Command line: [exonerate -m p2g --showtargetgff -q /homes/users/U63741/seqaamm/selW2.mm.fa -t selw2.mm.subseq.fa]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000118_1.0 # Protein # Selenoprotein W2 (SelW2) # Mus musculus # Complete
        Target: GL194160.1:subseq(229810,20239) dna:scaffold scaffold:ailMel1:GL194160.1:1:326334:1 REF
         Model: protein2genome:local
     Raw score: 521
   Query range: 0 -> 115
  Target range: 9223 -> 10239

     1 : MetSerGlyGluProAlaProValSerValValProProProGlyGluValGluAlaGly :    20
         |||||||||||||||!.!|||..!|||! !!.!|||||||||||||||:!!||| !!|||
         MetSerGlyGluProGlyProThrSerGluAlaProProProGlyGluIleGluProGly
  9224 : ATGAGCGGGGAGCCGGGGCCGACGTCTGAAGCGCCCCCTCCCGGGGAGATTGAACCGGGT :  9281

    21 : SerGlyValHisIleValValGluTyr{Cy}  >>>> Target Intron 1 >>>>   :    30
         |||||||||!.!|||||||||||||||{||}            103 bp           
         SerGlyValArgIleValValGluTyr{Cy}++                         ++
  9282 : AGTGGGGTGCGCATCGTCGTGGAATAC{TG}gt.........................ag :  9414

    31 : {s}LysProCysGlyPheGluAlaThrTyrLeuGluLeuAlaSerAlaValLysGluGlu :    49
         {|}:!!|||||||||||||||||||||||||||||||||||||||||||||||||||:!!
         {s}GluProCysGlyPheGluAlaThrTyrLeuGluLeuAlaSerAlaValLysGluGln
  9415 : {T}GAACCCTGTGGATTTGAGGCGACCTACCTGGAGCTGGCGAGTGCCGTGAAGGAGCAG :  9471

    50 : TyrProGlyIleGluIleGluSerArgLeuGlyGlyThr{G}  >>>> Target Intr :    63
         |||||||||||||||||||||||||||!!!|||||||||{|}            487 bp
         TyrProGlyIleGluIleGluSerArgPheGlyGlyThr{G}++                
  9472 : TATCCTGGCATTGAGATCGAGTCGCGCTTTGGGGGCACA{G}gt................ :  9516

    64 : on 2 >>>>  {ly}AlaPheGluIleGluIleAsnGlyGlnLeuValPheSerLysLeu :    78
                    {||}|||||||||||||||||||||||||||||||||||||||||||||
                  ++{ly}AlaPheGluIleGluIleAsnGlyGlnLeuValPheSerLysLeu
  9517 : .........ag{GG}GCCTTTGAGATCGAAATCAATGGACAGCTGGTGTTCTCCAAGCTG : 10045

    79 : GluAsnGlyGlyPheProTyrGluLysAsp  >>>> Target Intron 3 >>>>  L :    89
         ||||||||||||||||||||||||||||||            81 bp            |
         GluAsnGlyGlyPheProTyrGluLysAsp++                         ++L
 10046 : GAGAATGGGGGCTTCCCTTATGAGAAAGATgt.........................agC : 10159

    90 : euMetGluAlaIleArgArgAlaSerAsnGlyGluProValGluLysIleThrAsnSerA :   109
         ||!!:|||||||||||||||||||||||||||||||||:!!|||||||||||||||||||
         euIleGluAlaIleArgArgAlaSerAsnGlyGluProLeuGluLysIleThrAsnSerA
 10160 : TCATTGAGGCCATCCGAAGAGCCAGTAACGGAGAACCCCTAGAAAAGATCACGAACAGCC : 10219

   110 : rgProProCysValIleLeu :   115
         ||||||||||||||||||||
         rgProProCysValIleLeu
 10220 : GTCCTCCCTGCGTCATCCTG : 10239

vulgar: SPP00000118_1.0 0 115 . GL194160.1:subseq(229810,20239) 9223 10239 + 521 M 29 87 S 0 2 5 0 2 I 0 99 3 0 2 S 1 1 M 32 96 S 0 1 5 0 2 I 0 483 3 0 2 S 1 2 M 25 75 5 0 2 I 0 77 3 0 2 M 27 81
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2012-12-01
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	gene	9224	10239	521	+	.	gene_id 1 ; sequence SPP00000118_1.0 ; gene_orientation +
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	cds	9224	9312	.	+	.	
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	exon	9224	9312	.	+	.	insertions 0 ; deletions 0
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	splice5	9313	9314	.	+	.	intron_id 1 ; splice_site "GT"
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	intron	9313	9415	.	+	.	intron_id 1
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	splice3	9414	9415	.	+	.	intron_id 0 ; splice_site "AG"
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	cds	9416	9513	.	+	.	
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	exon	9416	9513	.	+	.	insertions 0 ; deletions 0
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	splice5	9514	9515	.	+	.	intron_id 2 ; splice_site "GT"
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	intron	9514	10000	.	+	.	intron_id 2
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	splice3	9999	10000	.	+	.	intron_id 1 ; splice_site "AG"
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	cds	10001	10077	.	+	.	
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	exon	10001	10077	.	+	.	insertions 0 ; deletions 0
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	splice5	10078	10079	.	+	.	intron_id 3 ; splice_site "GT"
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	intron	10078	10158	.	+	.	intron_id 3
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	splice3	10157	10158	.	+	.	intron_id 2 ; splice_site "AG"
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	cds	10159	10239	.	+	.	
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	exon	10159	10239	.	+	.	insertions 0 ; deletions 0
GL194160.1:subseq(229810,20239)	exonerate:protein2genome:local	similarity	9224	10239	521	+	.	alignment_id 1 ; Query SPP00000118_1.0 ; Align 9224 1 87 ; Align 9417 31 96 ; Align 10003 64 75 ; Align 10159 89 81
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
