Command line: [exonerate -m p2g --showtargetgff -q MSRB3.fa -t MSRB3.subseq] Hostname: [ws101069u] C4 Alignment: ------------ Query: SPP00000092_2.0 # Protein # Methionine-R-sufoxide reductase 3 (MSRB3) # Human Target: JSZB01006555.1:subseq(360000,225000) Manis javanica isolate MP_PG03-UM SCAFFOLD7521, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 769 Query range: 32 -> 192 Target range: 176660 -> 51789 33 : GlySerCysArgAspLysLysAsnCysLysValValPheSerGlnGlnGluLeuArgL : 52 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GlySerCysArgAspLysLysAsnCysLysValValPheSerGlnGlnGluLeuArgL 176660 : GGGTCATGTAGGGATAAAAAGAACTGTAAGGTGGTCTTTTCCCAGCAGGAGCTGAGGA : 176603 53 : ysArgLeuThrProLeuGlnTyrHisValThrGlnGluLysGlyThrGlu{Se} >> : 69 ||||||||||||||||||||||||||||||||||||||||||||||||||{||} ysArgLeuThrProLeuGlnTyrHisValThrGlnGluLysGlyThrGlu{Se}++ 176602 : AGCGGCTAACACCCCTGCAGTACCATGTCACTCAGGAGAAAGGGACTGAA{AG}gt.. : 176548 70 : >> Target Intron 1 >>>> {r}AlaPheGluGlyGluTyrThrHisHisLys : 79 1588 bp {|}|||||||||||||||||||||||||||||| ++{r}AlaPheGluGlyGluTyrThrHisHisLys 176547 : .......................ag{T}GCCTTCGAAGGAGAATACACACATCACAAA : 174934 80 : AspProGlyIleTyrLysCysValValCysGlyThrProLeuPhe{Ly} >>>> Ta : 95 |||||||||||||||||||||||||||||||||||||||||||||{||} AspProGlyIleTyrLysCysValValCysGlyThrProLeuPhe{Ly}++ 174933 : GATCCTGGAATATATAAGTGTGTTGTTTGTGGAACTCCATTGTTC{AA}gt....... : 174882 96 : rget Intron 2 >>>> {s}SerGluThrLysPheAspSerGlySer{G} >>> : 105 28994 bp {|}|||||||||||||||||||||||||||{|} ++{s}SerGluThrLysPheAspSerGlySer{G}++ 174881 : ..................ag{G}TCAGAAACCAAATTTGACTCCGGGTCA{G}gt... : 145859 106 : > Target Intron 3 >>>> {ly}TrpProSerPheHisAspValIleAsnSer : 115 85780 bp {||}|||||||||||||||||||||||||||||| ++{ly}TrpProSerPheHisAspValIleAsnSer 145858 : ......................ag{GT}TGGCCTTCATTCCATGATGTGATCAATTCT : 60052 116 : GluAlaIleThrPheThrAspAspPheSerTyrGlyMetHisArgValGluThrSerC : 135 !!:|||:!!.!!|||||||||||||||||||||||||||||||||||||||||||||| AspAlaValAlaPheThrAspAspPheSerTyrGlyMetHisArgValGluThrSerC 60051 : GATGCAGTCGCATTCACAGATGACTTTTCCTACGGGATGCACAGGGTGGAAACAAGCT : 59992 136 : ysSerGln >>>> Target Intron 4 >>>> CysGlyAlaHisLeuGlyHis : 144 |||||||| 8032 bp ||||||||||||||||||||| ysSerGln++ ++CysGlyAlaHisLeuGlyHis 59991 : GCTCTCAGgt.........................agTGTGGTGCTCACCTTGGGCAT : 51933 145 : IlePheAspAspGlyProArgProThrGlyLysArgTyrCysIleAsnSerAlaAlaL : 164 ||||||||||||||||||||||||||||||||||||||||||:!:|||||||||:!!| IlePheAspAspGlyProArgProThrGlyLysArgTyrCysValAsnSerAlaSerL 51932 : ATTTTTGATGATGGGCCTCGTCCAACCGGCAAAAGATACTGCGTGAACTCGGCTTCCT : 51873 165 : euSerPheThrProAlaAspSerSerGlyThrAlaGluGlyGlySerGlyValAlaSe : 183 |||||||||||||||||!!:|||!!!|||.!!.!!! !|||! !|||||| !.!.! euSerPheThrProAlaGluSerArgGlyAlaThrGlyGlyAspSerGly---GlyGl 51872 : TGTCTTTCACACCTGCAGAGAGCAGAGGTGCCACCGGAGGTGACAGCGGG---GGCGG : 51819 184 : rProAlaGlnAlaAspLysAlaGluLeu : 192 !|||!.!::!|||||||||.!!|||||| yProGlyArgAlaAspLysThrGluLeu 51818 : CCCCGGCAGGGCAGACAAGACAGAGCTG : 51790 vulgar: SPP00000092_2.0 32 192 . JSZB01006555.1:subseq(360000,225000) 176660 51789 - 769 M 36 108 S 0 2 5 0 2 I 0 1584 3 0 2 S 1 1 M 25 75 S 0 2 5 0 2 I 0 28990 3 0 2 S 1 1 M 9 27 S 0 1 5 0 2 I 0 85776 3 0 2 S 1 2 M 32 96 5 0 2 I 0 8028 3 0 2 M 43 129 G 1 0 M 11 33 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-14 ##type DNA # # # seqname source feature start end score strand frame attributes # JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local gene 51790 176660 769 - . gene_id 1 ; sequence SPP00000092_2.0 ; gene_orientation + JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local cds 176551 176660 . - . JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local exon 176551 176660 . - . insertions 0 ; deletions 0 JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local splice5 176549 176550 . - . intron_id 1 ; splice_site "GT" JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local intron 174963 176550 . - . intron_id 1 JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local splice3 174963 174964 . - . intron_id 0 ; splice_site "AG" JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local cds 174885 174962 . - . JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local exon 174885 174962 . - . insertions 0 ; deletions 0 JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local splice5 174883 174884 . - . intron_id 2 ; splice_site "GT" JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local intron 145891 174884 . - . intron_id 2 JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local splice3 145891 145892 . - . intron_id 1 ; splice_site "AG" JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local cds 145862 145890 . - . JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local exon 145862 145890 . - . insertions 0 ; deletions 0 JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local splice5 145860 145861 . - . intron_id 3 ; splice_site "GT" JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local intron 60082 145861 . - . intron_id 3 JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local splice3 60082 60083 . - . intron_id 2 ; splice_site "AG" JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local cds 59984 60081 . - . JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local exon 59984 60081 . - . insertions 0 ; deletions 0 JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local splice5 59982 59983 . - . intron_id 4 ; splice_site "GT" JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local intron 51952 59983 . - . intron_id 4 JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local splice3 51952 51953 . - . intron_id 3 ; splice_site "AG" JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local cds 51790 51951 . - . JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local exon 51790 51951 . - . insertions 0 ; deletions 1 JSZB01006555.1:subseq(360000,225000) exonerate:protein2genome:local similarity 51790 176660 769 - . alignment_id 1 ; Query SPP00000092_2.0 ; Align 176661 33 108 ; Align 174962 70 75 ; Align 145890 96 27 ; Align 60080 106 96 ; Align 51952 138 129 ; Align 51823 182 33 # --- END OF GFF DUMP --- # -- completed exonerate analysis