Command line: [exonerate -m p2g --showtargetgff -q msra1_zf.aa.fa.canviat -t genomemsra1_JXSJ01000021.1.fa] Hostname: [ws116078U] C4 Alignment: ------------ Query: SPP00000625_2.0 # Protein # Methionine sulfoxide reductase A (MsrA) # Zebrafish Target: JXSJ01000021.1:subseq(749275,124207) Miichthys miiuy scaffold21, whole genome shotgun sequence Model: protein2genome:local Raw score: 828 Query range: 17 -> 238 Target range: 43680 -> 74207 18 : ValValAlaGlnLeuGluMetAlaAsnLysSerValLeuProThrLysGluArgAlaLeu : 37 :!!!.!||| !..!||||||||||||!:!! !||||||!:!!:!!!:||||||||| LeuAlaAlaAlaAspSerMetAlaAsnLysAsnGluLeuProSerArgAspArgAlaLeu 43681 : CTCGCTGCCGCTGACTCGATGGCAAATAAGAATGAGCTGCCAAGCAGAGACCGCGCTctg : 43738 38 : LysGlyArgGluGluLysValValValAla{A} >>>> Target Intron 1 >>>> : 48 ||||||||||||||||||:::|||||||||{!} 6214 bp LysGlyArgGluGluLysMetValValAla{A}++ 43739 : aaaggaagagaggagaaaatggtCGTGGCA{G}gt......................... : 43774 49 : {la}LysHisAlaAlaAsnGlyAsnThrThrValGluProPheProAspGlyMetGlu : 66 { !}|||||||||!.!||||||||| !!||||||||||||||||||!!:||||||||| ++{sp}LysHisAlaValAsnGlyAsnProThrValGluProPheProGluGlyMetGlu 43775 : ag{AC}AAGCATGCCGTCAATGGAAATCCCACTGTGGAGCCTTTTCCAGAAGGCATGGAG : 50039 67 : MetIleMetPhe{G} >>>> Target Intron 2 >>>> {ly}MetGlyCysPhe : 75 ! |||||||||{|} 177 bp {||}|||||||||||| ThrIleMetPhe{G}++ ++{ly}MetGlyCysPhe 50040 : ACCATCATGTTT{G}gt.........................ag{GT}ATGGGCTGTTTC : 50243 76 : TrpGlyAlaGluArgArgPheTrpLysIleThrGlyValPheSerThrGlnValGlyTyr : 95 ||||||||||||!:!!.!||||||::!:!! !!||||||||||||||||||||||||||| TrpGlyAlaGluLysHisPheTrpArgLeuProGlyValPheSerThrGlnValGlyTyr 50244 : TGGGGAGCTGAGAAACATTTCTGGCGGCTTCCTGGAGTGTTCTCCACACAGGTGGGCTAC : 50303 96 : AlaGlyGlyPheThrSerAsnProThrTyrHisGluValCysSer{G} >>>> Targe : 111 ||||||||||||||| !!|||||||||||| ! ||||||||||||{|} 2 AlaGlyGlyPheThrProAsnProThrTyrLysGluValCysSer{G}++ 50304 : GCCGGCGGCTTTACACCCAACCCCACTTACAAAGAAGTCTGTTCA{G}gt.......... : 50354 112 : t Intron 3 >>>> {ly}LeuThrGlyHisThrGluValValArgValValPheSer : 124 854 bp {||}||||||||||||||||||||||||||||||||||||||| ++{ly}LeuThrGlyHisThrGluValValArgValValPheSer 50355 : ...............ag{GT}CTGACGGGTCACACTGAGGTGGTGAGGGTGGTCTTCTCC : 53244 125 : ProLysAspValSerLeuGluLysLeuLeuLysValPheTrpGluSerHisAspProThr : 144 |||:!!|||:!!!:!||||||:!!||||||!!. !|||||||||!:!|||||||||||| ProGluAspIleAsnLeuGluGluLeuLeuAsnHisPheTrpGluAsnHisAspProThr 53245 : CCTGAAGACATCAACCTTGAGGAGCTGCTCAACCACTTTTGGGAGAACCACGATCCTACC : 53304 145 : Gln{G} >>>> Target Intron 4 >>>> {ly}MetAlaGlnGlyAsnAspHis : 153 |||{|} 11491 bp {||}||| !||| ! !||| ! Gln{G}++ ++{ly}MetLysGlnHisAlaAspCys 53305 : CAA{G}gt.........................ag{gt}ATGAAGCAGCATGCTGACTGT : 64822 154 : GlyThrGlnTyrArgSerAlaIleTyrThrTyrSerProGluGlnGlnAspLeuAlaMet : 173 ||||||||||||||||||||||||||||||! !!:!|||! ||||||!!:||||||:!! GlyThrGlnTyrArgSerAlaIleTyrThrSerAsnProAlaGlnGlnGluLeuAlaLeu 64823 : GGTACTCAGTATCGCTCAGCCATTTACACATCCAACCCCGCTCAACAGGAGCTTGCGTTG : 64882 174 : LysSerLysHisMetTyrGlnGlu >>>> Target Intron 5 >>>> AlaLeuS : 184 ||||||||| ||||||:!! 9128 bp ! !|||. LysSerLysValAlaTyrGlnGln++ ++GluLeuA 64883 : AAGAGCAAAGTGGCCTACCAGCAGgt.........................agGAGCTGG : 74043 185 : erArgLysGlyLeuGlyGluIleThrThrAspIleArgGlnLeuThrValPheTyrTyrA : 204 .!!:!||||||! !.!!! |||||||||!!:|||!:!:!! ! ! !|||||||||| spLysLysGlyTyrSerAlaIleThrThrGluIleGlnGluGlyHisGlnPheTyrTyrA 74044 : ATAAAAAAGGCTACAGTGCTATCACTACAGAGATCCAGGAGGGGCATCAGTTTTACTACG : 74103 205 : laGluAspTyrHisGlnGlnTyrLeuHisLysValProLysGlyTyrCysGlyLeuLysG : 224 |||||||||||||||||||||||||| ! ||||||||||||||||||||||||||||||| laGluAspTyrHisGlnGlnTyrLeuLysLysValProLysGlyTyrCysGlyLeuLysG 74104 : CTGAGGACTATCACCAGCAGTACCTGAAGAAGGTACCTAAGGGCTATTGTGGCCTCAAAG : 74163 225 : lyThrGlyValThrCysSerIleThrGluGlyArgAspGluLeu : 238 |||||||||||:!!||| !!||| !! |||!:!||||||||| lyThrGlyValSerCysProIleGlyAlaGlyLysAspGluLeu 74164 : GCACCGGTGTCTCTTGTCCCATCGGAGCCGGTAAAGATGAGCTG : 74207 vulgar: SPP00000625_2.0 17 238 . JXSJ01000021.1:subseq(749275,124207) 43680 74207 + 828 M 30 90 S 0 1 5 0 2 I 0 6210 3 0 2 S 1 2 M 22 66 S 0 1 5 0 2 I 0 173 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 2850 3 0 2 S 1 2 M 34 102 S 0 1 5 0 2 I 0 11487 3 0 2 S 1 2 M 35 105 5 0 2 I 0 9124 3 0 2 M 57 171 # --- 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 # JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local gene 43681 74207 828 + . gene_id 1 ; sequence SPP00000625_2.0 ; gene_orientation + JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local cds 43681 43771 . + . JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local exon 43681 43771 . + . insertions 0 ; deletions 0 JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local splice5 43772 43773 . + . intron_id 1 ; splice_site "GT" JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local intron 43772 49985 . + . intron_id 1 JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local splice3 49984 49985 . + . intron_id 0 ; splice_site "AG" JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local cds 49986 50054 . + . JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local exon 49986 50054 . + . insertions 0 ; deletions 0 JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local splice5 50055 50056 . + . intron_id 2 ; splice_site "GT" JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local intron 50055 50231 . + . intron_id 2 JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local splice3 50230 50231 . + . intron_id 1 ; splice_site "AG" JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local cds 50232 50351 . + . JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local exon 50232 50351 . + . insertions 0 ; deletions 0 JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local splice5 50352 50353 . + . intron_id 3 ; splice_site "GT" JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local intron 50352 53205 . + . intron_id 3 JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local splice3 53204 53205 . + . intron_id 2 ; splice_site "AG" JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local cds 53206 53310 . + . JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local exon 53206 53310 . + . insertions 0 ; deletions 0 JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local splice5 53311 53312 . + . intron_id 4 ; splice_site "GT" JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local intron 53311 64801 . + . intron_id 4 JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local splice3 64800 64801 . + . intron_id 3 ; splice_site "ag" JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local cds 64802 64908 . + . JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local exon 64802 64908 . + . insertions 0 ; deletions 0 JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local splice5 64909 64910 . + . intron_id 5 ; splice_site "GT" JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local intron 64909 74036 . + . intron_id 5 JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local splice3 74035 74036 . + . intron_id 4 ; splice_site "AG" JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local cds 74037 74207 . + . JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local exon 74037 74207 . + . insertions 0 ; deletions 0 JXSJ01000021.1:subseq(749275,124207) exonerate:protein2genome:local similarity 43681 74207 828 + . alignment_id 1 ; Query SPP00000625_2.0 ; Align 43681 18 90 ; Align 49988 49 66 ; Align 50234 72 117 ; Align 53208 112 102 ; Align 64804 147 105 ; Align 74037 182 171 # --- END OF GFF DUMP --- # -- completed exonerate analysis