Command line: [exonerate -m p2g --showtargetgff -q SELENOT1/SELENOT1_x.fa -t SELENOT1/SUBSEQ/CM004417.1_0_subseq.txt --exhaustive] Hostname: [ws112615u] C4 Alignment: ------------ Query: SPP00000649_2.0 Protein Selenoprotein T1 (SELENOT1) Zebrafish Target: CM004417.1:subseq(376650,50128) Ictalurus punctatus breed USDA103 chromosome 4, whole genome shotgun sequence Model: protein2genome:local Raw score: 646 Query range: 8 -> 178 Target range: 24283 -> 26168 9 : PheSerAlaLeuLeuLeuTrpAlaLeuCysLeuHisSerAlaSerAlaAspAsnAsnGly : 28 |||||| !!!!:!!|||!! !.!|||! !|||:!! !..!!!!|||||||||..!.!! PheSerLeuPheValLeuCysValLeuSerLeuTyrHisCysThrAlaAspAsnGlySer 24284 : TTCTCGCTGTTTGTCCTGTGTGTGCTGTCTCTGTACCACTGCACAGCGGATAACGGCAGT : 24341 29 : ValLysLysMetLysMetGlnPheAlaThrGlyProLeuLeuLysPheGlnIle{Cy} : 47 ||||||||||||||||||!!.!:!.!!.!!||||||||||||||||||||||||{||} ValLysLysMetLysMetHisTyrThrAlaGlyProLeuLeuLysPheGlnIle{Cy}++ 24342 : GTTAAAAAGATGAAGATGCACTACACAGCTGGACCTCTGCTCAAGTTCCAGATT{TG}gt : 24400 48 : >>>> Target Intron 1 >>>> {s}ValSerUnkGlyTyrLysArgValPheGlu : 57 599 bp {|}:!!||| ||||||||||||||||||||| ++{s}IleSer***GlyTyrLysArgValPheGlu 24401 : .........................ag{C}ATCTCCTGAGGCTACAAGCGGGTGTTTGAG : 25027 58 : GluTyrThrGlnAlaLeuTyrGlnArgTyrProAspIleArgIleGluGlyGluAsnTyr : 77 ||||||.!!|||!.!||| !!|||||||||||||||||||||||||||||||||!:!||| GluTyrAlaGlnValLeuAsnGlnArgTyrProAspIleArgIleGluGlyGluSerTyr 25028 : GAGTACGCTCAGGTTCTTAACCAGAGGTATCCAGACATCCGCATAGAAGGGGAGAGCTAC : 25087 78 : LeuProLeuProLeuTyr{Ar} >>>> Target Intron 2 >>>> {g}HisIle : 86 ||||||! !|||:::|||{||} 89 bp {|}|||:!: LeuProGlnProValTyr{Ar}++ ++{g}HisLeu 25088 : CTCCCTCAACctgtgtac{ag}gt.........................ag{A}CACCTG : 25203 87 : AlaSerPheLeuSerMetPheLysLeuLeuLeuIleGlyValIleIleLeuGlyLysAsp : 106 ||||||||||||||||||!!.|||!!! !:!!||| !:!!:!!|||:!!||||||||| AlaSerPheLeuSerMetLeuLysPheAlaValIleIleLeuValIleValGlyLysAsp 25204 : GCCTCCTTCCTCTCCATGTTGAAGTTCGCTGTAATCATCCTTGTTATTGTGGGAAAGGAT : 25263 107 : ProPheAlaLeuCysGlyMetGlnAlaProGlyIleTrpValTrpSerGlnGluAsnLys : 126 ||||||.!!|||! !|||!!:! !.!!||||||:!!|||..!|||.!!|||||||||||| ProPheThrLeuPheGlyIleProThrProGlyValTrpThrTrpGlyGlnGluAsnLys 25264 : CCGTTCACGCTGTTCGGAATACCGACTCCTGGAGTCTGGACCTGGGGGCAGGAGAACAAG : 25323 127 : >>>> Target Intron 3 >>>> IleTyrAlaCysMetMetValPhePhePheS : 137 503 bp :::|||||||||||||||||||||||||||! ++ ++ValTyrAlaCysMetMetValPhePhePheT 25324 : gt.........................aggtgtacgCCTGTATGATGGTGTTCTTCTTCA : 25859 138 : erAsnMetIleGluAsnGlnCysMetSerThrGlyAlaPheGluIleThrLeuAsn{A} : 156 !!||||||!!:||||||||||||:!:|||||||||||||||||||||:!!||||||{|} hrAsnMetMetGluAsnGlnCysLeuSerThrGlyAlaPheGluIleSerLeuAsn{A}+ 25860 : CGAACATGATGGAGAACCAGTGTTTATCTACAGGAGCCTTTGAGATTTCACTGAAT{G}g : 25917 157 : >>>> Target Intron 4 >>>> {sp}ValProValTrpSerLysLeuGluSerG : 166 184 bp {||}|||||||||||||||||||||||||||| + ++{sp}ValProValTrpSerLysLeuGluSerG 25918 : t.........................ag{ac}gTCCCTGTGTGGTCGAAGCTGGAATCGG : 26130 167 : lyHisLeuProSerMetGlnGlnLeuValGlnIleLeu : 178 ||||||||||||||||||||||||||:!!||||||||| lyHisLeuProSerMetGlnGlnLeuLeuGlnIleLeu 26131 : GTCATCTTCCCTCCATGCAGCAGCTTCTTCAGATCCTG : 26168 vulgar: SPP00000649_2.0 8 178 . CM004417.1:subseq(376650,50128) 24283 26168 + 646 M 38 114 S 0 2 5 0 2 I 0 595 3 0 2 S 1 1 M 36 108 S 0 2 5 0 2 I 0 85 3 0 2 S 1 1 M 42 126 5 0 2 I 0 499 3 0 2 M 29 87 S 0 1 5 0 2 I 0 180 3 0 2 S 1 2 M 22 66 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-15 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004417.1:subseq(376650,50128) exonerate:protein2genome:local gene 24284 26168 646 + . gene_id 1 ; sequence SPP00000649_2.0 ; gene_orientation + CM004417.1:subseq(376650,50128) exonerate:protein2genome:local cds 24284 24399 . + . CM004417.1:subseq(376650,50128) exonerate:protein2genome:local exon 24284 24399 . + . insertions 0 ; deletions 0 CM004417.1:subseq(376650,50128) exonerate:protein2genome:local splice5 24400 24401 . + . intron_id 1 ; splice_site "GT" CM004417.1:subseq(376650,50128) exonerate:protein2genome:local intron 24400 24998 . + . intron_id 1 CM004417.1:subseq(376650,50128) exonerate:protein2genome:local splice3 24997 24998 . + . intron_id 0 ; splice_site "AG" CM004417.1:subseq(376650,50128) exonerate:protein2genome:local cds 24999 25109 . + . CM004417.1:subseq(376650,50128) exonerate:protein2genome:local exon 24999 25109 . + . insertions 0 ; deletions 0 CM004417.1:subseq(376650,50128) exonerate:protein2genome:local splice5 25110 25111 . + . intron_id 2 ; splice_site "gt" CM004417.1:subseq(376650,50128) exonerate:protein2genome:local intron 25110 25198 . + . intron_id 2 CM004417.1:subseq(376650,50128) exonerate:protein2genome:local splice3 25197 25198 . + . intron_id 1 ; splice_site "AG" CM004417.1:subseq(376650,50128) exonerate:protein2genome:local cds 25199 25325 . + . CM004417.1:subseq(376650,50128) exonerate:protein2genome:local exon 25199 25325 . + . insertions 0 ; deletions 0 CM004417.1:subseq(376650,50128) exonerate:protein2genome:local splice5 25326 25327 . + . intron_id 3 ; splice_site "GT" CM004417.1:subseq(376650,50128) exonerate:protein2genome:local intron 25326 25828 . + . intron_id 3 CM004417.1:subseq(376650,50128) exonerate:protein2genome:local splice3 25827 25828 . + . intron_id 2 ; splice_site "ag" CM004417.1:subseq(376650,50128) exonerate:protein2genome:local cds 25829 25916 . + . CM004417.1:subseq(376650,50128) exonerate:protein2genome:local exon 25829 25916 . + . insertions 0 ; deletions 0 CM004417.1:subseq(376650,50128) exonerate:protein2genome:local splice5 25917 25918 . + . intron_id 4 ; splice_site "GT" CM004417.1:subseq(376650,50128) exonerate:protein2genome:local intron 25917 26100 . + . intron_id 4 CM004417.1:subseq(376650,50128) exonerate:protein2genome:local splice3 26099 26100 . + . intron_id 3 ; splice_site "ag" CM004417.1:subseq(376650,50128) exonerate:protein2genome:local cds 26101 26168 . + . CM004417.1:subseq(376650,50128) exonerate:protein2genome:local exon 26101 26168 . + . insertions 0 ; deletions 0 CM004417.1:subseq(376650,50128) exonerate:protein2genome:local similarity 24284 26168 646 + . alignment_id 1 ; Query SPP00000649_2.0 ; Align 24284 9 114 ; Align 25000 48 108 ; Align 25200 85 126 ; Align 25829 127 87 ; Align 26103 157 66 # --- END OF GFF DUMP --- # -- completed exonerate analysis