C4 Alignment:
------------
         Query: SPP00000105_1.0 # Protein # Glutathione peroxidase 8 (GPx8) # Mus musculus # Complete
        Target: GL193930.1:subseq(70315,20300) dna:scaffold scaffold:ailMel1:GL193930.1:1:427026:1 REF:[revcomp]
         Model: protein2genome:local
     Raw score: 907
   Query range: 0 -> 209
  Target range: 11020 -> 6868

     1 : MetGluProPheAlaAlaTyrProLeuLysCysSerGlyProLysAlaLysIlePheAla :    20
         |||||||||.!!.!!||||||||||||!:!||||||||| !!|||||||||:!!||||||
         MetGluProLeuThrAlaTyrProLeuArgCysSerGlySerLysAlaLysValPheAla
 11020 : ATGGAGCCTCTTACAGCGTACCCTTTAAGATGTTCAGGGTCAAAAGCAAAGGTATTTGCA : 10963

    21 : ValLeuLeuSerMetValLeuCysThrValMetLeuPheLeuLeuGlnLeuLysPheLeu :    40
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         ValLeuLeuSerMetValLeuCysThrValMetLeuPheLeuLeuGlnLeuLysPheLeu
 10962 : GTTTTACTATCTATGGTTCTATGCACAGTAATGCTATTTCTTCTACAACTAAAATTCCTA : 10903

    41 : LysProArgThrAsnSerPheTyrSerPheGluValLysAspAlaLysGlyArgThrVal :    60
         ||||||!:!! !||||||||||||!!!|||||||||||||||!.!|||||||||||||||
         LysProLysIleAsnSerPheTyrThrPheGluValLysAspValLysGlyArgThrVal
 10902 : AAACCTAAAATCAACAGCTTTTATACCTTTGAAGTGAAAGATGTGAAAGGAAGAACGGTT : 10843

    61 : SerLeuGluLysPheLysGlyLys  >>>> Target Intron 1 >>>>  AlaSerL :    71
         ||||||||||||||||||||||||            556 bp           !.!:!!|
         SerLeuGluLysPheLysGlyLys++                         ++ValAlaL
 10842 : TCTCTGGAAAAGTTTAAAGGCAAAgt.........................agGTTGCAC : 10254

    72 : euValValAsnValAlaSerAspCysArgPheThrAspLysSerTyrGlnThrLeuArgG :    91
         ||||||||||||||||||||||||||!:!.!!||||||!:!!:!|||  !.!!|||!:!|
         euValValAsnValAlaSerAspCysGlnLeuThrAspArgAsnTyrLeuAlaLeuGlnG
 10253 : TAGTTGTAAACGTGGCTAGTGACTGCCAACTCACAGACAGAAATTACTTAGCACTGCAGG : 10194

    92 : luLeuHisLysGluPheGlyProTyrHisPheAsnValLeuAlaPheProCysAsnGlnP :   111
         |||||||||||||||||||||||!:!||||||!:!|||||||||||||||||||||||||
         luLeuHisLysGluPheGlyProPheHisPheSerValLeuAlaPheProCysAsnGlnP
 10193 : AACTGCACAAAGAGTTTGGACCATTCCACTTCAGCGTCTTGGCCTTTCCATGCAATCAGT : 10134

   112 : heGlyGluSerGluProLysSerSerLysGluValGluSerPheAlaArgGlnAsnTyrG :   131
         |||||||||||||||||::: !!||||||||||||! !||||||||||||.!.|||||||
         heGlyGluSerGluProArgProSerLysGluValValSerPheAlaArgAsnAsnTyrG
 10133 : TCGGAGAATCGGAGCCCCGCCCAAGCAAGGAAGTAGTATCTTTTGCAAGAAATAACTACG : 10074

   132 : lyValThrPheProIlePheHisLysIleLysIleLeuGlyProGluAlaGluProAlaP :   151
         ||||||||||||||||||||||||||||||||||||||||| !!||||||!!:|||||||
         lyValThrPheProIlePheHisLysIleLysIleLeuGlySerGluAlaAspProAlaP
 10073 : GGGTGACGTTCCCCATCTTCCACAAGATTAAGATTCTAGGATCTGAAGCAGACCCTGCGT : 10014

   152 : heArgPheIleVal{A}  >>>> Target Intron 2 >>>>  {sp}SerSerLysL :   160
         ||||||||:!!|||{|}           2969 bp           {||}||||||||||
         heArgPheLeuVal{A}++                         ++{sp}SerSerLysL
 10013 : TTAGATTTCTTGTT{G}gt.........................ag{AT}TCTTCAAAGA :  7018

   161 : ysGluProArgTrpAsnPheTrpLysTyrLeuValAsnProGluGlyGlnValValLysP :   180
         |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||!
         ysGluProArgTrpAsnPheTrpLysTyrLeuValAsnProGluGlyGlnValValLysS
  7017 : AGGAACCAAGGTGGAATTTTTGGAAGTATCTGGTCAACCCTGAGGGCCAAGTTGTGAAGT :  6958

   181 : heTrpArgProGluGluProLeuGluAlaIleArgProHisValSerGlnMetIleGlyG :   200
          !||||||||||||||||||:!!|||!.!|||||||||.!.:!!:!!   :!!||| !!|
         erTrpArgProGluGluProIleGluValIleArgProGluIleAlaAlaLeuIleArgG
  6957 : CCTGGAGGCCAGAGGAACCCATTGAAGTCATCAGGCCTGAGATAGCAGCTCTGATTAGAC :  6898

   201 : lnIleIleLeuLysLysLysGluAspLeu :   209
         ||!!:|||:!!!:!|||||||||||||||
         lnMetIleIleArgLysLysGluAspLeu
  6897 : AAATGATCATAAGAAAGAAAGAGGACCTG :  6869

vulgar: SPP00000105_1.0 0 209 . GL193930.1:subseq(70315,20300) 11020 6868 - 907 M 68 204 5 0 2 I 0 552 3 0 2 M 87 261 S 0 1 5 0 2 I 0 2965 3 0 2 S 1 2 M 53 159
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2012-11-09
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	gene	6869	11020	907	-	.	gene_id 1 ; sequence SPP00000105_1.0 ; gene_orientation +
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	cds	10817	11020	.	-	.	
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	exon	10817	11020	.	-	.	insertions 0 ; deletions 0
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	splice5	10815	10816	.	-	.	intron_id 1 ; splice_site "GT"
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	intron	10261	10816	.	-	.	intron_id 1
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	splice3	10261	10262	.	-	.	intron_id 0 ; splice_site "AG"
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	cds	9999	10260	.	-	.	
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	exon	9999	10260	.	-	.	insertions 0 ; deletions 0
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	splice5	9997	9998	.	-	.	intron_id 2 ; splice_site "GT"
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	intron	7030	9998	.	-	.	intron_id 2
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	splice3	7030	7031	.	-	.	intron_id 1 ; splice_site "AG"
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	cds	6869	7029	.	-	.	
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	exon	6869	7029	.	-	.	insertions 0 ; deletions 0
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	similarity	6869	11020	907	-	.	alignment_id 1 ; Query SPP00000105_1.0 ; Align 11021 1 204 ; Align 10261 69 261 ; Align 7028 157 159
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis

U63741@luke:~> more Gpx8mm.exon.gff
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	exon	10817	11020	.	-	.	insertions 0 
; deletions 0
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	exon	9999	10260	.	-	.	insertions 0 
; deletions 0
GL193930.1:subseq(70315,20300)	exonerate:protein2genome:local	exon	6869	7029	.	-	.	insertions 0 
; deletions 0