Command line: [exonerate -m p2g --showtargetgff -q SELENOM.fa.txt -t SELENOM.subseq.txt] Hostname: [ws116044u] C4 Alignment: ------------ Query: SPP00000077_2.0 # Protein # Selenoprotein M (SELENOM) # Human Target: JSZB01032570.1:subseq(37000,102000) Manis javanica isolate MP_PG03-UM SCAFFOLD43260, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 521 Query range: 0 -> 145 Target range: 52457 -> 50231 1 : MetSerLeuLeuLeuProProLeuAlaLeuLeuLeuLeuLeuAlaAlaLeuValAlaPro : 20 ||| !:!!! !|||||||||! !||||||||||||||||||||||||!!! MetHisValProLeuProProProAlaLeuLeuLeuLeuLeuAlaAlaPhe--------- 52457 : ATGCACGTCCCGCTGCCTCCGCCGGCGCTGCTGCTCCTACTTGCGGCGTTC--------- : 52406 21 : AlaThrAlaAlaThrAlaTyrArgProAspTrpAsnArgLeuSerGlyLeuThrArgAla : 40 |||:!!|||||||||.!!!:!||||||||||||||||||||| !||||||.!!|||||| AlaSerAlaAlaThrThrPheArgProAspTrpAsnArgLeuHisGlyLeuAlaArgAla 52405 : GCGTCCGCCGCCACCACCTTCCGGCCCGACTGGAACCGTCTGCATGGCCTGGCCCGAGCC : 52349 41 : ArgValGlu >>>> Target Intron 1 >>>> ThrCysGlyGlyUnkGlnLeuA : 51 ||||||||| 1191 bp |||||||||||| ||||||| ArgValGlu++ ++ThrCysGlyGly***GlnLeuA 52348 : CGGGTGGAGgt.........................agACCTGCGGGGGATGACAGCTGA : 51125 52 : snArgLeuLysGlu >>>> Target Intron 2 >>>> ValLysAlaPheValTh : 61 |||||||||||||| 182 bp ||||||||||||||||| snArgLeuLysGlu++ ++ValLysAlaPheValTh 51124 : ATCGCCTGAAGGAGgt.........................agGTGAAGGCCTTCGTCAC : 50913 62 : rGlnAspIleProPhe{Ty} >>>> Target Intron 3 >>>> {r}HisAsnLe : 70 ||||||||||||||||{||} 354 bp {|}|||||||| rGlnAspIleProPhe{Ty}++ ++{r}HisAsnLe 50912 : CCAGGACATCCCATTC{TA}gt.........................ag{T}CACAACCT : 50532 71 : uValMetLysHisLeuProGlyAlaAspProGluLeuValLeuLeuGlyArgArgTyrGl : 90 |||||||||||||||||||||||||||||||||||||||||||||||||!.!|||||||| uValMetLysHisLeuProGlyAlaAspProGluLeuValLeuLeuGlyHisArgTyrGl 50531 : GGTAATGAAACACCTTCCGGGAGCCGACCCAGAGCTCGTGCTGCTGGGCCACCGCTACGA : 50472 91 : uGluLeuGlu >>>> Target Intron 4 >>>> ArgIleProLeuSerGluMet : 100 |||||||||| 73 bp ||||||||||||||||||||| uGluLeuGlu++ ++ArgIleProLeuSerGluMet 50471 : GGAACTGGAGgt.........................agCGAATCCCACTCAGCGAGATG : 50369 101 : ThrArgGluGluIleAsnAlaLeuValGlnGluLeuGlyPheTyrArgLysAlaAlaPro : 120 ||||||||||||||||||! !||||||||||||||||||||||||||||||||||||||| ThrArgGluGluIleAsnGluLeuValGlnGluLeuGlyPheTyrArgLysAlaAlaPro 50368 : ACCCGTGAGGAGATCAACGAGCTGGTGCAGGAGCTCGGCTTCTACCGCAAGGCGGCGCCC : 50309 121 : AspAlaGlnValProProGluTyrValTrpAlaProAlaLysProProGluGluThrSer : 140 |||! !! |||||| !!||||||:!! !!|||||||||!:! !! !!|||....!! !! AspGluProValProThrGluTyrLeuArgAlaProAlaArgSerAlaGluSerAlaPro 50308 : GACGAGCCTGTTCCTACCGAGTACCTGCGGGCGCCCGCTAGGTCCGCCGAAAGCGCTCCG : 50249 141 : AspHisAlaAspLeu : 145 |||!.!!.!|||||| AspArgGlyAspLeu 50248 : GACCGCGGCGACCTG : 50232 vulgar: SPP00000077_2.0 0 145 . JSZB01032570.1:subseq(37000,102000) 52457 50231 - 521 M 17 51 G 3 0 M 23 69 5 0 2 I 0 1187 3 0 2 M 12 36 5 0 2 I 0 178 3 0 2 M 11 33 S 0 2 5 0 2 I 0 350 3 0 2 S 1 1 M 26 78 5 0 2 I 0 69 3 0 2 M 52 156 # --- 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 # JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local gene 50232 52457 521 - . gene_id 1 ; sequence SPP00000077_2.0 ; gene_orientation + JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local cds 52338 52457 . - . JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local exon 52338 52457 . - . insertions 0 ; deletions 3 JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local splice5 52336 52337 . - . intron_id 1 ; splice_site "GT" JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local intron 51147 52337 . - . intron_id 1 JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local splice3 51147 51148 . - . intron_id 0 ; splice_site "AG" JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local cds 51111 51146 . - . JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local exon 51111 51146 . - . insertions 0 ; deletions 0 JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local splice5 51109 51110 . - . intron_id 2 ; splice_site "GT" JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local intron 50929 51110 . - . intron_id 2 JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local splice3 50929 50930 . - . intron_id 1 ; splice_site "AG" JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local cds 50894 50928 . - . JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local exon 50894 50928 . - . insertions 0 ; deletions 0 JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local splice5 50892 50893 . - . intron_id 3 ; splice_site "GT" JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local intron 50540 50893 . - . intron_id 3 JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local splice3 50540 50541 . - . intron_id 2 ; splice_site "AG" JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local cds 50461 50539 . - . JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local exon 50461 50539 . - . insertions 0 ; deletions 0 JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local splice5 50459 50460 . - . intron_id 4 ; splice_site "GT" JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local intron 50388 50460 . - . intron_id 4 JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local splice3 50388 50389 . - . intron_id 3 ; splice_site "AG" JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local cds 50232 50387 . - . JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local exon 50232 50387 . - . insertions 0 ; deletions 0 JSZB01032570.1:subseq(37000,102000) exonerate:protein2genome:local similarity 50232 52457 521 - . alignment_id 1 ; Query SPP00000077_2.0 ; Align 52458 1 51 ; Align 52407 21 69 ; Align 51147 44 36 ; Align 50929 56 33 ; Align 50539 68 78 ; Align 50388 94 156 # --- END OF GFF DUMP --- # -- completed exonerate analysis