Command line: [exonerate -m p2g --showtargetgff --exhaustive yes -q danio.fa -t genome_selh_owc_subseq.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: D.rerio
        Target: supercontig_1.12:subseq(834258,50000) of Capsaspora owczarzaki ATCC 30864:[revcomp]
         Model: protein2genome:local
     Raw score: 186
   Query range: 30 -> 125
  Target range: 25576 -> 24999

    31 : AspLysAspGluGluThrGlyLeuArgValValIleGluHis{Cy}  >>>> Target  :    45
         |||||| !    ..!  !||||||||| !!|||||||||!..{||}            94
         AspLysLysProArgLeuGlyLeuArgPheValIleGluArg{Cy}++            
 25576 : GACAAGAAACCTCGGCTGGGGTTGCGCTTTGTGATTGAACGA{TG}gt............ : 25530

    46 : Intron 1 >>>>  {s}LysSerUnkArgValTyrGlyArgAsnAlaValValValArg :    59
          bp            {|}!!.|||   |||..!|||!.!  !...|||  !! !:!!|||
                      ++{s}AsnSer***ArgThrTyrAlaSerArgAlaAsnGlyLeuArg
 25529 : .............ag{C}AATTCCTGACGAACGTACGCGTCGCGGGCCAACGGGCTGCGC : 25398

    60 : GluAlaLeuAlaAsp  >>>> Target Intron 2 >>>>  SerHisProGluLeuL :    70
         !!:.!!|||  !!!:            88 bp            :!!  !|||!!:  !:
         AspThrLeuGlnGlu++                         ++AlaPheProAspAlaG
 25397 : GACACACTTCAGGAGgt.........................agGCTTTCCCGGATGCTG : 25277

    71 : ysValMetIleAsnProHisAsnProArgArgAsnSerPheGluIleThrLeuMetAspG :    90
         !!:!!:!:|||||||||:!!!!.|||||||||..!|||||||||  !|||:!!..!   |
         luIleLeuIleAsnProAsnLysProArgArgGlySerPheGluCysThrMetGlnLeuG
 25276 : AAATTCTCATCAATCCGAACAAACCGCGACGTGGCAGCTTTGAGTGCACAATGCAGCTGG : 25217

    91 : lyGluArg{A}  >>>> Target Intron 3 >>>>  {la}AspValLeuTrpSerG :    99
         ||!    !{!}            110 bp           { !}...:!!:!!|||!!!|
         lyGlyAla{G}++                         ++{lu}SerLeuValTrpThrG
 25216 : GCGGCGCA{G}gt.........................ag{AA}TCGCTTGTGTGGACTG : 25080

   100 : lyIleLysLysGlyProProArgLysLeuLysPheProGluProAlaGluValValThrA :   119
         ||:!!|||:::||||||||||||!!.  !|||||||||!!:  !|||:!!:!!|||.!!!
         lyValLysArgGlyProProArgAsnAspLysPheProAspGlyAlaLysLeuValAlaA
 25079 : GCGTCAAGCGCGGACCGCCGCGCAACGACAAGTTCCCGGACGGCGCCAAGCTGGTCGCGG : 25020

   120 : laLeuLysGlnAlaLeuGlu :   125
          !:!!:::|||  !:!!:!!
         spIleArgGlnLeuIleGln
 25019 : ACATTCGCCAGCTCATACAG : 25000

vulgar: D.rerio 30 125 . supercontig_1.12:subseq(834258,50000) 25576 24999 - 186 M 14 42 S 0 2 5 0 2 I 0 90 3 0 2 S 1 1 M 19 57 5 0 2 I 0 84 3 0 2 M 28 84 S 0 1 5 0 2 I 0 106 3 0 2 S 1 2 M 32 96
# --- 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_1.12:subseq(834258,50000)	exonerate:protein2genome:local	gene	25000	25576	186	-	.	gene_id 1 ; sequence D.rerio ; gene_orientation +
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	cds	25533	25576	.	-	.	
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	exon	25533	25576	.	-	.	insertions 0 ; deletions 0
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	splice5	25531	25532	.	-	.	intron_id 1 ; splice_site "GT"
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	intron	25439	25532	.	-	.	intron_id 1
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	splice3	25439	25440	.	-	.	intron_id 0 ; splice_site "AG"
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	cds	25381	25438	.	-	.	
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	exon	25381	25438	.	-	.	insertions 0 ; deletions 0
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	splice5	25379	25380	.	-	.	intron_id 2 ; splice_site "GT"
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	intron	25293	25380	.	-	.	intron_id 2
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	splice3	25293	25294	.	-	.	intron_id 1 ; splice_site "AG"
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	cds	25208	25292	.	-	.	
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	exon	25208	25292	.	-	.	insertions 0 ; deletions 0
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	splice5	25206	25207	.	-	.	intron_id 3 ; splice_site "GT"
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	intron	25098	25207	.	-	.	intron_id 3
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	splice3	25098	25099	.	-	.	intron_id 2 ; splice_site "AG"
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	cds	25000	25097	.	-	.	
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	exon	25000	25097	.	-	.	insertions 0 ; deletions 0
supercontig_1.12:subseq(834258,50000)	exonerate:protein2genome:local	similarity	25000	25576	186	-	.	alignment_id 1 ; Query D.rerio ; Align 25577 31 42 ; Align 25438 46 57 ; Align 25293 65 84 ; Align 25096 94 96
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis