Command line: [exonerate -m p2g --showtargetgff -q selenou1a_zf.aa.fa.canviat -t genomeselenou1a_JXSJ01000036.1.fa]
Hostname: [ws101073u]

C4 Alignment:
------------
         Query: SPP00000652_2.0 # Protein # Selenoprotein U1a (SELENOU1a) # Zebrafish 
        Target: JXSJ01000036.1:subseq(1864154,52277) Miichthys miiuy scaffold36, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 483
   Query range: 67 -> 222
  Target range: 2238 -> 1499

   68 : LysAlaLysAlaLeuTrpGluLysSerGlyAlaValIleMetAlaValArgArgProGlyUn :   88
        |||||||||.!!||||||||||||!!!|||||||||||||||!.!|||||||||||||||  
        LysAlaLysThrLeuTrpGluLysThrGlyAlaValIleMetValValArgArgProGly**
 2238 : AAAGCAAAAACTCTGTGGGAGAAGACTGGAGCTGTGATCATGGTTGTACGGCGACCTGGATG : 2178

   89 : kPheLeuCysArgGlu  >>>> Target Intron 1 >>>>  GluAlaSerGluLeuSe :   99
         !!.||||||||||||            84 bp            ||||||:!!||||||||
        *LeuLeuCysArgGlu++                         ++GluAlaAlaGluLeuSe
 2177 : ATTATTGTGCAGAGAGgt.........................agGAGGCTGCTGAGCTGTC : 2061

  100 : rSerLeuLysProGlnLeuAspGluLeuGlyValProLeuTyrAlaValValLysGluAsnV :  120
        |||||||:!! !!||||||.!.!!:|||! !|||||||||!:!||||||||||||||||||:
        rSerLeuGlnSerGlnLeuGlnAspLeuGluValProLeuPheAlaValValLysGluAsnL
 2060 : CTCTCTACAGTCCCAGCTGCAGGACCTCGAGGTTCCTCTATTTGCCGTGGTCAAAGAAAACC : 1998

  121 : alGlyThrGluIleGlnAspPheArgProHisPheAlaGlyGluIlePheLeuAspGluLys :  140
        !!|||! !|||:!:.!.  !|||!:!  !:!!|||:!!|||:!!:!!!:!:!!|||.!.|||
        euGlyLysGluLeuAspCysPheLysLysTyrPheSerGlyLysValTyrValAspHisLys
 1997 : TTGGCAAGGAGCTGGACTGCTTCAAGAAGTACTTCTCTGGAAAGGTCTACGTGGATCACAAG : 1938

  141 :   >>>> Target Intron 2 >>>>  GlnAlaPheTyrGlyProGlnGlnArgLysMet :  151
                    109 bp           ::!  !||||||||||||! !:!!|||  !|||
        ++                         ++ArgAsnPheTyrGlyProLeuGluArgTrpMet
 1937 : gt.........................agAGAAATTTCTACGGCCCTCTAGAGAGATGGATG : 1796

  152 : GlyGlyLeuGlyPheIleArgLeuGlyValTrpGlnAsnPheValArgAlaTrpArgAlaGl :  172
          !  !! !  ! !!:!:|||:!!|||||||||::!|||.!!  !||||||   |||  !||
        PheLeuSerMetValLeuArgIleGlyValTrpArgAsnLeuTrpArgAlaAsnArgLysGl
 1795 : TTTCTCTCCATGGTCCTGCGTATTGGTGTGTGGAGGAATCTCTGGCGAGCGAACCGGAAAGG : 1733

  173 : yTyrGlnGlyAsnMetAsnGlyGluGlyPheIleLeuGlyGlyValPheValMetGlySerG :  193
        |!:!::!||||||.!.!..||||||||||||:!!||||||||||||||||||!!:||| !!|
        yPheArgGlyAsnPheArgGlyGluGlyPheValLeuGlyGlyValPheValIleGlyProG
 1732 : CTTTAGGGGAAACTTTAGAGGTGAAGGATTTGTCCTGGGTGGAGTCTTCGTCATTGGGCCCG : 1670

  194 : lyGlyGln  >>>> Target Intron 3 >>>>  GlyValLeuLeuGluHisArgGluL :  204
        ||! !|||            81 bp            |||:!!|||||||||||||||||||
        lyAspGln++                         ++GlyIleLeuLeuGluHisArgGluL
 1669 : GAGATCAGgt.........................agGGCATTTTACTGGAGCACCGTGAGA : 1556

  205 : ysGluPheGlyAspLysValSerLeuGluSerValLeuGluAlaAlaLysLysVal :  222
        ||||||||||||||||||||!:!:!!  !:!!:!!|||  !.!!|||:::|||:!!
        ysGluPheGlyAspLysValAsnMetLeuAlaLeuLeuThrThrAlaArgLysMet
 1555 : AGGAGTTTGGGGACAAAGTGAATATGTTGGCTTTACTCACGACAGCCCGCAAAATG : 1500

vulgar: SPP00000652_2.0 67 222 . JXSJ01000036.1:subseq(1864154,52277) 2238 1499 - 483 M 26 78 5 0 2 I 0 80 3 0 2 M 47 141 5 0 2 I 0 105 3 0 2 M 55 165 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 2016-11-21
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	gene	1500	2238	483	-	.	gene_id 1 ; sequence SPP00000652_2.0 ; gene_orientation +
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	cds	2161	2238	.	-	.	
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	exon	2161	2238	.	-	.	insertions 0 ; deletions 0
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	splice5	2159	2160	.	-	.	intron_id 1 ; splice_site "GT"
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	intron	2077	2160	.	-	.	intron_id 1
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	splice3	2077	2078	.	-	.	intron_id 0 ; splice_site "AG"
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	cds	1936	2076	.	-	.	
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	exon	1936	2076	.	-	.	insertions 0 ; deletions 0
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	splice5	1934	1935	.	-	.	intron_id 2 ; splice_site "GT"
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	intron	1827	1935	.	-	.	intron_id 2
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	splice3	1827	1828	.	-	.	intron_id 1 ; splice_site "AG"
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	cds	1662	1826	.	-	.	
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	exon	1662	1826	.	-	.	insertions 0 ; deletions 0
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	splice5	1660	1661	.	-	.	intron_id 3 ; splice_site "GT"
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	intron	1581	1661	.	-	.	intron_id 3
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	splice3	1581	1582	.	-	.	intron_id 2 ; splice_site "AG"
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	cds	1500	1580	.	-	.	
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	exon	1500	1580	.	-	.	insertions 0 ; deletions 0
JXSJ01000036.1:subseq(1864154,52277)	exonerate:protein2genome:local	similarity	1500	2238	483	-	.	alignment_id 1 ; Query SPP00000652_2.0 ; Align 2239 68 78 ; Align 2077 94 141 ; Align 1827 141 165 ; Align 1581 196 81
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis