Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/E.SelR3.1.fa.x.fa -t 3B.fastasub.dir/1.E.SelR3.1.fa.x.fa]
Hostname: [ws116063]

C4 Alignment:
------------
         Query: SPP00000879_2.0 # Protein # Methionine-R-sufoxide reductase 3 (SelR3) # Horse (Equus caballus)
        Target: gi|398923229|gb|JH767750.1|:subseq(22093843,211093) Ceratotherium simum simum unplaced genomic scaffold scaffold00028, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 794
   Query range: 15 -> 189
  Target range: 44582 -> 161156

     16 : LeuArgLeuCysLeuSerLeuCysValTyrProAlaSer  >>>> Target Intro :     29
          ||||||||||||:!!|||||| !   !  ! !!..!|||           5378 bp 
          LeuArgLeuCysValSerLeuArgAsnValSerCysSer++                 
  44583 : CTCAGATTGTGTGTTAGTCTCAGGAATGTTTCCTGTAGTgt................. :  44624

     30 : n 1 >>>>  LeuSerProGlySerCysArgAspGlnLysSerCysLysValValPhe :     44
                    |||! !||||||||||||||||||:!!|||||||||||||||||||||
                  +-LeuPheProGlySerCysArgAspLysLysSerCysLysValValPhe
  44625 : ........atCTCTTTCCAGGGTCATGTAGGGATAAAAAGAGCTGTAAGGTGGTCTTT :  50045

     45 : SerGlnGlnGluLeuArgLysArgLeuThrProLeuGlnTyrHisValThrGlnGluL :     64
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          SerGlnGlnGluLeuArgLysArgLeuThrProLeuGlnTyrHisValThrGlnGluL
  50046 : TCCCAGCAGGAACTGAGGAAGCGGCTCACACCCCTGCAGTACCATGTCACTCAGGAGA :  50105

     65 : ysGlyThrGlu{Se}  >>>> Target Intron 2 >>>>  {r}AlaPheGluGl :     72
          |||||||||||{||}           1612 bp           {|}|||||||||||
          ysGlyThrGlu{Se}++                         ++{r}AlaPheGluGl
  50106 : AAGGGACGGAA{AG}gt.........................ag{T}GCCTTCGAAGG :  51741

     73 : yGluTyrIleArgHisLysAspProGlyIleTyrLysCysValValCysGlyThrPro :     91
          |||||||! !!.!|||||||||||||||||||||||||||||||||||||||||||||
          yGluTyrThrHisHisLysAspProGlyIleTyrLysCysValValCysGlyThrPro
  51742 : AGAATATACACATCACAAAGATCCTGGAATCTATAAATGTGTTGTTTGTGGAACTCCA :  51798

     92 : LeuPhe{Ly}  >>>> Target Intron 3 >>>>  {s}SerGluThrLysPheA :    100
          ||||||{||}           31336 bp          {|}||||||||||||||||
          LeuPhe{Ly}++                         ++{s}SerGluThrLysPheA
  51799 : TTGTTC{AA}gt.........................ag{G}TCAGAAACCAAATTTG :  83161

    101 : spSerGlySer{G}  >>>> Target Intron 4 >>>>  {ly}TrpProSerPh :    108
          |||||||||||{|}           69032 bp          {||}|||||||||||
          spSerGlySer{G}++                         ++{ly}TrpProSerPh
  83162 : ACTCCGGTTCA{G}gt.........................ag{GT}TGGCCTTCATT : 152217

    109 : eHisAspValIleSerSerAspAlaIleThrPheThrAspAspPheSerTyrGlyMet :    127
          |||||||||||||||||||||||||||||||.!!||||||||||||||||||||||||
          eHisAspValIleSerSerAspAlaIleThrLeuThrAspAspPheSerTyrGlyMet
 152218 : CCACGACGTGATCAGCTCGGACGCAATCACGCTCACAGATGACTTTTCCTACGGGATG : 152274

    128 : HisArgValGluThrSerCysSerGln  >>>> Target Intron 5 >>>>  Cy :    137
          |||||||||||||||||||||||||||           8697 bp           ||
          HisArgValGluThrSerCysSerGln++                         ++Cy
 152275 : CACAGGGTGGAAACAAGCTGCTCCCAGgt.........................agTG : 161001

    138 : sGlyAlaHisLeuGlyHisIlePheAspAspGlyProArgProThrGlyLysArgTyr :    156
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          sGlyAlaHisLeuGlyHisIlePheAspAspGlyProArgProThrGlyLysArgTyr
 161002 : CGGGGCTCACCTTGGGCACATTTTTGATGACGGACCTCGTCCGACGGGCAAAAGATAC : 161058

    157 : CysIleAsnSerAlaSerLeuSerPheThrProAlaAspGlyLeuGlyAlaGlyGlyS :    176
          ||||||||||||||||||||||||||||||||||||||||||  !|||||||||||| 
          CysIleAsnSerAlaSerLeuSerPheThrProAlaAspGlySerGlyAlaGlyGly-
 161059 : TGCATCAACTCGGCATCCCTGTCTTTCACACCTGCAGATGGCAGCGGCGCCGGCGGC- : 161118

    177 : erGlyAlaGlySerGluGlyArgAlaAspLysAlaGluLeu :    189
            ||||||||||||  !!.!!:!|||||||||.!!||||||
          --GlyAlaGlySerProAlaGlnAlaAspLysThrGluLeu
 161119 : --GGGGCGGGCAGCCCGGCCCAGGCGGACAAGACCGAGCTG : 161156

vulgar: SPP00000879_2.0 15 189 . gi|398923229|gb|JH767750.1|:subseq(22093843,211093) 44582 161156 + 794 M 13 39 5 0 2 I 0 5374 3 0 2 M 39 117 S 0 2 5 0 2 I 0 1608 3 0 2 S 1 1 M 25 75 S 0 2 5 0 2 I 0 31332 3 0 2 S 1 1 M 9 27 S 0 1 5 0 2 I 0 69028 3 0 2 S 1 2 M 32 96 5 0 2 I 0 8693 3 0 2 M 39 117 G 1 0 M 13 39
# --- 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|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	gene	44583	161156	794	+	.	gene_id 1 ; sequence SPP00000879_2.0 ; gene_orientation +
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	cds	44583	44621	.	+	.	
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	exon	44583	44621	.	+	.	insertions 0 ; deletions 0
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	splice5	44622	44623	.	+	.	intron_id 1 ; splice_site "GT"
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	intron	44622	49999	.	+	.	intron_id 1
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	splice3	49998	49999	.	+	.	intron_id 0 ; splice_site "AT"
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	cds	50000	50118	.	+	.	
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	exon	50000	50118	.	+	.	insertions 0 ; deletions 0
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	splice5	50119	50120	.	+	.	intron_id 2 ; splice_site "GT"
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	intron	50119	51730	.	+	.	intron_id 2
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	splice3	51729	51730	.	+	.	intron_id 1 ; splice_site "AG"
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	cds	51731	51808	.	+	.	
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	exon	51731	51808	.	+	.	insertions 0 ; deletions 0
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	splice5	51809	51810	.	+	.	intron_id 3 ; splice_site "GT"
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	intron	51809	83144	.	+	.	intron_id 3
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	splice3	83143	83144	.	+	.	intron_id 2 ; splice_site "AG"
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	cds	83145	83173	.	+	.	
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	exon	83145	83173	.	+	.	insertions 0 ; deletions 0
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	splice5	83174	83175	.	+	.	intron_id 4 ; splice_site "GT"
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	intron	83174	152205	.	+	.	intron_id 4
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	splice3	152204	152205	.	+	.	intron_id 3 ; splice_site "AG"
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	cds	152206	152303	.	+	.	
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	exon	152206	152303	.	+	.	insertions 0 ; deletions 0
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	splice5	152304	152305	.	+	.	intron_id 5 ; splice_site "GT"
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	intron	152304	161000	.	+	.	intron_id 5
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	splice3	160999	161000	.	+	.	intron_id 4 ; splice_site "AG"
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	cds	161001	161156	.	+	.	
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	exon	161001	161156	.	+	.	insertions 0 ; deletions 1
gi|398923229|gb|JH767750.1|:subseq(22093843,211093)	exonerate:protein2genome:local	similarity	44583	161156	794	+	.	alignment_id 1 ; Query SPP00000879_2.0 ; Align 44583 16 39 ; Align 50000 29 117 ; Align 51732 69 75 ; Align 83146 95 27 ; Align 152208 105 96 ; Align 161001 137 117 ; Align 161118 177 39
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
