9444 9539 . - . insertions 0 ; deletions 0 CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local splice5 9442 9443 . - . intron_id 1 ; splice_site "GT" CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local intron 7953 9443 . - . intron_id 1 CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local splice3 7953 7954 . - . intron_id 0 ; splice_site "AG" CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local cds 7917 7952 . - . CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local exon 7917 7952 . - . insertions 0 ; deletions 0 CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local splice5 7915 7916 . - . intron_id 2 ; splice_site "GT" CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local intron 7632 7916 . - . intron_id 2 CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local splice3 7632 7633 . - . intron_id 1 ; splice_site "AG" CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local cds 7597 7631 . - . CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local exon 7597 7631 . - . insertions 0 ; deletions 0 CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local splice5 7595 7596 . - . intron_id 3 ; splice_site "GT" CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local intron 7171 7596 . - . intron_id 3 CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local splice3 7171 7172 . - . intron_id 2 ; splice_site "AG" CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local cds 7092 7170 . - . CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local exon 7092 7170 . - . insertions 0 ; deletions 0 CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local splice5 7090 7091 . - . intron_id 4 ; splice_site "GT" CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local intron 4956 7091 . - . intron_id 4 CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local splice3 4956 4957 . - . intron_id 3 ; splice_site "AG" CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local cds 4818 4955 . - . CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local exon 4818 4955 . - . insertions 0 ; deletions 0 CM004435.1:subseq(14750000,150000) exonerate:protein2genome:local similarity 4818 9539 509 - . alignment_id 1 ; Query sp|Q802G7|SELM_DANRE ; Align 9540 2 96 ; Align 7953 34 36 ; Align 7632 46 33 ; Align 7170 58 78 ; Align 4956 84 138 # --- END OF GFF DUMP --- # -- completed exonerate analysis