Command line: [exonerate -m p2g --showtargetgff -q query_Chlamydomonas_reinhardtii_MsrA.senseU.fa -t ChlamydomonasMsrACONTRAAureococcus_anophagefferens.2009.senseU.Scaffold4.fastafetch.fa]
Hostname: [ws101133.aulescm.upf.edu]

C4 Alignment:
------------
         Query: gi|23452038|gb|AAN32904.1| methionine-S-sulfoxide reductase MsrA1 [Chlamydomonas reinhardtii] 
        Target: scaffold_4
         Model: protein2genome:local
     Raw score: 259
   Query range: 7 -> 149
  Target range: 1209100 -> 1209514

       8 : AlaSerGlyAlaGluLeuAlaThrPheAlaLeuGlyUnkPheTrpHisProGluAl :      26
           ||| !!.!!  !...:!!||||||||||||||||||   ||||||   |||:!!  
           AlaProSerArgArgValAlaThrPheAlaLeuGly***PheTrpThrProGlnGl
 1209101 : GCGCCGAGCCGACGCGTCGCCACCTTCGCGCTCGGATGATTCTGGACGCCGCAGCA : 1209155

      27 : aSerPheAlaAsnValProGlyValValLysThrArgValGlyTyrThrGlyGlyS :      45
           !!.!|||! !     !  !||||||:!!  !!:!! !||||||||||||..!|||!
           nLysPheAspLeuArgAspGlyValIleTrpSerThrValGlyTyrThrSerGlyT
 1209156 : GAAGTTCGACCTGCGCGACGGCGTCATCTGGAGCACCGTGGGCTACACGTCGGGCA : 1209212

      46 : erArgProAsnProThrTyrGluSerValCysAlaGlyAspGlyHisThrGluAla :      63
           !!! !|||   |||!.!|||!!:..!:!!      ||||||   ||||||||||||
           hrThrProAlaProAsnTyrAspAspLeu------GlyAsp---HisThrGluAla
 1209213 : CGACGCCCGCACCGAACTACGACGACCTC------GGCGAC---CACACGGAGGCG : 1209257

      64 : MetArgValTrpPheAspProAlaIleIleSerTyrGluAspLeuLeuLysGlnPh :      82
           :!!|||:!!   ||||||  !! !:!!:!:|||||||||!  |||:!!:!!|||||
           LeuArgLeuGluPheAspGluAspValValSerTyrGluAlaLeuValGluGlnPh
 1209258 : CTGCGGCTCGAATTCGACGAGGACGTCGTGAGCTACGAGGCGCTCGTAGAGCAGTT : 1209314

      83 : ePheArgGluHisAspProThrGlnLysSerLysCysGlnTyrLysSerAlaValT :     101
           |!::  !   |||!  |||!.!:!!  !|||:::   ||||||::!||||||:!!!
           eTrpAspLeuHisAlaProAsnLysGlySerArg---GlnTyrArgSerAlaIleP
 1209315 : CTGGGACCTCCACGCGCCGAACAAGGGGAGCCGC---CAGTACCGGAGCGCCATCT : 1209368

     102 : rpTyrHisSerGluAlaHisGlyThrAlaLeuAlaAlaValMetLysGluLeuGlu :     119
           ::||||||..!||||||!!. !!  !..!  !! !  !|||..!  !:!!|||   
           heTyrHisAspGluAlaGlnArgGluCysAlaGluArgValGlnAlaGlnLeuPhe
 1209369 : TCTATCACGACGAGGCGCAGCGCGAGTGCGCGGAGCGCGTGCAGGCGCAGCTCTTC : 1209422

     120 : GlyLysTyrArgValArgLeuAlaThrThrValAspProAlaGlyAspTrpTrpAs :     138
             !..! ! |||  !  !! !! !|||.!!:!!!!:||||||!.!!!:!::!::  
           ProSerLysArgTyrValArgAspThrAlaIleGluProAlaAlaGluPhePhePr
 1209423 : CCCTCGAAGCGTTACGTCCGCGACACGGCCATCGAGCCGGCGGCCGAGTTCTTCCC : 1209479

     139 : pAlaGluGluTyrHisGlnLysTyrIleGluLys :     149
            ||||||! !|||||||||||||||  !||||||
           oAlaGluAlaTyrHisGlnLysTyrArgGluLys
 1209480 : GGCGGAGGCGTACCACCAGAAGTACCGCGAGAAG : 1209514

vulgar: gi|23452038|gb|AAN32904.1| 7 149 . scaffold_4 1209100 1209514 + 259 M 47 141 G 2 0 M 2 6 G 1 0 M 34 102 G 1 0 M 55 165
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-03-03
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_4	exonerate:protein2genome:local	gene	1209101	1209514	259	+	.	gene_id 1 ; sequence gi|23452038|gb|AAN32904.1| ; gene_orientation .
scaffold_4	exonerate:protein2genome:local	cds	1209101	1209514	.	+	.	
scaffold_4	exonerate:protein2genome:local	exon	1209101	1209514	.	+	.	insertions 0 ; deletions 4
scaffold_4	exonerate:protein2genome:local	similarity	1209101	1209514	259	+	.	alignment_id 1 ; Query gi|23452038|gb|AAN32904.1| ; Align 1209101 8 141 ; Align 1209242 57 6 ; Align 1209248 60 102 ; Align 1209350 95 165
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
