Command line: [/mnt/NFS_UPF/soft/exonerate/exonerate-2.2.0-x86_64/bin/exonerate -m p2g --showtargetgff --exhaustive yes -q query11 -t q_subseq] Hostname: [am30751-101042u] C4 Alignment: ------------ Query: SPP00000078_1.0 # Protein # Methionine sulfoxide reductase A (MsrA) # Mus musculus # Complete Target: PVKD010004692.1:subseq(1,109209) Cricetomys gambianus isolate US082 CriGam_scaffold_9379, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 372 Query range: 21 -> 124 Target range: 102269 -> 2875 22 : GlyAspSerAlaSerLysValIleSerAlaGluGluAlaLeuPro{G} >>>> Tar : 37 ||||||! ! !|||!.. !:!!:!!.!!||| !|||! !|||{|} GlyAspLeuAsnSerSerSerLeuAlaThrGluMetAlaTrpPro{G}++ 102269 : GGTGACTTAAACAGTAGCAGTCTAGCCACTGAGATGGCATGGCCA{G}gt........ : 102221 38 : get Intron 1 >>>> {ly}ArgThrGluProIleProValThr{A} >>>> T : 46 51895 bp {||}!:! ! ||| !||| !|||{|} ++{ly}GlnLeuProProHisProHisThr{A}-+ 102220 : .................ag{GC}CAGCTTCCTCCTCATCCCCACACT{G}ct...... : 50299 47 : arget Intron 2 >>>> {la}LysHisHisValSerGlyAsnArgThrValGlu : 57 17642 bp {||}||||||||||||||||||||||||||||||||| ++{la}LysHisHisValSerGlyAsnArgThrValGlu 50298 : ...................ag{cc}AAACACCATGTCAGTGGCAACAGAACGGTTGAA : 32627 58 : ProPheProGluGlyThrGlnMetAlaValPhe{G} >>>> Target Intron 3 : 69 |||||||||||||||||||||||||||||||||{|} 23382 bp ProPheProGluGlyThrGlnMetAlaValPhe{G}++ 32626 : CCTTTCCCAGAGGGAACACAGATGGCTGTATTT{G}gt.................... : 32588 70 : >>>> {ly}MetGlyCysPheTrpGlyAlaGluArgLysPheTrpValLeuLysGl : 85 {||}||||||||||||||||||||||||||||||||||||:!!|||||||| ++{ly}MetGlyCysPheTrpGlyAlaGluArgLysPheTrpLeuLeuLysGl 32587 : .....ag{GA}ATGGGCTGCTTCTGGGGAGCTGAACGCAAGTTCTGGCTCTTGAAAGG : 9161 86 : yValTyrSerThrGlnValGlyPheAlaGlyGlyHisThrArgAsnProThrTyrLys : 104 ||||||||||||||||||||||||||||||||||:!!||||||||||||||||||||| yValTyrSerThrGlnValGlyPheAlaGlyGlyTyrThrArgAsnProThrTyrLys 9160 : CGTGTATTCAACCCAAGTGGGCTTTGCAGGAGGCTACACACGAAATCCCACCTACAAA : 9104 105 : GluValCysSer{G} >>>> Target Intron 4 >>>> {lu}LysThrGlyH : 113 ||||||||||||{!} 6166 bp { } ! !|||| GluValCysSer{G}++ ++{ly}ValHisGlyH 9103 : GAAGTGTGTTCA{G}gt.........................ag{GC}GTGCACGGCC : 2911 114 : isAlaGluValValArgValValTyrArgProGlu : 124 |||||:!! !:!!!.!..! !!::...|||||| isAlaGlnProLeuHisThrCysTrpGluProGlu 2910 : ATGCTCAGCCTTTACACACGTGCTGGGAacctgaa : 2876 vulgar: SPP00000078_1.0 21 124 . PVKD010004692.1:subseq(1,109209) 102269 2875 - 372 M 15 45 S 0 1 5 0 2 I 0 51891 3 0 2 S 1 2 M 8 24 S 0 1 5 0 2 I 0 17638 3 0 2 S 1 2 M 22 66 S 0 1 5 0 2 I 0 23378 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 6162 3 0 2 S 1 2 M 15 45 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2019-11-20 ##type DNA # # # seqname source feature start end score strand frame attributes # PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local gene 2876 102269 372 - . gene_id 1 ; sequence SPP00000078_1.0 ; gene_orientation + PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local cds 102224 102269 . - . PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local exon 102224 102269 . - . insertions 0 ; deletions 0 PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local splice5 102222 102223 . - . intron_id 1 ; splice_site "GT" PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local intron 50329 102223 . - . intron_id 1 PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local splice3 50329 50330 . - . intron_id 0 ; splice_site "AG" PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local cds 50302 50328 . - . PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local exon 50302 50328 . - . insertions 0 ; deletions 0 PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local splice5 50300 50301 . - . intron_id 2 ; splice_site "CT" PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local intron 32660 50301 . - . intron_id 2 PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local splice3 32660 32661 . - . intron_id 1 ; splice_site "ag" PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local cds 32591 32659 . - . PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local exon 32591 32659 . - . insertions 0 ; deletions 0 PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local splice5 32589 32590 . - . intron_id 3 ; splice_site "GT" PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local intron 9209 32590 . - . intron_id 3 PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local splice3 9209 9210 . - . intron_id 2 ; splice_site "AG" PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local cds 9089 9208 . - . PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local exon 9089 9208 . - . insertions 0 ; deletions 0 PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local splice5 9087 9088 . - . intron_id 4 ; splice_site "GT" PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local intron 2923 9088 . - . intron_id 4 PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local splice3 2923 2924 . - . intron_id 3 ; splice_site "AG" PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local cds 2876 2922 . - . PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local exon 2876 2922 . - . insertions 0 ; deletions 0 PVKD010004692.1:subseq(1,109209) exonerate:protein2genome:local similarity 2876 102269 372 - . alignment_id 1 ; Query SPP00000078_1.0 ; Align 102270 22 45 ; Align 50327 38 24 ; Align 32658 47 66 ; Align 9207 70 117 ; Align 2921 110 45 # --- END OF GFF DUMP --- # -- completed exonerate analysis