Command line: [exonerate -m p2g --showtargetgff -q SELENOJ1.x.fa -t SELENOJ1.extraction.KV884754.1.fa] Hostname: [sitdoc] C4 Alignment: ------------ Query: SELENOJ1 # Protein # Selenoprotein J1 (SELENOJ1) # Zebrafish Target: KV884754.1:subseq(1752858,100000) Monopterus albus unplaced genomic scaffold scaffold66.1, whole genome shotgun sequence Model: protein2genome:local Raw score: 1334 Query range: 0 -> 341 Target range: 48577 -> 52162 1 : MetAlaLeuAlaLeuSerAsnArgAlaIleGlyAlaIleIleGlySerAlaValAlaAsp : 20 |||||| !|||||| !:!!||||||:!!|||||||||:!!|||:!!|||||||||||| MetAlaAlaAlaLeuValAspArgAlaValGlyAlaIleValGlyAlaAlaValAlaAsp 48578 : ATGGCTGCAGCTCTGGTCGACAGAGCAGTCGGGGCCATTGTAGGAGCAGCTGTTGCAGAT : 48635 21 : AlaAla{A} >>>> Target Intron 1 >>>> {la}GlnProLeuHisTrpVal : 29 ||||||{|} 290 bp {||}|||||||||||||||||| AlaAla{A}++ ++{la}GlnProLeuHisTrpVal 48636 : GCAGCA{G}gt.........................ag{CA}CAGCCTCTCCACTGGGTG : 48952 30 : TyrAspLeuSerLysLeuSerValLeuLeuSerGlnSerProGlnProGluPheArgPro : 49 ||||||||| !!||||||..! !:!!|||:!!|||..!|||.!.|||||||||||| !! TyrAspLeuProLysLeuGlnLysIleLeuAlaGlnAspProAsnProGluPheArgSer 48953 : TATGACCTCCCGAAGCTACAGAAGATTCTGGCTCAGGATCCAAACCCTGAATTCCGCTCT : 49012 50 : GluSerAlaAsnProPheTyrArgArgAsnThrGlyGlnGlnSerCysTyrGlyAspGln : 69 |||||||||||||||||||||||||||.!.||||||:!!||||||||||||||||||||| GluSerAlaAsnProPheTyrArgArgGlnThrGlyGluGlnSerCysTyrGlyAspGln 49013 : GAATCTGCCAACCCGTTCTACAGGAGGCAGACAGGCGAGCAGAGCTGCTATGGAGACCAG : 49072 70 : AlaPheIleLeuLeuGluSerLeuSerGluCysGly{G} >>>> Target Intron : 82 |||!:!:!!||||||||||||||||||! !||||||{|} 889 bp AlaTyrValLeuLeuGluSerLeuSerValCysGly{G}++ 49073 : GCGTATGTCCTGCTGGAGTCCCTGTCTGTATGTGGA{G}gt................... : 49114 83 : 2 >>>> {ly}LeuAsnValGluAspPheLysGlnArgThrTyrLysPhePheGlyPro : 98 {||}|||:!!|||||||||.!.|||||||||||| ||||||||||||||| ++{ly}LeuAspValGluAspLeuLysGlnArgThrLeuLysPhePheGlyPro 49115 : ......ag{GT}CTAGATGTTGAAGATCTGAAACAACGCACACTGAAATTCTTTGGACCC : 50048 99 : GlySerGluTyrAspThrProValAsnAspProTyrArgAspLysGly{A} >>>> Ta : 115 |||||||||||||||||||||||||||||||||||||||.!.!:!|||{!} GlySerGluTyrAspThrProValAsnAspProTyrArgGlnArgGly{G}++ 50049 : GGATCAGAGTATGACACACCTGTCAATGATCCTTACAGGCAGAGAGGA{G}gt....... : 50102 116 : rget Intron 3 >>>> {la}ProArgProGlnLeuProIleGluGlyProTrpArg : 127 102 bp {.!}|||||||||||||||||||||||||||||||||||| ++{ly}ProArgProGlnLeuProIleGluGlyProTrpArg 50103 : ..................ag{GG}CCAAGACCTCAGCTTCCCATCGAGGGGCCATGGAGA : 50237 128 : HisAlaSerLeuLysGlyPheIleLysAsnValAspAlaGlyLysGluGluThr{G} > : 146 !!.||||||||||||.!!|||:!:||||||||||||||||||||||||||||||{|} GlnAlaSerLeuLysSerPheLeuLysAsnValAspAlaGlyLysGluGluThr{G}++ 50238 : CAGGCAAGTTTAAAGAGCTTCCTGAAAAATGTGGATGCTGGCAAAGAGGAGACA{G}gt. : 50297 147 : >>> Target Intron 4 >>>> {ly}CysGluThrAspThrGlnIleAspGlyVal : 156 83 bp {||}||||||!:!||| !||||||||||||:!! ++{ly}CysGluSerAspCysGlnIleAspGlyIle 50298 : ........................ag{GC}TGTGAGAGCGACTGCCAGATTGATGGAATA : 50407 157 : ThrLysLeuAlaProIleValAlaCysTyrAlaGlyLysProGluMetLeuGluLysVal : 176 .!!|||||||||||||||||||||! !|||||||||!!. !!!!:||||||||||||||| AlaLysLeuAlaProIleValAlaPheTyrAlaGlyAsnThrAspMetLeuGluLysVal 50408 : GCTAAACTGGCTCCTATAGTGGCGTTTTACGCGGGAAATACTGACATGCTGGAAAAAGTG : 50467 177 : GluGluAlaValArgValThrGlnAsnAsnAspLeuCysValAlaGluThrLeuAlaAla : 196 |||:!!|||:!!||||||||||||||||||||| !|||||||||||||||||||||||| GluGlnAlaIleArgValThrGlnAsnAsnAspAlaCysValAlaGluThrLeuAlaAla 50468 : GAACAGGCCATCCGTGTCACACAGAACAATGACGCGTGTGTGGCAGAGACTCTGGCAGCA : 50527 197 : Ala{Ar} >>>> Target Intron 5 >>>> {g}PheLeuGluHisPheIleLeu : 205 |||{||} 753 bp {|}||||||||||||||||||||| Ala{Ar}++ ++{g}PheLeuGluHisPheIleLeu 50528 : GCA{AG}gt.........................ag{G}TTCCTGGAGCATTTCATCCTG : 51307 206 : AsnGlyProAspProLysAlaLeuAspAlaValLeuLysGlnLeuSerAspProGluArg : 225 |||||||||||||||||||||||||||||||||||| ! |||||||||||| !.!.||| AsnGlyProAspProLysAlaLeuAspAlaValLeuAspGlnLeuSerAspArgAsnArg 51308 : AATGGTCCTGATCCCAAAGCCTTAGATGCAGTGCTTGATCAGCTCAGTGACAGGAACAGG : 51367 226 : LysAsnProGlnGluLeuAspLysAlaValIle{G} >>>> Target Intron 6 > : 237 |||.!.||||||!!:|||||||||:::||| {|} 183 bp LysGlnProGlnAspLeuAspLysSerValThr{G}++ 51368 : AAGCAGCCCCAGGACCTGGACAAATcagtcact{g}gt...................... : 51406 238 : >>> {ly}HisIleHisGlnValLysAspAsnLeuAsnLysLysProLysGluLeuIle : 254 {||}||||||!!.|||||||||!!:||||||::!|||! |||:!!|||:!!||| ++{ly}HisIleGlnGlnValLysGluAsnLeuSerLysThrProGlnGluIleIle 51407 : ...ag{GG}CACATCCAACAGGTGAAGGAGAATTTATCCAAGACTCCTCAGGAGATAATT : 51637 255 : ProAlaValPheProAsnThrUnk{G} >>>> Target Intron 7 >>>> {ly} : 263 |||::!|||||| !!|||||| {|} 176 bp {||} ProSerValPheThrAsnThr***{G}++ ++{ly} 51638 : CCCAGTGTGTTTACTAACACTTGA{G}gt.........................ag{gt} : 51841 264 : LeuProGlyAlaPheGlnAlaAlaLeuHisGlyValLeuThrAlaSerSerTyrGluGln : 283 |||||||||||||||||||||||||||||||||!.!|||||||||!!!..!||||||||| LeuProGlyAlaPheGlnAlaAlaLeuHisGlyAlaLeuThrAlaThrGlnTyrGluGln 51842 : ttGCCAGGTGCATTCCAAGCAGCGCTGCATGGAGCCCTGACAGCCACACAGTATGAACAG : 51900 284 : AlaValArgAspThrMetSerCysGlyGlyCysThrCysSerArgSerSerPheIleGly : 303 |||:!!|||||||||||||||||||||||||||||||||||||||.!!|||||||||||| AlaIleArgAspThrMetSerCysGlyGlyCysThrCysSerArgGlySerPheIleGly 51901 : GCTATTAGAGACACCATGAGCTGTGGGGGATGCACCTGCAGCCGAGGATCCTTCATTGGG : 51960 304 : AlaCysIleGlyAlaGln >>>> Target Intron 8 >>>> ValGlyLeuGluG : 314 ||||||:!!||||||||| 86 bp !!|||||||||| AlaCysLeuGlyAlaGln++ ++PheGlyLeuGluG 51961 : GCATGTCTTGGGGCCCAGgt.........................agTTTGGGCTTGAGG : 52079 315 : lyIleProAlaSerTrpLysSerLysThrLeuArgCysAsnThrLeuLeuAspLeuSerA : 334 ||||||||:!!||||||! !|||||||||||||||! !..!:!!:!!|||!!:! !:!!! lyIleProSerSerTrpThrSerLysThrLeuArgTyrGlySerValLeuGluHisAlaL 52080 : GAATTCCTTCCTCCTGGACATCCAAAACCCTGCGATATGGCTCTGTGTTGGAACATGCCA : 52139 335 : rgLysValValAlaLeuGlnGln : 341 :!! !:!!..! !! !!!.||| ysThrIleThrLysHisHisGln 52140 : AGACGATAACCAAACACCACCAG : 52162 vulgar: SELENOJ1 0 341 . KV884754.1:subseq(1752858,100000) 48577 52162 + 1334 M 22 66 S 0 1 5 0 2 I 0 286 3 0 2 S 1 2 M 58 174 S 0 1 5 0 2 I 0 885 3 0 2 S 1 2 M 32 96 S 0 1 5 0 2 I 0 98 3 0 2 S 1 2 M 30 90 S 0 1 5 0 2 I 0 79 3 0 2 S 1 2 M 51 153 S 0 2 5 0 2 I 0 749 3 0 2 S 1 1 M 38 114 S 0 1 5 0 2 I 0 179 3 0 2 S 1 2 M 25 75 S 0 1 5 0 2 I 0 172 3 0 2 S 1 2 M 46 138 5 0 2 I 0 82 3 0 2 M 32 96 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2017-11-23 ##type DNA # # # seqname source feature start end score strand frame attributes # KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local gene 48578 52162 1334 + . gene_id 1 ; sequence SELENOJ1 ; gene_orientation + KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local cds 48578 48644 . + . KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local exon 48578 48644 . + . insertions 0 ; deletions 0 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice5 48645 48646 . + . intron_id 1 ; splice_site "GT" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local intron 48645 48934 . + . intron_id 1 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice3 48933 48934 . + . intron_id 0 ; splice_site "AG" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local cds 48935 49111 . + . KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local exon 48935 49111 . + . insertions 0 ; deletions 0 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice5 49112 49113 . + . intron_id 2 ; splice_site "GT" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local intron 49112 50000 . + . intron_id 2 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice3 49999 50000 . + . intron_id 1 ; splice_site "AG" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local cds 50001 50099 . + . KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local exon 50001 50099 . + . insertions 0 ; deletions 0 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice5 50100 50101 . + . intron_id 3 ; splice_site "GT" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local intron 50100 50201 . + . intron_id 3 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice3 50200 50201 . + . intron_id 2 ; splice_site "AG" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local cds 50202 50294 . + . KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local exon 50202 50294 . + . insertions 0 ; deletions 0 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice5 50295 50296 . + . intron_id 4 ; splice_site "GT" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local intron 50295 50377 . + . intron_id 4 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice3 50376 50377 . + . intron_id 3 ; splice_site "AG" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local cds 50378 50534 . + . KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local exon 50378 50534 . + . insertions 0 ; deletions 0 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice5 50535 50536 . + . intron_id 5 ; splice_site "GT" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local intron 50535 51287 . + . intron_id 5 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice3 51286 51287 . + . intron_id 4 ; splice_site "AG" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local cds 51288 51403 . + . KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local exon 51288 51403 . + . insertions 0 ; deletions 0 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice5 51404 51405 . + . intron_id 6 ; splice_site "gt" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local intron 51404 51586 . + . intron_id 6 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice3 51585 51586 . + . intron_id 5 ; splice_site "ag" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local cds 51587 51664 . + . KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local exon 51587 51664 . + . insertions 0 ; deletions 0 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice5 51665 51666 . + . intron_id 7 ; splice_site "GT" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local intron 51665 51840 . + . intron_id 7 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice3 51839 51840 . + . intron_id 6 ; splice_site "ag" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local cds 51841 51980 . + . KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local exon 51841 51980 . + . insertions 0 ; deletions 0 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice5 51981 51982 . + . intron_id 8 ; splice_site "GT" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local intron 51981 52066 . + . intron_id 8 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local splice3 52065 52066 . + . intron_id 7 ; splice_site "AG" KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local cds 52067 52162 . + . KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local exon 52067 52162 . + . insertions 0 ; deletions 0 KV884754.1:subseq(1752858,100000) exonerate:protein2genome:local similarity 48578 52162 1334 + . alignment_id 1 ; Query SELENOJ1 ; Align 48578 1 66 ; Align 48937 24 174 ; Align 50003 83 96 ; Align 50204 116 90 ; Align 50380 147 153 ; Align 51289 199 114 ; Align 51589 238 75 ; Align 51843 264 138 ; Align 52067 310 96 # --- END OF GFF DUMP --- # -- completed exonerate analysis