Command line: [exonerate -m p2g --showtargetgff -q query_Chlamydomonas_reinhardtii_MsrA.x.fa -t chlamydomonasCONTRAEmiliania_huxleyi.2009.MsrA.2.fastarevcomp.fa]
Hostname: [ws101145.aulescm.upf.edu]

C4 Alignment:
------------
         Query: gi|23452038|gb|AAN32904.1| methionine-S-sulfoxide reductase MsrA1 [Chlamydomonas reinhardtii] 
        Target: scaffold_31:subseq(711193,4407) [revcomp]
         Model: protein2genome:local
     Raw score: 259
   Query range: 14 -> 153
  Target range: 2000 -> 2408

   15 : ThrPheAlaLeuGlyUnkPheTrpHisProGluAlaSerPheAlaAsnValProGlyValVa :   35
        |||.!!|||||||||   |||||||||||||||! !..!.!!|||  !:!!|||||||||  
        ThrLeuAlaLeuGly***PheTrpHisProGluGluGluLeuAlaAlaLeuProGlyValSe
 2001 : ACACTCGCGCTCGGGTGATTCTGGCACCCTGAGGAGGAGCTTGCAGCTCTCCCCGGGGTCTC : 2061

   36 : lLysThrArgValGlyTyrThrGlyGlySerArgProAsnProThrTyrGluSerValCysA :   56
        !:!!|||  !|||||||||  !|||||||||! ! !!:!!|||||||||:!!|||:!!    
        rGluThrValValGlyTyrCysGlyGlySerThrAlaAspProThrTyrLysSerIle----
 2062 : GGAGACCGTGGTTGGCTACTGCGGTGGCAGCACCGCCGATCCGACCTACAAGTCGATT---- : 2121

   57 : laGlyAspGlyHisThrGluAlaMetArgValTrpPheAspProAlaIleIleSerTyrGlu :   76
          ||||||   ||||||||||||:!!||||||   |||||| !!  !:!::!:|||   |||
        --GlyAsp---HisThrGluAlaLeuArgValThrPheAspSerArgValValSerAlaGlu
 2122 : --GGCGAT---CACACAGAGGCCTTGCGTGTCACCTTCGACTCGCGTGTGGTGTCGGCGGAG : 2175

   77 : AspLeuLeuLysGlnPhePheArgGluHisAspProThrGlnLys<-><->SerLysCysGl :   95
        ..!:!!|||:!!!::||||||..!  !|||||||||! !! !:::      !!!     !||
        SerMetLeuGluArgPhePheGluMetHisAspProMetProArgAlaPheThrGlyThrGl
 2176 : AGCATGCTCGAGCGCTTCTTTGAGATGCACGACCCGATGCCGCGTGCCTTCACGGGCACTCA : 2238

   96 : nTyrLysSerAlaValTrpTyrHisSerGluAlaHisGlyThrAlaLeuAlaAlaValMetL :  116
        ||||:::||||||:!!!::||||||!:!!!:|||!!.!.!  !.!!  !|||||||||  ! 
        nTyrArgSerAlaIlePheTyrHisAsnAspAlaGlnAlaGluThrAlaAlaAlaValAlaG
 2239 : GTACCGCTCCGCCATCTTCTATCACAACGACGCGCAGGCCGAGACGGCGGCGGCCGTGGCGG : 2301

  117 : ysGluLeuGluGlyLysTyrArgValArgLeuAlaThrThrValAspProAlaGlyAspTrp :  136
          ..!! !! !..!..! !   !  !!.!      |||:!!:!!!!:|||||||||   !::
        lyArgGlnAlaSerSerGlnAlaLysHis------ThrSerIleGluProAlaGlyProPhe
 2302 : GCCGGCAGGCGTCCTCGCAAGCGAAGCAC------ACCTCGATCGAGCCGGCCGGTCCATTT : 2355

  137 : TrpAspAlaGluGluTyrHisGlnLysTyrIleGluLysSerMetMetArg :  153
        !::  !||||||||||||||||||:::!:!:!:!  |||..!! !  !|||
        TyrArgAlaGluGluTyrHisGlnArgPheLeuAlaLysGlnThrGlyArg
 2356 : TACCGCGCTGAAGAGTACCACCAGCGCTTTCTGGCTAAGCAGACGGGGCGG : 2408

vulgar: gi|23452038|gb|AAN32904.1| 14 153 . scaffold_31:subseq(711193,4407) 2000 2408 + 259 M 40 120 G 2 0 M 2 6 G 1 0 M 32 96 G 0 6 M 34 102 G 2 0 M 26 78
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-02-26
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_31:subseq(711193,4407)	exonerate:protein2genome:local	gene	2001	2408	259	+	.	gene_id 1 ; sequence gi|23452038|gb|AAN32904.1| ; gene_orientation .
scaffold_31:subseq(711193,4407)	exonerate:protein2genome:local	cds	2001	2408	.	+	.	
scaffold_31:subseq(711193,4407)	exonerate:protein2genome:local	exon	2001	2408	.	+	.	insertions 6 ; deletions 5
scaffold_31:subseq(711193,4407)	exonerate:protein2genome:local	similarity	2001	2408	259	+	.	alignment_id 1 ; Query gi|23452038|gb|AAN32904.1| ; Align 2001 15 120 ; Align 2121 57 6 ; Align 2127 60 96 ; Align 2229 92 102 ; Align 2331 128 78
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
