Command line: [exonerate -m p2g --showtargetgff -q eEFsecn/eEFsecn_U.fa -t eEFsecn/SUBSEQ/KB228921.1_0_subseq.txt --exhaustive yes] Hostname: [luke] C4 Alignment: ------------ Query: SPP00000144_2.0 # Protein # Eukaryotic elongation factor (eEFsec) # Human (Homo sapiens) Target: KB228921.1:subseq(4150114,25659) Odobenus rosmarus divergens isolate Ivan unplaced genomic scaffold Scaffold44, whole genome shotgun sequence:[revcomp] Model: protein2genome:local Raw score: 1320 Query range: 261 -> 578 Target range: 25659 -> 1564 262 : LysValValLysLysValLysSerMetGlnMetPheHisMetProIleThrSerAlaMet : 281 :!!||||||||||||||||||||||||||||||||||||||||||:!!|||||||||||| GlnValValLysLysValLysSerMetGlnMetPheHisMetProValThrSerAlaMet 25659 : CAGGTGGTGAAGAAGGTGAAGTCCATGCAGATGTTTCACATGCCTGTCACCTCAGCCATG : 25602 282 : GlnGlyAspArgLeuGlyIleCysValThrGlnPheAspProLysLeuLeuGluArgGly : 301 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GlnGlyAspArgLeuGlyIleCysValThrGlnPheAspProLysLeuLeuGluArgGly 25601 : CAGGGAGACCGACTGGGCATCTGCGTCACCCAGTTTGACCCCAAGCTACTGGAGCGCGGC : 25542 302 : LeuValCysAlaProGluSerLeuHisThrValHisAlaAlaLeuIleSerValGluLys : 321 ||||||||||||||||||||||||||||||||||||||||||:!!||||||||||||||| LeuValCysAlaProGluSerLeuHisThrValHisAlaAlaIleIleSerValGluLys 25541 : CTGGTGTGTGCCCCTGAGTCCCTGCACACTGTCCACGCGGCCATCATCTCTGTGGAGAAG : 25482 322 : IleProTyrPheArgGlyProLeuGlnThrLysAlaLysPheHisIleThrValGlyHis : 341 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| IleProTyrPheArgGlyProLeuGlnThrLysAlaLysPheHisIleThrValGlyHis 25481 : ATCCCGTATTTCCGGGGGCCCCTGCAGACCAAAGCCAAGTTCCACATCACGGTGGGCCAT : 25422 342 : GluThrValMetGlyArgLeuMetPhePheSerProAlaProAspAsnPheAspGlnGlu : 361 |||||||||||||||||||||||||||||||||! !|||||||||!:!||||||!!.||| GluThrValMetGlyArgLeuMetPhePheSerLeuAlaProAspSerPheAspHisGlu 25421 : GAGACAGTCATGGGCCGGTTGATGTTCTTCAGCCTTGCCCCCGATAGCTTTGACCATGAG : 25362 362 : ProIleLeuAspSerPheAsnPheSerGlnGluTyrLeuPheGlnGluGlnTyrLeuSer : 381 |||:!:||||||||||||:!!||||||!:!|||||||||||||||||||||||||||..! ProValLeuAspSerPheAspPheSerArgGluTyrLeuPheGlnGluGlnTyrLeuAsp 25361 : CCTGTGCTGGACTCCTTCGACTTCTCTCGAGAATACCTTTTCCAGGAGCAGTACCTAGAT : 25302 382 : LysAspLeuThrProAlaValThrAspAsnAspGluAlaAspLysLysAlaGlyGlnAla : 401 |||||||||.!!|||!.!!.!||||||!:!|||||||||:!!||||||.!!||||||||| LysAspLeuAlaProValAlaThrAspSerAspGluAlaAsnLysLysThrGlyGlnAla 25301 : AAGGATTTGGCACCAGTGGCGACAGACAGTGATGAGGCTAACAAGAAGACGGGCCAGGCC : 25242 402 : ThrGluGlyHisCysProArgGlnGlnTrpAlaLeuValGluPheGluLysProValThr : 421 ||||||||| !|||||||||||||||||||||||||||||||||||||||||||||||| ThrGluGlyCysCysProArgGlnGlnTrpAlaLeuValGluPheGluLysProValThr 25241 : ACAGAAGGCTGCTGCCCTCGGCAGCAGTGGGCCCTCGTGGAATTTGAGAAGCCTGTCACC : 25182 422 : CysProArgLeuCysLeuValIleGlySerArgLeuAspAlaAspIleHisThrAsnThr : 441 |||||||||||||||||||||||||||||||||||||||||||||||||||.!!|||! ! CysProArgLeuCysLeuValIleGlySerArgLeuAspAlaAspIleHisAlaAsnMet 25181 : TGCCCTCGGCTGTGCCTGGTGATTGGCTCCAGGCTAGATGCAGACATTCATGCCAACATG : 25122 442 : CysArgLeuAlaPheHisGlyIleLeuLeuHisGlyLeuGluAspArgAsnTyrAlaAsp : 461 |||||||||||||||||||||:!!|||||||||||||||||||||!:!:!!||||||!!: CysArgLeuAlaPheHisGlyValLeuLeuHisGlyLeuGluAspLysAspTyrAlaGlu 25121 : TGCCGACTGGCCTTCCACGGTGTCCTGCTCCACGGGCTGGAGGACAAGGACTATGCTGAG : 25062 462 : SerPheLeuProArgLeuLysValTyrLysLeuLysHisLysHisGlyLeuValGluArg : 481 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| SerPheLeuProArgLeuLysValTyrLysLeuLysHisLysHisGlyLeuValGluArg 25061 : AGCTTCTTGCCCAGGCTGAAAGTGTATAAGCTCAAGCACAAACATGGCCTTGTAGAACGG : 25002 482 : >>>> Target Intron 1 >>>> AlaMetAspAspTyrSerValIleGlyArgS : 492 16935 bp !.!|||||||||:!!|||||||||||||||| ++ ++ValMetAspAspHisSerValIleGlyArgS 25001 : gt.........................agGTGATGGATGACCACAGCGTGATCGGCCGCT : 8034 493 : erLeuPheLysLysGluThrAsnIleGlnLeuPheValGlyLeuLysValHisLeuSerT : 512 ||||||||||||||||||||||||||||||||||||||||||||||||||:!!||||||| erLeuPheLysLysGluThrAsnIleGlnLeuPheValGlyLeuLysValTyrLeuSerT 8033 : CCCTGTTCAAAAAGGAGACCAACATCCAGCTCTTTGTGGGCCTCAAGGTGTACCTATCCA : 7974 513 : hrGlyGluLeuGlyIleIleAspSerAlaPheGlyGlnSerGlyLysPheLysIleHisI : 532 ||||||||||||||:!!||||||||||||||||||||||||||||||||||||||||||| hrGlyGluLeuGlyValIleAspSerAlaPheGlyGlnSerGlyLysPheLysIleHisI 7973 : CTGGGGAGCTGGGGGTCATCGACAGCGCCTTCGGCCAGAGTGGCAAGTTCAAGATCCACA : 7914 533 : lePro{G} >>>> Target Intron 2 >>>> {ly}GlyLeuSerProGluSerL : 541 |||||{|} 4542 bp {||}||| !|||! !! !|||: lePro{G}++ ++{ly}GlyAlaSerLeuGlySerG 7913 : TCCCT{G}gt.........................ag{GA}GGAGCATCACTCGGGAGCC : 3345 542 : ys >>>> Target Intron 3 >>>> LysIleLeuThrProAlaLeuLysLysAr : 551 !! 1667 bp :!!! !..!|||!.!||| :!! ! ln+- ++AlaLeuGlnValProGlyLeuValGlnGl 3344 : AGga.........................agGCCCTTCAGGTGCCCGGCCTTGTCCAAGG : 1648 552 : gAlaArgAlaGlyArgGlyGluAlaThrArgGlnGluGluSerAlaGluArgSerGluPr : 571 ! !......||||||||||||... !:!!... ! !! !:!!..!|||... ! yLeuGluCysGlyArgGlyGluGlyGlyProGluArgTrpLeuGluLysGluSerArgAl 1647 : CCTGGAatgtggcagaggggagggaggtccTGAACGTTGGCTGGAGAAGGAGAGTCGTGC : 1588 572 : oSerGlnHisValValLeuSer : 578 ! !! |||:!! !|||||| aValLeuHisLeuSerLeuSer 1587 : AGTGCTCCATCTTAGCCTGAGC : 1565 vulgar: SPP00000144_2.0 261 578 . KB228921.1:subseq(4150114,25659) 25659 1564 - 1320 M 220 660 5 0 2 I 0 16931 3 0 2 M 52 156 S 0 1 5 0 2 I 0 4538 3 0 2 S 1 2 M 7 21 5 0 2 I 0 1663 3 0 2 M 37 111 # --- START OF GFF DUMP --- # # ##gff-version 2 ##source-version exonerate:protein2genome:local 2.2.0 ##date 2015-11-25 ##type DNA # # # seqname source feature start end score strand frame attributes # KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local gene 1565 25659 1320 - . gene_id 1 ; sequence SPP00000144_2.0 ; gene_orientation + KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local cds 25000 25659 . - . KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local exon 25000 25659 . - . insertions 0 ; deletions 0 KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local splice5 24998 24999 . - . intron_id 1 ; splice_site "GT" KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local intron 8065 24999 . - . intron_id 1 KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local splice3 8065 8066 . - . intron_id 0 ; splice_site "AG" KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local cds 7908 8064 . - . KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local exon 7908 8064 . - . insertions 0 ; deletions 0 KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local splice5 7906 7907 . - . intron_id 2 ; splice_site "GT" KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local intron 3366 7907 . - . intron_id 2 KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local splice3 3366 3367 . - . intron_id 1 ; splice_site "AG" KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local cds 3343 3365 . - . KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local exon 3343 3365 . - . insertions 0 ; deletions 0 KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local splice5 3341 3342 . - . intron_id 3 ; splice_site "GA" KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local intron 1676 3342 . - . intron_id 3 KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local splice3 1676 1677 . - . intron_id 2 ; splice_site "AG" KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local cds 1565 1675 . - . KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local exon 1565 1675 . - . insertions 0 ; deletions 0 KB228921.1:subseq(4150114,25659) exonerate:protein2genome:local similarity 1565 25659 1320 - . alignment_id 1 ; Query SPP00000144_2.0 ; Align 25660 262 660 ; Align 8065 482 156 ; Align 3364 535 21 ; Align 1676 542 111 # --- END OF GFF DUMP --- # -- completed exonerate analysis