Command line: [exonerate -m p2g --showtargetgff -q secp43.2_zf.aa.fa.canviat -t genomesecp43.2_JXSJ01000502.1.fa] Hostname: [ws101072u] C4 Alignment: ------------ Query: SPP00000665_2.0 # Protein # tRNA Sec 1 associated protein 1 (SECp43) # Zebrafish Target: JXSJ01000502.1:subseq(30134,104190) Miichthys miiuy scaffold502, whole genome shotgun sequence Model: protein2genome:local Raw score: 895 Query range: 0 -> 314 Target range: 49087 -> 54202 1 : MetPheAsnArgMetThrSerLeuTrpMetGlyAsp >>>> Target Intron 1 > : 13 ||||||||||||..!||||||||||||||||||||| 876 bp MetPheAsnArgGlnThrSerLeuTrpMetGlyAsp++ 49088 : ATGTTTAACAGACAGACCAGCCTGTGGATGGGTGACgt...................... : 49126 14 : >>> LeuAspProTyrMetAspGluAsnPheIleLysGlnAlaPheSerThrMetGlyG : 31 |||||||||||||||||||||||||||||||||||||||||||||.!!||||||| ++LeuAspProTyrMetAspGluAsnPheIleLysGlnAlaPheSerAlaMetGlyG 49127 : ...agttGGACCCATACATGGATGAGAATTTCATCAAGCAGGCCTTTAGTGCTATGGGAG : 50054 32 : luThrAlaPheGlyValLysIleIleThrHisArgValThr{Gl} >>>> Target I : 45 ||:!! !!|||||||||||||||||||||||||||:!!|||{||} 583 luSerProPheGlyValLysIleIleThrHisArgIleThr{Gl}++ 50055 : AGTCACCGTTTGGAGTGAAGATCATCACTCACAGGATAACA{GG}gt............. : 50100 46 : ntron 2 >>>> {y}GlySerAlaGlyTyrCysPheValGluMetAlaAspGluAlaS : 60 bp {|}|||||||||||||||||||||||||||:!!||||||||||||| ++{y}GlySerAlaGlyTyrCysPheValGluLeuAlaAspGluAlaS 50101 : ............ag{T}GGTTCAGCAGGATACTGCTTTGTGGAGCTGGCTGATGAAGCAA : 50724 61 : erValAspArgCysValGlnArgLeuAsnGlyLysLeuValProGlySerAsnPro >> : 79 |||||||||||||||||||||||||||||||||||||||||||||||||||||||| erValAspArgCysValGlnArgLeuAsnGlyLysLeuValProGlySerAsnPro++ 50725 : GTGTTGACCGCTGTGTCCAAAGACTCAATGGAAAACTGGTTCCCGGATCAAACCCGgt.. : 50783 80 : >> Target Intron 3 >>>> ProArgLysPheLysLeuAsnTyrAlaThrTyrGl : 90 889 bp ||||||||||||||||||||||||||||||||||| ++ProArgLysPheLysLeuAsnTyrAlaThrTyrGl 50784 : .......................agCCCCGGAAGTTTAAGCTAAACTATGCCACGTATGG : 51703 91 : yLysArgProGluPro{Gl} >>>> Target Intron 4 >>>> {y}ProGluPh : 99 ||||||||||||| !!{||} 937 bp {|}|||||||| yLysArgProGluAla{Gl}++ ++{y}ProGluPh 51704 : AAAACGGCCAGAGGCA{GG}gt.........................ag{G}CCGGagtt : 52667 100 : eSerValPheValGlyAspLeuThrSerGluValAspAspTyrGlnLeuHisGlnPhePh : 119 ||||||||||||||||||||||.!!|||||||||||||||!:!|||||||||||| !!|| eSerValPheValGlyAspLeuAlaSerGluValAspAspPheGlnLeuHisGlnValPh 52668 : ctctgtgtttgtgggcGACTTGGCCTCTGAGGTGGATGACTTCCAACTGCACCAAGTTTT : 52727 120 : eLeuLysLysPheProSerCysLysGlyAlaLysValValThrAspProTyrGlyAsnSe : 139 | ||||||!:!! !||||||||||||||||||||||||||||||! !|||||| !!|| e---LysLysTyrLeuSerCysLysGlyAlaLysValValThrAspGlnTyrGlyTyrSe 52728 : C---AAGAAGTACCTCTCCTGCAAAGGAGCCAAAGTGGTCACTGATCAGTATGGATACTC : 52784 140 : r{Ar} >>>> Target Intron 5 >>>> {g}GlyTyrGlyPheValLysPheSe : 148 |{||} 395 bp {|}|||||||||||||||||||||.! r{Ar}++ ++{g}GlyTyrGlyPheValLysPheGl 52785 : C{AG}gt.........................ag{A}GGTTACGGCTTTGTCAAGTTTGG : 53206 149 : rAspGluAsnGluGlnLysLysAlaLeuGluGluPheGlnAsnAlaSerGlyLeuGlyGl : 168 !!!:|||!:!|||||||||||||||:!!||||||! !|||..!.!!! ! |||||||| yGluGluSerGluGlnLysLysAlaIleGluGluCysGlnGlyThrMet---LeuGlyGl 53207 : GGAGGAGAGCGAGCAGAAGAAGGCGATCGAGGAGTGCCAGGGTACGATG---CTTGGGGG : 53263 169 : yLysProIleArgIleSerIleAlaValAsnLys{Gl} >>>> Target Intron 6 : 180 |||||||:!!|||:!!|||||||||||| |||{ !} 169 bp yLysProLeuArgLeuSerIleAlaValAlaLys{Ar}++ 53264 : GAAGCCGCTCAGGCTCAGTATCGCCGTGGCAAAG{AG}gt.................... : 53303 181 : >>>> {y}AsnLysAlaSerThrTyrHisAsnGlnAsnAsnThrTyrAsnThrAsnTy : 197 {!}..!:!!!.!..!!.!|||||||||.!. !!||| !! !.!.:!!!:!|| -+{g}GlyGlnGlyGlnAsnTyrHisAsnAsnTyrAsnGlnSerGlnSerSerTy 53304 : .....gg{G}GGCCAGGGCCAGAATTACCATAACAACTATAACCAGTCCCAGTCCAGTTA : 53519 198 : rGlnGlnGlnTyrTyrGlnGlnProTyrAsnSerTyrTyrProGlnTrp<->GlyTyrAs : 216 | ! ... !! ! ! ! ! ....!!|||||| !!|||||| |||||||| rTyrGlySerAsnSerThrAlaGlyGlnGlyGlyTyrTyrSerGlnTrpGlyGlyTyrAs 53520 : CTATGGCAGCAATAGCACCGCAGGTCAAGGGGGCTACTACTCTCAGTGGGGTGGCTATGA : 53579 217 : pGlnTyrSerGlyTyr<->AsnTyrGlyTyrAsnProTyrAlaAlaProProProMetMe : 235 |||||||||||||||| ||| !||||||||| ! ! !::! ! ! !! ! pGlnTyrSerGlyTyrAsnAsnSerGlyTyrAsnSerGlyTyrSerSerGlyTyrAsnSe 53580 : CCAGTACAGCGGCTACAACAACAGCGGCTATAACAGTGGCTACAGCAGCGGCTACAACAG : 53639 236 : tGlyProProProProMetGlyMetProProMetProProAspMetGlnGlySerThrGl : 255 ||| ! ! ! ! ||| ! ! |||||| !!. !! ! !! rGlyTyrAsnTyrSerTyrGlyProTyrGlyTyrProProProGlyHisMetMetProPr 53640 : TGGCTACAACTATAGCTACGGGCCTTATGGATACCCCCCACCAGGCCACATGATGCCACC : 53699 256 : uAlaHisAspGlyThrGluGluValGluGluAspProSerGluAsp >>>> Target : 271 ! !!! !! ! !! !.....!!!: !... !:!! !!!: 32 oProProValProProMetSerThrAspMetSerGlyAlaThrGlu++ 53700 : ACCTCCCGTGCCACCCATGTCCACTGACATGTCAGGAGCTACAGAGgt............ : 53749 272 : Intron 7 >>>> ProAsnProGlnValAspValGluGluLeuAsnArgGlnTyrMet : 285 4 bp |||! !|||:!! !|||||||||:!!! !|||!:!.!.!:!||| ++ProIleProGluCysAspValGluGlnTrpAsnLysAspPheMet 53750 : .............agCCGATCCCTGAATGTGACGTGGAGCAGTGGAACAAAGATTTTATG : 54113 286 : GluArgSerGluGluLeuTyrAspSerLeuMetGluCysHisTrpLeuProMetAspThr : 305 :!!|||||||||||||||||||||:!!:!!|||!!:|||!.!||| !|||!!:|||:!! GlnArgSerGluGluLeuTyrAspAlaMetMetAspCysArgTrpGluProIleAspSer 54114 : CAACGCAGCGAGGAACTCTACGACGCCATGATGGACTGTCGCTGGGAGCCCATAGACTCT : 54173 306 : IleThrSerAspIleSerMetMetAsn : 314 :!!!.!||| ||| :::::: ValAsnSerProIleProSerLeuSer 54174 : GTTAACTCTCCcattccctccctctct : 54202 vulgar: SPP00000665_2.0 0 314 . JXSJ01000502.1:subseq(30134,104190) 49087 54202 + 895 M 12 36 5 0 2 I 0 872 3 0 2 M 32 96 S 0 2 5 0 2 I 0 579 3 0 2 S 1 1 M 33 99 5 0 2 I 0 885 3 0 2 M 17 51 S 0 2 5 0 2 I 0 933 3 0 2 S 1 1 M 23 69 G 1 0 M 19 57 S 0 2 5 0 2 I 0 391 3 0 2 S 1 1 M 24 72 G 1 0 M 14 42 S 0 2 5 0 2 I 0 165 3 0 2 S 1 1 M 33 99 G 0 3 M 8 24 G 0 3 M 49 147 5 0 2 I 0 320 3 0 2 M 44 132 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-21 ##type DNA # # # seqname source feature start end score strand frame attributes # JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local gene 49088 54202 895 + . gene_id 1 ; sequence SPP00000665_2.0 ; gene_orientation + JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local cds 49088 49123 . + . JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local exon 49088 49123 . + . insertions 0 ; deletions 0 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local splice5 49124 49125 . + . intron_id 1 ; splice_site "GT" JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local intron 49124 49999 . + . intron_id 1 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local splice3 49998 49999 . + . intron_id 0 ; splice_site "ag" JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local cds 50000 50097 . + . JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local exon 50000 50097 . + . insertions 0 ; deletions 0 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local splice5 50098 50099 . + . intron_id 2 ; splice_site "GT" JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local intron 50098 50680 . + . intron_id 2 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local splice3 50679 50680 . + . intron_id 1 ; splice_site "AG" JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local cds 50681 50780 . + . JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local exon 50681 50780 . + . insertions 0 ; deletions 0 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local splice5 50781 50782 . + . intron_id 3 ; splice_site "GT" JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local intron 50781 51669 . + . intron_id 3 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local splice3 51668 51669 . + . intron_id 2 ; splice_site "AG" JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local cds 51670 51722 . + . JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local exon 51670 51722 . + . insertions 0 ; deletions 0 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local splice5 51723 51724 . + . intron_id 4 ; splice_site "GT" JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local intron 51723 52659 . + . intron_id 4 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local splice3 52658 52659 . + . intron_id 3 ; splice_site "AG" JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local cds 52660 52788 . + . JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local exon 52660 52788 . + . insertions 0 ; deletions 1 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local splice5 52789 52790 . + . intron_id 5 ; splice_site "GT" JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local intron 52789 53183 . + . intron_id 5 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local splice3 53182 53183 . + . intron_id 4 ; splice_site "AG" JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local cds 53184 53300 . + . JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local exon 53184 53300 . + . insertions 0 ; deletions 1 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local splice5 53301 53302 . + . intron_id 6 ; splice_site "GT" JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local intron 53301 53469 . + . intron_id 6 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local splice3 53468 53469 . + . intron_id 5 ; splice_site "GG" JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local cds 53470 53746 . + . JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local exon 53470 53746 . + . insertions 6 ; deletions 0 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local splice5 53747 53748 . + . intron_id 7 ; splice_site "GT" JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local intron 53747 54070 . + . intron_id 7 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local splice3 54069 54070 . + . intron_id 6 ; splice_site "ag" JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local cds 54071 54202 . + . JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local exon 54071 54202 . + . insertions 0 ; deletions 0 JXSJ01000502.1:subseq(30134,104190) exonerate:protein2genome:local similarity 49088 54202 895 + . alignment_id 1 ; Query SPP00000665_2.0 ; Align 49088 1 36 ; Align 50000 13 96 ; Align 50682 46 99 ; Align 51670 79 51 ; Align 52661 97 69 ; Align 52730 121 57 ; Align 53185 141 72 ; Align 53257 166 42 ; Align 53471 181 99 ; Align 53573 214 24 ; Align 53600 222 147 ; Align 54071 271 132 # --- END OF GFF DUMP --- # -- completed exonerate analysis