Command line: [exonerate -m p2g --showtargetgff --exhaustive yes -q selw_artemia_w2.aa.fa -t genome_selw_owc_subseq.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query:  Artemia franciscana SelW2
        Target: supercontig_1.4:subseq(1763183,50000) of Capsaspora owczarzaki ATCC 30864:[revcomp]
         Model: protein2genome:local
     Raw score: 147
   Query range: 0 -> 91
  Target range: 25487 -> 15404

     1 : MetValLysIleHisValGluTyr{Cy}  >>>> Target Intron 1 >>>>  {s} :     9
         :!::!!|||:!::!!:!!||||||{||}            104 bp           {|}
         ValLeuLysValAsnIleGluTyr{Cy}++                         ++{s}
 25487 : GTTCTCAAAGTGAACATTGAATAC{TG}gt.........................ag{C} : 25357

    10 : GlyAlaUnkGlyTyrAlaProArgTyrGln  >>>> Target Intron 2 >>>>  G :    20
         ..!|||   ||||||  !||||||   :!!            174 bp           |
         SerAlaCysGlyTyrPheProArgMetLys++                         ++G
 25356 : TCGGCATGCGGCTACTTTCCACGCATGAAGgt.........................agG : 25152

    21 : luLeuAlaAlaLysIleArgLysAlaAlaProAspAlaGluValSerGlyAsnValGlyA :    40
         ||:!!! !  !   |||!:!|||! !  !|||   |||:!!|||!!!|||.!.! !||||
         luIleGluArgAlaIleGlnLysGluPheProThrAlaLysValThrGlyGluGlyGlyA
 25151 : AGATTGAGCGAGCCATCCAGAAAGAGTTCCCCACGGCCAAGGTGACTGGCGAGGGCGGCC : 25092

    41 : rgArgSerSerPheGluValThrValAsnGlyGluLeuIleHisSerLysLeuSerThrA :    60
         ||!!!!.!|||||||||||||||:!!||||||||||||:!!||||||||||||!!!:!!.
         rgSerLysSerPheGluValThrIleAsnGlyGluLeuValHisSerLysLeuThrSerG
 25091 : GAAGCAAGTCGTTCGAGGTCACCATCAACGGCGAGCTCGTCCACTCCAAGCTCACCTCGG : 25032

    61 : snGlyPheProAspPheAspGluValValGluIleValIleSerVal{T}  >>>> Tar :    76
         .!  !|||  !:!!      !  :!!||||||  !!.!!  :!!:!!{.}          
         lyLysPheValAsnProProValIleValGluAlaAlaLysAlaIle{A}-+        
 25031 : GCAAGTTTGTCAACCCGCCAGTCATTGTCGAAGCTGCAAAGGCGATT{G}ct........ : 24981

    77 : get Intron 3 >>>>  {hr}LysGlyAspLysProArgThrValGluLysThrHisS :    89
          9532 bp           {!!}   ..!..!  !||||||  !! !|||:!!  !|||:
                          ++{la}CysSerSerProProArgAspAspGluGlnArgHisA
 24980 : .................ag{CT}TGCTCAAGCCCGCCGCGAGATGATGAGCAGCGCCACG : 15413

    90 : erSerCys :    91
         !!||||||
         laSerCys
 15412 : CAAGTTGC : 15405

vulgar:  0 91 . supercontig_1.4:subseq(1763183,50000) 25487 15404 - 147 M 8 24 S 0 2 5 0 2 I 0 100 3 0 2 S 1 1 M 10 30 5 0 2 I 0 170 3 0 2 M 56 168 S 0 1 5 0 2 I 0 9528 3 0 2 S 1 2 M 15 45
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-03-17
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	gene	15405	25487	147	-	.	gene_id 1 ; sequence  ; gene_orientation +
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	cds	25462	25487	.	-	.	
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	exon	25462	25487	.	-	.	insertions 0 ; deletions 0
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	splice5	25460	25461	.	-	.	intron_id 1 ; splice_site "GT"
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	intron	25358	25461	.	-	.	intron_id 1
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	splice3	25358	25359	.	-	.	intron_id 0 ; splice_site "AG"
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	cds	25327	25357	.	-	.	
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	exon	25327	25357	.	-	.	insertions 0 ; deletions 0
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	splice5	25325	25326	.	-	.	intron_id 2 ; splice_site "GT"
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	intron	25153	25326	.	-	.	intron_id 2
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	splice3	25153	25154	.	-	.	intron_id 1 ; splice_site "AG"
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	cds	24984	25152	.	-	.	
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	exon	24984	25152	.	-	.	insertions 0 ; deletions 0
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	splice5	24982	24983	.	-	.	intron_id 3 ; splice_site "CT"
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	intron	15452	24983	.	-	.	intron_id 3
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	splice3	15452	15453	.	-	.	intron_id 2 ; splice_site "AG"
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	cds	15405	15451	.	-	.	
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	exon	15405	15451	.	-	.	insertions 0 ; deletions 0
supercontig_1.4:subseq(1763183,50000)	exonerate:protein2genome:local	similarity	15405	25487	147	-	.	alignment_id 1 ; Query  ; Align 25488 1 24 ; Align 25357 10 30 ; Align 25153 20 168 ; Align 15450 77 45
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis