Command line: [exonerate -m p2g --showtargetgff -q SelU2.fa.U_to_X -t gi|511782581|gb|CM001953.1|.fastasubseq]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000114_2.0 # Protein # Selenoprotein U2 (SelU2) # Human (Homo sapiens) 
        Target: gi|511782581|gb|CM001953.1|:subseq(106386811,212804) Chlorocebus sabaeus isolate 1994-021 chromosome 12, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 1112
   Query range: 0 -> 226
  Target range: 99999 -> 112804

      1 : MetAlaAlaProAlaProValThrArgGlnValSerGlyAlaAlaAlaLeuValProA :     20
          |||||||||||||||||||||||||||||||||||||||!.!.!!|||! !|||||||
          MetAlaAlaProAlaProValThrArgGlnValSerGlyGlyThrAlaProValProA
 100000 : ATGGCCGCGCCCGCCCCGGTCACGCGGCAGGTTAGCGGCGGCACCGCCCCGGTCCCGG : 100057

     21 : laProSerGlyProAspSerGlyGlnProLeuAlaAlaAlaValAlaGluLeuProVa :     39
          ||||||||||||||||| !!||||||||||||||||||||||||||||||||||||||
          laProSerGlyProAspArgGlyGlnProLeuAlaAlaAlaValAlaGluLeuProVa
 100058 : CCCCGAGCGGCCCCGACCGTGGGCAGCCCCTGGCAGCCGCCGTGGCCGAGCTGCCGGT : 100114

     40 : lLeuAspAlaArgGlyGlnArgValProPheGlyAlaLeuPheArgGluArgArgAla :     58
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          lLeuAspAlaArgGlyGlnArgValProPheGlyAlaLeuPheArgGluArgArgAla
 100115 : GCTGGACGCCCGCGGGCAGCGGGTACCTTTCGGCGCGCTGTTCCGGGAGCGCCGCGCC : 100171

     59 : ValValValPheValArg  >>>> Target Intron 1 >>>>  HisPheLeuCy :     68
          ||||||||||||||||||            309 bp           |||||||||||
          ValValValPheValArg++                         ++HisPheLeuCy
 100172 : GTGGTGGTGTTCGTGCGGgt.........................agCATTTTCTGTG : 100510

     69 : sTyrIleCysLysGluTyrValGluAspLeuAlaLysIleProArgSerPheLeuGln :     87
          |||||||||||||||||||||||||||||||||||||||||||!:!||||||||||||
          sTyrIleCysLysGluTyrValGluAspLeuAlaLysIleProLysSerPheLeuGln
 100511 : TTACATCTGCAAGGAATACGTAGAGGATCTGGCCAAAATCCCGAAGAGTTTCTTACAA : 100567

     88 :   >>>> Target Intron 2 >>>>  GluAlaAsnValThrLeuIleValIleGl :     97
                     2832 bp           ||||||:!!||||||||||||||||||||
          ++                         ++GluAlaAspValThrLeuIleValIleGl
 100568 : gt.........................agGAAGCAGATGTCACCCTTATAGTGATTGG : 103429

     98 : yGlnSerSerTyrHisHisIleGlu  >>>> Target Intron 3 >>>>  ProP :    107
          |||||||||||||||||||||||||            163 bp           ||||
          yGlnSerSerTyrHisHisIleGlu++                         ++ProP
 103430 : ACAGTCATCCTACCATCATATTGAGgt.........................agCCTT : 103622

    108 : heCysLysLeuThrGlyTyrSerHisGluIleTyrValAspProGluArgGluIleTy :    126
          |||||!:!||||||||||||||||||||||||||||||||||||||||||||||||||
          heCysArgLeuThrGlyTyrSerHisGluIleTyrValAspProGluArgGluIleTy
 103623 : TTTGCAGACTGACTGGATATTCTCATGAAATCTATGTCGATCCTGAGAGAGAAATTTA : 103679

    127 : rLysArgLeuGlyMetLysArgGlyGluGluIleAlaSerSer{G}  >>>> Targe :    141
          |||||||||||||||||||||||||||||||||||||||||||{|}           4
          rLysArgLeuGlyMetLysArgGlyGluGluIleAlaSerSer{G}++          
 103680 : TAAAAGATTGGGAATGAAACGAGGTGAAGAAATTGCCTCCTCA{G}gt.......... : 103727

    142 : t Intron 4 >>>>  {ly}GlnSerProHisIleLysSerAsnLeuLeuSerGlyS :    154
          830 bp           {||}||||||||||||:!!||||||||||||||||||||||
                         ++{ly}GlnSerProHisValLysSerAsnLeuLeuSerGlyS
 103728 : ...............ag{GA}CAGAGCCCCCACGTAAAATCAAATCTACTCTCAGGAA : 108593

    155 : erLeuGlnSerLeuTrpArgAlaValThrGlyProLeuPheAspPheGlnGlyAspPr :    173
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          erLeuGlnSerLeuTrpArgAlaValThrGlyProLeuPheAspPheGlnGlyAspPr
 108594 : GCCTTCAGAGCCTGTGGCGGGCAGTGACCGGCCCGCTCTTTGATTTTCAAGGAGACCC : 108650

    174 : oAlaGlnGlnGlyGlyThrLeuIleLeuGlyPro{G}  >>>> Target Intron  :    185
          ||||||||||||||||! !|||||||||||||||{|}           3993 bp   
          oAlaGlnGlnGlyGlyIleLeuIleLeuGlyPro{G}++                   
 108651 : AGCTCAGCAAGGTGGAATCCTCATTTTAGGTCCA{G}gt................... : 108689

    186 : 5 >>>>  {ly}AsnAsnIleHisPheIleHisArgAspArgAsnArgLeuAspHisL :    201
                  {||}||||||||||||||||||||||||||||||||||||||||||||||
                ++{ly}AsnAsnIleHisPheIleHisArgAspArgAsnArgLeuAspHisL
 108690 : ......ag{GT}AACAACATCCATTTTATACACCGCGATAGGAATAGGTTGGATCACA : 112727

    202 : ysProIleAsnSerValLeuGlnLeuValGlyValGlnHisValAsnPheThrAsnAr :    220
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          ysProIleAsnSerValLeuGlnLeuValGlyValGlnHisValAsnPheThrAsnAr
 112728 : AACCTATCAACTCTGTTTTACAGCTTGTCGGAGTTCAGCATGTGAACTTTACAAACAG : 112784

    221 : gProSerValIleHisVal :    226
          |||||||||||||||||||
          gProSerValIleHisVal
 112785 : ACCTTCAGTTATCCATGTG : 112804

vulgar: SPP00000114_2.0 0 226 . gi|511782581|gb|CM001953.1|:subseq(106386811,212804) 99999 112804 + 1112 M 64 192 5 0 2 I 0 305 3 0 2 M 23 69 5 0 2 I 0 2828 3 0 2 M 18 54 5 0 2 I 0 159 3 0 2 M 35 105 S 0 1 5 0 2 I 0 4826 3 0 2 S 1 2 M 43 129 S 0 1 5 0 2 I 0 3989 3 0 2 S 1 2 M 41 123
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-04
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	gene	100000	112804	1112	+	.	gene_id 1 ; sequence SPP00000114_2.0 ; gene_orientation +
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	cds	100000	100191	.	+	.	
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	exon	100000	100191	.	+	.	insertions 0 ; deletions 0
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	splice5	100192	100193	.	+	.	intron_id 1 ; splice_site "GT"
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	intron	100192	100500	.	+	.	intron_id 1
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	splice3	100499	100500	.	+	.	intron_id 0 ; splice_site "AG"
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	cds	100501	100569	.	+	.	
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	exon	100501	100569	.	+	.	insertions 0 ; deletions 0
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	splice5	100570	100571	.	+	.	intron_id 2 ; splice_site "GT"
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	intron	100570	103401	.	+	.	intron_id 2
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	splice3	103400	103401	.	+	.	intron_id 1 ; splice_site "AG"
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	cds	103402	103455	.	+	.	
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	exon	103402	103455	.	+	.	insertions 0 ; deletions 0
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	splice5	103456	103457	.	+	.	intron_id 3 ; splice_site "GT"
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	intron	103456	103618	.	+	.	intron_id 3
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	splice3	103617	103618	.	+	.	intron_id 2 ; splice_site "AG"
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	cds	103619	103724	.	+	.	
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	exon	103619	103724	.	+	.	insertions 0 ; deletions 0
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	splice5	103725	103726	.	+	.	intron_id 4 ; splice_site "GT"
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	intron	103725	108554	.	+	.	intron_id 4
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	splice3	108553	108554	.	+	.	intron_id 3 ; splice_site "AG"
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	cds	108555	108686	.	+	.	
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	exon	108555	108686	.	+	.	insertions 0 ; deletions 0
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	splice5	108687	108688	.	+	.	intron_id 5 ; splice_site "GT"
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	intron	108687	112679	.	+	.	intron_id 5
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	splice3	112678	112679	.	+	.	intron_id 4 ; splice_site "AG"
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	cds	112680	112804	.	+	.	
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	exon	112680	112804	.	+	.	insertions 0 ; deletions 0
gi|511782581|gb|CM001953.1|:subseq(106386811,212804)	exonerate:protein2genome:local	similarity	100000	112804	1112	+	.	alignment_id 1 ; Query SPP00000114_2.0 ; Align 100000 1 192 ; Align 100501 65 69 ; Align 103402 88 54 ; Align 103619 106 105 ; Align 108557 142 129 ; Align 112682 186 123
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis