Command line: [exonerate -m p2g --showtargetgff -q /homes/users/U63741/seqaahs/selU1.hs.fa -t selu1.hs.subseq.fa]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000026_1.0 # Protein # Selenoprotein U1 (SelU1) # Homo sapiens # Complete
        Target: GL192914.1:subseq(1068998,20179) dna:scaffold scaffold:ailMel1:GL192914.1:1:1188742:1 REF
         Model: protein2genome:local
     Raw score: 1080
   Query range: 0 -> 229
  Target range: 4074 -> 13275

     1 : MetSerPheLeuGlnAspProSerPhePheThrMetGlyMetTrpSerIleGlyAlaGly :    20
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         MetSerPheLeuGlnAspProSerPhePheThrMetGlyMetTrpSerIleGlyAlaGly
  4075 : ATGTCTTTCCTCCAGGATCCGAGTTTCTTCACCATGGGGATGTGGTCCATCGGTGCGGGG :  4132

    21 : AlaLeuGlyAlaAlaAlaLeuAlaLeuLeuLeuAlaAsnThrAspValPheLeuSerLys :    40
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         AlaLeuGlyAlaAlaAlaLeuAlaLeuLeuLeuAlaAsnThrAspValPheLeuSerLys
  4133 : GCCCTGGGGGCAGCTGCCTTGGCCCTGCTCCTGGCCAACACAGACGTGTTTCTGTCCAAG :  4192

    41 : ProGlnLysAlaAlaLeuGluTyrLeuGluAspIleAspLeuLysThrLeuGluLys{G} :    60
          !!|||||||||.!!||||||||||||||||||||||||||||||||||||||||||{|}
         SerGlnLysAlaThrLeuGluTyrLeuGluAspIleAspLeuLysThrLeuGluLys{G}
  4193 : TCCCAGAAAGCGACGCTGGAGTATCTGGAGGACATAGACCTGAAAACCCTGGAGAAG{G} :  4252

    61 :   >>>> Target Intron 1 >>>>  {lu}ProArgThrPheLysAlaLysGluLeu :    69
                    1881 bp           {||}|||||||||||||||||||||||||||
         ++                         ++{lu}ProArgThrPheLysAlaLysGluLeu
  4253 : gt.........................ag{AA}CCAAGGACTTTCAAAGCAAAGGAGCTC :  6160

    70 : TrpGluLysAsnGlyAlaValIleMetAlaValArgArgProGlyCysPheLeuCysArg :    89
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         TrpGluLysAsnGlyAlaValIleMetAlaValArgArgProGlyCysPheLeuCysArg
  6161 : TGGGAAAAGAATGGAGCTGTGATTATGGCTGTGCGCAGGCCTGGCTGTTTCCTCTGCCGA :  6220

    90 : Glu  >>>> Target Intron 2 >>>>  GluAlaAlaAspLeuSerSerLeuLysS :   100
         |||           2997 bp           ||||||||||||||||||||||||||| 
         Glu++                         ++GluAlaAlaAspLeuSerSerLeuLysP
  6221 : GAGgt.........................agGAGGCTGCCGACCTGTCCTCCCTGAAGC :  9250

   101 : erMetLeuAspGlnLeuGlyValProLeuTyrAlaValValLysGluHisIleArgThrG :   120
         !!! !||||||:!!|||||||||||||||||||||||||||||||||!!.||||||||||
         roLysLeuAspGluLeuGlyValProLeuTyrAlaValValLysGluGlnIleArgThrG
  9251 : CCAAGCTGGACGAGCTGGGAGTCCCCCTGTATGCAGTGGTGAAGGAACAAATCAGGACCG :  9310

   121 : luValLysAspPheGlnProTyrPheLysGlyGluIlePheLeuAspGluLys  >>>>  :   138
         |||||:!!|||||||||||||||||||||||||||||||||||||||||||||       
         luValGlnAspPheGlnProTyrPheLysGlyGluIlePheLeuAspGluLys++     
  9311 : AAGTGCAGGACTTCCAGCCTTATTTCAAAGGAGAAATCTTCCTGGATGAAAAGgt..... :  9366

   139 : Target Intron 3 >>>>  LysLysPheTyrGlyProGlnArgArgLysMetMetPh :   150
              651 bp           ||||||||||||||||||||||||||||||||||||||
                             ++LysLysPheTyrGlyProGlnArgArgLysMetMetPh
  9367 : ....................agAAAAAGTTCTACGGTCCCCAAAGGCGGAAGATGATGTT : 10051

   151 : eMetGlyPheIleArgLeuGlyValTrpTyrAsnPhePheArgAlaTrpAsnGlyGlyPh :   170
         ||||||||||:!!||||||||||||||||||||||||||||||||| !!|||||||||||
         eMetGlyPheValArgLeuGlyValTrpTyrAsnPhePheArgAlaArgAsnGlyGlyPh
 10052 : TATGGGATTTGTCCGTCTGGGTGTTTGGTACAACTTCTTCCGGGCCCGGAACGGAGGCTT : 10111

   171 : eSerGlyAsnLeuGluGlyGluGlyPheIleLeuGlyGlyValPheValValGlySerGl :   190
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         eSerGlyAsnLeuGluGlyGluGlyPheIleLeuGlyGlyValPheValValGlySerGl
 10112 : TTCTGGAAACCTGGAAGGCGAAGGCTTCATCCTTGGGGGAGTTTTTGTGGTGGGATCAGG : 10171

   191 : yLysGln  >>>> Target Intron 4 >>>>  GlyIleLeuLeuGluHisArgGlu :   200
         |||||||           2985 bp           ||||||||||||||||||||||||
         yLysGln++                         ++GlyIleLeuLeuGluHisArgGlu
 10172 : AAAGCAGgt.........................agGGCATTCTTCTCGAGCATCGGGAA : 13186

   201 : LysGluPheGlyAspLysValAsnLeuLeuSerValLeuGluAlaAlaLysMetIleLys :   220
         ||||||||||||||||||||||||! !:!!||||||||||||||||||!:!! !|||:!!
         LysGluPheGlyAspLysValAsnProValSerValLeuGluAlaAlaArgLysIleGln
 13187 : AAAGAATTTGGAGACAAAGTGAACCCAGTTTCTGTTCTGGAAGCTGCTAGGAAGATCCAA : 13246

   221 : ProGlnThrLeuAlaSerGluLysLys :   229
         |||||||||! !|||:!!|||! !|||
         ProGlnThrSerAlaAlaGluThrLys
 13247 : CCCCAGACTTCAGCCGCAGAGACAAAG : 13275

vulgar: SPP00000026_1.0 0 229 . GL192914.1:subseq(1068998,20179) 4074 13275 + 1080 M 59 177 S 0 1 5 0 2 I 0 1877 3 0 2 S 1 2 M 30 90 5 0 2 I 0 2993 3 0 2 M 47 141 5 0 2 I 0 647 3 0 2 M 55 165 5 0 2 I 0 2981 3 0 2 M 37 111
# --- 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
#
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	gene	4075	13275	1080	+	.	gene_id 1 ; sequence SPP00000026_1.0 ; gene_orientation +
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	cds	4075	4252	.	+	.	
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	exon	4075	4252	.	+	.	insertions 0 ; deletions 0
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	splice5	4253	4254	.	+	.	intron_id 1 ; splice_site "GT"
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	intron	4253	6133	.	+	.	intron_id 1
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	splice3	6132	6133	.	+	.	intron_id 0 ; splice_site "AG"
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	cds	6134	6225	.	+	.	
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	exon	6134	6225	.	+	.	insertions 0 ; deletions 0
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	splice5	6226	6227	.	+	.	intron_id 2 ; splice_site "GT"
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	intron	6226	9222	.	+	.	intron_id 2
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	splice3	9221	9222	.	+	.	intron_id 1 ; splice_site "AG"
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	cds	9223	9363	.	+	.	
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	exon	9223	9363	.	+	.	insertions 0 ; deletions 0
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	splice5	9364	9365	.	+	.	intron_id 3 ; splice_site "GT"
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	intron	9364	10014	.	+	.	intron_id 3
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	splice3	10013	10014	.	+	.	intron_id 2 ; splice_site "AG"
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	cds	10015	10179	.	+	.	
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	exon	10015	10179	.	+	.	insertions 0 ; deletions 0
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	splice5	10180	10181	.	+	.	intron_id 4 ; splice_site "GT"
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	intron	10180	13164	.	+	.	intron_id 4
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	splice3	13163	13164	.	+	.	intron_id 3 ; splice_site "AG"
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	cds	13165	13275	.	+	.	
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	exon	13165	13275	.	+	.	insertions 0 ; deletions 0
GL192914.1:subseq(1068998,20179)	exonerate:protein2genome:local	similarity	4075	13275	1080	+	.	alignment_id 1 ; Query SPP00000026_1.0 ; Align 4075 1 177 ; Align 6136 61 90 ; Align 9223 91 141 ; Align 10015 138 165 ; Align 13165 193 111
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
