Command line: [exonerate -m p2g --showtargetgff -q ./proteins/SPP00000012_1.0.fa -t ./exonerate/SPP00000012_1.0_1_genomic.fa_exonerate.fa]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000012_1.0 # Protein # Methionine sulfoxide reductase A (MsrA) # Homo sapiens # Complete
        Target: gi|357434168|gb|JH378195.1|:subseq(8562110,586247) Saimiri boliviensis boliviensis unplaced genomic scaffold scaffold00091, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 1150
   Query range: 0 -> 235
  Target range: 149999 -> 527920

      1 : MetLeuSerAlaThrArgArgAlaCysGlnLeuLeuLeuLeuHisSerLeuPheProV :     20
          |||||||||||||||||||||||| !!|||      ||||||||||||||||||||||
          MetLeuSerAlaThrArgArgAlaArgGln------LeuLeuHisSerLeuPheProV
 150000 : ATGCTGTCGGCCACGCGGAGGGCTCGCCAA------CTCCTCCACAGCCTCTTTCCAG : 150051

     21 : alProArgMetGlyAsnSerAlaSerAsnIleValSerProGlnGluAlaLeuProGl :     39
          ||||||||||||||:!!|||||||||!!.|||||||||||||||||||||||||||||
          alProArgMetGlyAspSerAlaSerLysIleValSerProGlnGluAlaLeuProGl
 150052 : TCCCGAGGATGGGCGACTCGGCATCGAAGATCGTCAGCCCCCAGGAGGCCTTGCCGGG : 150108

     40 : yArgLysGluGlnThrProValAla{A}  >>>> Target Intron 1 >>>>  { :     48
          ||||||||||! !||||||||||||{|}          154130 bp          {
          yArgLysGluProThrProValAla{A}++                         ++{
 150109 : CCGGAAGGAGCCGACCCCAGTAGCG{G}gt.........................ag{ : 304266

     49 : la}LysHisHisValAsnGlyAsnArgThrValGluProPheProGluGlyThrGlnM :     67
          ||}|||||||||||||||||||||||||||||||||||||||||||||||||||||||
          la}LysHisHisValAsnGlyAsnArgThrValGluProPheProGluGlyThrGlnM
 304267 : CC}AAACATCATGTCAATGGCAACAGAACAGTCGAACCTTTCCCAGAGGGAACACAGA : 304322

     68 : etAlaValPhe{G}  >>>> Target Intron 2 >>>>  {ly}MetGlyCysPh :     75
          |||||:!!|||{|}           36890 bp          {||}|||||||||||
          etAlaIlePhe{G}++                         ++{ly}MetGlyCysPh
 304323 : TGGCTATATTT{G}gt.........................ag{GA}ATGGGCTGTTT : 341236

     76 : eTrpGlyAlaGluArgLysPheTrpValLeuLysGlyValTyrSerThrGlnValGly :     94
          |||||||||||||||||||||||||!.!||||||||||||||||||||||||||||||
          eTrpGlyAlaGluArgLysPheTrpAlaLeuLysGlyValTyrSerThrGlnValGly
 341237 : CTGGGGAGCTGAAAGGAAATTCTGGGCCTTGAAAGGAGTATATTCAACTCAAGTTGGT : 341293

     95 : PheAlaGlyGlyTyrThrSerAsnProThrTyrLysGluValCysSer{G}  >>>>  :    111
          ||||||||||||||||||||||||||||||||||||||||||||||||{|}       
          PheAlaGlyGlyTyrThrSerAsnProThrTyrLysGluValCysSer{G}++     
 341294 : TTTGCAGGAGGGTACACTTCAAATCCTACTTATAAAGAAGTCTGCTCA{G}gt..... : 341347

    112 : Target Intron 3 >>>>  {lu}LysThrGlyHisAlaGluValValArgValVa :    122
              54192 bp          {||}||||||||||||||||||||||||||||||||
                              ++{lu}LysThrGlyHisAlaGluValValArgValVa
 341348 : ....................ag{AA}AAAACTGGCCATGCAGAAGTCGTCCGAGTTGT : 395569

    123 : lTyrGlnProGluHisMetSerPheGluGluLeuLeuLysValPheTrpGluAsnHis :    141
          ||||||||||||||||!!:|||||||||||||||||||||||||||||||||||||||
          lTyrGlnProGluHisIleSerPheGluGluLeuLeuLysValPheTrpGluAsnHis
 395570 : GTACCAGCCAGAACACATCAGTTTTGAGGAACTGCTCAAGGTCTTCTGGGAGAATCAC : 395626

    142 : AspProThrGln{G}  >>>> Target Intron 4 >>>>  {ly}MetArgGlnG :    150
          ||||||||||||{|}           18355 bp          {||}||||||||||
          AspProThrGln{G}++                         ++{ly}MetArgGlnG
 395627 : GACCCGACCCAA{G}gt.........................ag{GT}ATGCGCCAGG : 414008

    151 : lyAsnAspHisGlyThrGlnTyrArgSerAlaIleTyrProThrSerAlaLysGlnMe :    169
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          lyAsnAspHisGlyThrGlnTyrArgSerAlaIleTyrProThrSerAlaLysGlnMe
 414009 : GCAACGACCACGGCACTCAGTACCGCTCAGCCATCTACCCAACCTCCGCCAAGCAGAT : 414065

    170 : tGluAlaAlaLeuSerSerLysGluAsnTyrGlnLys  >>>> Target Intron  :    182
          |||||||||||||||||||||||||:!!|||||||||          113655 bp  
          tGluAlaAlaLeuSerSerLysGluAspTyrGlnLys++                   
 414066 : GGAGGCAGCCCTGAGCTCCAAAGAGGACTACCAGAAGgt................... : 414106

    183 : 5 >>>>  ValLeuSerGluHisGlyPheGlyProIleThrThrAspIleArgGluGl :    198
                  |||||||||||||||||||||||||||||||||||||||||||||||| !
                ++ValLeuSerGluHisGlyPheGlyProIleThrThrAspIleArgGluAr
 414107 : ......agGTTCTTTCTGAGCACGGCTTTGGCCCCATCACTACCGACATCCGGGAGAG : 527807

    199 : yGlnThrPheTyrTyrAlaGluAspTyrHisGlnGlnTyrLeuSerLysAsnProAsn :    217
          !||||||||||||||||||||||||||||||||||||||||||||||||||||||:!!
          gGlnThrPheTyrTyrAlaGluAspTyrHisGlnGlnTyrLeuSerLysAsnProHis
 527808 : ACAGACTTTCTACTACGCGGAAGACTACCACCAGCAGTACCTGAGCAAGAACCCCCAC : 527864

    218 : GlyTyrCysGlyLeuGlyGlyThrGlyValSerCysProValGlyIleLysLys :    235
          |||||||||||||||||||||||||||||||||||||||:!!||||||||||||
          GlyTyrCysGlyLeuGlyGlyThrGlyValSerCysProMetGlyIleLysLys
 527865 : GGCTACTGCGGCCTGGGGGGCACCGGCGTGTCCTGCCCAATGGGTATTAAAAAA : 527920

vulgar: SPP00000012_1.0 0 235 . gi|357434168|gb|JH378195.1|:subseq(8562110,586247) 149999 527920 + 1150 M 10 30 G 2 0 M 35 105 S 0 1 5 0 2 I 0 154126 3 0 2 S 1 2 M 22 66 S 0 1 5 0 2 I 0 36886 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 54188 3 0 2 S 1 2 M 34 102 S 0 1 5 0 2 I 0 18351 3 0 2 S 1 2 M 35 105 5 0 2 I 0 113651 3 0 2 M 54 162
# --- 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|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	gene	150000	527920	1150	+	.	gene_id 1 ; sequence SPP00000012_1.0 ; gene_orientation +
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	cds	150000	150135	.	+	.	
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	exon	150000	150135	.	+	.	insertions 0 ; deletions 2
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	splice5	150136	150137	.	+	.	intron_id 1 ; splice_site "GT"
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	intron	150136	304265	.	+	.	intron_id 1
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	splice3	304264	304265	.	+	.	intron_id 0 ; splice_site "AG"
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	cds	304266	304334	.	+	.	
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	exon	304266	304334	.	+	.	insertions 0 ; deletions 0
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	splice5	304335	304336	.	+	.	intron_id 2 ; splice_site "GT"
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	intron	304335	341224	.	+	.	intron_id 2
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	splice3	341223	341224	.	+	.	intron_id 1 ; splice_site "AG"
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	cds	341225	341344	.	+	.	
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	exon	341225	341344	.	+	.	insertions 0 ; deletions 0
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	splice5	341345	341346	.	+	.	intron_id 3 ; splice_site "GT"
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	intron	341345	395536	.	+	.	intron_id 3
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	splice3	395535	395536	.	+	.	intron_id 2 ; splice_site "AG"
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	cds	395537	395641	.	+	.	
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	exon	395537	395641	.	+	.	insertions 0 ; deletions 0
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	splice5	395642	395643	.	+	.	intron_id 4 ; splice_site "GT"
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	intron	395642	413996	.	+	.	intron_id 4
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	splice3	413995	413996	.	+	.	intron_id 3 ; splice_site "AG"
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	cds	413997	414103	.	+	.	
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	exon	413997	414103	.	+	.	insertions 0 ; deletions 0
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	splice5	414104	414105	.	+	.	intron_id 5 ; splice_site "GT"
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	intron	414104	527758	.	+	.	intron_id 5
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	splice3	527757	527758	.	+	.	intron_id 4 ; splice_site "AG"
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	cds	527759	527920	.	+	.	
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	exon	527759	527920	.	+	.	insertions 0 ; deletions 0
gi|357434168|gb|JH378195.1|:subseq(8562110,586247)	exonerate:protein2genome:local	similarity	150000	527920	1150	+	.	alignment_id 1 ; Query SPP00000012_1.0 ; Align 150000 1 30 ; Align 150030 13 105 ; Align 304268 49 66 ; Align 341227 72 117 ; Align 395539 112 102 ; Align 413999 147 105 ; Align 527759 182 162
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis