Command line: [exonerate -m p2g --showtargetgff -q SBP2.fa -t genomic.fa] Hostname: [ws101074U] C4 Alignment: ------------ Query: SPP00000054_2.0 # Protein # SECIS binding protein 2 (SBP2) # Human Target: CM004417.1:subseq(33270000,150000) Ictalurus punctatus breed USDA103 chromosome 4, whole genome shotgun sequence Model: protein2genome:local Raw score: 523 Query range: 618 -> 787 Target range: 3304 -> 4389 619 : ThrThrPheProLysIleHisSerArgArgPheArg{As} >>>> Target Intron 1 : 631 :!!|||.!! !!||||||||||||||||||||||||{!!} 118 bp SerThrIleThrLysIleHisSerArgArgPheArg{Gl}++ 3305 : TCCACCATCACCAAGATTCACAGCAGGAGGTTCAGA{GA}gt.................... : 3345 632 : >>>> {p}TyrCysSerGlnMetLeuSerLysGluValAspAlaCysValThrAspLeuL : 649 {:}||||||!:!|||:!!|||!:!||||||:!!|||! ! !!|||||| |||| ++{u}TyrCysAsnGlnValLeuAsnLysGluIleAspGluSerValThrLeuLeuL 3346 : .....ag{g}tactGTAACCAGGTGCTGAATAAGGAGATTGATGAGAGCGTCACTCTGCTGC : 3513 650 : euLysGluLeuValArgPheGlnAspArgMetTyrGlnLysAspProValLysAlaLysThr : 669 ||:!!||||||||||||||||||!!:|||:!!|||||||||!!:||| !|||||||||.!! euGlnGluLeuValArgPheGlnGluArgValTyrGlnLysGluProAsnLysAlaLysAla 3514 : TGCAGGAGCTTGTGCGTTTTCAGGAGCGAGTGTATCAGAAGGAGCCCAATAAAGCTAAAGCT : 3573 670 : LysArgArgLeuValLeuGlyLeuArgGluValLeuLysHisLeuLysLeuLysLysLeuLy : 690 |||||||||||||||:!!||||||||||||||| !||||||:!!||||||!!.|||:!!:: LysArgArgLeuValMetGlyLeuArgGluValThrLysHisMetLysLeuAsnLysIleAr 3574 : AAGCGCCGCCTGGTCATGGGTTTGCGTGAGGTCACCAAGCACATGAAGCTCAACAAGATACG : 3636 691 : sCysValIleIleSerProAsnCysGluLysIleGlnSerLys{G} >>>> Target In : 705 !||||||||||||||||||||||||||||||||||||:!!|||{|} 185 gCysValIleIleSerProAsnCysGluLysIleGlnAlaLys{G}++ 3637 : ATGTGTGATCATCTCGCCTAACTGTGAGAAGATCCAGGCCAAG{G}gt.............. : 3684 706 : tron 2 >>>> {ly}GlyLeuAspAspThrLeuHisThrIleIleAspTyrAlaCysGlu : 720 bp {||}|||||||||!!:.!!|||:!!!.!:!:|||! ||| !!||| ++{ly}GlyLeuAspGluAlaLeuTyrAsnValIleAlaMetAlaArgGlu 3685 : ...........ag{gt}GGTCTGGATGAGGCTCTGTACAATGTGATAGCGATGGCCCGTGAG : 3911 721 : GlnAsnIleProPheValPheAlaLeuAsnArgLysAlaLeuGlyArgSerLeuAsnLysAl : 741 |||.!.|||||||||||||||||||||...||||||||||||||||||!!!:!!|||||| GlnGluIleProPheValPheAlaLeuGlyArgLysAlaLeuGlyArgCysValAsnLysLe 3912 : CAGGAGATCCCGTTTGTTTTCGCTCTGGGGCGTAAAGCTCTCGGCCGCTGCGTTAACAAACT : 3974 742 : aValProValSerValValGlyIlePheSerTyrAspGlyAlaGln >>>> Target In : 757 !|||||||||||||||||||||||||||!:!|||..!||||||:!: 275 uValProValSerValValGlyIlePheAsnTyrSerGlyAlaGlu++ 3975 : CGTCCCCGTCAGTGTAGTGGGAATCTTCAACTACTCCGGAGCAGAggt.............. : 4024 758 : tron 3 >>>> AspGlnPheHisLysMetValGluLeuThrValAlaAlaArgGlnAlaT : 773 bp ! !|||:!!::::!!|||...||||||! !! !||||||::!|||| ++AlaLeuPheAsnArgLeuValSerLeuThrGluGluAlaArgArgAlaT 4025 : ...........aggctCTGTTTAACCGCCTGGTGTCTCTGACGGAGGAGGCGCGCAGGGCGT : 4345 774 : yrLysThrMetLeuGluAsnValGlnGlnGluLeuValGlyGlu : 787 ||||| !|||:!! !:!!:!!||||||! !!.!! !||| yrLysGluMetValCysAlaLeuGluGlnGluGlnAlaGluGlu 4346 : ATAAGGAGATGGTTTGTGCTCTGGAGCAGGAGCAGGCTGAGGAG : 4389 vulgar: SPP00000054_2.0 618 787 . CM004417.1:subseq(33270000,150000) 3304 4389 + 523 M 12 36 S 0 2 5 0 2 I 0 114 3 0 2 S 1 1 M 73 219 S 0 1 5 0 2 I 0 181 3 0 2 S 1 2 M 51 153 5 0 2 I 0 271 3 0 2 M 31 93 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-25 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local gene 3305 4389 523 + . gene_id 1 ; sequence SPP00000054_2.0 ; gene_orientation + CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local cds 3305 3342 . + . CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local exon 3305 3342 . + . insertions 0 ; deletions 0 CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local splice5 3343 3344 . + . intron_id 1 ; splice_site "Gt" CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local intron 3343 3460 . + . intron_id 1 CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local splice3 3459 3460 . + . intron_id 0 ; splice_site "ag" CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local cds 3461 3681 . + . CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local exon 3461 3681 . + . insertions 0 ; deletions 0 CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local splice5 3682 3683 . + . intron_id 2 ; splice_site "GT" CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local intron 3682 3866 . + . intron_id 2 CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local splice3 3865 3866 . + . intron_id 1 ; splice_site "ag" CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local cds 3867 4021 . + . CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local exon 3867 4021 . + . insertions 0 ; deletions 0 CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local splice5 4022 4023 . + . intron_id 3 ; splice_site "gt" CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local intron 4022 4296 . + . intron_id 3 CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local splice3 4295 4296 . + . intron_id 2 ; splice_site "ag" CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local cds 4297 4389 . + . CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local exon 4297 4389 . + . insertions 0 ; deletions 0 CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local similarity 3305 4389 523 + . alignment_id 1 ; Query SPP00000054_2.0 ; Align 3305 619 36 ; Align 3462 632 219 ; Align 3869 706 153 ; Align 4297 757 93 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000054_2.0 # Protein # SECIS binding protein 2 (SBP2) # Human Target: CM004417.1:subseq(33270000,150000) Ictalurus punctatus breed USDA103 chromosome 4, whole genome shotgun sequence Model: protein2genome:local Raw score: 178 Query range: 441 -> 535 Target range: 1258 -> 1945 442 : LysLysSerGlnLeuProValGlnLeuAspLeuGlyGlyMetLeuThrAlaLeuGluLysLy : 462 |||||||||::! !|||||||||||||||||||||! !||||||.!!||||||||||||:! LysLysSerArgThrProValGlnLeuAspLeuGlyAspMetLeuAlaAlaLeuGluLysGl 1259 : AAGAAGAGCAGGACTCCAGTACAGCTGGATCTGGGGGACATGCTCGCTGCACTGGAGAAACA : 1319 463 : sGlnHisSerGlnHisAlaLysGlnSerSerLysProValValValSerValGly{A} >> : 481 !|||!!.:!!..! ! |||::!||| !!:!!!. !! ! !:!!||| {!} nGlnGlnAlaMetLysAlaArgGlnLeuAsnAsnThrLysProLeuSerTyrThr{V}++ 1320 : ACAACAGGCCATGAAGGCACGACAACTCAACAACACCAAACCCCTTTCATacaca{g}gt.. : 1379 482 : >> Target Intron 1 >>>> {la}ValProValLeuSerLysGluCysAlaSerGly : 492 405 bp {.!} !!..!! ! ! .!. ! !..!!.! ++{al}GlyThrThrSerLeuPheHisAsnLysAspAla 1380 : .......................ag{tg}ggtACGACCTCACTGTTCCACAATAAGGATGCA : 1814 493 : GluArgGlyArgArgMetSerGlnMetLysThrProHisAsnProLeuAspSerSerAlaPr : 513 ! !!! ! !! !|||!.!..! ! |||||||||||| !|||||||||!!!||||| ValSerLysGlyValMetLysSerTyrThrThrProHisAsnMetLeuAspSerThrAlaPr 1815 : GTCAGTAAGGGTGTGATGAAATCATATACTACCCCCCACAACATGCTCGACTCCACAGCACC : 1877 514 : oLeuMetLysLysGlyLysGlnArgGluIleProLysAlaLysLysProThrSerLeuLysL : 534 | !!!:|||!::||||||:::|||||||||||||||!.!|||!:!||||||:!!||||||| oLysIleLysArgGlyLysGluArgGluIleProLysValLysArgProThrAlaLeuLysL 1878 : CAAAATCAAGAggggtaaagagagagagatacctaAAGTGAAGAGACCTACTGCCCTCAAGA : 1940 535 : ysIle : 535 ||:!! ysVal 1941 : AGGTA : 1945 vulgar: SPP00000054_2.0 441 535 . CM004417.1:subseq(33270000,150000) 1258 1945 + 178 M 39 117 S 0 1 5 0 2 I 0 401 3 0 2 S 1 2 M 54 162 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-25 ##type DNA # # # seqname source feature start end score strand frame attributes # CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local gene 1259 1945 178 + . gene_id 2 ; sequence SPP00000054_2.0 ; gene_orientation + CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local cds 1259 1376 . + . CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local exon 1259 1376 . + . insertions 0 ; deletions 0 CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local splice5 1377 1378 . + . intron_id 1 ; splice_site "gt" CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local intron 1377 1781 . + . intron_id 1 CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local splice3 1780 1781 . + . intron_id 0 ; splice_site "ag" CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local cds 1782 1945 . + . CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local exon 1782 1945 . + . insertions 0 ; deletions 0 CM004417.1:subseq(33270000,150000) exonerate:protein2genome:local similarity 1259 1945 178 + . alignment_id 2 ; Query SPP00000054_2.0 ; Align 1259 442 117 ; Align 1784 482 162 # --- END OF GFF DUMP --- # -- completed exonerate analysis