Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/E.MsrA.1.fa.x.fa -t 3B.fastasub.dir/1.E.MsrA.1.fa.x.fa]
Hostname: [ws116063]

C4 Alignment:
------------
         Query: SPP00000861_2.0 # Protein # Methionine sulfoxide reductase A (MsrA) # Horse (Equus caballus)
        Target: gi|398922613|gb|JH767767.1|:subseq(12645953,419023) Ceratotherium simum simum unplaced genomic scaffold scaffold00045, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 263
   Query range: 133 -> 186
  Target range: 50128 -> 50287

   134 : LysValLeuSerGluHisGlyTyrGlyLeuIleThrThrAspIleArgGluGlyGlnThr :   153
         :!!|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         GlnValLeuSerGluHisGlyTyrGlyLeuIleThrThrAspIleArgGluGlyGlnThr
 50129 : CAGGTTCTTTCAGAGCACGGCTACGGCCTGATCACCACCGACATCCGGGAGGGACAGACT : 50186

   154 : PheTyrTyrAlaGluAspTyrHisGlnGlnTyrLeuSerLysAsnProAspGlyTyrCys :   173
         |||:!!||||||:!!|||||||||||||||||||||||||||||||||||||||||||||
         PheHisTyrAlaLysAspTyrHisGlnGlnTyrLeuSerLysAsnProAspGlyTyrCys
 50187 : TTCCACTACGCCAAGGATTACCACCAGCAGTACCTGAGCAAGAACCCTGACGGGTACTGC : 50246

   174 : GlyLeuGlyGlyThrGlyValSerCysProLeuGlyIle :   186
         |||||||||.!!||||||!.!||||||  !|||||||||
         GlyLeuGlySerThrGlyAlaSerCysMetLeuGlyIle
 50247 : GGCCTCGGGAGCACTGGAGCGTCCTGTATGCTGGGTATT : 50287

vulgar: SPP00000861_2.0 133 186 . gi|398922613|gb|JH767767.1|:subseq(12645953,419023) 50128 50287 + 263 M 53 159
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-25
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	gene	50129	50287	263	+	.	gene_id 1 ; sequence SPP00000861_2.0 ; gene_orientation .
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	cds	50129	50287	.	+	.	
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	exon	50129	50287	.	+	.	insertions 0 ; deletions 0
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	similarity	50129	50287	263	+	.	alignment_id 1 ; Query SPP00000861_2.0 ; Align 50129 134 159
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000861_2.0 # Protein # Methionine sulfoxide reductase A (MsrA) # Horse (Equus caballus)
        Target: gi|398922613|gb|JH767767.1|:subseq(12645953,419023) Ceratotherium simum simum unplaced genomic scaffold scaffold00045, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 964
   Query range: 0 -> 188
  Target range: 369023 -> 125399

      1 : AlaLysHisHisValSerGlyAsnArgThrValGluProPheProGluGlyThrGlnM :     20
          |||||||||||||||!:!||||||||||||||||||||||||||||||||||||||||
          AlaLysHisHisValAsnGlyAsnArgThrValGluProPheProGluGlyThrGlnM
 369023 : GCCAAACATCATGTCAATGGCAACAGAACAGTTGAACCCTTCCCAGAGGGAACACAGA : 368966

     21 : etAlaValPhe{G}  >>>> Target Intron 1 >>>>  {ly}MetGlyCysPh :     28
          |||||:!!|||{|}           51653 bp          {||}|||||||||||
          etAlaLeuPhe{G}++                         ++{ly}MetGlyCysPh
 368965 : TGGCTCTATTT{G}gt.........................ag{GA}ATGGGTTGTTT : 317289

     29 : eTrpGlyAlaGluArgLysPheTrpThrLeuLysGlyValTyrSerThrGlnValGly :     47
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          eTrpGlyAlaGluArgLysPheTrpThrLeuLysGlyValTyrSerThrGlnValGly
 317288 : CTGGGGAGCTGAAAGGAAATTCTGGACCCTGAAAGGAGTCTATTCAACTCAAGTTGGC : 317232

     48 : PheAlaGlyGlyTyrThrProAsnProThrTyrLysGluValCysSer{G}  >>>>  :     64
          |||||||||||||||||||||||||||||||||||||||||||||!!!{|}       
          PheAlaGlyGlyTyrThrProAsnProThrTyrLysGluValCysThr{G}++     
 317231 : TTTGCAGGAGGCTACACTCCCAATCCTACTTACAAAGAAGTCTGCACA{G}gt..... : 317178

     65 : Target Intron 2 >>>>  {ly}LysThrGlyHisAlaGluValValArgValVa :     75
              65599 bp          {||}||||||||||||||||||||||||||||||||
                              ++{ly}LysThrGlyHisAlaGluValValArgValVa
 317177 : ....................ag{GA}AAAACCGGCCATGCAGAAGTAGTCCGAGTGGT : 251549

     76 : lTyrGlnProGluArgIleSerPheGluGluLeuLeuLysValPheTrpGluAsnHis :     94
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          lTyrGlnProGluArgIleSerPheGluGluLeuLeuLysValPheTrpGluAsnHis
 251548 : GTACCAGCCAGAACGCATCAGCTTTGAGGAACTGCTCAAGGTCTTCTGGGAGAATCAC : 251492

     95 : AspProThrGln{G}  >>>> Target Intron 3 >>>>  {ly}MetArgGlnG :    103
          ||||||||||||{|}           28893 bp          {||}||||||||||
          AspProThrGln{G}++                         ++{ly}MetArgGlnG
 251491 : GACCCGACCCAA{G}gt.........................ag{GC}ATGCGCCAAG : 222572

    104 : lyAsnAspTyrGlySerGlnTyrArgSerAlaIleTyrProThrSerAlaAspHisMe :    122
          ||!..|||||||||||||||||||||||||||||||||! !|||||||||||||||||
          lyArgAspTyrGlySerGlnTyrArgSerAlaIleTyrLeuThrSerAlaAspHisMe
 222571 : GCAGAGACTACGGCTCTCAGTACCGCTCAGCCATCTACCTAACCTCCGCCGACCACAT : 222515

    123 : tGluAlaAlaLeuArgSerLysGluAspTyrGlnLys  >>>> Target Intron  :    135
          ||||!.!||||||||||||||||||||||||||||||           96915 bp  
          tGluValAlaLeuArgSerLysGluAspTyrGlnLys++                   
 222514 : GGAGGTGGCCCTGAGGTCCAAAGAGGACTACCAGAAGgt................... : 222474

    136 : 4 >>>>  ValLeuSerGluHisGlyTyrGlyLeuIleThrThrAspIleArgGluGl :    151
                  ||||||||||||||||||||||||! !|||||||||||||||! !|||||
                ++ValLeuSerGluHisGlyTyrGlyProIleThrThrAspIleLeuGluGl
 222473 : ......agGTTCTTTCAGAGCACGGCTACGGCCCGATCACCACCGACATCCTGGAGGG : 125513

    152 : yGlnThrPheTyrTyrAlaGluAspTyrHisGlnGlnTyrLeuSerLysAsnProAsp :    170
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          yGlnThrPheTyrTyrAlaGluAspTyrHisGlnGlnTyrLeuSerLysAsnProAsp
 125512 : ACAGACTTTCTACTACGCCGAGGATTACCACCAGCAGTACCTGAGCAAGAACCCCGAT : 125456

    171 : GlyTyrCysGlyLeuGlyGlyThrGlyValSerCysProLeuGlyIleLysLys :    188
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||
          GlyTyrCysGlyLeuGlyGlyThrGlyValSerCysProLeuGlyIleLysLys
 125455 : GGGTACTGCGGCCTTGGGGGCACCGGAGTGTCCTGCCCGCTGGGTATTAAAAAG : 125400

vulgar: SPP00000861_2.0 0 188 . gi|398922613|gb|JH767767.1|:subseq(12645953,419023) 369023 125399 - 964 M 23 69 S 0 1 5 0 2 I 0 51649 3 0 2 S 1 2 M 39 117 S 0 1 5 0 2 I 0 65595 3 0 2 S 1 2 M 34 102 S 0 1 5 0 2 I 0 28889 3 0 2 S 1 2 M 35 105 5 0 2 I 0 96911 3 0 2 M 54 162
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-25
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	gene	125400	369023	964	-	.	gene_id 1 ; sequence SPP00000861_2.0 ; gene_orientation +
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	cds	368954	369023	.	-	.	
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	exon	368954	369023	.	-	.	insertions 0 ; deletions 0
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	splice5	368952	368953	.	-	.	intron_id 1 ; splice_site "GT"
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	intron	317301	368953	.	-	.	intron_id 1
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	splice3	317301	317302	.	-	.	intron_id 0 ; splice_site "AG"
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	cds	317181	317300	.	-	.	
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	exon	317181	317300	.	-	.	insertions 0 ; deletions 0
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	splice5	317179	317180	.	-	.	intron_id 2 ; splice_site "GT"
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	intron	251582	317180	.	-	.	intron_id 2
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	splice3	251582	251583	.	-	.	intron_id 1 ; splice_site "AG"
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	cds	251477	251581	.	-	.	
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	exon	251477	251581	.	-	.	insertions 0 ; deletions 0
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	splice5	251475	251476	.	-	.	intron_id 3 ; splice_site "GT"
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	intron	222584	251476	.	-	.	intron_id 3
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	splice3	222584	222585	.	-	.	intron_id 2 ; splice_site "AG"
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	cds	222477	222583	.	-	.	
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	exon	222477	222583	.	-	.	insertions 0 ; deletions 0
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	splice5	222475	222476	.	-	.	intron_id 4 ; splice_site "GT"
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	intron	125562	222476	.	-	.	intron_id 4
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	splice3	125562	125563	.	-	.	intron_id 3 ; splice_site "AG"
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	cds	125400	125561	.	-	.	
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	exon	125400	125561	.	-	.	insertions 0 ; deletions 0
gi|398922613|gb|JH767767.1|:subseq(12645953,419023)	exonerate:protein2genome:local	similarity	125400	369023	964	-	.	alignment_id 1 ; Query SPP00000861_2.0 ; Align 369024 1 69 ; Align 317299 25 117 ; Align 251580 65 102 ; Align 222582 100 105 ; Align 125562 135 162
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
