Command line: [exonerate -m p2g --showtargetgff -q SelU3.fa.U_to_X -t gi|511782573|gb|CM001961.1|.fastasubseq]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000116_2.0 # Protein # Selenoprotein U3 (SelU3) # Human (Homo sapiens) 
        Target: gi|511782573|gb|CM001961.1|:subseq(128865374,202231) Chlorocebus sabaeus isolate 1994-021 chromosome 20, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 993
   Query range: 5 -> 228
  Target range: 102231 -> 99615

      6 : GlySerArgSerGluGluProGlyAlaGlyAsnArgGluSerGly<-><->SerArgG :     23
          |||||| !!|||:!!|||||||||:!!||||||!:!||| !!|||      ||| !!|
          GlySerGlySerGlnGluProGlySerGlyAsnGlnGluProGlyAlaAlaSerTrpG
 102231 : GGATCTGGGAGCCAGGAGCCGGGATCTGGGAACCAGGAGCCGGGAGCGGCGAGCTGGG : 102174

     24 : luProGlyLeuAlaAlaAlaAlaMetSerThrValAspLeuAlaArgValGlyAlaCy :     42
          ||||||||! !|||||||||||||||||||||||||||||||||||||||||||||||
          luProGlyArgAlaAlaAlaAlaMetSerThrValAspLeuAlaArgValGlyAlaCy
 102173 : AACCAGGGCGGGCGGCCGCGGCCATGAGCACGGTGGACCTTGCCCGCGTGGGCGCGTG : 102117

     43 : sIleLeuLysHisAlaValThrGlyGlu  >>>> Target Intron 1 >>>>  A :     52
          ||||||||||||||||||||||||||||            141 bp           |
          sIleLeuLysHisAlaValThrGlyGlu++                         ++A
 102116 : CATCCTGAAGCATGCGGTGACTGGGGAGgt.........................agG : 101946

     53 : laValGluLeuArgSerLeuTrpArgGluHisAlaCysValValAlaGlyLeuArgAr :     71
          ||||||||||||||||||||||||||!!:!.!||||||||||||||||||||||||||
          laValGluLeuArgSerLeuTrpArgAspArgAlaCysValValAlaGlyLeuArgAr
 101945 : CCGTGGAGCTGCGGAGCCTGTGGCGGGATCGCGCGTGCGTGGTGGCCGGGCTGCGGCG : 101889

     72 : gPheGlyCysValValCysArgTrpIleAlaGlnAspLeuSerSerLeuAlaGlyLeu :     90
          |||||||||||||||||||||||||||||||||||||||||||.!!||||||||||||
          gPheGlyCysValValCysArgTrpIleAlaGlnAspLeuSerGlyLeuAlaGlyLeu
 101888 : CTTCGGCTGCGTGGTGTGCCGCTGGATCGCCCAGGACCTCAGCGGCCTCGCGGGGCTC : 101832

     91 : LeuAspGlnHisGlyValArgLeuValGlyValGlyProGluAlaLeuGlyLeuGlnG :    110
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          LeuAspGlnHisGlyValArgLeuValGlyValGlyProGluAlaLeuGlyLeuGlnG
 101831 : CTGGACCAGCACGGTGTGCGTCTGGTGGGCGTGGGGCCCGAGGCCCTGGGTCTGCAGG : 101772

    111 : luPheLeuAspGlyAspTyrPheAlaGly{G}  >>>> Target Intron 2 >>> :    120
          ||||||||||||||! !||||||||||||{|}            443 bp        
          luPheLeuAspGlyGlyTyrPheAlaGly{G}++                        
 101771 : AGTTCCTGGACGGCGGCTACTTCGCGGGA{G}gt........................ : 101739

    121 : >  {lu}LeuTyrLeuAspGluSerLysGlnLeuTyrLysGluLeuGlyPheLys{Ar :    137
             {||}||||||||||||||||||||||||||||||||||||||||||||||||{!:
           ++{lu}LeuTyrLeuAspGluSerLysGlnLeuTyrLysGluLeuGlyPheLys{Gl
 101738 : .ag{AG}CTCTACCTGGATGAGAGCAAGCAGCTTTATAAGGAGCTGGGCTTCAAG{CA : 101248

    138 : }  >>>> Target Intron 3 >>>>  {g}TyrAsnSerLeuSerIleLeuProA :    146
          }            596 bp           {!}|||||||||||||||:!!|||||||
          }++                         ++{n}TyrAsnSerLeuSerValLeuProA
 101247 : }gt.........................ag{G}TACAACAGCCTGAGCGTCCTCCCCG : 100625

    147 : laAlaLeuGlyLysProValArgAspValAlaAlaLys  >>>> Target Intron :    159
          ||||||||||||||||||||||||||||||||||||||            96 bp   
          laAlaLeuGlyLysProValArgAspValAlaAlaLys++                  
 100624 : CAGCTCTGGGGAAGCCTGTGCGTGATGTGGCTGCCAAGgt.................. : 100584

    160 :  4 >>>>  AlaLysAlaValGlyIleGlnGlyAsnLeuSerGlyAspLeuLeuGlnS :    175
                   |||||||||||||||||||||||||||||||||||||||||||||||||
                 ++AlaLysAlaValGlyIleGlnGlyAsnLeuSerGlyAspLeuLeuGlnS
 100583 : .......agGCCAAGGCTGTTGGCATCCAGGGGAACCTGTCTGGGGACCTGCTGCAGA : 100442

    176 : erGlyGlyLeuLeuValValSerLys{G}  >>>> Target Intron 5 >>>>   :    184
          ||||||||||||||||||||||||||{|}            296 bp           
          erGlyGlyLeuLeuValValSerLys{G}++                         ++
 100441 : GCGGAGGGCTGCTGGTGGTCAGCAAA{G}gt.........................ag : 100120

    185 : {ly}GlyAspLysValLeuLeuHisPheValGlnLysSerProGlyAspTyrValPro :    202
          {||}||||||||||||||||||||||||||||||||||||||||||||||||||||||
          {ly}GlyAspLysValLeuLeuHisPheValGlnLysSerProGlyAspTyrValPro
 100119 : {GT}GGTGACAAAGTGCTGCTGCATTTCGTTCAGAAGTCCCCAGGCGATTATGTCCCC : 100065

    203 : LysGluHisIleLeuGlnValLeuGlyIleSerAlaGluValCysAlaSerAspProP :    222
          :!!||||||||||||||||||||||||||||||||||||||||||||||||:!!||||
          GlnGluHisIleLeuGlnValLeuGlyIleSerAlaGluValCysAlaSerAsnProP
 100064 : CAGGAGCACATCCTGCAGGTCCTGGGCATCTCTGCGGAGGTCTGTGCCAGCAACCCGC : 100005

    223 : roGln  >>>> Target Intron 6 >>>>  CysAspArgGluVal :    228
          |||||            369 bp           |||||||||||||||
          roGln++                         ++CysAspArgGluVal
 100004 : CTCAGgt.........................agTGTGACAGAGAGGTG :  99616

vulgar: SPP00000116_2.0 5 228 . gi|511782573|gb|CM001961.1|:subseq(128865374,202231) 102231 99615 - 993 M 15 45 G 0 6 M 31 93 5 0 2 I 0 137 3 0 2 M 68 204 S 0 1 5 0 2 I 0 439 3 0 2 S 1 2 M 16 48 S 0 2 5 0 2 I 0 592 3 0 2 S 1 1 M 21 63 5 0 2 I 0 92 3 0 2 M 25 75 S 0 1 5 0 2 I 0 292 3 0 2 S 1 2 M 39 117 5 0 2 I 0 365 3 0 2 M 5 15
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-04
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	gene	99616	102231	993	-	.	gene_id 1 ; sequence SPP00000116_2.0 ; gene_orientation +
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	cds	102088	102231	.	-	.	
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	exon	102088	102231	.	-	.	insertions 6 ; deletions 0
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	splice5	102086	102087	.	-	.	intron_id 1 ; splice_site "GT"
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	intron	101947	102087	.	-	.	intron_id 1
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	splice3	101947	101948	.	-	.	intron_id 0 ; splice_site "AG"
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	cds	101742	101946	.	-	.	
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	exon	101742	101946	.	-	.	insertions 0 ; deletions 0
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	splice5	101740	101741	.	-	.	intron_id 2 ; splice_site "GT"
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	intron	101299	101741	.	-	.	intron_id 2
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	splice3	101299	101300	.	-	.	intron_id 1 ; splice_site "AG"
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	cds	101247	101298	.	-	.	
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	exon	101247	101298	.	-	.	insertions 0 ; deletions 0
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	splice5	101245	101246	.	-	.	intron_id 3 ; splice_site "GT"
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	intron	100651	101246	.	-	.	intron_id 3
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	splice3	100651	100652	.	-	.	intron_id 2 ; splice_site "AG"
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	cds	100587	100650	.	-	.	
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	exon	100587	100650	.	-	.	insertions 0 ; deletions 0
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	splice5	100585	100586	.	-	.	intron_id 4 ; splice_site "GT"
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	intron	100491	100586	.	-	.	intron_id 4
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	splice3	100491	100492	.	-	.	intron_id 3 ; splice_site "AG"
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	cds	100415	100490	.	-	.	
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	exon	100415	100490	.	-	.	insertions 0 ; deletions 0
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	splice5	100413	100414	.	-	.	intron_id 5 ; splice_site "GT"
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	intron	100119	100414	.	-	.	intron_id 5
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	splice3	100119	100120	.	-	.	intron_id 4 ; splice_site "AG"
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	cds	100000	100118	.	-	.	
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	exon	100000	100118	.	-	.	insertions 0 ; deletions 0
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	splice5	99998	99999	.	-	.	intron_id 6 ; splice_site "GT"
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	intron	99631	99999	.	-	.	intron_id 6
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	splice3	99631	99632	.	-	.	intron_id 5 ; splice_site "AG"
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	cds	99616	99630	.	-	.	
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	exon	99616	99630	.	-	.	insertions 0 ; deletions 0
gi|511782573|gb|CM001961.1|:subseq(128865374,202231)	exonerate:protein2genome:local	similarity	99616	102231	993	-	.	alignment_id 1 ; Query SPP00000116_2.0 ; Align 102232 6 45 ; Align 102181 21 93 ; Align 101947 52 204 ; Align 101297 121 48 ; Align 100650 138 63 ; Align 100491 159 75 ; Align 100117 185 117 ; Align 99631 224 15
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis