Command line: [exonerate --exhaustive yes -m p2g --showtargetgff -q SECp43softshell.anole.fa -t SECp43softshell.extraccio.KQ748792.1.fa] Hostname: [ws101069u] C4 Alignment: ------------ Query: SPP00002156_2.0 # Protein # tRNA Sec 1 associated protein 1 (SECp43) # Softshell turtle Target: KQ748792.1:subseq(105709,54920) Gekko japonicus isolate JY-2015 unplaced genomic scaffold scaffold167, whole genome shotgun sequence Model: protein2genome:local Raw score: 1272 Query range: 0 -> 271 Target range: 19999 -> 34920 1 : LeuGluProTyrMetAspGluAsnPheValSerArgAlaPheAlaThrMetGlyGluLeu : 20 |||||||||||||||||||||||||||:!!|||||||||||||||||||||||||||||| LeuGluProTyrMetAspGluAsnPheIleSerArgAlaPheAlaThrMetGlyGluLeu 20000 : ctGGAGCCATATATGGATGAGAACTTCATTTCAAGAGCCTTTGCCACTATGGGGGAGCTG : 20057 21 : ValLeuSerValLysIleIleArgAsnArgLeuThr{Gl} >>>> Target Intron : 33 ||||||||||||||||||||||||||||||||||||{||} 6710 bp ValLeuSerValLysIleIleArgAsnArgLeuThr{Gl}++ 20058 : GTTCTGAGCGTCAAAATAATTCGAAATAGATTGACG{GG}gt.................. : 20100 34 : 1 >>>> {y}IleProAlaGlyTyrCysPheValGluPheAlaAspLeuAlaThrAla : 49 {|}|||||||||||||||||||||||||||||||||||||||||||||||| ++{y}IleProAlaGlyTyrCysPheValGluPheAlaAspLeuAlaThrAla 20101 : .......ag{G}ATTCCGGCAGGCTATTGCTTTGTGGAATTTGCTGATCTAGCCACTGCT : 26854 50 : GluLysCysLeuHisLysIleAsnGlyLysProLeuProGlyAlaThrPro >>>> Ta : 67 ||||||||||||||||||||||||||||||||||||||||||||||||||| GluLysCysLeuHisLysIleAsnGlyLysProLeuProGlyAlaThrPro++ 26855 : GAAAAgtgtttacataaaatcaacgGCAAACCTCTTCCTGGTGCCACACCTgt....... : 26910 68 : rget Intron 2 >>>> AlaLysArgPheLysLeuAsnTyrAlaThrTyrGlyLysG : 80 1725 bp .!!||||||||||||||||||||||||||||||||||||| ++ThrLysArgPheLysLeuAsnTyrAlaThrTyrGlyLysG 26911 : ..................agACAAAGCGATTTAAATTAAACTACGCAACATATGGGAAGC : 28672 81 : lnProAspAsn{Se} >>>> Target Intron 3 >>>> {r}ProGluTyrSerL : 89 |||||||||||{||} 688 bp {|}||||||||||||| lnProAspAsn{Se}++ ++{r}ProGluTyrSerL 28673 : AGCCAGATAAC{AG}gt.........................ag{C}CCAGAATATTCAC : 29387 90 : euPheValGlyAspLeuThrProAspValAspAspGlyMetLeuTyrGluPhePheValL : 109 |||||||||||||||||:!!|||||||||||||||||||||:!!|||||||||||||||| euPheValGlyAspLeuSerProAspValAspAspGlyMetIleTyrGluPhePheValL 29388 : TATTTGTGGGAGATCTTTCCCCGGATGTGGATGACGGGATGATATACGAGTTCTTTGTAA : 29447 110 : ysValTyrProSerCysArgGlyGlyLysValValLeuAspGlnThrGlyValSer{Ly} : 128 |||||||||||||||||||||||||||||||||||:!!||||||||||||||||||{||} ysValTyrProSerCysArgGlyGlyLysValValValAspGlnThrGlyValSer{Ly} 29448 : AAGTGTACCCCTCGTGCAGGGGCGGCAAAGTTGTTGTAGACCAGACGGGCGTTTCC{AA} : 29504 129 : >>>> Target Intron 4 >>>> {s}GlyTyrGlyPheValLysPheThrAspG : 138 630 bp {|}|||||||||||||||||||||:!!|||| ++ ++{s}GlyTyrGlyPheValLysPheSerAspG 29505 : gt.........................ag{G}GGCTATGGTTTTGTGAAATTCTCAGATG : 30164 139 : luLeuGluGlnLysArgAlaLeuThrGluCysGlnGlyAlaValGlyLeuGlySerLysP : 158 |||||||||||||||||||||||..!|||||||||||||||||||||||||||||||||| luLeuGluGlnLysArgAlaLeuValGluCysGlnGlyAlaValGlyLeuGlySerLysP 30165 : AATTGGAACAGAAAAGAGCACTGGTAGAGTGCCAGGGTGCCGTGGGTCTTGGTTCCAAAC : 30224 159 : roValArgLeuSerValAlaIleProLys{Al} >>>> Target Intron 5 >>>> : 168 ||:!!||||||||||||||||||||||||{||} 2214 bp roIleArgLeuSerValAlaIleProLys{Al}++ 30225 : CAATACGCTTGAGCGTTGCCATACCAAAA{GC}gt......................... : 30258 169 : {a}SerAsnArgMetLysThrValGluTyrAsnGlnMetTyrSerTyrAsnTyrAsnG : 187 {|}|||||||||:!!|||||||||||||||||||||||||||!:!||||||||||||| --{a}SerAsnArgLeuLysThrValGluTyrAsnGlnMetTyrAsnTyrAsnTyrAsnG 30259 : ca{c}AGTAACCGGCTGAAGACAGTTGAATATAATCAGATGTACAACTATAACTACAACC : 32525 188 : lnTyrTyrGlnGlnTyrGlnAsnTyrTyrAlaGlnTrpGlyTyrAspGlnAsnThrGlyS : 207 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| lnTyrTyrGlnGlnTyrGlnAsnTyrTyrAlaGlnTrpGlyTyrAspGlnAsnThrGlyS 32526 : AGTACTACCAGCAATATCAGAACTATTATGCCCAGTGGGGGTATGACCAGAACACAGGCA : 32585 208 : erTyrSerTyrSerTyrProGlnTyrGlyTyrThrGlnSerThrMetGln >>>> Tar : 224 ||||||||||||||||||||||||||||||||||||||!:!||||||||| erTyrSerTyrSerTyrProGlnTyrGlyTyrThrGlnAsnThrMetGln++ 32586 : GTTACAGCTACAGCTATCCACAGTACGGCTACACACAAAACACCATGCAGgt........ : 32638 225 : get Intron 6 >>>> GluProPheValPro{T} >>>> Target Intron 7 : 229 917 bp ! !|||||||||{ } 1224 bp ++ProLeuPheValPro{G}-+ 32639 : .................agCCTCTATTTGTCCCA{G}ct..................... : 33571 230 : >>>> {yr}PhePheProProLeuAspProMetProGlnMetAspValSerGluAlaAs : 246 { !}|||.!!|||! !! !||||||||||||||||||||||||||||||||||| ++{ly}PheLeuProLeuProAspProMetProGlnMetAspValSerGluAlaAs 33572 : ....ag{GC}TTCCTTCCACTTCCAGATCCAATGCCCCAGATGGACGTGAGCGAAGCCAA : 34843 247 : nLysGlnPheMetGluGlnSerGluGluLeuTyrAspAlaLeuMetAspCysHisTrpGl : 266 |||||||||||||!!:|||||||||||||||||||||||||||!!:!!:||||||||||| nLysGlnPheMetAspGlnSerGluGluLeuTyrAspAlaLeuIleGluCysHisTrpGl 34844 : CAAACAGTTCATGGACCAGAGCGAGGAGCTCTACGACGCCTTGATAGAATGCCACTGGCA : 34903 267 : nProLeuAspThrVal : 271 ||||||||||!:!||| nProLeuAspSerVal 34904 : GCCTTTGGACAGTGTC : 34920 vulgar: SPP00002156_2.0 0 271 . KQ748792.1:subseq(105709,54920) 19999 34920 + 1272 M 32 96 S 0 2 5 0 2 I 0 6706 3 0 2 S 1 1 M 33 99 5 0 2 I 0 1721 3 0 2 M 17 51 S 0 2 5 0 2 I 0 684 3 0 2 S 1 1 M 43 129 S 0 2 5 0 2 I 0 626 3 0 2 S 1 1 M 39 117 S 0 2 5 0 2 I 0 2210 3 0 2 S 1 1 M 55 165 5 0 2 I 0 913 3 0 2 M 5 15 S 0 1 5 0 2 I 0 1220 3 0 2 S 1 2 M 42 126 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-24 ##type DNA # # # seqname source feature start end score strand frame attributes # KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local gene 20000 34920 1272 + . gene_id 1 ; sequence SPP00002156_2.0 ; gene_orientation + KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local cds 20000 20097 . + . KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local exon 20000 20097 . + . insertions 0 ; deletions 0 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local splice5 20098 20099 . + . intron_id 1 ; splice_site "GT" KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local intron 20098 26807 . + . intron_id 1 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local splice3 26806 26807 . + . intron_id 0 ; splice_site "AG" KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local cds 26808 26907 . + . KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local exon 26808 26907 . + . insertions 0 ; deletions 0 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local splice5 26908 26909 . + . intron_id 2 ; splice_site "GT" KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local intron 26908 28632 . + . intron_id 2 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local splice3 28631 28632 . + . intron_id 1 ; splice_site "AG" KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local cds 28633 28685 . + . KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local exon 28633 28685 . + . insertions 0 ; deletions 0 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local splice5 28686 28687 . + . intron_id 3 ; splice_site "GT" KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local intron 28686 29373 . + . intron_id 3 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local splice3 29372 29373 . + . intron_id 2 ; splice_site "AG" KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local cds 29374 29505 . + . KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local exon 29374 29505 . + . insertions 0 ; deletions 0 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local splice5 29506 29507 . + . intron_id 4 ; splice_site "GT" KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local intron 29506 30135 . + . intron_id 4 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local splice3 30134 30135 . + . intron_id 3 ; splice_site "AG" KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local cds 30136 30255 . + . KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local exon 30136 30255 . + . insertions 0 ; deletions 0 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local splice5 30256 30257 . + . intron_id 5 ; splice_site "GT" KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local intron 30256 32469 . + . intron_id 5 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local splice3 32468 32469 . + . intron_id 4 ; splice_site "ca" KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local cds 32470 32635 . + . KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local exon 32470 32635 . + . insertions 0 ; deletions 0 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local splice5 32636 32637 . + . intron_id 6 ; splice_site "GT" KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local intron 32636 33552 . + . intron_id 6 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local splice3 33551 33552 . + . intron_id 5 ; splice_site "AG" KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local cds 33553 33568 . + . KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local exon 33553 33568 . + . insertions 0 ; deletions 0 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local splice5 33569 33570 . + . intron_id 7 ; splice_site "CT" KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local intron 33569 34792 . + . intron_id 7 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local splice3 34791 34792 . + . intron_id 6 ; splice_site "AG" KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local cds 34793 34920 . + . KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local exon 34793 34920 . + . insertions 0 ; deletions 0 KQ748792.1:subseq(105709,54920) exonerate:protein2genome:local similarity 20000 34920 1272 + . alignment_id 1 ; Query SPP00002156_2.0 ; Align 20000 1 96 ; Align 26809 34 99 ; Align 28633 67 51 ; Align 29375 85 129 ; Align 30137 129 117 ; Align 32471 169 165 ; Align 33553 224 15 ; Align 34795 230 126 # --- END OF GFF DUMP --- # -- completed exonerate analysis