Command line: [exonerate -m p2g --showtargetgff -q /homes/users/U63741/seqaammx/selT.mm.fa -t selT.mm.subseq.fa]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000116_1.0 # Protein # Selenoprotein T (SelT) # Mus musculus # Complete
        Target: GL192476.1:subseq(15742,20131) dna:scaffold scaffold:ailMel1:GL192476.1:1:2486912:1 REF
         Model: protein2genome:local
     Raw score: 769
   Query range: 40 -> 195
  Target range: 9288 -> 14128

    41 : LeuLysPheGlnIleCysValSerUnkGlyTyrArgArgValPheGluGluTyrMetArg :    60
         |||..!|||     ! !!||||||   |||||||||||||||||||||||||||||||||
         LeuSerPhePheCysSerValSer***GlyTyrArgArgValPheGluGluTyrMetArg
  9289 : CTTTCATTTTTCTGCAGTGTTTCCTGAGGTTATAGGCGGGTGTTTGAGGAGTACATGCGG :  9346

    61 : ValIleSerGlnArgTyrProAspIleArgIleGluGlyGluAsnTyrLeuProGlnPro :    80
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         ValIleSerGlnArgTyrProAspIleArgIleGluGlyGluAsnTyrLeuProGlnPro
  9347 : GTTATAAGCCAGCGGTACCCAGACATCCGCATTGAAGGAGAAAATTACCTTCCTCAACCC :  9406

    81 : IleTyr{Ar}  >>>> Target Intron 1 >>>>  {g}HisIleAlaSerPheLeu :    89
         ||||||{||}            585 bp           {|}||||||||||||||||||
         IleTyr{Ar}++                         ++{g}HisIleAlaSerPheLeu
  9407 : ATATAT{AG}gt.........................ag{A}CACATAGCATCTTTCCTG : 10018

    90 : SerValPheLysLeuValLeuIleGlyLeuIleIleValGlyLysAspProPheAlaPhe :   109
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         SerValPheLysLeuValLeuIleGlyLeuIleIleValGlyLysAspProPheAlaPhe
 10019 : TCAGTCTTCAAACTAGTATTAATAGGCTTAATAATTGTTGGCAAGGATCCTTTTGCTTTC : 10078

   110 : PheGlyMetGlnAlaProSerIleTrpGlnTrpGlyGlnGluAsnLys  >>>> Targe :   126
         ||||||||||||||||||||||||||||||||||||||||||||||||           2
         PheGlyMetGlnAlaProSerIleTrpGlnTrpGlyGlnGluAsnLys++          
 10079 : TTTGGCATGCAAGCTCCTAGCATCTGGCAGTGGGGCCAAGAAAATAAGgt.......... : 10131

   127 : t Intron 2 >>>>  ValTyrAlaCysMetMetValPhePheLeuSerAsnMetIleG :   140
         051 bp           |||||||||||||||||||||||||||||||||||||||||||
                        ++ValTyrAlaCysMetMetValPhePheLeuSerAsnMetIleG
 10132 : ...............agGTCTATGCATGTATGATGGTTTTCTTCTTGAGCAACATGATTG : 12222

   141 : luAsnGlnCysMetSerThrGlyAlaPheGluIleThrLeuAsn{A}  >>>> Target :   155
         ||||||||||||||||||||||||||||||||||||||||||||{|}           17
         luAsnGlnCysMetSerThrGlyAlaPheGluIleThrLeuAsn{A}++           
 12223 : AGAACCAGTGTATGTCAACAGGTGCATTTGAGATAACTTTGAAT{G}gt........... : 12270

   156 :  Intron 3 >>>>  {sp}ValProValTrpSerLysLeuGluSerGlyHisLeuProS :   169
         39 bp           {||}||||||||||||||||||||||||||||||||||||||||
                       ++{sp}ValProValTrpSerLysLeuGluSerGlyHisLeuProS
 12271 : ..............ag{AT}GTGCCTGTGTGGTCCAAGCTAGAATCTGGTCACCTCCCAT : 14048

   170 : erMetGlnGlnLeuValGlnIleLeuAspAsnGluMetLysLeuAsnValHisMetAspS :   189
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         erMetGlnGlnLeuValGlnIleLeuAspAsnGluMetLysLeuAsnValHisMetAspS
 14049 : CCATGCAACAGCTTGTTCAAATTCTTGACAATGAAATGAAGCTCAATGTGCATATGGATT : 14108

   190 : erIleProHisHisArgSer :   195
         ||||||||||||||||||||
         erIleProHisHisArgSer
 14109 : CAATCCCACATCATCGATCA : 14128

vulgar: SPP00000116_1.0 40 195 . GL192476.1:subseq(15742,20131) 9288 14128 + 769 M 42 126 S 0 2 5 0 2 I 0 581 3 0 2 S 1 1 M 42 126 5 0 2 I 0 2047 3 0 2 M 29 87 S 0 1 5 0 2 I 0 1735 3 0 2 S 1 2 M 40 120
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2012-12-03
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	gene	9289	14128	769	+	.	gene_id 1 ; sequence SPP00000116_1.0 ; gene_orientation +
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	cds	9289	9416	.	+	.	
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	exon	9289	9416	.	+	.	insertions 0 ; deletions 0
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	splice5	9417	9418	.	+	.	intron_id 1 ; splice_site "GT"
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	intron	9417	10001	.	+	.	intron_id 1
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	splice3	10000	10001	.	+	.	intron_id 0 ; splice_site "AG"
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	cds	10002	10128	.	+	.	
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	exon	10002	10128	.	+	.	insertions 0 ; deletions 0
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	splice5	10129	10130	.	+	.	intron_id 2 ; splice_site "GT"
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	intron	10129	12179	.	+	.	intron_id 2
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	splice3	12178	12179	.	+	.	intron_id 1 ; splice_site "AG"
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	cds	12180	12267	.	+	.	
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	exon	12180	12267	.	+	.	insertions 0 ; deletions 0
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	splice5	12268	12269	.	+	.	intron_id 3 ; splice_site "GT"
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	intron	12268	14006	.	+	.	intron_id 3
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	splice3	14005	14006	.	+	.	intron_id 2 ; splice_site "AG"
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	cds	14007	14128	.	+	.	
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	exon	14007	14128	.	+	.	insertions 0 ; deletions 0
GL192476.1:subseq(15742,20131)	exonerate:protein2genome:local	similarity	9289	14128	769	+	.	alignment_id 1 ; Query SPP00000116_1.0 ; Align 9289 41 126 ; Align 10003 84 126 ; Align 12180 126 87 ; Align 14009 156 120
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
