Command line: [exonerate --showtargetgff --model protein2genome SelS.prot 
SelS.fa]
C4 Alignment display:
  Model: protein2genome
  Raw score: 835
  Aligned positions 0->189 of query
  Aligned positions 3801->8444 of target

Query: SelS
Target: 15 dna:chromosome chromosome:CHIMP1A:15:100806218:100823418:1

    1 : MetGluArgGlnGluGluSerLeuSerAlaArgProAlaLeuGluThrGluGlyLeuArgPh :   
20
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        MetGluArgGlnGluGluSerLeuSerAlaArgProAlaLeuGluThrGluGlyLeuArgPh
3802 : ATGGAACGCCAAGAGGAGTCCCTGTCCGCGCGGCCGGCCCTGGAGACCGAGGGGCTGCGCTT : 3861

   21 : eLeuHisThrThr{V}  >>>> Target Intron 1 >>>>  {al}GlySerLeuLeuA :   
30
        |||||||||||||{|}            666 bp           {||}|||||||||||||
        eLeuHisThrThr{V}                             {al}GlySerLeuLeuA
3862 : CCTGCACACCACG{G}gt.........................ag{TG}GGCTCCCTGCTGG : 4557

   31 : laThrTyrGlyTrpTyrIleValPheSerCysIleLeuLeuTyrValValPheGlnLysLeu :   
50
        |||||||||||||||||:!!||||||||||||||||||||||||||||||||||||||||||
        laThrTyrGlyTrpTyrValValPheSerCysIleLeuLeuTyrValValPheGlnLysLeu
4558 : CCACCTATGGCTGGTACGTCGTCTTCAGCTGCATCCTGCTCTACGTGGTCTTTCAGAAGCTT : 4617

   51 : SerAlaArgLeuArgAlaLeuArgGlnArgGlnLeuAspArgAlaAlaAlaAlaVal{G}   :   
70
        |||||||||||||||||||||||||||||||||||||||||||||||||||||||||{|}
        SerAlaArgLeuArgAlaLeuArgGlnArgGlnLeuAspArgAlaAlaAlaAlaVal{G}
4618 : TCCGCCCGGCTAAGAGCCTTGAGGCAGAGGCAGCTGGACCGAGCTGCGGCTGCTGTG{G}gt : 4678

   71 : >>>> Target Intron 2 >>>>  {lu}ProAspValValValLysArgGlnGluAlaL :   
81
                 1181 bp           {||}||||||||||||||||||||||||||||||:
                                   {lu}ProAspValValValLysArgGlnGluAlaV
4679 : .........................ag{AA}CCTGATGTTGTTGTTAAACGACAAGAAGCTG : 5891

   82 : euAlaAlaAlaArgLeuLysMetGlnGluGluLeuAsnAlaGlnValGluLysHisLysGlu :  
101
        !!||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        alAlaAlaAlaArgLeuLysMetGlnGluGluLeuAsnAlaGlnValGluLysHisLysGlu
5892 : TAGCAGCTGCTCGACTGAAAATGCAAGAAGAACTAAATGCGCAAGTTGAAAAGCATAAGGAA : 5951

  102 : LysLeuLysGln  >>>> Target Intron 3 >>>>  LeuGluGluGluLysArgArg :  
112
        ||||||||||||            573 bp           |||||||||||||||||||||
        LysLeuLysGln                             LeuGluGluGluLysArgArg
5952 : AAACTGAAACAGgt.........................agCTTGAAGAAGAAAAAAGGAGA : 6557

  113 : GlnLysIleGluMetTrpAspSerMetGlnGluGlyLysSerTyrLysGlyAsnAlaLysLy :  
133
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        GlnLysIleGluMetTrpAspSerMetGlnGluGlyLysSerTyrLysGlyAsnAlaLysLy
6558 : CAGAAGATTGAAATGTGGGACAGCATGCAAGAGGGAAAAAGTTACAAAGGAAATGCAAAGAA : 6620

  134 : sProGln  >>>> Target Intron 4 >>>>  GluGluAspSerProGlyProSerTh :  
144
        |||||||            96 bp            ||||||||||||||||||||||||||
        sProGln                             GluGluAspSerProGlyProSerTh
6621 : GCCCCAGgt.........................agGAGGAAGACAGTCCTGGGCCTTCCAC : 6749

  145 : rSerSerValLeuLysArgLysSerAspArgLysProLeuArgGlyGly{G}  >>>> Tar :  
161
        |||||||||||||||||||||||||||||||||||||||||||||||||{|}
        rSerSerValLeuLysArgLysSerAspArgLysProLeuArgGlyGly{G}
6750 : TTCATCTGTCCTGAAACGGAAATCGGACAGAAAGCCTTTGCGGGGAGGA{G}gt........ : 6803

  162 : get Intron 5 >>>>  {ly}TyrAsnProLeuSerGly-GluGlyGlyGlyAlaCysSe :  
174
         1559 bp           {||}||||||||||||||||||#||||||||||||||||||||
                           {ly}TyrAsnProLeuSerGly#GluGlyGlyGlyAlaCysSe
6804 : .................ag{GT}TATAACCCGTTGTCTGGTGGAAGGAGGCGGAGCTTGCTC : 8399

  175 : rTrpArgProGlyArgArgGlyProSerSerGlyGly***Gly :  189
        |||||||||||||||||||||||||||||||||||||||||||
        rTrpArgProGlyArgArgGlyProSerSerGlyGly***Gly
8400 : CTGGAGACCTGGACGCAGAGGCCCGTCATCTGGCGGATGAGGC : 8444

vulgar: SelS 0 189 . 15 3801 8444 - 835 M 25 75 S 0 1 5 0 2 I 0 662 3 0 2 S 
1 2 M 44 132 S 0 1 5 0 2 I 0 1177 3 0 2 S 1 2 M 35 105 5 0 2 I 0 569 3 0 2 M 
30 90 5 0 2 I 0 92 3 0 2 M 25 75 S 0 1 5 0 2 I 0 1555 3 0 2 S 1 2 M 6 18 F 0 
1 M 21 63
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 0.8.2
##date 2006-03-15
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
15	exonerate:protein2genome	gene	3802	8444	835	-	. gene_id 2 ; sequence SelS 
; gene_orientation + ;
15	exonerate:protein2genome	exon	3802	3877	.	-	. insertions 0 ; deletions 0 
;
15	exonerate:protein2genome	splice5	3878	3879	.	-	. intron_id 1 ; 
splice_site "GT" ;
15	exonerate:protein2genome	intron	3878	4543	.	-	. intron_id 1 ;
15	exonerate:protein2genome	splice3	4542	4543	.	-	. intron_id 0 ; 
splice_site "AG" ;
15	exonerate:protein2genome	exon	4546	4678	.	-	. insertions 0 ; deletions 0 
;
15	exonerate:protein2genome	splice5	4679	4680	.	-	. intron_id 2 ; 
splice_site "GT" ;
15	exonerate:protein2genome	intron	4679	5859	.	-	. intron_id 2 ;
15	exonerate:protein2genome	splice3	5858	5859	.	-	. intron_id 1 ; 
splice_site "AG" ;
15	exonerate:protein2genome	exon	5862	5966	.	-	. insertions 0 ; deletions 0 
;
15	exonerate:protein2genome	splice5	5967	5968	.	-	. intron_id 3 ; 
splice_site "GT" ;
15	exonerate:protein2genome	intron	5967	6539	.	-	. intron_id 3 ;
15	exonerate:protein2genome	splice3	6538	6539	.	-	. intron_id 2 ; 
splice_site "AG" ;
15	exonerate:protein2genome	exon	6540	6629	.	-	. insertions 0 ; deletions 0 
;
15	exonerate:protein2genome	splice5	6630	6631	.	-	. intron_id 4 ; 
splice_site "GT" ;
15	exonerate:protein2genome	intron	6630	6725	.	-	. intron_id 4 ;
15	exonerate:protein2genome	splice3	6724	6725	.	-	. intron_id 3 ; 
splice_site "AG" ;
15	exonerate:protein2genome	exon	6726	6801	.	-	. insertions 0 ; deletions 0 
;
15	exonerate:protein2genome	splice5	6802	6803	.	-	. intron_id 5 ; 
splice_site "GT" ;
15	exonerate:protein2genome	intron	6802	8360	.	-	. intron_id 5 ;
15	exonerate:protein2genome	splice3	8359	8360	.	-	. intron_id 4 ; 
splice_site "AG" ;
15	exonerate:protein2genome	exon	8363	8444	.	-	. insertions 0 ; deletions 0 
;
15	exonerate:protein2genome	similarity	3802	8444	835	-	. alignment_id 2 ; 
Align 3802 1 75 ; Align 4546 27 132 ; Align 5862 72 105 ; Align 6540 107 90 
; Align 6726 137 75 ; Align 8363 163 18 ; Align 8382 169 63 ;
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis