Command line: [exonerate -m p2g --showtargetgff -q SelT.fa.U_to_X -t gi|511782578|gb|CM001956.1|.fastasubseq]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00001359_2.0 # Protein # Selenoprotein T (SelT) # Macaque (Macaca mulatta) 
        Target: gi|511782578|gb|CM001956.1|:subseq(39963998,230579) Chlorocebus sabaeus isolate 1994-021 chromosome 15, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 942
   Query range: 0 -> 188
  Target range: 130579 -> 99999

      1 : LeuValAlaAlaSerAlaMetValArgSerGluAlaSerAlaAsnLeuGlyGlyValP :     20
          ||||||!.!|||||||||||||||||||||||||||||||||||||||||||||||||
          LeuValValAlaSerAlaMetValArgSerGluAlaSerAlaAsnLeuGlyGlyValP
 130579 : CTAGTGGTGGCGTCGGCGATGGTCCGGAGCGAGGCCTCGGCCAATCTGGGCGGCGTGC : 130522

     21 : roSerLysArgLeuLysMetGlnTyrAlaThrGlyProLeuLeuLysPheGlnIle{C :     39
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||{|
          roSerLysArgLeuLysMetGlnTyrAlaThrGlyProLeuLeuLysPheGlnIle{C
 130521 : CCAGCAAGAGATTAAAGATGCAGTACGCCACGGGGCCGCTGCTCAAGTTCCAGATT{T : 130465

     40 : y}  >>>> Target Intron 1 >>>>  {s}ValSerUnkGlyTyrArgArgVal :     47
          |}           25129 bp          {|}||||||   |||||||||||||||
          y}++                         ++{s}ValSer***GlyTyrArgArgVal
 130464 : G}gt.........................ag{T}GTCTCCTGAGGTTATAGGCGGGTG : 105312

     48 : PheGluGluTyrMetArgValIleSerGlnArgTyrProAspIleArgIleGluGlyG :     67
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          PheGluGluTyrMetArgValIleSerGlnArgTyrProAspIleArgIleGluGlyG
 105311 : TTTGAGGAGTACATGCGGGTTATCAGCCAGCGGTACCCAGACATCCGCATTGAAGGAG : 105252

     68 : luAsnTyrLeuProGlnProIleTyr{Ar}  >>>> Target Intron 2 >>>>  :     76
          ||||||||||||||||||||||||||{||}            878 bp          
          luAsnTyrLeuProGlnProIleTyr{Ar}++                         +
 105251 : AGAATTACCTCCCTCAACCAATATAT{AG}gt.........................a : 104347

     77 :  {g}HisIleAlaSerPheLeuSerValPheLysLeuValLeuIleGlyLeuIleIle :     94
           {|}||||||||||||||||||||||||||||||||||||||||||||||||||||||
          +{g}HisIleAlaSerPheLeuSerValPheLysLeuValLeuIleGlyLeuIleIle
 104346 : g{A}CACATAGCATCTTTCCTATCAGTCTTCAAACTAGTATTAATAGGCTTAATAATT : 104293

     95 : ValGlyLysAspProPheAlaPhePheGlyMetGlnAlaProSerIleTrpGlnTrpG :    114
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          ValGlyLysAspProPheAlaPhePheGlyMetGlnAlaProSerIleTrpGlnTrpG
 104292 : GTTGGCAAGGATCCTTTTGCTTTCTTTGGCATGCAAGCTCCTAGCATCTGGCAGTGGG : 104233

    115 : lyGlnGluAsnLys  >>>> Target Intron 3 >>>>  ValTyrAlaCysMet :    123
          ||||||||||||||           1925 bp           |||||||||||||||
          lyGlnGluAsnLys++                         ++ValTyrAlaCysMet
 104232 : GCCAAGAAAATAAGgt.........................agGTCTATGCATGTATG : 102281

    124 : MetValPhePheLeuSerAsnMetIleGluAsnGlnCysMetSerThrGlyAlaPheG :    143
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          MetValPhePheLeuSerAsnMetIleGluAsnGlnCysMetSerThrGlyAlaPheG
 102280 : ATGGTTTTCTTCTTGAGCAACATGATTGAGAACCAGTGTATGTCAACAGGTGCATTTG : 102221

    144 : luIleThrLeuAsn{A}  >>>> Target Intron 4 >>>>  {sp}ValProVa :    151
          ||||||||||||||{|}           2084 bp           {||}||||||||
          luIleThrLeuAsn{A}++                         ++{sp}ValProVa
 102220 : AGATAACTTTAAAT{G}gt.........................ag{AT}GTACCTGT : 100113

    152 : lTrpSerLysLeuGluSerGlyHisLeuProSerMetGlnGlnLeuValGlnIleLeu :    170
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          lTrpSerLysLeuGluSerGlyHisLeuProSerMetGlnGlnLeuValGlnIleLeu
 100112 : GTGGTCTAAGCTGGAATCTGGTCATCTTCCATCCATGCAACAACTTGTTCAAATTCTT : 100056

    171 : AspAsnGluMetLysLeuAsnValHisMetAspSerIleProHisHisArgSer :    188
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||
          AspAsnGluMetLysLeuAsnValHisMetAspSerIleProHisHisArgSer
 100055 : GACAATGAAATGAAGCTCAATGTGCATATGGATTCAATCCCACACCATCGATCA : 100000

vulgar: SPP00001359_2.0 0 188 . gi|511782578|gb|CM001956.1|:subseq(39963998,230579) 130579 99999 - 942 M 38 114 S 0 2 5 0 2 I 0 25125 3 0 2 S 1 1 M 36 108 S 0 2 5 0 2 I 0 874 3 0 2 S 1 1 M 42 126 5 0 2 I 0 1921 3 0 2 M 29 87 S 0 1 5 0 2 I 0 2080 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 2013-11-07
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	gene	100000	130579	942	-	.	gene_id 1 ; sequence SPP00001359_2.0 ; gene_orientation +
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	cds	130464	130579	.	-	.	
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	exon	130464	130579	.	-	.	insertions 0 ; deletions 0
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	splice5	130462	130463	.	-	.	intron_id 1 ; splice_site "GT"
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	intron	105335	130463	.	-	.	intron_id 1
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	splice3	105335	105336	.	-	.	intron_id 0 ; splice_site "AG"
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	cds	105224	105334	.	-	.	
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	exon	105224	105334	.	-	.	insertions 0 ; deletions 0
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	splice5	105222	105223	.	-	.	intron_id 2 ; splice_site "GT"
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	intron	104346	105223	.	-	.	intron_id 2
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	splice3	104346	104347	.	-	.	intron_id 1 ; splice_site "AG"
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	cds	104219	104345	.	-	.	
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	exon	104219	104345	.	-	.	insertions 0 ; deletions 0
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	splice5	104217	104218	.	-	.	intron_id 3 ; splice_site "GT"
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	intron	102294	104218	.	-	.	intron_id 3
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	splice3	102294	102295	.	-	.	intron_id 2 ; splice_site "AG"
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	cds	102206	102293	.	-	.	
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	exon	102206	102293	.	-	.	insertions 0 ; deletions 0
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	splice5	102204	102205	.	-	.	intron_id 4 ; splice_site "GT"
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	intron	100122	102205	.	-	.	intron_id 4
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	splice3	100122	100123	.	-	.	intron_id 3 ; splice_site "AG"
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	cds	100000	100121	.	-	.	
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	exon	100000	100121	.	-	.	insertions 0 ; deletions 0
gi|511782578|gb|CM001956.1|:subseq(39963998,230579)	exonerate:protein2genome:local	similarity	100000	130579	942	-	.	alignment_id 1 ; Query SPP00001359_2.0 ; Align 130580 1 114 ; Align 105334 40 108 ; Align 104345 77 126 ; Align 102294 119 87 ; Align 100120 149 120
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis