Command line: [exonerate -m p2g --showtargetgff -q selenoo2_zf.aa.fa.canviat -t genomeselenoo2_JXSJ01000232.1.fa] Hostname: [ws116078U] C4 Alignment: ------------ Query: SPP00000641_2.0 # Protein # Selenoprotein O2 (SELENOO2) # Zebrafish Target: JXSJ01000232.1:subseq(284614,104490) Miichthys miiuy scaffold232, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 1632 Query range: 146 -> 614 Target range: 54124 -> 49501 147 : GlyArgTrpGluIleGlnValLysGlyAlaGlyLeuThrProTyrSer{Ar} >>>> T : 163 |||||||||||||||||||||||||||||||||:!!||||||||||||{||} GlyArgTrpGluIleGlnValLysGlyAlaGlyValThrProTyrSer{Ar}++ 54124 : GGGCGATGGGAGATTCAGGTGAAAGGTGCAGGGGTCACACCTTATTCC{AG}gt...... : 54072 164 : arget Intron 1 >>>> {g}LeuSerAspGlyArgLysValLeuArgSerSerIle : 175 1314 bp {|} !.!!|||||||||||||||||||||||||||||| ++{g}AspGlyAspGlyArgLysValLeuArgSerSerIle 54071 : ...................ag{G}GATGGTGATGGCCGGAAGGTGCTTCGCTCCAGCATC : 52726 176 : ArgGluPheLeuCysSerGluAlaMetPheAlaLeuGlyIleProThrThrArgAlaGly : 195 ||||||||||||||||||||||||||| !|||||||||||||||!:!|||||||||!.! ArgGluPheLeuCysSerGluAlaMetAlaAlaLeuGlyIleProSerThrArgAlaAla 52725 : AGAGAATTCCTGTGCAGCGAGGCAATGGCTGCCCTGGGGATACCCAGCACTCGGGCAGCC : 52666 196 : SerLeuValThrSerAspLeuTyrValGlnArgAspGluPheTyrSerGlyAsnProLys : 215 |||||||||||||||||||||||||||.!.|||||| !.!! !!||||||!..! !! SerLeuValThrSerAspLeuTyrValAsnArgAspProLeuAsnSerGlyArgArgIle 52665 : TCCCtcgtgacctctgacctgtaCGTCAACAGAGATCCACTCAACAGTGGCAGGCGCATT : 52606 216 : ProGluArgCysSerValValLeuArgIleAlaProThrPheIle{Ar} >>>> Targ : 231 |||||||||||||||||||||||||||:!!||||||:!!||||||{||} ProGluArgCysSerValValLeuArgLeuAlaProSerPheIle{Ar}++ 52605 : CCCGAGCGCTGTTCAGTTGTCCTGCGTCTCGCCCCTTCCTTCATC{AG}gt......... : 52554 232 : et Intron 2 >>>> {g}PheGlySerPheGluIlePheHisProLeuAspAspPhe : 244 90 bp {|}.!!||||||||||||||||||! !! !||||||||| ++{g}IleGlySerPheGluIlePheLeuGlyArgAspAspPhe 52553 : ................ag{G}ATCGGCTCTTTTGAGATCTTTCTGGGCCGTGATGATTTC : 52429 245 : ThrGlyArgGlnGlyProSerValGlyArgProAspIleArgAlaGlyLeuLeuAspTyr : 264 :!!|||! !||||||||||||!.!||||||! !|||||||||||| !|||||||||||| SerGlyLeuGlnGlyProSerAlaGlyArgHisAspIleArgAlaGlnLeuLeuAspTyr 52428 : TCAGGACTGCAGGGTCCAAGTGCAGGCCGCCATGACATTCGCGCTCAGCTGCTGGATTAT : 52369 265 : ValIleGluThrPheTyrProGluIleGlnArgGlyHisLeuAspArgLysGluArgAsn : 284 ||||||||||||||||||||| ||||||!:! !||| !:!!||||||!!:|||||| ValIleGluThrPheTyrProCysIleGlnLysThrHisSerAsnArgLysAspArgAsn 52368 : GTCATTGAGACTTTTTATCCTTGCATCCAGAAGACTCATAGCAACCGGAAAGACAGGAAC : 52309 285 : AlaAlaPhePheArgGlu >>>> Target Intron 3 >>>> ValThrValArgT : 295 !||||||||||||||| 119 bp |||! !:!!|||| MetAlaPhePheArgGlu++ ++ValMetLeuArgT 52308 : ATGGCTTTTTTCAGAGAGgt.........................agGTGATGTTGCGAA : 52157 296 : hrAlaLysLeuValAlaLeuTrpGlnSerValGlyPheCysHisGlyValLeuAsnThrA : 315 |||||||||||||||||! !||||||!!!||||||||||||||||||||||||||||||| hrAlaLysLeuValAlaGlnTrpGlnCysValGlyPheCysHisGlyValLeuAsnThrA 52156 : CTGCTAAGCTAGTGGCCCAGTGGCAGTGTGTTGGTTTTTGCCATGGCGTCCTTAACACAG : 52097 316 : spAsnMetSerIleLeuGlyLeuThrIleAspTyrGlyProPheGlyPheMetAsp{Ar} : 334 ||||||||||||||||||||||||||:!:|||||||||||||||||||||||||||{||} spAsnMetSerIleLeuGlyLeuThrLeuAspTyrGlyProPheGlyPheMetAsp{Ar} 52096 : ACAACATGAGCATTCTGGGTCTTACTCTGGATTATGGCCCCTTTGGTTTCATGGAC{AG} : 52040 335 : >>>> Target Intron 4 >>>> {g}PheAspProGluPheValCysAsnAlaS : 344 169 bp {|}|||||||||!!:||||||||||||.!!| ++ ++{g}PheAspProAspPheValCysAsnThrS 52039 : gt.........................ag{A}TTTGATCCGGATTTCGTTTGCAACACCT : 51841 345 : erAspLysLysGlyArgTyrThrTyrGluAlaGlnProTyrValCysArgTrpAsnLeuA : 364 ||||||||!:!|||||||||:!!|||..!|||||||||! !||||||||||||||||||| erAspLysArgGlyArgTyrSerTyrArgAlaGlnProSerValCysArgTrpAsnLeuA 51840 : CGGACAAAAGAGGACGCTACTCATACCGAGCCCAGCCATCCGTGTGCCGCTGGAACCTGG : 51781 365 : laArgLeuAlaGluAlaLeuGlyAlaGluIleGlnSerIleLysAlaGlyValIleLeuA : 384 |||||||||||||||||||||||:!!|||:!:.!.:!! !:!!|||||||||:!!|||| laArgLeuAlaGluAlaLeuGlySerGluLeuAspAlaAlaGlnAlaGlyValValLeuA 51780 : CTCGTCTGGCAGAGGCATTGGGTTCTGAGCTGGATGCGGCTCAGGCAGGGGTTGTTCTGG : 51721 385 : spGluPheMetSerLeuTyrGluAspPheTyrLeuGlyAsnMetArgLysLysLeuGlyL : 404 ||||||||:!: !! !||||||! !|||||||||!.!! !||||||||||||||||||| spGluPheValProThrTyrGluAlaPheTyrLeuAlaIleMetArgLysLysLeuGlyL 51720 : ATGAATTTGTACCCACATACGAAGCCTTTTATCTGGCTATCATGAGAAAAAAGCTGGGCC : 51661 405 : euLeuArgLysGlnGluProGluAspGlyGluLeuValAlaAspMetLeuLysThrMetH : 424 ||:!!|||!:!:!!!!: !!|||||||||||||||:!!:!!|||:!!|||::: !|||| euValArgArgGluAspAlaGluAspGlyGluLeuIleSerAspLeuLeuArgLeuMetH 51660 : TTGTGAGAAGAGAAGATGCAGAGGACGGCGAGCTCATATCAGACCTGCTGCGCCTCATGC : 51601 425 : isIleThr{G} >>>> Target Intron 5 >>>> {ly}AlaAspPheThrAsnT : 433 || !|||{|} 182 bp {||}|||||||||||||||| isAspThr{G}++ ++{ly}AlaAspPheThrAsnT 51600 : ATGACACT{G}gt.........................ag{GT}GCAGATTTCACCAACA : 51392 434 : hrPheArgLeuLeuSerAspIleSerSerProValGlyAspProAlaGluLysAspAsnT : 453 ||||||||||||||||| !:!! !!!!!||||||! !! ! !::!|||!:!! !!... hrPheArgLeuLeuSerArgValProTrpProValAspGlyAspSerGluArgAlaThrV 51391 : CCTTCCGTCTGCTGAGCCGTGTCCCTTGGCCTGTGGATGGCGACAGTGAGAGGGCCACAG : 51332 454 : hrAspSerValValGluLeuIleValAspGlnCysAlaLeuLeuGluGluLeuLysValA : 473 .!! ! !!||||||!!:||||||:!!!!:||||||||| !:!!|||||||||||||||| alGlyProValValAspLeuIleLeuGluGlnCysAlaThrIleGluGluLeuLysValA 51331 : TGGGCCCAGTAGTGGACCTCATCCTAGAACAGTGTGCCACTATTGAGGAGCTAAAGGTGG : 51272 474 : laAsnHisProThrMetGlnPro{Gl} >>>> Target Intron 6 >>>> {y}G : 482 ||||| ! |||||||||:!! !{ !} 361 bp {!}| laAsnLysProThrMetGluAsp{Ar}++ ++{g}G 51271 : CTAATAAGCCAACTATGGAGGAC{CG}gt.........................ag{T}G : 50884 483 : luLeuGluMetIleLeuSerMetAlaGluThrAsnProGluMetPheAsnMetValAlaA : 502 |||||! !||||||||||||||||||:!!|||||||||! ||||||...!!:||||||: luLeuAlaMetIleLeuSerMetAlaGlnThrAsnProValMetPheGlyIleValAlaA 50883 : AACTGGCAATGATTCTGTCCATGGCACAAACCAACCCAGTCATGTTTGGGATAGTGGCAG : 50824 503 : snGlnProGluValThrLysGlnLeuGluLysIleGlyArgLeuArgGluLeuLeuMetI : 522 !! !|||!!:|||:!!:!!|||||||||::!!!:|||||||||!:!||||||||| !! spThrProAspValSerGlnGlnLeuGluArgMetGlyArgLeuLysGluLeuLeuGluT 50823 : ACACACCAGATGTGTCCCAGCAACTGGAACGAATGGGACGGCTAAAGGAACTGCTCGAGA : 50764 523 : leSerGluAlaGluLeuLysValLysGlnArgGluHisTrpGlnArgTrpValLysGlnT : 542 !...::: ||||||||| !|||||||||!!: !!||| |||||||||!..!:!| hrAspGlnGluGluLeuLysLysLysGlnArgAspAspTrpIleArgTrpValSerArgT 50763 : CAGatcaggaagagctcaagaaAAAGCAGCGAGATGACTGGATTCGATGGGTTAGCCGAT : 50704 543 : yr{Ar} >>>> Target Intron 7 >>>> {g}LysArgLeuAlaPheGluCysA : 551 ||{||} 522 bp {|}!:!||||||||| ||||||: yr{Ar}++ ++{g}ArgArgLeuAlaArgGluCysA 50703 : AC{AG}gt.........................ag{G}AGGCGTTTAGCCAGAGAGTGTG : 50155 552 : snGlnAlaSerAspProAlaSerValGluLysGluArgValArgPheMetAsnSerThrA : 571 !! .!!!.!|||! !:!! !:!!:!!|||||||||:!!!!! ! ||||||||||||| spGlyThrLysAspLeuSerLeuIleLysLysGluArgLeuSerValMetAsnSerThrA 50154 : ATGGCACAAAGGACCTGTCTCTCATCAAAAAGGAGAGGCTCAGCGTGATGAACAGCACCA : 50095 572 : snProAlaValValLeuArgAsnTyrIleAlaGlnAsnAlaIleAspAlaAlaGluLysG : 591 ||||| !|||:!!||||||||||||||||||||||||||||||.!.||||||||||||| snProHisValIleLeuArgAsnTyrIleAlaGlnAsnAlaIleGlnAlaAlaGluLysG 50094 : ACCCCCATGTCATCTTACGCAACTACATCGCCCAGAATGCAATTCAGGCTGCAGAAAAGG : 50035 592 : lyAspPheSerGlu >>>> Target Intron 8 >>>> ValGlnArgValLeuAr : 601 |||||||||||||| 462 bp |||.!.|||||||||!: lyAspPheSerGlu++ ++ValAsnArgValLeuLy 50034 : GAGATTTCTCTGAGgt.........................agGTCAACAGGGTCCTCAA : 49543 602 : gValLeuGluAsnProTyrSerValSerProAspLeuGlu : 614 !|||||||||!!.|||||||||! !..! !! |||||| sValLeuGluLysProTyrSerAspGluPheGlyLeuGlu 49542 : AGTTCTGGAGAAACCATATTCTGATGAATTTGGGCTGGAG : 49502 vulgar: SPP00000641_2.0 146 614 . JXSJ01000232.1:subseq(284614,104490) 54124 49501 - 1632 M 16 48 S 0 2 5 0 2 I 0 1310 3 0 2 S 1 1 M 67 201 S 0 2 5 0 2 I 0 86 3 0 2 S 1 1 M 59 177 5 0 2 I 0 115 3 0 2 M 43 129 S 0 2 5 0 2 I 0 165 3 0 2 S 1 1 M 92 276 S 0 1 5 0 2 I 0 178 3 0 2 S 1 2 M 53 159 S 0 2 5 0 2 I 0 357 3 0 2 S 1 1 M 61 183 S 0 2 5 0 2 I 0 518 3 0 2 S 1 1 M 52 156 5 0 2 I 0 458 3 0 2 M 19 57 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-18 ##type DNA # # # seqname source feature start end score strand frame attributes # JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local gene 49502 54124 1632 - . gene_id 1 ; sequence SPP00000641_2.0 ; gene_orientation + JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local cds 54075 54124 . - . JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local exon 54075 54124 . - . insertions 0 ; deletions 0 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice5 54073 54074 . - . intron_id 1 ; splice_site "GT" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local intron 52761 54074 . - . intron_id 1 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice3 52761 52762 . - . intron_id 0 ; splice_site "AG" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local cds 52557 52760 . - . JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local exon 52557 52760 . - . insertions 0 ; deletions 0 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice5 52555 52556 . - . intron_id 2 ; splice_site "Gt" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local intron 52467 52556 . - . intron_id 2 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice3 52467 52468 . - . intron_id 1 ; splice_site "AG" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local cds 52289 52466 . - . JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local exon 52289 52466 . - . insertions 0 ; deletions 0 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice5 52287 52288 . - . intron_id 3 ; splice_site "GT" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local intron 52170 52288 . - . intron_id 3 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice3 52170 52171 . - . intron_id 2 ; splice_site "AG" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local cds 52039 52169 . - . JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local exon 52039 52169 . - . insertions 0 ; deletions 0 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice5 52037 52038 . - . intron_id 4 ; splice_site "GT" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local intron 51870 52038 . - . intron_id 4 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice3 51870 51871 . - . intron_id 3 ; splice_site "AG" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local cds 51592 51869 . - . JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local exon 51592 51869 . - . insertions 0 ; deletions 0 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice5 51590 51591 . - . intron_id 5 ; splice_site "GT" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local intron 51410 51591 . - . intron_id 5 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice3 51410 51411 . - . intron_id 4 ; splice_site "AG" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local cds 51247 51409 . - . JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local exon 51247 51409 . - . insertions 0 ; deletions 0 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice5 51245 51246 . - . intron_id 6 ; splice_site "GT" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local intron 50886 51246 . - . intron_id 6 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice3 50886 50887 . - . intron_id 5 ; splice_site "ag" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local cds 50700 50885 . - . JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local exon 50700 50885 . - . insertions 0 ; deletions 0 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice5 50698 50699 . - . intron_id 7 ; splice_site "GT" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local intron 50178 50699 . - . intron_id 7 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice3 50178 50179 . - . intron_id 6 ; splice_site "AG" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local cds 50021 50177 . - . JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local exon 50021 50177 . - . insertions 0 ; deletions 0 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice5 50019 50020 . - . intron_id 8 ; splice_site "GT" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local intron 49559 50020 . - . intron_id 8 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local splice3 49559 49560 . - . intron_id 7 ; splice_site "AG" JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local cds 49502 49558 . - . JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local exon 49502 49558 . - . insertions 0 ; deletions 0 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local similarity 49502 54124 1632 - . alignment_id 1 ; Query SPP00000641_2.0 ; Align 54125 147 48 ; Align 52760 164 201 ; Align 52466 232 177 ; Align 52170 291 129 ; Align 51869 335 276 ; Align 51408 428 159 ; Align 50885 482 183 ; Align 50177 544 156 ; Align 49559 596 57 # --- END OF GFF DUMP --- # C4 Alignment: ------------ Query: SPP00000641_2.0 # Protein # Selenoprotein O2 (SELENOO2) # Zebrafish Target: JXSJ01000232.1:subseq(284614,104490) Miichthys miiuy scaffold232, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 387 Query range: 12 -> 129 Target range: 54490 -> 54136 13 : SerLeuThrProLeuGluArgLeuLysPheAsnAsnValAlaLeuLysAlaLeuProVal : 32 |||! !:!! !!||||||!.!||| |||||||||..!||||||||| !||||||||| SerSerSerAlaLeuGluHisLeuProPheAsnAsnThrAlaLeuLysArgLeuProVal 54490 : TCGTCCTCGGCTCTGGAGCATTTACCTTTCAACAACACCGCGCTGAAAAGGCTGCCGGTG : 54433 33 : AspSerSerLeuGluProGlySerArgThrValLysAlaAlaCysPheSerLeuValLys : 52 |||..!||| !||||||||||||||||||||| !|||||||||||||||! !:!!::! AspAspSerAspGluProGlySerArgThrValProAlaAlaCysPheSerArgIleArg 54432 : GATGACTCAGATGAGCCCGGGTCCCGAACGGTCCCGGCGGCATGTTTCTCTCGAATTCGG : 54373 53 : Pro<->GlnAlaLeuIleLysProThrIleValAlaLeuSerGlyProAlaLeuAlaLeu : 71 !! ||| !!||| !:::||||||.!!|||:!!! !||| ! !!|||||||||||| ThrLeuGlnProLeuProArgProThrPheValSerGlnSerGlnSerAlaLeuAlaLeu 54372 : ACTCTTCAGCCCCTTCCACGTCCGACCTTCGTGTCCCAGTCCCAGTCAGCTCTGGCTCTG : 54313 72 : LeuGlyLeuLysValGluAspValLeuGlnAspProHisAlaAlaGluTyrLeuSerGly : 91 |||! !|||! |||||||||||||||!:::!!|||! !.! !!||||||||||||||| LeuAspLeuThrValGluAspValLeuArgAsnProLeuGlyProGluTyrLeuSerGly 54312 : CTCGACCTGACCGTGGAGGATGTGTTGCGTAACCCTCTGGGCCCGGAGTATTTGAGCGGC : 54253 92 : SerArgLeuIleGlnGlySerGluProAlaAlaHisCysTyrCysGlyHisGlnPheGly : 111 |||||||||:!:! !||||||||||||||||||||||||||| !!||||||||||||||| SerArgLeuLeuProGlySerGluProAlaAlaHisCysTyrSerGlyHisGlnPheGly 54252 : TCCAGGCTGCTGCCGGGCTCCGAGCCGGCCGCGCACTGTTACAGCGGGCATCAATTCGGG : 54193 112 : GlnPheAlaGlyGlnLeuGlyAspGlyAlaValCysTyrLeuGlyGluValGlu : 129 ! !|||||||||||||||||||||||||||||| |||||||||||||||||| LeuPheAlaGlyGlnLeuGlyAspGlyAlaValValTyrLeuGlyGluValGlu 54192 : CTGTTCGCGGGACAGCTGGGAGACGGAGCGGTGGTGTACCTTGGGGAGGTGGAG : 54137 vulgar: SPP00000641_2.0 12 129 . JXSJ01000232.1:subseq(284614,104490) 54490 54136 - 387 M 41 123 G 0 3 M 76 228 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-18 ##type DNA # # # seqname source feature start end score strand frame attributes # JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local gene 54137 54490 387 - . gene_id 2 ; sequence SPP00000641_2.0 ; gene_orientation . JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local cds 54137 54490 . - . JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local exon 54137 54490 . - . insertions 3 ; deletions 0 JXSJ01000232.1:subseq(284614,104490) exonerate:protein2genome:local similarity 54137 54490 387 - . alignment_id 2 ; Query SPP00000641_2.0 ; Align 54491 13 123 ; Align 54365 54 228 # --- END OF GFF DUMP --- # -- completed exonerate analysis