Command line: [exonerate -m p2g --showtargetgff -q /homes/users/U63741/seqaahs/selU2.hs.fa -t selU2hssubseq.fa]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000027_1.0 # Protein # Selenoprotein U2 (SelU2) # Homo sapiens # Complete
        Target: GL193912.1:subseq(65390,20400) dna:scaffold scaffold:ailMel1:GL193912.1:1:435002:1 REF
         Model: protein2genome:local
     Raw score: 898
   Query range: 40 -> 226
  Target range: 8578 -> 17396

    41 : AspAlaArgGlyGlnArgValProPheGlyAlaLeuPheArgGluArgArgAlaValVal :    60
         ||||||  !|||::!!:!||||||||||||||||||||||||||||||||||||||||||
         AspAlaSerGlyArgGlnValProPheGlyAlaLeuPheArgGluArgArgAlaValVal
  8579 : GACGCCTCCGGAAGGCAGGTGCCGTTCGGCGCGCTGTTCCGGGAGCGTCGGGCTGTCGTA :  8636

    61 : ValPheValArg  >>>> Target Intron 1 >>>>  HisPheLeuCysTyrIleC :    71
         ||||||||||||            421 bp           |||||||||||||||||||
         ValPheValArg++                         ++HisPheLeuCysTyrIleC
  8637 : GTCTTCGTGCGGgt.........................agCATTTCCTGTGTTACATTT :  9090

    72 : ysLysGluTyrValGluAspLeuAlaLysIleProArgSerPheLeuGln  >>>> Tar :    88
         |||||||||||||||||||||||||||||||||||!:!||||||||||||          
         ysLysGluTyrValGluAspLeuAlaLysIleProLysSerPheLeuGln++        
  9091 : GCAAGGAATACGTAGAAGATCTGGCCAAAATCCCCAAGAGTTTTTTACAAgt........ :  9143

    89 : get Intron 2 >>>>  GluAlaAsnValThrLeuIleValIleGlyGlnSerSerTy :   101
           862 bp           ||||||:!!||||||||||||||||||||||||||||||||
                          ++GluAlaAspValThrLeuIleValIleGlyGlnSerSerTy
  9144 : .................agGAAGCAGATGTCACCCTAATAGTGATTGGACAGTCATCCTA : 10042

   102 : rHisHisIleGlu  >>>> Target Intron 3 >>>>  ProPheCysLysLeuThr :   111
         |||||||||||||            159 bp           ||||||||||||||||||
         rHisHisIleGlu++                         ++ProPheCysLysLeuThr
 10043 : CCATCATATCGAGgt.........................agCCGTTCTGCAAACTGACT : 10231

   112 : GlyTyrSerHisGluIleTyrValAspProGluArgGluIleTyrLysArgLeuGlyMet :   131
         ||||||||||||||||||||||||||||||||||||||||||||||||!:!|||||||||
         GlyTyrSerHisGluIleTyrValAspProGluArgGluIleTyrLysLysLeuGlyMet
 10232 : GGGTATTCTCATGAAATCTATGTTGATCCTGAGAGAGAAATTTATAAAAAATTGGGAATG : 10291

   132 : LysArgGlyGluGluIleAlaSerSer{G}  >>>> Target Intron 4 >>>>  { :   141
         |||||||||||||||||||||||||||{|}           4292 bp           {
         LysArgGlyGluGluIleAlaSerSer{G}++                         ++{
 10292 : AAAAGAGGTGAAGAAATTGCCTCCTCA{G}gt.........................ag{ : 14614

   142 : ly}GlnSerProHisIleLysSerAsnLeuLeuSerGlySerLeuGlnSerLeuTrpArg :   160
         ||}:!!|||||||||||||||||||||:!!||||||||||||:!!!:!||||||||||||
         ly}LysSerProHisIleLysSerAsnIleLeuSerGlySerIleArgSerLeuTrpArg
 14615 : GA}AAGAGCCCCCATATAAAATCAAATATACTCTCAGGAAGCATTCGGAGCCTGTGGAGG : 14670

   161 : AlaValThrGlyProLeuPheAspPheGlnGlyAspProAlaGlnGlnGlyGlyThrLeu :   180
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         AlaValThrGlyProLeuPheAspPheGlnGlyAspProAlaGlnGlnGlyGlyThrLeu
 14671 : GCAGTGACTGGCCCTCTTTTTGATTTTCAAGGAGACCCTGCTCAGCAAGGTGGAACCCTC : 14730

   181 : IleLeuGlyPro{G}  >>>> Target Intron 5 >>>>  {ly}AsnAsnIleHis :   189
         ||||||||||||{|}           2526 bp           {||}||||||||||||
         IleLeuGlyPro{G}++                         ++{ly}AsnAsnIleHis
 14731 : ATCTTAGGTCCA{G}gt.........................ag{GT}AACAACATCCAT : 17283

   190 : PheIleHisArgAspArgAsnArgLeuAspHisLysProIleAsnSerValLeuGlnLeu :   209
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         PheIleHisArgAspArgAsnArgLeuAspHisLysProIleAsnSerValLeuGlnLeu
 17284 : TTTATACACCGTGATAGAAATAGGTTGGATCACAAACCCATCAACTCTGTTTTACAGCTT : 17343

   210 : ValGlyValGlnHisValAsnPheThrAsnArgProSerValIleHisVal :   226
         |||||||||||||||||| !!||||||!:!|||||||||||||||||||||
         ValGlyValGlnHisValTyrPheThrSerArgProSerValIleHisVal
 17344 : GTAGGAGTTCAGCATGTGTACTTTACAAGCAGACCTTCAGTTATCCATGTG : 17396

vulgar: SPP00000027_1.0 40 226 . GL193912.1:subseq(65390,20400) 8578 17396 + 898 M 24 72 5 0 2 I 0 417 3 0 2 M 23 69 5 0 2 I 0 858 3 0 2 M 18 54 5 0 2 I 0 155 3 0 2 M 35 105 S 0 1 5 0 2 I 0 4288 3 0 2 S 1 2 M 43 129 S 0 1 5 0 2 I 0 2522 3 0 2 S 1 2 M 41 123
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2012-12-02
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	gene	8579	17396	898	+	.	gene_id 1 ; sequence SPP00000027_1.0 ; gene_orientation +
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	cds	8579	8650	.	+	.	
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	exon	8579	8650	.	+	.	insertions 0 ; deletions 0
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	splice5	8651	8652	.	+	.	intron_id 1 ; splice_site "GT"
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	intron	8651	9071	.	+	.	intron_id 1
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	splice3	9070	9071	.	+	.	intron_id 0 ; splice_site "AG"
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	cds	9072	9140	.	+	.	
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	exon	9072	9140	.	+	.	insertions 0 ; deletions 0
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	splice5	9141	9142	.	+	.	intron_id 2 ; splice_site "GT"
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	intron	9141	10002	.	+	.	intron_id 2
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	splice3	10001	10002	.	+	.	intron_id 1 ; splice_site "AG"
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	cds	10003	10056	.	+	.	
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	exon	10003	10056	.	+	.	insertions 0 ; deletions 0
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	splice5	10057	10058	.	+	.	intron_id 3 ; splice_site "GT"
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	intron	10057	10215	.	+	.	intron_id 3
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	splice3	10214	10215	.	+	.	intron_id 2 ; splice_site "AG"
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	cds	10216	10321	.	+	.	
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	exon	10216	10321	.	+	.	insertions 0 ; deletions 0
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	splice5	10322	10323	.	+	.	intron_id 4 ; splice_site "GT"
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	intron	10322	14613	.	+	.	intron_id 4
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	splice3	14612	14613	.	+	.	intron_id 3 ; splice_site "AG"
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	cds	14614	14745	.	+	.	
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	exon	14614	14745	.	+	.	insertions 0 ; deletions 0
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	splice5	14746	14747	.	+	.	intron_id 5 ; splice_site "GT"
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	intron	14746	17271	.	+	.	intron_id 5
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	splice3	17270	17271	.	+	.	intron_id 4 ; splice_site "AG"
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	cds	17272	17396	.	+	.	
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	exon	17272	17396	.	+	.	insertions 0 ; deletions 0
GL193912.1:subseq(65390,20400)	exonerate:protein2genome:local	similarity	8579	17396	898	+	.	alignment_id 1 ; Query SPP00000027_1.0 ; Align 8579 41 72 ; Align 9072 65 69 ; Align 10003 88 54 ; Align 10216 106 105 ; Align 14616 142 129 ; Align 17274 186 123
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
