Command line: [exonerate -m p2g --showtargetgff -q SELENOS.fa.txt -t SELENOS.subseq.txt] Hostname: [ws116044u] C4 Alignment: ------------ Query: SPP00000100_2.0 # Protein # Selenoprotein S (SELENOS) # Human Target: JSZB01022157.1:subseq(280000,77852) Manis javanica isolate MP_PG03-UM SCAFFOLD27863, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 845 Query range: 0 -> 189 Target range: 55603 -> 48023 1 : MetGluArgGlnGluGluSerLeuSerAlaArgProAlaLeuGluThrGluGlyLeuArg : 20 |||||||||.!.! !|||..!||||||||||||||||||||||||||||||||||||!.! MetGluArgAspGlyGluGlnLeuSerAlaArgProAlaLeuGluThrGluGlyLeuHis 55603 : ATGGAGCGGGACGGGGAGCAGCTGTCCGCGCGGCCGGCCCTGGAGACAGAGGGGTTGCAT : 55546 21 : PheLeuHisThrThr{V} >>>> Target Intron 1 >>>> {al}GlySerLeu : 29 |||||||||! !|||{|} 679 bp {||}||||||||| PheLeuHisIleThr{V}++ ++{al}GlySerLeu 55545 : TTTCTGCATATTACC{G}gt.........................ag{TG}GGCTCTCTG : 54840 30 : LeuAlaThrTyrGlyTrpTyrIleValPheSerCysIleLeuLeuTyrValValPheGln : 49 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| LeuAlaThrTyrGlyTrpTyrIleValPheSerCysIleLeuLeuTyrValValPheGln 54839 : CTGGCCACCTACGGCTGGTACATTGTCTTCAGCTGCATCCTTCTCTACGTGGTCTTCCAG : 54780 50 : LysLeuSerAlaArgLeuArgAlaLeuArgGlnArgGlnLeuAspArgAlaAlaAlaAla : 69 |||||||||.!!|||||||||||||||||||||||||||||||||||||||||||||||| LysLeuSerThrArgLeuArgAlaLeuArgGlnArgGlnLeuAspArgAlaAlaAlaAla 54779 : AAGCTCTCCACCCGGCTGAGGGCCTTGCGGCAGAGGCAGCTGGACCGAGCTGCGGCAGCT : 54720 70 : Val{G} >>>> Target Intron 2 >>>> {lu}ProAspValValValLysArg : 78 |||{|} 1976 bp {||}||||||||||||||||||||| Val{G}++ ++{lu}ProAspValValValLysArg 54719 : GTG{G}gt.........................ag{AA}CCTGATGTTGTTGTTAAGCGA : 52717 79 : GlnGluAlaLeuAlaAlaAlaArgLeuLysMetGlnGluGluLeuAsnAlaGlnValGlu : 98 ||||||||||||||||||||||||||||||||||||||||||||||||.!!||||||||| GlnGluAlaLeuAlaAlaAlaArgLeuLysMetGlnGluGluLeuAsnThrGlnValGlu 52716 : CAGGAGGCTTTAGCAGCTGCTCGACTGAAAATGCAAGAAGAATTAAATACACAAGTTGAA : 52657 99 : LysHisLysGluLysLeuLysGln >>>> Target Intron 3 >>>> LeuGluG : 109 ||||||||||||||||||!:!:!! 2496 bp ||||||| LysHisLysGluLysLeuArgLys++ ++LeuGluG 52656 : AAGCATAAGGAAAAACTAAGAAAGgt.........................agcttgaag : 50128 110 : luGluLysArgArgGlnLysIleGluMetTrpAspSerMetGlnGluGlyLysSerTyrL : 129 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| luGluLysArgArgGlnLysIleGluMetTrpAspSerMetGlnGluGlyLysSerTyrL 50127 : aagagaaaaggagacagaagatTGAAATGTGGGACAGCATGCAAGAAGGAAAAAGTTACA : 50068 130 : ysGlyAsnAlaLysLysProGln >>>> Target Intron 4 >>>> GluGluAs : 139 |||||||||||!:!!:!|||||| 101 bp ||||||!! ysGlyAsnAlaArgArgProGln++ ++GluGluGl 50067 : AAGGAAATGCAAGAAGGCCTCAGgt.........................agGAAGAAGA : 49937 140 : pSerProGlyProSerThrSerSerValLeu<->LysArgLysSerAspArgLysProLe : 158 :||||||||||||||||||||||||!.!:!! |||||||||||||||||||||||||| uSerProGlyProSerThrSerSerAlaIleProLysArgLysSerAspArgLysProLe 49936 : GAGTCCTGGGCCTTCTACTTCATCAGCCATCCCGAAACGAAAATCTGACAGAAAGCCTTT : 49877 159 : uArgGlyGly{G} >>>> Target Intron 5 >>>> {ly}TyrAsnProLeuSe : 167 ||||||||||{|} 1758 bp {||}|||||||||||||| uArgGlyGly{G}++ ++{ly}TyrAsnProLeuSe 49876 : GCGGGGAGGT{G}gt.........................ag{GT}TACAACCCTCtctc : 48092 168 : rGlyGluGlyGlyGlyAlaCysSerTrpArgProGlyArgArgGlyProSerSerGlyGl : 187 |||||||||||||||||||||||||||||||||||||||||||||||||!!!|||||||| rGlyGluGlyGlyGlyAlaCysSerTrpArgProGlyArgArgGlyProThrSerGlyGl 48091 : tggggaaggaggtggagCCTGCTCCTGGAGACCTGGGCGCAGAGGCCCGACATCTGGTGG : 48032 188 : yUnkGly : 189 | ||| y***Gly 48031 : ATGAGGC : 48024 vulgar: SPP00000100_2.0 0 189 . JSZB01022157.1:subseq(280000,77852) 55603 48023 - 845 M 25 75 S 0 1 5 0 2 I 0 675 3 0 2 S 1 2 M 44 132 S 0 1 5 0 2 I 0 1972 3 0 2 S 1 2 M 35 105 5 0 2 I 0 2492 3 0 2 M 30 90 5 0 2 I 0 97 3 0 2 M 13 39 G 0 3 M 12 36 S 0 1 5 0 2 I 0 1754 3 0 2 S 1 2 M 27 81 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-22 ##type DNA # # # seqname source feature start end score strand frame attributes # JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local gene 48024 55603 845 - . gene_id 1 ; sequence SPP00000100_2.0 ; gene_orientation + JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local cds 55528 55603 . - . JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local exon 55528 55603 . - . insertions 0 ; deletions 0 JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local splice5 55526 55527 . - . intron_id 1 ; splice_site "GT" JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local intron 54849 55527 . - . intron_id 1 JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local splice3 54849 54850 . - . intron_id 0 ; splice_site "AG" JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local cds 54714 54848 . - . JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local exon 54714 54848 . - . insertions 0 ; deletions 0 JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local splice5 54712 54713 . - . intron_id 2 ; splice_site "GT" JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local intron 52738 54713 . - . intron_id 2 JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local splice3 52738 52739 . - . intron_id 1 ; splice_site "AG" JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local cds 52631 52737 . - . JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local exon 52631 52737 . - . insertions 0 ; deletions 0 JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local splice5 52629 52630 . - . intron_id 3 ; splice_site "GT" JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local intron 50135 52630 . - . intron_id 3 JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local splice3 50135 50136 . - . intron_id 2 ; splice_site "Ag" JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local cds 50045 50134 . - . JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local exon 50045 50134 . - . insertions 0 ; deletions 0 JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local splice5 50043 50044 . - . intron_id 4 ; splice_site "GT" JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local intron 49944 50044 . - . intron_id 4 JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local splice3 49944 49945 . - . intron_id 3 ; splice_site "AG" JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local cds 49865 49943 . - . JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local exon 49865 49943 . - . insertions 3 ; deletions 0 JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local splice5 49863 49864 . - . intron_id 5 ; splice_site "GT" JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local intron 48107 49864 . - . intron_id 5 JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local splice3 48107 48108 . - . intron_id 4 ; splice_site "AG" JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local cds 48024 48106 . - . JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local exon 48024 48106 . - . insertions 0 ; deletions 0 JSZB01022157.1:subseq(280000,77852) exonerate:protein2genome:local similarity 48024 55603 845 - . alignment_id 1 ; Query SPP00000100_2.0 ; Align 55604 1 75 ; Align 54847 27 132 ; Align 52736 72 105 ; Align 50135 107 90 ; Align 49944 137 39 ; Align 49902 150 36 ; Align 48105 163 81 # --- END OF GFF DUMP --- # -- completed exonerate analysis