Command line: [exonerate -m p2g --showtargetgff -q MrsAaureococcus4.fa --exhaustive -t 1fastasubseq.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: MsrA.Aureococcus_anophagefferens.3 located on scaffold_4 strand + positions 1209101,1209514
        Target: gi|299737276|gb|GL376613.1|:subseq(584000,2000) Pythium ultimum DAOM BR144 unplaced genomic scaffold scf_1117875582016, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 168
   Query range: 2 -> 138
  Target range: 925 -> 1366

    3 : SerArgArgValAlaThrPheAlaLeuGlyUnkPheTrpThrProGlnGlnLysPheAspLe :   23
        !:!!:!!!!|||||||||||||||  !|||   ||||||  !  !:!!!    !|||.!.! 
        AsnGlnSerValAlaThrPheAlaAlaGlyCysPheTrpGlyValGluLeuAlaPheGlnAr
  926 : AACCAGAGCGTCGCCACGTTCGCCGCGGGTTGCTTTTGGGGTGTCGAGCTCGCGTTTCAGCG :  986

   24 : uArgAspGlyValIleTrpSerThrValGlyTyrThrSerGlyThrThrProAlaProAsnT :   44
        !  !   ||||||:!!   !!!! !|||||||||.!!..!|||  !! !  !  !|||!..|
        gValProGlyValValAspThrLysValGlyTyrAlaGlnGlyHisIleAspHisProThrT
  987 : CGTGCCGGGCGTCGTCGACACGAAGGTCGGCTACGCGCAGGGCCACATCGACCACCCTACGT : 1049

   45 : yrAspAspLeu<-><-><-><->GlyAspHisThrGluAlaLeuArgLeuGluPheAspGlu :   60
        || ! .!.:!!              !! !|||.!!||||||:!!!:!:!!! !||||||:!!
        yrLysGlnValCysSerGlyLysThrGlyHisAlaGluAlaIleLysIleValPheAspLys
 1050 : ACAAGCAAGTGTGCTCGGGCAAGACGGGCCACGCCGAGGCGATCAAGATCGTGTTCGACAAG : 1109

   61 : AspValValSerTyrGluAlaLeuValGluGlnPheTrpAspLeuHisAlaPro<-><-><- :   79
        :!!! !|||!!!|||  !  !|||:!!!!:  !|||||| ! :!!|||! !|||        
        AsnGluValThrTyrProGlnLeuLeuAspValPheTrpLysValHisAspProThrMetLe
 1110 : AACGAGGTGACGTACCCGCAGCTGCTGGACGTGTTTTGGAAGGTCCATGACCCGACGATGCT : 1172

   80 : ><-><-><-><->AsnLysGlySerArgGlnTyrArgSerAlaIlePheTyrHisAspGluA :   95
                     ||| ! ! !.!!! !||||||||||||!.!|||!:!||||||||||||!
        uAsnArgGlnLysAsnAspValGlyThrGlnTyrArgSerGlyIleTyrTyrHisAspGluA
 1173 : CAACCGCCAGAAGAACGACGTCGGCACGCAGTACCGCTCGGGCATCTACTACCACGACGAAG : 1235

   96 : laGlnArgGluCysAlaGluArgValGlnAlaGlnLeuPheProSerLysArgTyrValArg :  115
         !||||||:!!   |||  !  !  !:!!! !:!!! !     !!!!  !||| !!  !! !
        spGlnArgLysGluAlaLeuAlaSerLysGluGluHisGlnLysThrLeuArgAsnProIle
 1236 : ACCAGCGGAAGGAGGCGCTGGCGTCCAAGGAAGAGCACCAGAAGACGCTGCGCAATCCGATT : 1295

  116 : AspThrAlaIleGluProAlaAlaGluPhePheProAlaGluAlaTyrHisGlnLysTyrAr :  136
        !  |||! !||||||||||||  !...|||!::  !||||||.!!|||||||||||||||  
        ValThrGluIleGluProAlaGlnArgPheTrpGluAlaGluThrTyrHisGlnLysTyrLe
 1296 : GTGACGGAGATCGAACCTGCGCAGCGCTTCTGGGAAGCTGAGACGTACCACCAAAAGTACTT : 1358

  137 : gGluLys :  138
        !:!!|||
        uGlnLys
 1359 : GCAGAAA : 1366

vulgar: MsrA.Aureococcus_anophagefferens.3 2 138 . gi|299737276|gb|GL376613.1|:subseq(584000,2000) 925 1366 + 168 M 45 135 G 0 12 M 31 93 G 0 21 M 60 180
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-03-04
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|299737276|gb|GL376613.1|:subseq(584000,2000)	exonerate:protein2genome:local	gene	926	1366	168	+	.	gene_id 1 ; sequence MsrA.Aureococcus_anophagefferens.3 ; gene_orientation .
gi|299737276|gb|GL376613.1|:subseq(584000,2000)	exonerate:protein2genome:local	cds	926	1366	.	+	.	
gi|299737276|gb|GL376613.1|:subseq(584000,2000)	exonerate:protein2genome:local	exon	926	1366	.	+	.	insertions 33 ; deletions 0
gi|299737276|gb|GL376613.1|:subseq(584000,2000)	exonerate:protein2genome:local	similarity	926	1366	168	+	.	alignment_id 1 ; Query MsrA.Aureococcus_anophagefferens.3 ; Align 926 3 135 ; Align 1073 48 93 ; Align 1187 79 180
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis