Command line: [exonerate -m p2g --showtargetgff -q query_Chlamydomonas_reinhardtii_MsrA.fa -t chlamydomonasCONTRAEimeria_tenella.2009.MsrA.fastarevcomp.fa --exhaustive yes]
Hostname: [ws101146.aulescm.upf.edu]

C4 Alignment:
------------
         Query: Query_Chlamydomonas_reinhardtii.MsrA
        Target: pathogen_EIMER_contig_00031474 - eimer-2383d07.q1k low_quality_removed:[revcomp]
         Model: protein2genome:local
     Raw score: 132
   Query range: 1 -> 150
  Target range: 5897 -> 8676

    2 : AlaThrAsnGlyAsn{G}  >>>>                 Target Intron 1 >>>>  {ly}AlaSerGlyAl :   11
        |||..!  !|||...{!}            632 bp           {.!}|||:!!!.!||
        AlaValAlaGlyGly{A}++                         ++{la}AlaAlaAlaAl
 5898 : GCGGTGGCTGGCGGA{G}gt.........................ag{CA}GCAGCAGCAGC : 6557

   12 : aGluLeuAlaThrPheAlaLeuGlyUnkPheTrpHisProGluAlaSerPheAlaAsn<->< :   31
        ||||  !  !..!.!.!.!  !|||   ||||||  !! !|||  !  !|||!.!.!.    
        aGluSerIleValLeuGlyGlyGlyCysPheTrpGlyLeuGluLysLeuPheValGluGluP
 6558 : AGAAAGCATCGTCCTGGGGGGCGGCTGCTTCTGGGGCCTGGAGAAGCTGTTTGTGGAGGAGT : 6620

   32 : ->ValProGlyValValLysThrArgValGlyTyrThrGlyGlySerArgProAsnProThr :   50
            !  !  !:!!! !  !||| !!|||||||||.!!||||||  !! !|||.!.||||||
        heLysAspLysLeuGluAlaThrCysValGlyTyrAlaGlyGlyHisThrProGlnProThr
 6621 : TCAAAGACAAGTTGGAAGCAACTTGTGTGGGGTACGCAGGTGGACATACACCCCAGCCCACG : 6680

   51 : TyrGluSerValCysAlaGly<->AspGlyHisThrGluAlaMetArgValTrpPheAspPr :   70
        |||! !..!||||||::!.!!     !||||||  !||||||:!:!:!:!!!  |||  !||
        TyrAlaGlnValCysSerSerLysThrGlyHisPheGluAlaLeuLysIleSerPhePhePr
 6681 : TACGCGCAGGTCTGCAGCAGCAAAACTGGACACTTCGAAGCTCTCAAGATTTCTTTTTTTCC : 6743

   71 : oAlaIleIleSerTyrGluAspLeuLeuLysGlnPhePheArgGluHisAspProThrGlnL :   91
        |  !!  :!!  !!  ..!!!:||||||!     |||!::! !   ||||||||||||    
        oGlnLysValHisLeuArgGluLeuLeuThrPhePheTrpThrIleHisAspProThrThrP
 6744 : GCAAAAGGTCCATTTGCGGGAACTCCTCACTTTCTTCTGGACCATCCACGACCCCACCACTC : 6806

   92 : ysSerLysCysGlnTyrLysSerAlaValTrpTyrHisSerGluAlaHisGlyThrAlaLeu :  111
          ..!!:!! !     !   :!!|||  !  !   !    !  !  !|||!.!.!!|||  !
        roAspArgSerAlaAlaAlaAlaAlaProValLeuLeuLeuLeuGlnHisAlaAlaAlaAla
 6807 : CCGACAGGTCCGCTGCTGCTGCTGCTCCAGTGCTGCTGCTGCTGCAGCATGCTGCTGCTGCT : 6866

  112 : AlaAla  >>>> Target Intron 2 >>>>  ValMetLysGluLeuGluGlyLysTyr :  122
        ||||||           1682 bp           :!!!  !!.|||:!!:!!  !|||!::
        AlaAla+-                         +-IleLysAsnGluMetGlnLysLysTrp
 6867 : GCTGCAgc.........................aaATTAAAAACGAAATGCAAAAAAAATGG : 8581

  123 : ArgValArgLeuAlaThrThrVal<-><->AspPro<->AlaGlyAspTrpTrpAspAlaGl :  140
        !.! !!!:!:!!  !|||  !:!!      ||||||     ! !! !!!::|||   |||||
        AsnPheLysIleGlnThrGluIleIleSerAspProAsnLysCysHisPheTrpProAlaGl
 8582 : AATTTCAAAATCCAAACTGAAATCATTTCCGATCCCAACAAATGCCACTTCTGGCCAGCCGA : 8644

  141 : uGluTyrHisGlnLysTyrIleGluLysSer :  150
        |!!::!!||||||||||||:!!   |||!:!
        uAspHisHisGlnLysTyrLeuPheLysAsn
 8645 : AGACCACCACCAAAAGTACCTCTTCAAGAAC : 8676

vulgar: Query_Chlamydomonas_reinhardtii.MsrA 1 150 . pathogen_EIMER_contig_00031474 5897 8676 + 132 M 5 15 S 0 1 5 0 2 I 0 628 3 0 2 S 1 2 M 23 69 G 0 6 M 27 81 G 0 3 M 56 168 5 0 2 I 0 1678 3 0 2 M 17 51 G 0 6 M 2 6 G 0 3 M 18 54
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-03-04
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
pathogen_EIMER_contig_00031474	exonerate:protein2genome:local	gene	5898	8676	132	+	.	gene_id 1 ; sequence Query_Chlamydomonas_reinhardtii.MsrA ; gene_orientation +
pathogen_EIMER_contig_00031474	exonerate:protein2genome:local	cds	5898	5913	.	+	.	
pathogen_EIMER_contig_00031474	exonerate:protein2genome:local	exon	5898	5913	.	+	.	insertions 0 ; deletions 0
pathogen_EIMER_contig_00031474	exonerate:protein2genome:local	splice5	5914	5915	.	+	.	intron_id 1 ; splice_site "GT"
pathogen_EIMER_contig_00031474	exonerate:protein2genome:local	intron	5914	6545	.	+	.	intron_id 1
pathogen_EIMER_contig_00031474	exonerate:protein2genome:local	splice3	6544	6545	.	+	.	intron_id 0 ; splice_site "AG"
pathogen_EIMER_contig_00031474	exonerate:protein2genome:local	cds	6546	6874	.	+	.	
pathogen_EIMER_contig_00031474	exonerate:protein2genome:local	exon	6546	6874	.	+	.	insertions 9 ; deletions 0
pathogen_EIMER_contig_00031474	exonerate:protein2genome:local	splice5	6875	6876	.	+	.	intron_id 2 ; splice_site "GC"
pathogen_EIMER_contig_00031474	exonerate:protein2genome:local	intron	6875	8556	.	+	.	intron_id 2
pathogen_EIMER_contig_00031474	exonerate:protein2genome:local	splice3	8555	8556	.	+	.	intron_id 1 ; splice_site "AA"
pathogen_EIMER_contig_00031474	exonerate:protein2genome:local	cds	8557	8676	.	+	.	
pathogen_EIMER_contig_00031474	exonerate:protein2genome:local	exon	8557	8676	.	+	.	insertions 9 ; deletions 0
pathogen_EIMER_contig_00031474	exonerate:protein2genome:local	similarity	5898	8676	132	+	.	alignment_id 1 ; Query Query_Chlamydomonas_reinhardtii.MsrA ; Align 5898 2 15 ; Align 6548 8 69 ; Align 6623 31 81 ; Align 6707 58 168 ; Align 8557 114 51 ; Align 8614 131 6 ; Align 8623 133 54
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
