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: CM004435.1:subseq(11060000,150000) Ictalurus punctatus breed USDA103 chromosome 22, whole genome shotgun sequence Model: protein2genome:local Raw score: 864 Query range: 441 -> 788 Target range: 4735 -> 8623 442 : LysLysSerGlnLeuProValGlnLeuAspLeuGlyGlyMetLeuThrAlaLeuGluLysLy : 462 |||||||||:!! !! !||||||||||||||||||! !||||||! !!.!||||||:!!|| LysLysSerLysAlaLeuValGlnLeuAspLeuGlyAspMetLeuLysValLeuGluGlnLy 4736 : AAGAAGAGCAAGGCACTTGTTCAGCTTGACCTAGGGGACATGCTGAAAGTTCTGGAGCAGAA : 4796 463 : sGlnHisSerGlnHisAlaLysGlnSerSerLysProValValValSer{V} >>>> Tar : 479 ||||!!.|||||| ! :!!!:!|||..! !||||||:!!..!:!!!!!{!} sGlnGlnSerGlnLysSerArgGlnAspValLysProLeuThrLeuThr{G}++ 4797 : ACAACAGTCTCAAAAGTCCAGACAAGATGTTAAACCACTAACTCTTACA{G}gt........ : 4850 480 : get Intron 1 >>>> {al}GlyAlaValProValLeuSerLysGluCysAlaSerGly : 492 199 bp { !}||||||:!!||||||:!! !|||!!: !!!!!!.! ++{ly}GlyAlaLeuProValValHisLysAsp---ProThrAla 4851 : .................ag{GA}GGAGCCCTACCAGTTGTCCACAAGGAC---CCAACAGCT : 5082 493 : GluArgGlyArgArgMetSerGlnMetLysThrProHisAsnProLeuAspSerSerAlaPr : 513 :!!!:! !!.! ! !..!||| !!:!! ! !!||||||||||||||||||!!!..!|| GlnLysLysHisSerTrpGlnGlnGluArgIleAlaHisAsnProLeuAspSerThrCysPr 5083 : CAAAAGAAGCATTCATGGCAGCAAGAGAGGATAGCACACAACCCTTTGGATTCCACCTGCCC : 5145 514 : oLeuMetLysLysGlyLysGlnArgGluIleProLysAlaLysLysProThrSerLeuLysL : 534 ||||:!!|||||||||||||||||||||:!:||||||||||||||||||||| !!||||||| oLeuValLysLysGlyLysGlnArgGluValProLysAlaLysLysProThrProLeuLysL 5146 : TTTAGTGAAAAAGGGAAAACAGCGAGAGGTGCCTAAAGCTAAAAAGCCTACACCTCTTAAAA : 5208 535 : ys >>>> Target Intron 2 >>>> IleIleLeuLysGluArgGlnGluArgLysG : 545 || 100 bp :!!|||||||||||||||:::|||||||||| ys++ ++ValIleLeuLysGluArgGluGluArgLysG 5209 : AAgt.........................agGTCATTTTaaaggagagagaagaaaggaaac : 5341 546 : ln<->ArgLeuGlnGluAsnAlaValSerProAlaPheThrSerAspAspThrGlnAspGly : 564 || ||||||! !|||.!. !! ! !! !! !.!.||||||!!:! !||||||!!: ! lnAsnArgLeuLeuGluGluArgAspProThrArgMetThrSerGluAlaThrGlnGluPro 5342 : AGAACCGCTTGCTAGAAGAAAGAGATCCGACACGAATGACTAGTGAAGCCACTCAAGAGCCA : 5401 565 : GluSerGlyGlyAspAspGlnPheProGluGlnAlaGluLeuSerGlyProGluGly{M} : 584 :!!:!!.!!! !:!! !... !.!...!|||:!!! !!!! ! ! ! !{!} GlnAlaSerGluAsnLeuSerGluSerAsnSerAlaGlnHisCysProGluProThr{S}++ 5402 : CAAGCCAGTGAGAATCTTTCTGAGAGCAATTCAGCGCAGCACTGTCCTGAACCAACA{A}gt : 5462 585 : >>>> Target Intron 3 >>>> {et}AspGluLeuIleSerThrProSerValGluA : 595 144 bp { }|||:!! ! !:!! ! !:!!! !:!! ++{er}AspGlnSerGlyAlaGluGluAlaAspGlnT 5463 : .........................ag{GT}GACCAGAGTGGTGCTGAGGAGGCTGATCAAA : 5638 596 : spLysSer<->GluGluProProGlyThrGluLeuGlnArgAspThrGluAlaSerHisLeu : 614 ||| |||!!:||| !..! !||| !.!.!!!! !!... !!:! ! hrGlySerProGluAspProLysAsnLeuGluGluAspSerAlaProSerLysAsnTrpAsp 5639 : CAGGTTCACCTGAAGACCCGAAGAACCTTGAAGAAGATAGCGCGCCGTCTAAAAACTGGGAT : 5698 615 : AlaProAsnHisThrThrPheProLysIleHisSerArgArgPheArg{As} >>>> Tar : 631 :!! !::!:!! !!!:! !||||||||||||||||||!:!||||||{||} SerAsnSerAsnProSerArgProLysIleHisSerArgLysPheArg{As}++ 5699 : TCAAATTCCAACCCCAGTCGTCCGAAAATCCATAGCAGGAAATTCAGA{GA}gt........ : 5753 632 : get Intron 4 >>>> {p}TyrCysSerGlnMetLeuSerLysGluValAspAlaCysV : 645 135 bp {|}||||||||||||||||||||||||!!:||||||! !|||| ++{p}TyrCysSerGlnMetLeuSerLysAspValAspGluCysV 5754 : .................ag{C}TACTGCAGCCAGATGCTAAGCAAGGATGTAGACGAGTGTG : 5926 646 : alThrAspLeuLeuLysGluLeuValArgPheGlnAspArgMetTyrGlnLysAspProVal : 665 |||||! !|||||||||||||||||||||||||||||||||:!:|||||||||||||||:!! alThrValLeuLeuLysGluLeuValArgPheGlnAspArgLeuTyrGlnLysAspProMet 5927 : TGACTGTTCTGCTGAAGGAGCTGGTCAGGTTCCAGGACCGGCTTTACCAGAAAGATCCCATG : 5986 666 : LysAlaLysThrLysArgArgLeuValLeuGlyLeuArgGluValLeuLysHisLeuLysLe : 686 ||||||!:!! !|||||||||||||||:!!|||||||||||||||||||||||||||||||| LysAlaArgMetLysArgArgLeuValMetGlyLeuArgGluValLeuLysHisLeuLysLe 5987 : AAGGCCAGGATGAAGAGGCGGCTGGTCATGGGTCTCAGGGAGGTGCTGAAACACCTAAAGCT : 6049 687 : uLysLysLeuLysCysValIleIleSerProAsnCysGluLysIleGlnSerLys{G} >> : 705 |!:!|||:!!||||||||||||||||||||||||||||||::::!!|||||||||{|} uArgLysValLysCysValIleIleSerProAsnCysGluArgValGlnSerLys{G}++ 6050 : CAGGAAAGTCAAGTGTGTCATCATCTCTCCCAACTGTGAACGTGTACAGTCTAAA{G}gt.. : 6109 706 : >> Target Intron 5 >>>> {ly}GlyLeuAspAspThrLeuHisThrIleIleAsp : 716 485 bp {||}|||||||||!!:.!!|||||||||||||||||| ++{ly}GlyLeuAspGluAlaLeuHisThrIleIleAsp 6110 : .......................ag{GT}GGTCTCGATGAAGCTCTACACACAATCATTGAT : 6624 717 : TyrAlaCysGluGlnAsnIleProPheValPheAlaLeuAsnArgLysAlaLeuGlyArgSe : 737 ..! ||||||:!!:!!||||||||||||||||||:::||||||||||||||||||!! ThrCysLeuGluGlnAspValProPheValPheAlaLeuSerArgLysAlaLeuGlyArgCy 6625 : ACATGTCTGGAACAAGATGTTCCTTTTGTCTTTGCCTTGTCAAGGAAGGCTTTGGGTCGCTG : 6687 738 : rLeuAsnLysAlaValProValSerValValGlyIlePheSerTyrAspGlyAlaGln >> : 757 !:!!|||||||||||||||||||||:!!||||||||||||!:!||||||||||||||| sValAsnLysAlaValProValSerLeuValGlyIlePheAsnTyrAspGlyAlaGln++ 6688 : TGTGAACAAAGCCGTTCCCGTCAGTCTGGTGGGCATCTTCAACTACGATGGAGCACAGgt.. : 6749 758 : >> Target Intron 6 >>>> AspGlnPheHisLysMetValGluLeuThrValAlaA : 769 1781 bp |||!!.!:!|||||||||:!!||||||||| ! !| ++AspHisTyrHisLysMetIleGluLeuThrSerGlnA 6750 : .......................agGACCATTACCACAAAATGATTGAGCTCACATCACAGG : 8564 770 : laArgGlnAlaTyrLysThrMetLeuGluAsnValGlnGlnGluLeuValGlyGluPro : 788 |||||:!!||||||:!!! !|||:!!...|||:!!:!!:!!...:!! ! !|||||| laArgLysAlaTyrGluMetMetValSerAsnLeuGluGluSerValGlnLysGluPro 8565 : CAAGGAAAGCCTATGAGATGATGGTTTCCAACCTTGAGGAGAGTGTACAGAAGGAGCCG : 8623 vulgar: SPP00000054_2.0 441 788 . CM004435.1:subseq(11060000,150000) 4735 8623 + 864 M 37 111 S 0 1 5 0 2 I 0 195 3 0 2 S 1 2 M 9 27 G 1 0 M 45 135 5 0 2 I 0 96 3 0 2 M 11 33 G 0 3 M 38 114 S 0 1 5 0 2 I 0 140 3 0 2 S 1 2 M 13 39 G 0 3 M 33 99 S 0 2 5 0 2 I 0 131 3 0 2 S 1 1 M 73 219 S 0 1 5 0 2 I 0 481 3 0 2 S 1 2 M 51 153 5 0 2 I 0 1777 3 0 2 M 32 96 # --- 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 # CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local gene 4736 8623 864 + . gene_id 1 ; sequence SPP00000054_2.0 ; gene_orientation + CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local cds 4736 4847 . + . CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local exon 4736 4847 . + . insertions 0 ; deletions 0 CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local splice5 4848 4849 . + . intron_id 1 ; splice_site "GT" CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local intron 4848 5046 . + . intron_id 1 CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local splice3 5045 5046 . + . intron_id 0 ; splice_site "AG" CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local cds 5047 5210 . + . CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local exon 5047 5210 . + . insertions 0 ; deletions 1 CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local splice5 5211 5212 . + . intron_id 2 ; splice_site "GT" CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local intron 5211 5310 . + . intron_id 2 CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local splice3 5309 5310 . + . intron_id 1 ; splice_site "AG" CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local cds 5311 5461 . + . CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local exon 5311 5461 . + . insertions 3 ; deletions 0 CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local splice5 5462 5463 . + . intron_id 3 ; splice_site "GT" CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local intron 5462 5605 . + . intron_id 3 CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local splice3 5604 5605 . + . intron_id 2 ; splice_site "AG" CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local cds 5606 5750 . + . CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local exon 5606 5750 . + . insertions 3 ; deletions 0 CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local splice5 5751 5752 . + . intron_id 4 ; splice_site "GT" CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local intron 5751 5885 . + . intron_id 4 CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local splice3 5884 5885 . + . intron_id 3 ; splice_site "AG" CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local cds 5886 6106 . + . CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local exon 5886 6106 . + . insertions 0 ; deletions 0 CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local splice5 6107 6108 . + . intron_id 5 ; splice_site "GT" CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local intron 6107 6591 . + . intron_id 5 CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local splice3 6590 6591 . + . intron_id 4 ; splice_site "AG" CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local cds 6592 6746 . + . CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local exon 6592 6746 . + . insertions 0 ; deletions 0 CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local splice5 6747 6748 . + . intron_id 6 ; splice_site "GT" CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local intron 6747 8527 . + . intron_id 6 CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local splice3 8526 8527 . + . intron_id 5 ; splice_site "AG" CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local cds 8528 8623 . + . CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local exon 8528 8623 . + . insertions 0 ; deletions 0 CM004435.1:subseq(11060000,150000) exonerate:protein2genome:local similarity 4736 8623 864 + . alignment_id 1 ; Query SPP00000054_2.0 ; Align 4736 442 111 ; Align 5049 480 27 ; Align 5076 490 135 ; Align 5311 535 33 ; Align 5347 546 114 ; Align 5608 585 39 ; Align 5650 598 99 ; Align 5887 632 219 ; Align 6594 706 153 ; Align 8528 757 96 # --- END OF GFF DUMP --- # -- completed exonerate analysis