Command line: [exonerate -m p2g --showtargetgff -q ./proteins/SPP00000028_1.0.fa -t ./exonerate/SPP00000028_1.0_1_genomic.fa_exonerate.fa]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000028_1.0 # Protein # Selenoprotein U3 (SelU3) # Homo sapiens # Complete
        Target: gi|357434142|gb|JH378221.1|:subseq(5162851,303731) Saimiri boliviensis boliviensis unplaced genomic scaffold scaffold00117, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 538
   Query range: 35 -> 198
  Target range: 153731 -> 149572

     36 : ValAlaGlyLeuArgArgPheGlyCysValValCysArgTrpIleAlaGlnAspLeuS :     55
          |||||||||||||||||||||||||||! !|||||| !!! !||||||!:!||||||.
          ValAlaGlyLeuArgArgPheGlyCysGlyValCysGly***IleAlaArgAspLeuG
 153731 : GTGGCCGGGCTGCGGCGCTTCGGGTGCGGGGTGTGCGGCTAGATCGCCCGGGACCTCG : 153674

     56 : erSerLeuAlaGlyLeuLeuAspGlnHisGlyValArgLeuValGlyValGlyProGl :     74
          !!||||||||||||||||||!!:|||! !|||||||||||||||||||||||||||:!
          lySerLeuAlaGlyLeuLeuGluGlnProGlyValArgLeuValGlyValGlyProGl
 153673 : GCAGCCTCGCGGGGCTCCTGGAGCAGCCCGGCGTGCGCCTGGTGGGCGTGGGGCCCCA : 153617

     75 : uAlaLeuGlyLeuGlnGluPheLeuAspGlyAspTyrPheAlaGly{G}  >>>> Ta :     90
          !||||||||||||||||||||||||||||||! !||||||||||||{|}         
          nAlaLeuGlyLeuGlnGluPheLeuAspGlyGlyTyrPheAlaGly{G}++       
 153616 : GGCCCTGGGTCTGCAGGAGTTCCTGGACGGCGGCTACTTCGCGGGC{G}gt....... : 153566

     91 : rget Intron 1 >>>>  {lu}LeuTyrLeuAspGluSerLysGlnLeuTyrLysG :    102
             437 bp           {||}||||||||||||||||||||||||||||||||||
                            ++{lu}LeuTyrLeuAspGluSerLysGlnLeuTyrLysG
 153565 : ..................ag{AG}CTCTACCTGGATGAGAGCAAGCAGCTTTATAAGG : 153096

    103 : luLeuGlyPheLys{Ar}  >>>> Target Intron 2 >>>>  {g}TyrAsnSe :    110
          ||||||||||||||{||}            587 bp           {|}|||!:!||
          luLeuGlyPheLys{Ar}++                         ++{g}TyrSerSe
 153095 : AGCTGGGCTTCAAG{CG}gt.........................ag{G}TATAGCAG : 152485

    111 : rLeuSerIleLeuProAlaAlaLeuGlyLysProValArgAspValAlaAlaLysAla :    129
          ||||.!!:!!||||||!.!|||||||||||| !!|||||||||||||||||||||!.!
          rLeuGlyValLeuProValAlaLeuGlyLysSerValArgAspValAlaAlaLysVal
 152484 : CCTGGGTGTCCTCCCTGTGGCCCTCGGGAAGTCCGTGCGTGATGTAGCTGCCAAGGTT : 152428

    130 : LysAlaValGly{Il}  >>>> Target Intron 3 >>>>  {e}GlnGlyAsnL :    138
             |||! ! !!{  }           2237 bp           {!} !  !!   !
          CysAlaGlyArg{Gl}++                         ++{y}TyrArgTrp*
 152427 : TGTGCCGGACGG{GG}gt.........................ag{C}TACAGGTGGT : 150164

    139 : euSerGlyAspLeuLeuGlnSerGlyGlyLeuLeuValValSerLysGlyGlyAspLy :    157
           !  !|||.!.! !|||   :!!! !|||! !! !!.!!.!!!!   |||   |||! 
          **HisGlyGlnProLeuGlyAlaAspGlyProProAlaAlaThrGlyGly---AspTh
 150163 : GACACGGGCAGCCTCTGGGTGCTGACGGCCCGCCCGCTGCTACAGGTGGT---GACAC : 150110

    158 : sValLeuLeuHisPheValGlnLysSerProGlyAspTyrValProLysGluHisIle :    176
          !|||||||||||||||||||||||||||||||||||||||||||||  !|||||||||
          rValLeuLeuHisPheValGlnLysSerProGlyAspTyrValProTrpGluHisIle
 150109 : AGTGCTGCTGCATTTCGTCCAGAAGTCTCCAGGTGACTACGTTCCCTGGGAGCATATC : 150053

    177 : LeuGlnValLeuGlyIleSerAlaGluValCysAlaSerAspProProGln  >>>>  :    194
          |||||||||||||||||||||||||||||||||||||||!  |||||||||       
          LeuGlnValLeuGlyIleSerAlaGluValCysAlaSerGlyProProGln++     
 150052 : CTGCAGGTCCTGGGCATCTCTGCAGAGGTGTGTGCCAGCGGGCCGCCTCAGgt..... : 149997

    195 : Target Intron 4 >>>>  CysAspArgGluVal :    198
               412 bp           ||||||||||||:!!
                              ++CysAspArgGluLeu
 149996 : ....................agTGTGACAGAGAGTTG : 149573

vulgar: SPP00000028_1.0 35 198 . gi|357434142|gb|JH378221.1|:subseq(5162851,303731) 153731 149572 - 538 M 54 162 S 0 1 5 0 2 I 0 433 3 0 2 S 1 2 M 16 48 S 0 2 5 0 2 I 0 583 3 0 2 S 1 1 M 26 78 S 0 2 5 0 2 I 0 2233 3 0 2 S 1 1 M 20 60 G 1 0 M 38 114 5 0 2 I 0 408 3 0 2 M 5 15
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2012-11-14
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	gene	149573	153731	538	-	.	gene_id 1 ; sequence SPP00000028_1.0 ; gene_orientation +
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	cds	153569	153731	.	-	.	
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	exon	153569	153731	.	-	.	insertions 0 ; deletions 0
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	splice5	153567	153568	.	-	.	intron_id 1 ; splice_site "GT"
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	intron	153132	153568	.	-	.	intron_id 1
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	splice3	153132	153133	.	-	.	intron_id 0 ; splice_site "AG"
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	cds	153080	153131	.	-	.	
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	exon	153080	153131	.	-	.	insertions 0 ; deletions 0
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	splice5	153078	153079	.	-	.	intron_id 2 ; splice_site "GT"
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	intron	152493	153079	.	-	.	intron_id 2
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	splice3	152493	152494	.	-	.	intron_id 1 ; splice_site "AG"
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	cds	152412	152492	.	-	.	
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	exon	152412	152492	.	-	.	insertions 0 ; deletions 0
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	splice5	152410	152411	.	-	.	intron_id 3 ; splice_site "GT"
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	intron	150175	152411	.	-	.	intron_id 3
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	splice3	150175	150176	.	-	.	intron_id 2 ; splice_site "AG"
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	cds	150000	150174	.	-	.	
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	exon	150000	150174	.	-	.	insertions 0 ; deletions 1
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	splice5	149998	149999	.	-	.	intron_id 4 ; splice_site "GT"
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	intron	149588	149999	.	-	.	intron_id 4
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	splice3	149588	149589	.	-	.	intron_id 3 ; splice_site "AG"
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	cds	149573	149587	.	-	.	
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	exon	149573	149587	.	-	.	insertions 0 ; deletions 0
gi|357434142|gb|JH378221.1|:subseq(5162851,303731)	exonerate:protein2genome:local	similarity	149573	153731	538	-	.	alignment_id 1 ; Query SPP00000028_1.0 ; Align 153732 36 162 ; Align 153130 91 48 ; Align 152492 108 78 ; Align 150174 135 60 ; Align 150114 156 114 ; Align 149588 194 15
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis