Command line: [exonerate -m p2g --showtargetgff -q msra.query.U_to_X -t gi|511782585|gb|CM001948.1|.fastasubseq]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000044_2.0 # Protein # Methionine sulfoxide reductase A (MsrA) # Human (Homo sapiens) 
        Target: gi|511782585|gb|CM001948.1|:subseq(8614616,460606) Chlorocebus sabaeus isolate 1994-021 chromosome 8, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 1214
   Query range: 0 -> 235
  Target range: 410606 -> 49999

      1 : MetLeuSerAlaThrArgArgAlaCysGlnLeuLeuLeuLeuHisSerLeuPheProV :     20
          |||||||||||||||||||||||| !!|||||||||||||||||||||||||||||||
          MetLeuSerAlaThrArgArgAlaArgGlnLeuLeuLeuLeuHisSerLeuPheProV
 410606 : ATGCTCTCGGCCACCCGGAGGGCTCGCCAGCTCCTCCTCCTCCACAGCCTCTTTCCCG : 410549

     21 : alProArgMetGlyAsnSerAlaSerAsnIleValSerProGlnGluAlaLeuProGl :     39
          ||||||||||||||||||||||||||!:!|||||||||||||||||||||||||||||
          alProArgMetGlyAsnSerAlaSerSerIleValSerProGlnGluAlaLeuProGl
 410548 : TCCCGAGGATGGGCAACTCGGCCTCGAGCATCGTCAGCCCCCAGGAGGCCTTGCCGGG : 410492

     40 : yArgLysGluGlnThrProValAla{A}  >>>> Target Intron 1 >>>>  { :     48
          |||||||||||||||||||||||||{|}          143735 bp          {
          yArgLysGluGlnThrProValAla{A}++                         ++{
 410491 : CCGGAAGGAACAGACCCCTGTAGCG{G}gt.........................ag{ : 266729

     49 : la}LysHisHisValAsnGlyAsnArgThrValGluProPheProGluGlyThrGlnM :     67
          ||}|||||||||||||||||||||||||||||||||||||||||||||||||||||||
          la}LysHisHisValAsnGlyAsnArgThrValGluProPheProGluGlyThrGlnM
 266728 : CC}AAACATCATGTCAATGGCAACAGAACAGTCGAACCTTTCCCAGAGGGAACACAGA : 266673

     68 : etAlaValPhe{G}  >>>> Target Intron 2 >>>>  {ly}MetGlyCysPh :     75
          |||||||||||{|}           35944 bp          {||}|||||||||||
          etAlaValPhe{G}++                         ++{ly}MetGlyCysPh
 266672 : TGGCTGTATTT{G}gt.........................ag{GA}ATGGGCTGTTT : 230705

     76 : eTrpGlyAlaGluArgLysPheTrpValLeuLysGlyValTyrSerThrGlnValGly :     94
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          eTrpGlyAlaGluArgLysPheTrpValLeuLysGlyValTyrSerThrGlnValGly
 230704 : CTGGGGAGCTGAAAGGAAATTCTGGGTCTTGAAAGGAGTGTATTCAACTCAAGTTGGT : 230648

     95 : PheAlaGlyGlyTyrThrSerAsnProThrTyrLysGluValCysSer{G}  >>>>  :    111
          ||||||||||||||||||||||||||||||||||||||||||||||||{|}       
          PheAlaGlyGlyTyrThrSerAsnProThrTyrLysGluValCysSer{G}++     
 230647 : TTTGCAGGAGGCTATACTTCAAATCCTACTTATAAAGAAGTCTGCTCA{G}gt..... : 230594

    112 : Target Intron 3 >>>>  {lu}LysThrGlyHisAlaGluValValArgValVa :    122
              57863 bp          {||}||||||||||||||||||||||||||||||||
                              ++{lu}LysThrGlyHisAlaGluValValArgValVa
 230593 : ....................ag{AA}AAAACTGGCCATGCAGAAGTCGTCCGAGTGGT : 172701

    123 : lTyrGlnProGluHisMetSerPheGluGluLeuLeuLysValPheTrpGluAsnHis :    141
          ||||||||||||||||!!:|||||||||||||||||||||||||||||||||||||||
          lTyrGlnProGluHisIleSerPheGluGluLeuLeuLysValPheTrpGluAsnHis
 172700 : GTACCAGCCAGAACACATCAGTTTTGAGGAACTGCTCAAGGTCTTCTGGGAGAATCAC : 172644

    142 : AspProThrGln{G}  >>>> Target Intron 4 >>>>  {ly}MetArgGlnG :    150
          ||||||||||||{|}           18208 bp          {||}||||||||||
          AspProThrGln{G}++                         ++{ly}MetArgGlnG
 172643 : GACCCGACCCAA{G}gt.........................ag{GT}ATGCGCCAGG : 154409

    151 : lyAsnAspHisGlyThrGlnTyrArgSerAlaIleTyrProThrSerAlaLysGlnMe :    169
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          lyAsnAspHisGlyThrGlnTyrArgSerAlaIleTyrProThrSerAlaLysGlnMe
 154408 : GGAATGACCATGGCACTCAGTACCGCTCGGCCATCTACCCGACTTCCGCCAAGCAAAT : 154352

    170 : tGluAlaAlaLeuSerSerLysGluAsnTyrGlnLys  >>>> Target Intron  :    182
          |||||||||||||||||||||||||:!!|||||||||          104152 bp  
          tGluAlaAlaLeuSerSerLysGluAspTyrGlnLys++                   
 154351 : GGAGGCGGCCCTGAGCTCCAAAGAGGACTACCAAAAGgt................... : 154311

    183 : 5 >>>>  ValLeuSerGluHisGlyPheGlyProIleThrThrAspIleArgGluGl :    198
                  ||||||||||||||||||||||||||||||||||||||||||||||||||
                ++ValLeuSerGluHisGlyPheGlyProIleThrThrAspIleArgGluGl
 154310 : ......agGTTCTTTCAGAGCACGGCTTTGGCCCCATCACTACCGACATCCGGGAAGG :  50113

    199 : yGlnThrPheTyrTyrAlaGluAspTyrHisGlnGlnTyrLeuSerLysAsnProAsn :    217
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          yGlnThrPheTyrTyrAlaGluAspTyrHisGlnGlnTyrLeuSerLysAsnProAsn
  50112 : ACAGACATTCTACTACGCGGAAGACTACCACCAGCAGTACCTGAGCAAGAACCCCAAC :  50056

    218 : GlyTyrCysGlyLeuGlyGlyThrGlyValSerCysProValGlyIleLysLys :    235
          |||||||||||||||||||||||||||||||||||||||:!!||||||||||||
          GlyTyrCysGlyLeuGlyGlyThrGlyValSerCysProMetGlyIleLysLys
  50055 : GGCTACTGCGGCCTGGGGGGCACCGGCGTGTCCTGCCCAATGGGTATTAAAAAA :  50000

vulgar: SPP00000044_2.0 0 235 . gi|511782585|gb|CM001948.1|:subseq(8614616,460606) 410606 49999 - 1214 M 47 141 S 0 1 5 0 2 I 0 143731 3 0 2 S 1 2 M 22 66 S 0 1 5 0 2 I 0 35940 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 57859 3 0 2 S 1 2 M 34 102 S 0 1 5 0 2 I 0 18204 3 0 2 S 1 2 M 35 105 5 0 2 I 0 104148 3 0 2 M 54 162
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-05
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	gene	50000	410606	1214	-	.	gene_id 1 ; sequence SPP00000044_2.0 ; gene_orientation +
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	cds	410465	410606	.	-	.	
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	exon	410465	410606	.	-	.	insertions 0 ; deletions 0
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	splice5	410463	410464	.	-	.	intron_id 1 ; splice_site "GT"
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	intron	266730	410464	.	-	.	intron_id 1
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	splice3	266730	266731	.	-	.	intron_id 0 ; splice_site "AG"
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	cds	266661	266729	.	-	.	
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	exon	266661	266729	.	-	.	insertions 0 ; deletions 0
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	splice5	266659	266660	.	-	.	intron_id 2 ; splice_site "GT"
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	intron	230717	266660	.	-	.	intron_id 2
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	splice3	230717	230718	.	-	.	intron_id 1 ; splice_site "AG"
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	cds	230597	230716	.	-	.	
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	exon	230597	230716	.	-	.	insertions 0 ; deletions 0
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	splice5	230595	230596	.	-	.	intron_id 3 ; splice_site "GT"
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	intron	172734	230596	.	-	.	intron_id 3
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	splice3	172734	172735	.	-	.	intron_id 2 ; splice_site "AG"
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	cds	172629	172733	.	-	.	
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	exon	172629	172733	.	-	.	insertions 0 ; deletions 0
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	splice5	172627	172628	.	-	.	intron_id 4 ; splice_site "GT"
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	intron	154421	172628	.	-	.	intron_id 4
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	splice3	154421	154422	.	-	.	intron_id 3 ; splice_site "AG"
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	cds	154314	154420	.	-	.	
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	exon	154314	154420	.	-	.	insertions 0 ; deletions 0
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	splice5	154312	154313	.	-	.	intron_id 5 ; splice_site "GT"
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	intron	50162	154313	.	-	.	intron_id 5
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	splice3	50162	50163	.	-	.	intron_id 4 ; splice_site "AG"
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	cds	50000	50161	.	-	.	
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	exon	50000	50161	.	-	.	insertions 0 ; deletions 0
gi|511782585|gb|CM001948.1|:subseq(8614616,460606)	exonerate:protein2genome:local	similarity	50000	410606	1214	-	.	alignment_id 1 ; Query SPP00000044_2.0 ; Align 410607 1 141 ; Align 266728 49 66 ; Align 230715 72 117 ; Align 172732 112 102 ; Align 154419 147 105 ; Align 50162 182 162
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis