Command line: [exonerate -m p2g --showtargetgff -q query_Chlamydomonas_reinhardtii_MsrA.senseU.fa -t ChlamydomonasMsrACONTRAAureococcus_anophagefferens.2009.senseU.fastafetch.fa]
Hostname: [ws101143.aulescm.upf.edu]

C4 Alignment:
------------
         Query: gi|23452038|gb|AAN32904.1| methionine-S-sulfoxide reductase MsrA1 [Chlamydomonas reinhardtii] 
        Target: scaffold_5
         Model: protein2genome:local
     Raw score: 255
   Query range: 8 -> 158
  Target range: 1244392 -> 1244830

       9 : SerGlyAlaGluLeuAlaThrPheAlaLeuGlyUnkPheTrpHisProGluAlaSe :      27
           !!!..! !!...:!!..!|||.!!|||:!!|||   ||||||||||||:!!!.!||
           ThrSerProArgValCysThrLeuAlaMetGly***PheTrpHisProGlnGlySe
 1244393 : ACGTCGCCGCGCGTCTGCACGCTCGCCATGGGCTGATTCTGGCACCCGCAGGGCTC : 1244447

      28 : rPheAlaAsnValProGlyValValLysThrArgValGlyTyrThrGlyGlySerA :      46
           ||||! !  !:!! !!||||||! !||||||! !||||||||||||||||||..! 
           rPheAspAlaLeuAlaGlyValGluLysThrLeuValGlyTyrThrGlyGlyAspA
 1244448 : CTTCGACGCCCTGGCGGGCGTCGAGAAGACCCTCGTGGGCTACACGGGCGGCGACG : 1244504

      47 : rgProAsnProThrTyrGluSerValCysAlaGlyAspGlyHisThrGluAlaMet :      64
            !  !.!.|||||||||:!! !!:!!      ||||||   |||||||||||||||
           spPheGluProThrTyrGlnArgIle------GlyAsp---HisThrGluAlaMet
 1244505 : ACTTCGAGCCGACGTACCAGCGCATC------GGCGAC---CACACGGAGGCCATG : 1244549

      65 : ArgValTrpPheAspProAlaIleIleSerTyrGluAspLeuLeuLysGlnPhePh :      83
           ! !|||  !||||||  !:!!   :!!:!!!:!||||||||||||   :!!|||!:
           LeuValGluPheAspGluSer---LeuAlaPheGluAspLeuLeuValLysPheTr
 1244550 : CTCGTCGAGTTCGACGAGTCG---CTCGCGTTCGAGGATTTGCTGGTCAAGTTCTG : 1244603

      84 : eArgGluHisAspProThrGlnLysSerLysCysGlnTyrLysSerAlaValTrpT :     102
           :..!||||||   |||! !     !|||:::   ||||||::!|||||||||!::!
           pGluGluHisThrProMetValGlySerArg---GlnTyrArgSerAlaValPheP
 1244604 : GGAGGAGCACACGCCCATGGTCGGGAGCCGC---CAGTACCGATCAGCGGTGTTCT : 1244657

     103 : yrHisSerGluAlaHisGlyThrAlaLeuAlaAlaValMetLysGluLeuGluGly :     120
           :!|||..!!!:|||!!. !!  !|||  !! !:!!:!!! !   ! !|||   !.!
           heHisAspAspAlaGlnArgAspAlaAlaGluSerMetLysAlaAlaLeuIleAla
 1244658 : TCCACGACGACGCGCAGCGGGACGCCGCGGAGTCCATGAAGGCCGCGCTCATCGCC : 1244711

     121 : LysTyrArgValArgLeuAla<->ThrThrValAspProAlaGlyAspTrpTrpAs :     138
            !   !!:!  ! !!:!!  !   |||.!!|||!!:||||||  !|||!::|||.!
           AspGlyLysLysTrpValLysAsnThrAlaValGluProAlaLysAspPheTrpGl
 1244712 : GACGGCAAGAAATGGGTCAAGAACACGGCCGTCGAGCCGGCCAAGGACTTCTGGCA : 1244768

     139 : pAlaGluGluTyrHisGlnLysTyrIleGluLysSerMetMetArgArgGlySerA :     157
           .||||||||||||||||||||||||:!!! !|||! !:!:! !! !|||  !! !:
           nAlaGluGluTyrHisGlnLysTyrLeuAlaLysMetLeuThrProArgTyrTyrS
 1244769 : GGCCGAGGAGTACCACCAAAAGTACCTCGCGAAGATGCTCACGCCGCGGTACTACT : 1244825

     158 : laGly :     158
           !!|||
           erGly
 1244826 : CCGGC : 1244830

vulgar: gi|23452038|gb|AAN32904.1| 8 158 . scaffold_5 1244392 1244830 + 255 M 46 138 G 2 0 M 2 6 G 1 0 M 12 36 G 1 0 M 21 63 G 1 0 M 33 99 G 0 3 M 31 93
# --- 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_5	exonerate:protein2genome:local	gene	1244393	1244830	255	+	.	gene_id 1 ; sequence gi|23452038|gb|AAN32904.1| ; gene_orientation .
scaffold_5	exonerate:protein2genome:local	cds	1244393	1244830	.	+	.	
scaffold_5	exonerate:protein2genome:local	exon	1244393	1244830	.	+	.	insertions 3 ; deletions 5
scaffold_5	exonerate:protein2genome:local	similarity	1244393	1244830	255	+	.	alignment_id 1 ; Query gi|23452038|gb|AAN32904.1| ; Align 1244393 9 138 ; Align 1244531 57 6 ; Align 1244537 60 36 ; Align 1244573 73 63 ; Align 1244636 95 99 ; Align 1244738 128 93
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
