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

C4 Alignment:
------------
         Query: SPP00000023_1.0 # Protein # Methionine-R-sufoxide reductase 3 (SelR3) # Homo sapiens # Complete
        Target: gi|398923229|gb|JH767750.1|:subseq(22093861,211138) Ceratotherium simum simum unplaced genomic scaffold scaffold00028, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 823
   Query range: 11 -> 192
  Target range: 1 -> 161138

     12 : SerLeuCysLeuSerLeuCysLeuCysLeuCysLeuAlaAlaAlaLeuGlySerAlaG :     31
          |||||| !!|||.!!||| !!||||||||||||||||||||||||! !|||:!!|||!
          SerLeuGlyLeuGlyLeuGlyLeuCysLeuCysLeuAlaAlaAlaArgGlyAlaAlaH
      2 : TCGCTCGGCCTCGGCCTCGGCCTCTGCCTCTGCCTGGCCGCGGCGCGGGGAGCCGCGC :     59

     32 : lnSer{G}  >>>> Target Intron 1 >>>>  {ly}SerCysArgAspLysLy :     39
          !. !!{|}           49926 bp          {||}|||||||||||||||||
          isPro{G}++                         ++{ly}SerCysArgAspLysLy
     60 : ACCCG{G}gt.........................ag{GG}TCATGTAGGGATAAAAA :  50009

     40 : sAsnCysLysValValPheSerGlnGlnGluLeuArgLysArgLeuThrProLeuGln :     58
          |!:!||||||||||||||||||||||||||||||||||||||||||||||||||||||
          sSerCysLysValValPheSerGlnGlnGluLeuArgLysArgLeuThrProLeuGln
  50010 : GAGCTGTAAGGTGGTCTTTTCCCAGCAGGAACTGAGGAAGCGGCTCACACCCCTGCAG :  50066

     59 : TyrHisValThrGlnGluLysGlyThrGlu{Se}  >>>> Target Intron 2 > :     69
          ||||||||||||||||||||||||||||||{||}           1612 bp      
          TyrHisValThrGlnGluLysGlyThrGlu{Se}++                      
  50067 : TACCATGTCACTCAGGAGAAAGGGACGGAA{AG}gt...................... :  50103

     70 : >>>  {r}AlaPheGluGlyGluTyrThrHisHisLysAspProGlyIleTyrLysCy :     86
               {|}||||||||||||||||||||||||||||||||||||||||||||||||||
             ++{r}AlaPheGluGlyGluTyrThrHisHisLysAspProGlyIleTyrLysCy
  50104 : ...ag{T}GCCTTCGAAGGAGAATATACACATCACAAAGATCCTGGAATCTATAAATG :  51762

     87 : sValValCysGlyThrProLeuPhe{Ly}  >>>> Target Intron 3 >>>>   :     95
          |||||||||||||||||||||||||{||}           31336 bp          
          sValValCysGlyThrProLeuPhe{Ly}++                         ++
  51763 : TGTTGTTTGTGGAACTCCATTGTTC{AA}gt.........................ag :  83125

     96 : {s}SerGluThrLysPheAspSerGlySer{G}  >>>> Target Intron 4 >> :    105
          {|}|||||||||||||||||||||||||||{|}           69032 bp      
          {s}SerGluThrLysPheAspSerGlySer{G}++                       
  83126 : {G}TCAGAAACCAAATTTGACTCCGGTTCA{G}gt....................... :  83158

    106 : >>  {ly}TrpProSerPheHisAspValIleAsnSerGluAlaIleThrPheThrAs :    122
              {||}||||||||||||||||||||||||!:!|||!!:|||||||||.!!|||||
            ++{ly}TrpProSerPheHisAspValIleSerSerAspAlaIleThrLeuThrAs
  83159 : ..ag{GT}TGGCCTTCATTCCACGACGTGATCAGCTCGGACGCAATCACGCTCACAGA : 152238

    123 : pAspPheSerTyrGlyMetHisArgValGluThrSerCysSerGln  >>>> Targe :    138
          ||||||||||||||||||||||||||||||||||||||||||||||           8
          pAspPheSerTyrGlyMetHisArgValGluThrSerCysSerGln++          
 152239 : TGACTTTTCCTACGGGATGCACAGGGTGGAAACAAGCTGCTCCCAGgt.......... : 152288

    139 : t Intron 5 >>>>  CysGlyAlaHisLeuGlyHisIlePheAspAspGlyProAr :    151
          697 bp           |||||||||||||||||||||||||||||||||||||||||
                         ++CysGlyAlaHisLeuGlyHisIlePheAspAspGlyProAr
 152289 : ...............agTGCGGGGCTCACCTTGGGCACATTTTTGATGACGGACCTCG : 161022

    152 : gProThrGlyLysArgTyrCysIleAsnSerAlaAlaLeuSerPheThrProAlaAsp :    170
          ||||||||||||||||||||||||||||||||||:!!|||||||||||||||||||||
          gProThrGlyLysArgTyrCysIleAsnSerAlaSerLeuSerPheThrProAlaAsp
 161023 : TCCGACGGGCAAAAGATACTGCATCAACTCGGCATCCCTGTCTTTCACACCTGCAGAT : 161079

    171 : SerSerGlyThrAlaGluGlyGlySerGlyValAlaSerProAlaGlnAlaAspLysA :    190
          .!!||||||         !.!|||.!!|||!.!!.!|||||||||||||||||||||.
          GlySerGly---------AlaGlyGlyGlyAlaGlySerProAlaGlnAlaAspLysT
 161080 : GGCAGCGGC---------GCCGGCGGCGGGGCGGGCAGCCCGGCCCAGGCGGACAAGA : 161130

    191 : laGluLeu :    192
          !!||||||
          hrGluLeu
 161131 : CCGAGCTG : 161138

vulgar: SPP00000023_1.0 11 192 . gi|398923229|gb|JH767750.1|:subseq(22093861,211138) 1 161138 + 823 M 21 63 S 0 1 5 0 2 I 0 49922 3 0 2 S 1 2 M 35 105 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 36 108 G 3 0 M 16 48
# --- 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(22093861,211138)	exonerate:protein2genome:local	gene	2	161138	823	+	.	gene_id 1 ; sequence SPP00000023_1.0 ; gene_orientation +
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	cds	2	65	.	+	.	
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	exon	2	65	.	+	.	insertions 0 ; deletions 0
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	splice5	66	67	.	+	.	intron_id 1 ; splice_site "GT"
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	intron	66	49991	.	+	.	intron_id 1
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	splice3	49990	49991	.	+	.	intron_id 0 ; splice_site "AG"
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	cds	49992	50100	.	+	.	
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	exon	49992	50100	.	+	.	insertions 0 ; deletions 0
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	splice5	50101	50102	.	+	.	intron_id 2 ; splice_site "GT"
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	intron	50101	51712	.	+	.	intron_id 2
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	splice3	51711	51712	.	+	.	intron_id 1 ; splice_site "AG"
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	cds	51713	51790	.	+	.	
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	exon	51713	51790	.	+	.	insertions 0 ; deletions 0
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	splice5	51791	51792	.	+	.	intron_id 3 ; splice_site "GT"
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	intron	51791	83126	.	+	.	intron_id 3
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	splice3	83125	83126	.	+	.	intron_id 2 ; splice_site "AG"
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	cds	83127	83155	.	+	.	
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	exon	83127	83155	.	+	.	insertions 0 ; deletions 0
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	splice5	83156	83157	.	+	.	intron_id 4 ; splice_site "GT"
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	intron	83156	152187	.	+	.	intron_id 4
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	splice3	152186	152187	.	+	.	intron_id 3 ; splice_site "AG"
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	cds	152188	152285	.	+	.	
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	exon	152188	152285	.	+	.	insertions 0 ; deletions 0
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	splice5	152286	152287	.	+	.	intron_id 5 ; splice_site "GT"
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	intron	152286	160982	.	+	.	intron_id 5
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	splice3	160981	160982	.	+	.	intron_id 4 ; splice_site "AG"
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	cds	160983	161138	.	+	.	
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	exon	160983	161138	.	+	.	insertions 0 ; deletions 3
gi|398923229|gb|JH767750.1|:subseq(22093861,211138)	exonerate:protein2genome:local	similarity	2	161138	823	+	.	alignment_id 1 ; Query SPP00000023_1.0 ; Align 2 12 63 ; Align 49994 34 105 ; Align 51714 70 75 ; Align 83128 96 27 ; Align 152190 106 96 ; Align 160983 138 108 ; Align 161091 177 48
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
