Command line: [exonerate -m p2g --showtargetgff -q especialqueryarabidopsis.fa -t arabidopsisgenomic.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: gi|301120252|ref|XP_002907853.1| methionine-R-sulfoxide reductase [Phytophthora infestans T30-4]
        Target: gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500) Hyaloperonospora parasitica strain Emoy2 v-7.0.1_Cont0.45, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 365
   Query range: 58 -> 138
  Target range: 2 -> 408

  59 : TyrThrSerThrThrLysPheAspSerGlyCysGlyTrpProAlaPheTyrAspAlaIleProG :  80
       ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
       TyrThrSerThrThrLysPheAspSerGlyCysGlyTrpProAlaPheTyrAspAlaIleProG
   3 : TACACGTCCACGACCAAGTTTGACTCGGGCTGTGGCTGGCCAGCGTTTTATGACGCGATTCCAG :  66

  81 : lyAlaIleLys  >>>> Target Intron 1 >>>>  AlaValProAspAlaAspGlyArg :  91
       |||||||||||            73 bp            .!!:!!||||||||||||||||||
       lyAlaIleLys++                         ++ThrIleProAspAlaAspGlyArg
  67 : GCGCAATTAAGgt.........................agACTATTCCTGATGCGGATGGACGA : 172

  92 : ArgThrGluIleMetCysAlaLysCysAsp{Gl}  >>>> Target Intron 2 >>>>  { : 102
       |||! !||||||:!!|||||||||||||||{||}            93 bp            {
       ArgIleGluIleValCysAlaLysCysAsp{Gl}++                         ++{
 173 : CGTATCGAGATCGTGTGCGCCAAGTGTGAC{GG}gt.........................ag{ : 300

 103 : y}HisMetGlyHisValPheLysGlyGluGlyPheLysThrProThrAspGluArgHisUnkVa : 123
       |}|||||||||||||||||||||||||||||||||!!.|||||||||||||||||||||   ||
       y}HisMetGlyHisValPheLysGlyGluGlyPheAsnThrProThrAspGluArgHisCysVa
 301 : T}CATATGGGTCACGTGTTCAAGGGCGAAGGATTCAATACGCCAACGGATGAGCGTCACTGTGT : 361

 124 : lAsnSerValSerLeuValPheHisAlaSerGluValProProGln : 138
       |||||||!.!||||||||||||:!!!.!!:!|||||||||||||||
       lAsnSerAlaSerLeuValPheTyrGlyAsnGluValProProGln
 362 : GAACAGTGCGTCGCTCGTGTTTTATGGCAATGAAGTCCCACCTCAG : 408

vulgar: gi|301120252|ref|XP_002907853.1| 58 138 . gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500) 2 408 + 365 M 25 75 5 0 2 I 0 69 3 0 2 M 18 54 S 0 2 5 0 2 I 0 89 3 0 2 S 1 1 M 36 108
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-03-10
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500)	exonerate:protein2genome:local	gene	3	408	365	+	.	gene_id 1 ; sequence gi|301120252|ref|XP_002907853.1| ; gene_orientation +
gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500)	exonerate:protein2genome:local	cds	3	77	.	+	.	
gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500)	exonerate:protein2genome:local	exon	3	77	.	+	.	insertions 0 ; deletions 0
gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500)	exonerate:protein2genome:local	splice5	78	79	.	+	.	intron_id 1 ; splice_site "GT"
gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500)	exonerate:protein2genome:local	intron	78	150	.	+	.	intron_id 1
gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500)	exonerate:protein2genome:local	splice3	149	150	.	+	.	intron_id 0 ; splice_site "AG"
gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500)	exonerate:protein2genome:local	cds	151	206	.	+	.	
gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500)	exonerate:protein2genome:local	exon	151	206	.	+	.	insertions 0 ; deletions 0
gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500)	exonerate:protein2genome:local	splice5	207	208	.	+	.	intron_id 2 ; splice_site "GT"
gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500)	exonerate:protein2genome:local	intron	207	299	.	+	.	intron_id 2
gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500)	exonerate:protein2genome:local	splice3	298	299	.	+	.	intron_id 1 ; splice_site "AG"
gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500)	exonerate:protein2genome:local	cds	300	408	.	+	.	
gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500)	exonerate:protein2genome:local	exon	300	408	.	+	.	insertions 0 ; deletions 0
gi|199611566|gb|ABWE01000246.1|:subseq(53464,2500)	exonerate:protein2genome:local	similarity	3	408	365	+	.	alignment_id 1 ; Query gi|301120252|ref|XP_002907853.1| ; Align 3 59 75 ; Align 151 84 54 ; Align 301 103 108
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis