Command line: [exonerate -m p2g --showtargetgff -q query_Chlamydomonas_reinhardtii_MsrA.senseU.fa -t ChlamydomonasMsrACONTRAAureococcus_anophagefferens.2009.senseU.Scaffold2.fastasubseq.5e21.fa]
Hostname: [ws101144.aulescm.upf.edu]

C4 Alignment:
------------
         Query: gi|23452038|gb|AAN32904.1| methionine-S-sulfoxide reductase MsrA1 [Chlamydomonas reinhardtii] 
        Target: scaffold_2:subseq(3316000,2000) [revcomp]
         Model: protein2genome:local
     Raw score: 180
   Query range: 1 -> 83
  Target range: 1423 -> 1174

    2 : AlaThrAsnGlyAsnGlyAlaSerGlyAlaGluLeuAlaThrPheAlaLeuGlyUnkPheTr :   22
        .!!|||  !! !!!..!!|||..!|||  !!  :!!||||||||||||  !|||   |||||
        ThrThrProValLysSerAlaAspGlyTyrAlaIleAlaThrPheAlaAlaGlyCysPheTr
 1423 : ACGACGCCCGTGAAGAGCGCCGACGGCTACGCCATCGCGACGTTCGCCGCGGGCTGCTTCTG : 1363

   23 : pHisProGluAlaSerPheAlaAsnValProGlyValValLysThrArgValGlyTyrThrG :   43
        |  !  !|||  !..!|||  !...:!!|||||||||:!!  !|||!!!|||||||||..! 
        pGlyValGluLeuGluPheGlnArgLeuProGlyValIleAlaThrSerValGlyTyrValG
 1362 : GGGCGTCGAGCTCGAGTTCCAGCGGCTGCCCGGCGTCATCGCGACGAGCGTGGGCTACGTGC : 1300

   44 : lyGlySerArgProAsnProThrTyrGluSerValCysAlaGly<->AspGlyHisThrGlu :   62
         !|||  !!:!! !!!.||||||||||||..!||| !!|||!.!   ..!||||||||||||
        lnGlyHisLysGlnLysProThrTyrGluGluValSerAlaAlaThrSerGlyHisThrGlu
 1299 : AGGGCCACAAGCAGAAGCCGACCTACGAGGAGGTGAGCGCCGCGACGTCCGGCCACACGGAG : 1240

   63 : AlaMetArgValTrpPheAspProAlaIleIleSerTyrGluAspLeuLeuLysGlnPhePh :   83
        |||:!!!:!:!!   !:!||||||!.!:!:|||||||||! !   |||! !:!!  !|||!:
        AlaValGlnLeuIleTyrAspProGlyValIleSerTyrAlaArgLeuCysGluAlaPheTr
 1239 : GCCGTGCAGTTGATCTACGACCCGGGCGTGATCTCCTACGCGCGGCTCTGCGAGGCGTTCTG : 1177

   84 : e :   83
        :
        p
 1176 : G : 1175

vulgar: gi|23452038|gb|AAN32904.1| 1 83 . scaffold_2:subseq(3316000,2000) 1423 1174 - 180 M 56 168 G 0 3 M 26 78
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-03-15
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_2:subseq(3316000,2000)	exonerate:protein2genome:local	gene	1175	1423	180	-	.	gene_id 1 ; sequence gi|23452038|gb|AAN32904.1| ; gene_orientation .
scaffold_2:subseq(3316000,2000)	exonerate:protein2genome:local	cds	1175	1423	.	-	.	
scaffold_2:subseq(3316000,2000)	exonerate:protein2genome:local	exon	1175	1423	.	-	.	insertions 3 ; deletions 0
scaffold_2:subseq(3316000,2000)	exonerate:protein2genome:local	similarity	1175	1423	180	-	.	alignment_id 1 ; Query gi|23452038|gb|AAN32904.1| ; Align 1424 2 168 ; Align 1253 58 78
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
