Command line: [exonerate -m p2g --showtargetgff -q query_Chlamydomonas_reinhardtii_MsrA.senseU.fa -t ChlamydomonasMsrACONTRAAureococcus_anophagefferens.2009.senseU.Scaffold7.e16.fastasubseq.fa]
Hostname: [ws101095.aulescm.upf.edu]

C4 Alignment:
------------
         Query: gi|23452038|gb|AAN32904.1| methionine-S-sulfoxide reductase MsrA1 [Chlamydomonas reinhardtii] 
        Target: scaffold_7:subseq(1742909,4500)
         Model: protein2genome:local
     Raw score: 171
   Query range: 13 -> 149
  Target range: 1999 -> 2416

   14 : AlaThrPheAlaLeuGlyUnkPheTrpHisProGluAlaSerPheAlaAsnValProGlyVa :   34
        ||||||!!.!.!||||||   ||||||   |||...! !..!.!.  !..!|||  !|||||
        AlaThrLeuGlyLeuGlyCysPheTrpAlaProSerGluGluLeuLeuGlyValGluGlyVa
 2000 : GCCACCTTGGGCCTGGGCTGCTTCTGGGCGCCGTCCGAGGAGCTGCTCGGCGTCGAGGGCGT : 2060

   35 : lValLysThrArgValGlyTyrThrGlyGlySerArgProAsn<-><->ProThrTyrGluS :   53
        |||| ! ||| !!  !||||||.!!|||!.!  !  !|||:!!      |||!:!|||! !|
        lValAspThrCysCysGlyTyrAlaGlyAlaValPheProAspAlaArgProSerTyrAlaS
 2061 : CGTGGACACGTGCTGCGGCTACGCGGGCGCCGTTTTCCCGGACGCGCGGCCGAGCTACGCGT : 2123

   54 : erValCysAlaGlyAspGlyHisThrGluAlaMetArgValTrpPheAspProAlaIleIle :   73
        ||||||||!.!|||||||||:!!..!||||||:!:!:!|||  !!:!|||  !|||:!!:!:
        erValCysGlyGlyAspGlyAsnValGluAlaValGlnValThrTyrAspAspAlaValVal
 2124 : CGGTCTGCGGCGGCGACGGCAACGTCGAGGCCGTCCAGGTCACGTACGACGACGCCGTCGTG : 2183

   74 : SerTyrGluAspLeuLeuLysGlnPhePheArgGluHisAspProThrGlnLysSerLysCy :   94
        |||||||||!  :!!||| !   !   |||  !! !  ! ! |||..!!     |||::!  
        SerTyrGluAlaValLeuAspAlaAlaPheAlaAlaSerLysProValLeuGlySerArgGl
 2184 : TCCTACGAGGCGGTGCTCGACGCGGCATTTGCCGCGAGCAAACCGGTACTCGGCTCGCGACA : 2246

   95 : sGlnTyrLysSerAlaValTrpTyrHisSerGluAlaHisGlyThrAlaLeuAlaAlaVal< :  115
          !   !   ! !!.! !!  !  ! !!.!!!!:! !   ..!  !|||  !|||  !||| 
        nTyrAlaProIleValPheAlaSerAspGlyAspGluAlaSerArgAlaAlaAlaTrpValG
 2247 : ATACGCCCCCATCGTCTTCGCGAGCGACGGCGACGAGGCGTCGCGCGCCGCGGCGTGGGTCG : 2309

  116 : ->MetLysGluLeuGluGlyLysTyrArgValArgLeuAlaThrThrValAspProAlaGly :  134
          :!!   !  :!!...! ! !   !! !! !|||! !  !  !.!!|||!!:  !.!!! !
        lyLeuGlyGlyValArgAspAspGlyLeuGluArgArgGlnPheAlaValGluGluThrAsp
 2310 : GGCTGGGCGGCGTGCGCGACGACGGCCTCGAGCGGCGCCAGTTCGCCGTCGAGGAGACGGAC : 2369

  135 : AspTrpTrpAspAlaGluGluTyrHisGlnLysTyrIleGluLys :  149
           !::|||  !||||||...|||||||||:!!|||   :!!|||
        ThrPheTrpLeuAlaGluSerTyrHisGlnGluTyrTrpGlnLys
 2370 : ACGTTCTGGCTCGCGGAAAGCTACCACCAGGAGTACTGGCAGAAG : 2416

vulgar: gi|23452038|gb|AAN32904.1| 13 149 . scaffold_7:subseq(1742909,4500) 1999 2416 + 171 M 35 105 G 0 6 M 66 198 G 0 3 M 35 105
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-03-12
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_7:subseq(1742909,4500)	exonerate:protein2genome:local	gene	2000	2416	171	+	.	gene_id 1 ; sequence gi|23452038|gb|AAN32904.1| ; gene_orientation .
scaffold_7:subseq(1742909,4500)	exonerate:protein2genome:local	cds	2000	2416	.	+	.	
scaffold_7:subseq(1742909,4500)	exonerate:protein2genome:local	exon	2000	2416	.	+	.	insertions 9 ; deletions 0
scaffold_7:subseq(1742909,4500)	exonerate:protein2genome:local	similarity	2000	2416	171	+	.	alignment_id 1 ; Query gi|23452038|gb|AAN32904.1| ; Align 2000 14 105 ; Align 2111 49 198 ; Align 2312 115 105
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
