Command line: [exonerate -m p2g --showtargetgff -q SELENOU.fa -t SELENOU.subseq] Hostname: [ws101098U] C4 Alignment: ------------ Query: SPP00000114_2.0 # Protein # Selenoprotein U2 (SELENOU2) # Human Target: JSZB01000054.1:subseq(0,60000) Manis javanica isolate MP_PG03-UM SCAFFOLD59, whole genome shotgun sequence Model: protein2genome:local Raw score: 775 Query range: 57 -> 226 Target range: 158 -> 6965 58 : AlaValValValPheValArgHisPheLeuCysTyrIleCysLysGluTyrValGluAspLe : 78 !.!!.!|||:!! !!!:!||||||||||||||||||||||||||||||||||||||||| ValAlaValLeuGlyPheGlnHisPheLeuCysTyrIleCysLysGluTyrValGluAspLe 159 : GTTGCCGTGTTGGGGTTTCAGCATTTCCTGTGTTACATCTGCAAGGAATACGTAGAGGATCT : 219 79 : uAlaLysIleProArgSerPheLeuGln >>>> Target Intron 1 >>>> GluAl : 89 ||||:!!|||||| !|||||||||||| 587 bp ||||| uAlaGlnIleProAlaSerPheLeuGln++ ++GluAl 220 : GGCCCAAATCCCCGCGAGTTTCTTACAGgt.........................agGAAGC : 839 90 : aAsnValThrLeuIleValIleGlyGlnSerSerTyrHisHisIleGlu >>>> Target : 106 |||||||!:!||||||||||||||||||||||||||||||||||||||| 1 aAsnValSerLeuIleValIleGlyGlnSerSerTyrHisHisIleGlu++ 840 : AAATGTCAGCCTTATAGTGATTGGACAGTCATCCTACCATCATATTGAGgt........... : 892 107 : Intron 2 >>>> ProPheCysLysLeuThrGlyTyrSerHisGluIleTyrValAspP : 121 52 bp |||||||||||||||||||||||||||:!!|||||||||||||||| ++ProPheCysLysLeuThrGlyTyrSerTyrGluIleTyrValAspP 893 : ..............agcCTTTCTGTAAACTGACTGGGTATTCTTATGAAATCTACGTTGATC : 1087 122 : roGluArgGluIleTyrLysArgLeuGlyMetLysArgGlyGluGluIleAlaSerSer{G} : 141 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||{|} roGluArgGluIleTyrLysArgLeuGlyMetLysArgGlyGluGluIleAlaSerSer{G} 1088 : CTGAGAGAGAGATTTATAAAAGATTGGGAATGAAAAGAGGTGAAGAAATTGCCTCCTCG{G} : 1147 142 : >>>> Target Intron 3 >>>> {ly}GlnSerProHisIleLysSerAsnLeuLe : 151 3707 bp {||}:!!|||||||||:!!|||||||||:!!|| ++ ++{ly}LysSerProHisValLysSerAsnIleLe 1148 : gt.........................ag{GA}AAGAGCCCCCATGTAAAATCAAACATACT : 4884 152 : uSerGlySerLeuGlnSerLeuTrpArgAlaValThrGlyProLeuPheAspPheGlnGlyA : 172 ||||||||||:!!!:!|||||||||||||||||||||||||||||||||||||||||||||| uSerGlySerIleArgSerLeuTrpArgAlaValThrGlyProLeuPheAspPheGlnGlyA 4885 : CTCAGGAAGCATTCGGAGCCTGTGGCGGGCAGTGACTGGCCCGCTCTTTGATTTCCAAGGAG : 4947 173 : spProAlaGlnGlnGlyGlyThrLeuIleLeuGlyPro{G} >>>> Target Intron : 185 ||||||||||||||||||||||||||||||||||||||{|} 1857 bp spProAlaGlnGlnGlyGlyThrLeuIleLeuGlyPro{G}++ 4948 : ACCCAGCTCAGCAAGGCGGAACCCTTATTTTAGGTCCA{G}gt................... : 4989 186 : 4 >>>> {ly}AsnAsnIleHisPheIleHisArgAspArgAsnArgLeuAspHisLysPr : 202 {||}|||||||||||||||||||||||||||||||||||||||||||||||||| ++{ly}AsnAsnIleHisPheIleHisArgAspArgAsnArgLeuAspHisLysPr 4990 : ......ag{GT}AACAACATCCATTTCATACACCGTGATAGGAATAGGTTGGATCATAAACC : 6894 203 : oIleAsnSerValLeuGlnLeuValGlyValGlnHisValAsnPheThrAsnArgProSerV : 223 |||||||||||||||||||||||||||||||:!!||||||:!!|||||| ||||||:!!| oIleAsnSerValLeuGlnLeuValGlyValGluHisValAspPheThr---ArgProAlaV 6895 : CATCAACTCTGTTTTACAGTTGGTAGGAGTTGAGCACGTGGACTTTACA---AGACCTGCAG : 6954 224 : alIleHisVal : 226 ||||||||||| alIleHisVal 6955 : TTATCCACGTG : 6965 vulgar: SPP00000114_2.0 57 226 . JSZB01000054.1:subseq(0,60000) 158 6965 + 775 M 30 90 5 0 2 I 0 583 3 0 2 M 18 54 5 0 2 I 0 148 3 0 2 M 35 105 S 0 1 5 0 2 I 0 3703 3 0 2 S 1 2 M 43 129 S 0 1 5 0 2 I 0 1853 3 0 2 S 1 2 M 33 99 G 1 0 M 7 21 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2016-11-09 ##type DNA # # # seqname source feature start end score strand frame attributes # JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local gene 159 6965 775 + . gene_id 1 ; sequence SPP00000114_2.0 ; gene_orientation + JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local cds 159 248 . + . JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local exon 159 248 . + . insertions 0 ; deletions 0 JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local splice5 249 250 . + . intron_id 1 ; splice_site "GT" JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local intron 249 835 . + . intron_id 1 JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local splice3 834 835 . + . intron_id 0 ; splice_site "ag" JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local cds 836 889 . + . JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local exon 836 889 . + . insertions 0 ; deletions 0 JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local splice5 890 891 . + . intron_id 2 ; splice_site "GT" JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local intron 890 1041 . + . intron_id 2 JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local splice3 1040 1041 . + . intron_id 1 ; splice_site "ag" JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local cds 1042 1147 . + . JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local exon 1042 1147 . + . insertions 0 ; deletions 0 JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local splice5 1148 1149 . + . intron_id 3 ; splice_site "GT" JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local intron 1148 4854 . + . intron_id 3 JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local splice3 4853 4854 . + . intron_id 2 ; splice_site "AG" JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local cds 4855 4986 . + . JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local exon 4855 4986 . + . insertions 0 ; deletions 0 JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local splice5 4987 4988 . + . intron_id 4 ; splice_site "GT" JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local intron 4987 6843 . + . intron_id 4 JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local splice3 6842 6843 . + . intron_id 3 ; splice_site "AG" JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local cds 6844 6965 . + . JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local exon 6844 6965 . + . insertions 0 ; deletions 1 JSZB01000054.1:subseq(0,60000) exonerate:protein2genome:local similarity 159 6965 775 + . alignment_id 1 ; Query SPP00000114_2.0 ; Align 159 58 90 ; Align 836 88 54 ; Align 1042 106 105 ; Align 4857 142 129 ; Align 6846 186 99 ; Align 6945 220 21 # --- END OF GFF DUMP --- # -- completed exonerate analysis