Command line: [exonerate -m p2g --showtargetgff -q ./proteins/SPP00000020_1.0.fa -t ./exonerate/SPP00000020_1.0_1_genomic.fa_exonerate.fa]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000020_1.0 # Protein # Selenoprotein P (SelP) # Homo sapiens # Complete
        Target: gi|357434243|gb|JH378120.1|:subseq(24855656,307324) Saimiri boliviensis boliviensis unplaced genomic scaffold scaffold00016, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 1676
   Query range: 0 -> 381
  Target range: 149999 -> 157324

      1 : MetTrpArgSerLeuGlyLeuAlaLeuAlaLeuCysLeuLeuProSerGlyGlyThrG :     20
          |||||||||||||||||||||||||||||||||||||||||||||:!!||||||||||
          MetTrpArgSerLeuGlyLeuAlaLeuAlaLeuCysLeuLeuProAlaGlyGlyThrG
 150000 : ATGTGGAGAAGCCTGGGGCTTGCCCTGGCTCTCTGTCTCCTCCCCGCAGGAGGAACAG : 150057

     21 : luSerGlnAspGlnSerSerLeuCysLysGlnProProAlaTrpSerIleArgAspGl :     39
          ||||||||||||||||||||||||||||||||||||||||||||!:!|||||||||||
          luSerGlnAspGlnSerSerLeuCysLysGlnProProAlaTrpAsnIleArgAspGl
 150058 : AGAGCCAGGACCAAAGCTCCTTGTGTAAGCAACCCCCAGCCTGGAACATAAGAGATCA : 150114

     40 : nAspProMetLeuAsnSerAsnGlySerValThrValValAlaLeuLeuGlnAlaSer :     58
          |||||||||||||||||||!:!||||||||||||||||||||||||||||||||||||
          nAspProMetLeuAsnSerSerGlySerValThrValValAlaLeuLeuGlnAlaSer
 150115 : AGATCCAATGCTGAACTCCAGTGGTTCAGTGACTGTGGTTGCTCTCCTTCAAGCAAGC : 150171

     59 : UnkTyrLeuCysIleLeuGlnAlaSer{Ly}  >>>> Target Intron 1 >>>> :     68
             ||||||||||||||||||||||||{!:}           1062 bp         
          ***TyrLeuCysIleLeuGlnAlaSer{Ar}++                         
 150172 : TGATACCTGTGCATTCTGCAGGCATCT{AG}gt......................... : 150205

     69 :   {s}LeuGluAspLeuArgValLysLeuLysLysGluGlyTyrSerAsnIleSerTy :     86
            {!}||||||||||||||||||||||||:!!||||||||||||||||||||||||||
          ++{g}LeuGluAspLeuArgValLysLeuGluLysGluGlyTyrSerAsnIleSerTy
 150206 : ag{A}TTGGAAGACCTGCGAGTAAAACTGGAGAAAGAAGGATATTCTAATATTTCTTA : 151317

     87 : rIleValValAsnHisGlnGlyIleSerSerArgLeuLysTyrThrHisLeuLysAsn :    105
          ||||:!!|||||||||||||||:!!||||||!:!|||!:!||||||||||||||||||
          rIleIleValAsnHisGlnGlyLeuSerSerGlnLeuArgTyrThrHisLeuLysAsn
 151318 : TATTATTGTTAATCATCAAGGACTCTCTTCTCAATTAAGATACACACATCTTAAGAAT : 151374

    106 : LysValSerGluHisIleProValTyrGlnGlnGluGluAsnGlnThrAspValTrpT :    125
          :!!|||||||||||||||||||||||||||||||||||||||||| !!|||||||||.
          GlnValSerGluHisIleProValTyrGlnGlnGluGluAsnGlnProAspValTrpA
 151375 : CAGGTTTCAGAGCATATTCCTGTTTATCAGCAAGAAGAAAACCAACCAGATGTCTGGG : 151434

    126 : hrLeuLeuAsnGlySerLysAspAspPheLeuIleTyrAsp{Ar}  >>>> Target :    139
          !!||||||||||||!:!||||||||||||||||||||||||{||}           21
          laLeuLeuAsnGlyAsnLysAspAspPheLeuIleTyrAsp{Ar}++           
 151435 : CTCTTTTAAATGGAAACAAAGATGACTTCCTTATATATGAC{AG}gt........... : 151480

    140 :  Intron 2 >>>>  {g}CysGlyArgLeuValTyrHisLeuGlyLeuProPheSer :    152
          22 bp           {|}|||||||||||||||||||||||||||||||||||||||
                        ++{g}CysGlyArgLeuValTyrHisLeuGlyLeuProPheSer
 151481 : ..............ag{A}TGTGGCCGTCTTGTGTATCATCTTGGTTTGCCTTTTTCC : 153637

    153 : PheLeuThrPheProTyrValGluGluAlaIleLysIleAlaTyrCysGluLysLysC :    172
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          PheLeuThrPheProTyrValGluGluAlaIleLysIleAlaTyrCysGluLysLysC
 153638 : TTCCTAACATTCCCATATGTAGAAGAAGCCATTAAGATTGCCTACTGTGAAAAGAAAT : 153697

    173 : ysGlyAsnCysSerLeuThr  >>>> Target Intron 3 >>>>  ThrLeuLys :    181
          ||||||||||||||||||||           2998 bp           |||||||||
          ysGlyAsnCysSerLeuThr++                         ++ThrLeuLys
 153698 : GTGGAAACTGCTCTCTCACGgt.........................agACTCTCAAA : 156722

    182 : AspGluAspPheCysLysArgValSerLeuAlaThrValAspLysThrValGluThrP :    201
          ||||||||||||||||||!.!||||||||||||||||||:!!||||||..!|||.!!|
          AspGluAspPheCysLysAsnValSerLeuAlaThrValAsnLysThrThrGluAlaP
 156723 : GATGAAGACTTTTGTAAAAATGTATCTTTGGCTACTGTGAATAAAACAACTGAAGCTC : 156782

    202 : roSerProHisTyrHisHisGluHisHisHisAsnHisGlyHisGlnHisLeuGlySe :    220
          ||..!||||||:!!||||||:!!|||||||||||||||||||||||||||||||||||
          roGlnProHisHisHisHisLysHisHisHisAsnHisGlyHisGlnHisLeuGlySe
 156783 : CACAGCCCCATCACCATCATAAGCATCATCACAATCATGGACATCAGCACCTTGGCAG : 156839

    221 : rSerGluLeuSerGluAsnGlnGlnProGlyAlaProAsnAlaProThrHisProAla :    239
          |||||||||||||:!!|||:!!|||||||||||||||:!!||||||||||||! !.!!
          rSerGluLeuSerLysAsnGluGlnProGlyAlaProAspAlaProThrHisLeuThr
 156840 : CAGTGAGCTTTCAAAGAATGAGCAACCAGGAGCACCAGATGCTCCTACTCATCTTACT : 156896

    240 : ProProGlyLeuHisHisHisHisLysHisLysGlyGlnHisArgGlnGlyHisProG :    259
           !!|||! !|||||||||||||||||||||||||||||||||||||||||||||||||
          SerProAspLeuHisHisHisHisLysHisLysGlyGlnHisArgGlnGlyHisProG
 156897 : TCTCCAGACCTTCATCACCACCATAAGCACAAGGGTCAACATAGACAGGGTCACCCAG : 156956

    260 : luAsnArgAspMetProAlaSerGluAspLeuGlnAspLeuGlnLysLysLeuCysAr :    278
          ||||| !! !!||||||!.!||||||! !|||||| !!! !|||!!.||||||!! !:
          luAsn***TyrMetProGlySerGluGlyLeuGlnHisProGlnAsnLysLeu***Gl
 156957 : AGAACTGATACATGCCAGGAAGTGAAGGTTTACAACATCCACAAAACAAGCTCTGACA : 157013

    279 : gLysArgCysIleAsnGlnLeuLeuCysLysLeuProThrAspSerGluLeuAlaPro :    297
          !||||||||||||||||||||||||!! |||||||||! !||||||||||||||||||
          nLysArgCysIleAsnGlnLeuLeu***LysLeuProLysAspSerGluLeuAlaPro
 157014 : AAAGAGATGTATAAATCAATTACTCTGAAAATTGCCCAAAGATTCAGAGTTGGCTCCT : 157070

    298 : ArgSerUnkCysCysHisCysArgHisLeuIlePheGluLysThrGlySerAlaIleT :    317
          ||||||   |||!! |||||||||||||||||||||||||||||||||||||||||||
          ArgSer***Cys***HisCysArgHisLeuIlePheGluLysThrGlySerAlaIleT
 157071 : AGGAGCTGATGCTGACATTGTCGACATCTGATATTTGAAAAAACGGGGTCTGCAATCA : 157130

    318 : hrUnkGlnCysLysGluAsnLeuProSerLeuCysSerUnkGlnGlyLeuArgAlaGl :    336
          ||   |||||||||||||||||||||||||||||||||   |||||||||||||||||
          hr***GlnCysLysGluAsnLeuProSerLeuCysSer***GlnGlyLeuArgAlaGl
 157131 : CCTGACAGTGTAAAGAAAACCTCCCATCCTTATGTAGCTGACAGGGACTTCGGGCAGA : 157187

    337 : uGluAsnIleThrGluSerCysGlnUnkArgLeuProProAlaAlaUnkGlnIleSer :    355
          ||||!.!||||||||||||||||||   ||||||||||||||||||   |||! !|||
          uGluThrIleThrGluSerCysGln***ArgLeuProProAlaAla***GlnThrSer
 157188 : GGAGACTATAACTGAATCTTGTCAGTGACGTTTGCCTCCAGCTGCCTGACAGACAAGT : 157244

    356 : GlnGlnLeuIleProThrGluAlaSerAlaSerUnkArgUnkLysAsnGlnAlaLysL :    375
          |||||||||||||||||||||||||||.!!!:!   !!!   ||||||:!!|||||||
          GlnGlnLeuIleProThrGluAlaSerThrAsn***Ser***LysAsnLysAlaLysL
 157245 : CAGCAGCTTATACCCACAGAAGCCAGTACCAACTGAAGCTGAAAGAATAAGGCGAAAA : 157304

    376 : ysUnkGluUnkProSerAsn :    381
          ||   |||   |||||||||
          ys***Glu***ProSerAsn
 157305 : AGTGAGAATGACCTTCAAAC : 157324

vulgar: SPP00000020_1.0 0 381 . gi|357434243|gb|JH378120.1|:subseq(24855656,307324) 149999 157324 + 1676 M 67 201 S 0 2 5 0 2 I 0 1058 3 0 2 S 1 1 M 70 210 S 0 2 5 0 2 I 0 2118 3 0 2 S 1 1 M 39 117 5 0 2 I 0 2994 3 0 2 M 203 609
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2012-11-14
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	gene	150000	157324	1676	+	.	gene_id 1 ; sequence SPP00000020_1.0 ; gene_orientation +
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	cds	150000	150202	.	+	.	
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	exon	150000	150202	.	+	.	insertions 0 ; deletions 0
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	splice5	150203	150204	.	+	.	intron_id 1 ; splice_site "GT"
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	intron	150203	151264	.	+	.	intron_id 1
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	splice3	151263	151264	.	+	.	intron_id 0 ; splice_site "AG"
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	cds	151265	151477	.	+	.	
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	exon	151265	151477	.	+	.	insertions 0 ; deletions 0
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	splice5	151478	151479	.	+	.	intron_id 2 ; splice_site "GT"
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	intron	151478	153599	.	+	.	intron_id 2
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	splice3	153598	153599	.	+	.	intron_id 1 ; splice_site "AG"
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	cds	153600	153717	.	+	.	
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	exon	153600	153717	.	+	.	insertions 0 ; deletions 0
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	splice5	153718	153719	.	+	.	intron_id 3 ; splice_site "GT"
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	intron	153718	156715	.	+	.	intron_id 3
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	splice3	156714	156715	.	+	.	intron_id 2 ; splice_site "AG"
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	cds	156716	157324	.	+	.	
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	exon	156716	157324	.	+	.	insertions 0 ; deletions 0
gi|357434243|gb|JH378120.1|:subseq(24855656,307324)	exonerate:protein2genome:local	similarity	150000	157324	1676	+	.	alignment_id 1 ; Query SPP00000020_1.0 ; Align 150000 1 201 ; Align 151266 69 210 ; Align 153601 140 117 ; Align 156716 179 609
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis