Command line: [exonerate -m p2g --showtargetgff -q SelR3.1.U_to_X -t gi|511782582|gb|CM001952.1|.fastasubseq]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000092_2.0 # Protein # Methionine-R-sufoxide reductase 3 (SelR3) # Human (Homo sapiens) 
        Target: gi|511782582|gb|CM001952.1|:subseq(60920431,333925) Chlorocebus sabaeus isolate 1994-021 chromosome 11, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 956
   Query range: 0 -> 192
  Target range: 49875 -> 233925

      1 : MetSerProArgArgThrLeuProArgProLeuSerLeuCysLeuSerLeuCysLeuC :     20
          ||||||||||||||||||||||||||||||            ||||||||||||||||
          MetSerProArgArgThrLeuProArgPro------------LeuSerLeuCysLeuC
  49876 : ATGAGCCCGCGGCGGACCCTCCCGCGCCCC------------CTCTCGCTCTGCCTCT :  49921

     21 : ysLeuCysLeuAlaAlaAlaLeuGlySerAlaGlnSer{G}  >>>> Target Int :     33
          ||||||||||||||||||||||||||||||||||||||{|}           50031 
          ysLeuCysLeuAlaAlaAlaLeuGlySerAlaGlnSer{G}++               
  49922 : GCCTCTGCCTGGCCGCGGCTCTGGGAAGTGCGCAGTCC{G}gt............... :  49963

     34 : ron 1 >>>>  {ly}SerCysArgAspLysLysAsnCysLysValValPheSerGln :     47
          bp          {||}||||||||||||||||||||||||||||||||||||||||||
                    ++{ly}SerCysArgAspLysLysAsnCysLysValValPheSerGln
  49964 : ..........ag{GG}TCATGTAGGGATAAAAAGAACTGTAAGGTGGTCTTTTCCCAG : 100033

     48 : GlnGluLeuArgLysArgLeuThrProLeuGlnTyrHisValThrGlnGluLysGlyT :     67
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          GlnGluLeuArgLysArgLeuThrProLeuGlnTyrHisValThrGlnGluLysGlyT
 100034 : CAGGAACTGAGGAAGCGGCTAACACCCCTGCAGTACCATGTCACTCAGGAGAAAGGGA : 100093

     68 : hrGlu{Se}  >>>> Target Intron 2 >>>>  {r}AlaPheGluGlyGluTy :     75
          |||||{||}           1601 bp           {|}|||||||||||||||||
          hrGlu{Se}++                         ++{r}AlaPheGluGlyGluTy
 100094 : CCGAA{AG}gt.........................ag{T}GCCTTTGAAGGAGAGTA : 101718

     76 : rThrHisHisLysAspProGlyIleTyrLysCysValValCysGlyThrProLeuPhe :     94
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          rThrHisHisLysAspProGlyIleTyrLysCysValValCysGlyThrProLeuPhe
 101719 : CACACATCACAAAGATCCTGGAATATATAAATGTGTTGTTTGTGGAACTCCATTGTTT : 101775

     95 : {Ly}  >>>> Target Intron 3 >>>>  {s}SerGluThrLysPheAspSerG :    103
          {||}           32028 bp          {|}||||||||||||||||||||||
          {Ly}++                         ++{s}SerGluThrLysPheAspSerG
 101776 : {AA}gt.........................ag{G}TCAGAAACCAAATTTGACTCCG : 133830

    104 : lySer{G}  >>>> Target Intron 4 >>>>  {ly}TrpProSerPheHisAs :    111
          |||||{|}           90465 bp          {||}|||||||||||||||||
          lySer{G}++                         ++{ly}TrpProSerPheHisAs
 133831 : GTTCA{G}gt.........................ag{GT}TGGCCTTCATTCCACGA : 224319

    112 : pValIleAsnSerGluAlaIleThrPheThrAspAspPheSerTyrGlyMetHisArg :    130
          |||||||!:!||||||||||||||||||||||||||||||||||||||||||||||||
          pValIleSerSerGluAlaIleThrPheThrAspAspPheSerTyrGlyMetHisArg
 224320 : TGTGATCAGTTCTGAGGCAATCACATTCACAGATGACTTTTCCTATGGGATGCACCGG : 224376

    131 : ValGluThrSerCysSerGln  >>>> Target Intron 5 >>>>  CysGlyAl :    140
          |||||||||||||||||||||           9361 bp           ||||||||
          ValGluThrSerCysSerGln++                         ++CysGlyAl
 224377 : GTGGAAACAAGCTGCTCTCAGgt.........................agTGTGGTGC : 233767

    141 : aHisLeuGlyHisIlePheAspAspGlyProArgProThrGlyLysArgTyrCysIle :    159
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          aHisLeuGlyHisIlePheAspAspGlyProArgProThrGlyLysArgTyrCysIle
 233768 : TCACCTTGGGCACATTTTTGATGATGGGCCTCGTCCAACTGGGAAAAGATACTGCATA : 233824

    160 : AsnSerAlaAlaLeuSerPheThrProAlaAspSerSerGlyThrAlaGluGlyGlyS :    179
          ||||||||||||||||||||||||||||||||||||||||||.!!|||||||||||||
          AsnSerAlaAlaLeuSerPheThrProAlaAspSerSerGlyAlaAlaGluGlyGlyS
 233825 : AATTCGGCTGCCTTGTCTTTCACACCTGCGGATAGCAGTGGCGCCGCCGAGGGAGGCA : 233884

    180 : erGlyValAlaSerProAlaGlnAlaAspLysAlaGluLeu :    192
          |||||||||||||||||||||||||||||||||||||||||
          erGlyValAlaSerProAlaGlnAlaAspLysAlaGluLeu
 233885 : GTGGGGTCGCCAGCCCAGCCCAGGCAGACAAAGCGGAGCTC : 233925

vulgar: SPP00000092_2.0 0 192 . gi|511782582|gb|CM001952.1|:subseq(60920431,333925) 49875 233925 + 956 M 10 30 G 4 0 M 18 54 S 0 1 5 0 2 I 0 50027 3 0 2 S 1 2 M 35 105 S 0 2 5 0 2 I 0 1597 3 0 2 S 1 1 M 25 75 S 0 2 5 0 2 I 0 32024 3 0 2 S 1 1 M 9 27 S 0 1 5 0 2 I 0 90461 3 0 2 S 1 2 M 32 96 5 0 2 I 0 9357 3 0 2 M 55 165
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-06
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	gene	49876	233925	956	+	.	gene_id 1 ; sequence SPP00000092_2.0 ; gene_orientation +
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	cds	49876	49960	.	+	.	
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	exon	49876	49960	.	+	.	insertions 0 ; deletions 4
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	splice5	49961	49962	.	+	.	intron_id 1 ; splice_site "GT"
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	intron	49961	99991	.	+	.	intron_id 1
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	splice3	99990	99991	.	+	.	intron_id 0 ; splice_site "AG"
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	cds	99992	100100	.	+	.	
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	exon	99992	100100	.	+	.	insertions 0 ; deletions 0
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	splice5	100101	100102	.	+	.	intron_id 2 ; splice_site "GT"
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	intron	100101	101701	.	+	.	intron_id 2
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	splice3	101700	101701	.	+	.	intron_id 1 ; splice_site "AG"
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	cds	101702	101779	.	+	.	
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	exon	101702	101779	.	+	.	insertions 0 ; deletions 0
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	splice5	101780	101781	.	+	.	intron_id 3 ; splice_site "GT"
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	intron	101780	133807	.	+	.	intron_id 3
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	splice3	133806	133807	.	+	.	intron_id 2 ; splice_site "AG"
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	cds	133808	133836	.	+	.	
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	exon	133808	133836	.	+	.	insertions 0 ; deletions 0
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	splice5	133837	133838	.	+	.	intron_id 4 ; splice_site "GT"
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	intron	133837	224301	.	+	.	intron_id 4
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	splice3	224300	224301	.	+	.	intron_id 3 ; splice_site "AG"
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	cds	224302	224399	.	+	.	
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	exon	224302	224399	.	+	.	insertions 0 ; deletions 0
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	splice5	224400	224401	.	+	.	intron_id 5 ; splice_site "GT"
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	intron	224400	233760	.	+	.	intron_id 5
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	splice3	233759	233760	.	+	.	intron_id 4 ; splice_site "AG"
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	cds	233761	233925	.	+	.	
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	exon	233761	233925	.	+	.	insertions 0 ; deletions 0
gi|511782582|gb|CM001952.1|:subseq(60920431,333925)	exonerate:protein2genome:local	similarity	49876	233925	956	+	.	alignment_id 1 ; Query SPP00000092_2.0 ; Align 49876 1 30 ; Align 49906 15 54 ; Align 99994 34 105 ; Align 101703 70 75 ; Align 133809 96 27 ; Align 224304 106 96 ; Align 233761 138 165
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis