Command line: [exonerate -m p2g --showtargetgff -q especialquerypultimum.fa -t ultimum2genomic.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: gi|301120252|ref|XP_002907853.1| methionine-R-sulfoxide reductase [Phytophthora infestans T30-4]
        Target: gi|299737303|gb|GL376586.1|:subseq(30763,2700) Pythium ultimum DAOM BR144 unplaced genomic scaffold scf_1117875581794, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 582
   Query range: 0 -> 136
  Target range: 1624 -> 999

    1 : MetSerSerSerAsnAspValValLysLeuSerAsnGluGluTrpLysGlnArgLeuThrPr :   21
        |||!!!..!!:!!:!..!  !|||! !||||||:!!!  |||||||||  !!:!||||||||
        MetThrAspAsnSerSerArgValThrLeuSerAspValGluTrpLysAlaGlnLeuThrPr
 1624 : ATGACGGACAACAGCAGCAGAGTGACGCTCTCGGACGTCGAGTGGAAGGCGCAGCTGACGCC : 1564

   22 : oMetGlnPheGlnValLeuArgLeuLysGlyThrGluArgAlaGlyThrGlyGluTyrAsnL :   42
        |:!!|||!:!||||||||||||||||||||||||||||||||||||||||||||||||||||
        oValGlnTyrGlnValLeuArgLeuLysGlyThrGluArgAlaGlyThrGlyGluTyrAsnL
 1563 : CGTGCAGTACCAGGTGCTGCGTCTCAAGGGCACGGAGCGCGCCGGCACAGGCGAGTACAACA : 1501

   43 : ysAsnLysGluThrGlyValTyrValCysAlaGlyCysLysThrProValTyrThrSerThr :   62
        ||:!! ! :!!  !|||..!|||||||||||||||||||||.!!|||:!!|||||||||  !
        ysHisTyrGlnAspGlyThrTyrValCysAlaGlyCysLysAlaProLeuTyrThrSerGlu
 1500 : AGCACTACCAGGACGGCACGTACGTCTGCGCCGGCTGCAAGGCGCCGCTCTACACGTCCGAG : 1441

   63 : ThrLysPheAspSerGlyCysGlyTrpProAlaPheTyrAspAlaIleProGlyAlaIleLy :   83
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        ThrLysPheAspSerGlyCysGlyTrpProAlaPheTyrAspAlaIleProGlyAlaIleLy
 1440 : ACCAAGTTCGACTCGGGCTGTGGGTGGCCCGCGTTCTACGACGCCATCCCCGGTGCCATCAA : 1378

   84 : s  >>>> Target Intron 1 >>>>  AlaValProAspAlaAspGlyArgArgThrGl :   94
        |            110 bp           |||:!!|||||| !!|||||||||||||||||
        s++                         ++AlaIleProAspProAspGlyArgArgThrGl
 1377 : Ggt.........................agGCGATCCCTGATCCGGACGGACGCCGCACGGA : 1235

   95 : uIleMetCysAlaLysCysAsp{Gl}  >>>> Target Intron 2 >>>>  {y}HisM :  104
        ||||:!!|||||||||||||||{||}            107 bp           {|}||||
        uIleValCysAlaLysCysAsp{Gl}++                         ++{y}HisM
 1234 : AATTGTGTGTGCCAAGTGCGAT{GG}gt.........................ag{C}CACA : 1098

  105 : etGlyHisValPheLysGlyGluGlyPheLysThrProThrAspGluArgHisUnkValAsn :  124
        |||||||||||||||||||||||||||||||||||||||||||||||||||||   ||||||
        etGlyHisValPheLysGlyGluGlyPheLysThrProThrAspGluArgHisCysValAsn
 1097 : TGGGCCACGTTTTCAAGGGAGAGGGCTTCAAGACGCCAACGGACGAACGCCACTGCGTCAAC : 1038

  125 : SerValSerLeuValPheHisAlaSerGluValPro :  136
        ||||||||||||||||||||||||.!!|||||||||
        SerValSerLeuValPheHisAlaGlyGluValPro
 1037 : AGCGTGTCGCTTGTGTTCCACGCTGGCGAAGTGCCA : 1000

vulgar: gi|301120252|ref|XP_002907853.1| 0 136 . gi|299737303|gb|GL376586.1|:subseq(30763,2700) 1624 999 - 582 M 83 249 5 0 2 I 0 106 3 0 2 M 18 54 S 0 2 5 0 2 I 0 103 3 0 2 S 1 1 M 34 102
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-03-09
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|299737303|gb|GL376586.1|:subseq(30763,2700)	exonerate:protein2genome:local	gene	1000	1624	582	-	.	gene_id 1 ; sequence gi|301120252|ref|XP_002907853.1| ; gene_orientation +
gi|299737303|gb|GL376586.1|:subseq(30763,2700)	exonerate:protein2genome:local	cds	1376	1624	.	-	.	
gi|299737303|gb|GL376586.1|:subseq(30763,2700)	exonerate:protein2genome:local	exon	1376	1624	.	-	.	insertions 0 ; deletions 0
gi|299737303|gb|GL376586.1|:subseq(30763,2700)	exonerate:protein2genome:local	splice5	1374	1375	.	-	.	intron_id 1 ; splice_site "GT"
gi|299737303|gb|GL376586.1|:subseq(30763,2700)	exonerate:protein2genome:local	intron	1266	1375	.	-	.	intron_id 1
gi|299737303|gb|GL376586.1|:subseq(30763,2700)	exonerate:protein2genome:local	splice3	1266	1267	.	-	.	intron_id 0 ; splice_site "AG"
gi|299737303|gb|GL376586.1|:subseq(30763,2700)	exonerate:protein2genome:local	cds	1210	1265	.	-	.	
gi|299737303|gb|GL376586.1|:subseq(30763,2700)	exonerate:protein2genome:local	exon	1210	1265	.	-	.	insertions 0 ; deletions 0
gi|299737303|gb|GL376586.1|:subseq(30763,2700)	exonerate:protein2genome:local	splice5	1208	1209	.	-	.	intron_id 2 ; splice_site "GT"
gi|299737303|gb|GL376586.1|:subseq(30763,2700)	exonerate:protein2genome:local	intron	1103	1209	.	-	.	intron_id 2
gi|299737303|gb|GL376586.1|:subseq(30763,2700)	exonerate:protein2genome:local	splice3	1103	1104	.	-	.	intron_id 1 ; splice_site "AG"
gi|299737303|gb|GL376586.1|:subseq(30763,2700)	exonerate:protein2genome:local	cds	1000	1102	.	-	.	
gi|299737303|gb|GL376586.1|:subseq(30763,2700)	exonerate:protein2genome:local	exon	1000	1102	.	-	.	insertions 0 ; deletions 0
gi|299737303|gb|GL376586.1|:subseq(30763,2700)	exonerate:protein2genome:local	similarity	1000	1624	582	-	.	alignment_id 1 ; Query gi|301120252|ref|XP_002907853.1| ; Align 1625 1 249 ; Align 1266 84 54 ; Align 1102 103 102
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis