Command line: [exonerate -m p2g --showtargetgff -q sbp2.1_zf.aa.fa.canviat -t genomesbp2.1_JXSJ01000013.1.fa] Hostname: [ws101184u] C4 Alignment: ------------ Query: SPP00000627_2.0 # Protein # SECIS binding protein 2 (SBP2) # Zebrafish Target: JXSJ01000013.1:subseq(156138,101975) Miichthys miiuy scaffold13, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 725 Query range: 159 -> 349 Target range: 51098 -> 49975 160 : SerGluAsnProThrLeuGlnThrGluIleProAsnSerAsnProIleSerLysValPro : 179 ..!|||!.. ! !! !|||||| !||| !!! !||| !|||::! ||| AspGluThrValGluGlnGlnThrThrSerProValThrCysProAlaSerArg---Pro 51098 : GACGAGACAGTAGAGCAACAAACCACCTCACCTGTAACCTGCCCAGCCAGTCGG---CCC : 51044 180 : LysIleHisSerArgLysPheArg{As} >>>> Target Intron 1 >>>> {p} : 188 ||||||||||||||||||||||||{||} 111 bp {|} LysIleHisSerArgLysPheArg{As}++ ++{p} 51043 : AAAATCCACAGCAGAAAGTTCAGA{GA}gt.........................ag{C} : 50904 189 : TyrCysAsnGlnValLeuSerLysAspValAspGluCysValSerAsnLeuLeuLysGlu : 208 ||||||!:!|||:!!|||||||||||||||||||||||||||!!!::!|||||||||||| TyrCysSerGlnMetLeuSerLysAspValAspGluCysValThrSerLeuLeuLysGlu 50903 : TATTGCAGCCAGATGCTGAGCAAAGACGTGGATGAGTGTGTGACGTCTCTGCTAAAGGAG : 50846 209 : LeuValArgPheGlnAspArgLeuTyrGlnLysAspProMetLysAlaArgMetLysArg : 228 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| LeuValArgPheGlnAspArgLeuTyrGlnLysAspProMetLysAlaArgMetLysArg 50845 : CTGGTTCGTTTCCAGGACCGCCTGTACCAGAAGGACCCCATGAAGGCCCGCATGAAGAGA : 50786 229 : ArgLeuValMetGlyLeuArgGluValLeuLysHisLeuLysLeuLysLysValLysCys : 248 |||:!!|||||||||||||||||||||||||||||||||||||||!:!|||||||||||| ArgIleValMetGlyLeuArgGluValLeuLysHisLeuLysLeuArgLysValLysCys 50785 : CGGATCGTGATGGGACTCAGAGAGGTCCTGAAACACCTCAAACTCAGGAAGGTCAAGTGT : 50726 249 : ValIleIleSerProAsnCysGluArgIleGlnSerLys{G} >>>> Target Intr : 262 |||||||||||||||||||||||||||||||||||||||{|} 362 bp ValIleIleSerProAsnCysGluArgIleGlnSerLys{G}++ 50725 : GTCATCATCTCACCCAACTGTGAACGCATCCAGTCCAAA{G}gt................ : 50681 263 : on 2 >>>> {ly}GlyLeuAspGluAlaLeuHisAsnIleIleAspThrCysArgAsp : 277 {||}||||||||||||||||||:!!!.!||||||||||||||||||!!: ++{ly}GlyLeuAspGluAlaLeuTyrThrIleIleAspThrCysArgGlu 50680 : .........ag{GA}GGCCTGGATGAGGCTCTCTACACCATCATCGACACTTGTCGTGAA : 50277 278 : GlnSerValProPheValPheAlaLeuSerArgLysAlaLeuGlyArgCysValAsnLys : 297 |||.!!|||||||||||||||||||||||||||||||||||||||||||||||||||||| GlnGlyValProPheValPheAlaLeuSerArgLysAlaLeuGlyArgCysValAsnLys 50276 : CAGGGGGTGCCATTCGTTTTTGCTCTCTCCAGGAAAGCTTTGGGTCGCTGTGTCAACAAG : 50217 298 : AlaValProValSerLeuValGlyIlePheAsnTyrAspGlyAlaGln >>>> Targe : 314 |||||||||||||||||||||||||||||||||||||||||||||||| AlaValProValSerLeuValGlyIlePheAsnTyrAspGlyAlaGln++ 50216 : GCAGTGCCTGTGAGCCTGGTGGGCATCTTCAACTACGATGGTGCACAGgt.......... : 50164 315 : t Intron 3 >>>> AspHisTyrHisLysMetIleGluLeuSerAlaGluAlaArgL : 328 83 bp |||:!!||||||||||||||||||||||||:!!|||||||||! ++AspTyrTyrHisLysMetIleGluLeuSerSerGluAlaArgT 50163 : ...............agGACTACTATCATAAGATGATCGAGTTGTCCTCTGAGGCCAGGA : 50041 329 : ysSerTyrGluValMetIleAlaAsnLeuAspGluGluGlyGluGlyArgLeuSerLeuL : 348 !:!!||||||||||||:!::!!!:!|||!!::!! !||| !!.!..! !..!! !: hrAlaTyrGluValMetValSerSerLeuGluGlnThrGlyProAlaGluAlaGluGlnV 50040 : CAGCCTATGAGGTGATGGTGTCCAGCCTGGAGCAGACGGGTCCGGCAGAGGCGGAGCAGG : 49981 349 : euAla : 349 !!||| alAla 49980 : TGGCG : 49976 vulgar: SPP00000627_2.0 159 349 . JXSJ01000013.1:subseq(156138,101975) 51098 49975 - 725 M 18 54 G 1 0 M 9 27 S 0 2 5 0 2 I 0 107 3 0 2 S 1 1 M 73 219 S 0 1 5 0 2 I 0 358 3 0 2 S 1 2 M 51 153 5 0 2 I 0 79 3 0 2 M 36 108 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-29 ##type DNA # # # seqname source feature start end score strand frame attributes # JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local gene 49976 51098 725 - . gene_id 1 ; sequence SPP00000627_2.0 ; gene_orientation + JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local cds 51016 51098 . - . JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local exon 51016 51098 . - . insertions 0 ; deletions 1 JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local splice5 51014 51015 . - . intron_id 1 ; splice_site "GT" JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local intron 50905 51015 . - . intron_id 1 JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local splice3 50905 50906 . - . intron_id 0 ; splice_site "AG" JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local cds 50684 50904 . - . JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local exon 50684 50904 . - . insertions 0 ; deletions 0 JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local splice5 50682 50683 . - . intron_id 2 ; splice_site "GT" JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local intron 50322 50683 . - . intron_id 2 JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local splice3 50322 50323 . - . intron_id 1 ; splice_site "AG" JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local cds 50167 50321 . - . JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local exon 50167 50321 . - . insertions 0 ; deletions 0 JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local splice5 50165 50166 . - . intron_id 3 ; splice_site "GT" JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local intron 50084 50166 . - . intron_id 3 JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local splice3 50084 50085 . - . intron_id 2 ; splice_site "AG" JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local cds 49976 50083 . - . JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local exon 49976 50083 . - . insertions 0 ; deletions 0 JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local similarity 49976 51098 725 - . alignment_id 1 ; Query SPP00000627_2.0 ; Align 51099 160 54 ; Align 51045 179 27 ; Align 50904 189 219 ; Align 50320 263 153 ; Align 50084 314 108 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000627_2.0 # Protein # SECIS binding protein 2 (SBP2) # Zebrafish Target: JXSJ01000013.1:subseq(156138,101975) Miichthys miiuy scaffold13, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 422 Query range: 0 -> 116 Target range: 51975 -> 51398 1 : SerGlnGlnThrSerGlnLysLysSerLysValProValGlnLeuAspLeuGlyAsnMet : 20 :!!:!!:!!..!||| !||||||||||||||||||||||||||||||:!!||||||||| AlaGluLysValSerGlyLysLysSerLysValProValGlnLeuAspIleGlyAsnMet 51975 : GCTGAAAAGGTGTCTGGGAAGAAGAGCAAAGTTCCTGTTCAGCTGGACATTGGAAACATG : 51918 21 : LeuAlaPheLeuGluGlnLysGlnGlnSerGlnLysSerLysGlnAspGlnArgProVal : 40 |||||| !||||||:!!||||||||| ||||||...||||||||| !:!|||||| LeuAlaAlaLeuGluLysLysGlnGlnPheGlnLysAspLysGlnAspThrLysProVal 51917 : TTGGCGGCCCTAGAAAAGAAGCAACAGtttcaaaaagacaaacaggatACCAAGCCAGTC : 51858 41 : ThrLeuThr{V} >>>> Target Intron 1 >>>> {al}GlyGlyAlaLeuPro : 49 ! !|||:!!{|} 124 bp {||}||||||!.!|||||| IleLeuSer{V}++ ++{al}GlyGlyGlyLeuPro 51857 : ATTCTCTCA{G}gt.........................ag{TT}GGTGGAGGACTACCT : 51707 50 : ValValHisLysGluProSerValGlnLysLys<->GlnTrpGlnGlnGluLysThrPro : 68 ||||||!!.|||:!!|||! !|||||||||||| !!.|||||||||! |||! ! !! ValValGlnLysGlnProLeuValGlnLysLysLeuHisTrpGlnGlnAlaLysIleAla 51706 : GTTGTCCAGAAGCAACCATTAGTCCAAAAGAAGCTTCACTGGCAGCAGGCTAAAATTGCT : 51647 69 : HisAsnProLeuAspSerThrCysProSerValLysLysGlyLysGlnArgGluValPro : 88 ||||||||||||||||||||| !!|||! |||||||||||||||||||||||||||||| HisAsnProLeuAspSerThrSerProLeuValLysLysGlyLysGlnArgGluValPro 51646 : CACAACCCCCTGGACTCTACCAGCCCTTTggtgaaaaaagggaaacagagagaggtgCCC : 51587 89 : LysAlaLysLysProThrProLeuLysArg >>>> Target Intron 2 >>>> V : 99 |||||||||||||||||||||||||||!:! 102 bp | LysAlaLysLysProThrProLeuLysLys++ ++V 51586 : AAAGCCAAGAAACCCACTCCTCTCAAGAAGgt.........................agG : 51452 100 : alIleLeuArgGluArgGluGluArgLysGlnAsnArgLeuLeuGluGluArg : 116 ||||||||:::|||||||||||||||||||||...|||||||||||||||||| alIleLeuLysGluArgGluGluArgLysGlnArgArgLeuLeuGluGluArg 51451 : TCATAttgaaagaaagggaggagaggaaacaaagacgtttgctggaggagaga : 51399 vulgar: SPP00000627_2.0 0 116 . JXSJ01000013.1:subseq(156138,101975) 51975 51398 - 422 M 43 129 S 0 1 5 0 2 I 0 120 3 0 2 S 1 2 M 16 48 G 0 3 M 38 114 5 0 2 I 0 98 3 0 2 M 18 54 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-29 ##type DNA # # # seqname source feature start end score strand frame attributes # JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local gene 51399 51975 422 - . gene_id 2 ; sequence SPP00000627_2.0 ; gene_orientation + JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local cds 51846 51975 . - . JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local exon 51846 51975 . - . insertions 0 ; deletions 0 JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local splice5 51844 51845 . - . intron_id 1 ; splice_site "GT" JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local intron 51722 51845 . - . intron_id 1 JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local splice3 51722 51723 . - . intron_id 0 ; splice_site "aG" JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local cds 51555 51721 . - . JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local exon 51555 51721 . - . insertions 3 ; deletions 0 JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local splice5 51553 51554 . - . intron_id 2 ; splice_site "GT" JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local intron 51453 51554 . - . intron_id 2 JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local splice3 51453 51454 . - . intron_id 1 ; splice_site "AG" JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local cds 51399 51452 . - . JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local exon 51399 51452 . - . insertions 0 ; deletions 0 JXSJ01000013.1:subseq(156138,101975) exonerate:protein2genome:local similarity 51399 51975 422 - . alignment_id 2 ; Query SPP00000627_2.0 ; Align 51976 1 129 ; Align 51720 45 48 ; Align 51669 61 114 ; Align 51453 99 54 # --- END OF GFF DUMP --- # -- completed exonerate analysis