Command line: [exonerate -m p2g --showtargetgff -q DI1.aa.fa.U_to_X -t gi|511782573|gb|CM001961.1|.fastasubseq]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000002_2.0 # Protein # Iodothyronine deiodinase 1 (DI1) # Human (Homo sapiens) 
        Target: gi|511782573|gb|CM001961.1|:subseq(78925275,215869) Chlorocebus sabaeus isolate 1994-021 chromosome 20, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 1272
   Query range: 0 -> 249
  Target range: 115869 -> 99999

      1 : MetGlyLeuProGlnProGlyLeuTrpLeuLysArgLeuTrpValLeuLeuGluValA :     20
          ||||||||||||||| !!|||||||||:!!|||!:!||||||||||||||||||||||
          MetGlyLeuProGlnSerGlyLeuTrpValLysLysLeuTrpValLeuLeuGluValA
 115869 : ATGGGGCTGCCCCAGTCAGGGCTGTGGGTGAAGAAGCTCTGGGTGCTCCTGGAGGTGG : 115812

     21 : laValHisValValValGlyLysValLeuLeuIleLeuPheProAspArgValLysAr :     39
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          laValHisValValValGlyLysValLeuLeuIleLeuPheProAspArgValLysAr
 115811 : CTGTCCATGTGGTCGTGGGTAAAGTGCTTCTGATATTGTTTCCAGACAGAGTCAAGCG : 115755

     40 : gAsnIleLeuAlaMetGlyGluLysThrGlyMetThrArgAsnProHisPheSerHis :     58
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          gAsnIleLeuAlaMetGlyGluLysThrGlyMetThrArgAsnProHisPheSerHis
 115754 : GAACATCCTGGCCATGGGCGAGAAGACCGGTATGACCAGGAACCCCCATTTCAGCCAC : 115698

     59 : AspAsnTrpIleProThrPhePheSerThrGlnTyrPheTrpPheValLeuLysValA :     78
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          AspAsnTrpIleProThrPhePheSerThrGlnTyrPheTrpPheValLeuLysValA
 115697 : GACAACTGGATCCCGACCTTTTTCAGCACCCAGTATTTCTGGTTCGTCTTGAAGGTCC : 115638

     79 : rgTrpGlnArgLeuGluAspThrThrGluLeuGlyGlyLeuAlaProAsnCysProVa :     97
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          rgTrpGlnArgLeuGluAspThrThrGluLeuGlyGlyLeuAlaProAsnCysProVa
 115637 : GTTGGCAGCGACTAGAGGACACGACTGAGCTAGGGGGTCTGGCCCCAAACTGCCCAGT : 115581

     98 : lValArgLeuSerGlyGlnArgCysAsnIleTrpGluPheMetGln{G}  >>>> Ta :    113
          ||||||||||||||||||||||||||||||||||!!:|||||||||{|}         
          lValArgLeuSerGlyGlnArgCysAsnIleTrpAspPheMetGln{G}++       
 115580 : GGTCCGCCTCTCAGGACAGAGGTGCAACATTTGGGACTTTATGCAA{G}gt....... : 115530

    114 : rget Intron 1 >>>>  {ly}AsnArgProLeuValLeuAsnPheGlySerCysT :    125
            9982 bp           {||}||||||||||||||||||||||||||||||||||
                            ++{ly}AsnArgProLeuValLeuAsnPheGlySerCysT
 115529 : ..................ag{GC}AATAGGCCACTGGTGCTGAATTTTGGAAGTTGTA : 105515

    126 : hrUnkProSerPheMetPheLysPheAspGlnPheLysArgLeuIleGluAspPheSe :    144
          ||   |||||||||||||||||||||||||||||||||||||||||||||||||||||
          hr***ProSerPheMetPheLysPheAspGlnPheLysArgLeuIleGluAspPheSe
 105514 : CCTGACCTTCATTTATGTTCAAATTTGACCAATTCAAGAGGCTTATTGAAGACTTTAG : 105458

    145 : rSerIleAlaAspPheLeuValIleTyrIleGluGluAlaHisAlaSer{A}  >>>> :    161
          |||||||||||||||||||:!!|||||||||||||||||||||||||||{|}      
          rSerIleAlaAspPheLeuIleIleTyrIleGluGluAlaHisAlaSer{A}++    
 105457 : TTCCATAGCAGATTTTCTCATCATTTACATTGAAGAAGCACATGCATCA{G}gt.... : 105404

    162 :  Target Intron 2 >>>>  {sp}GlyTrpAlaPheLysAsnAsnMetAspIleA :    172
               1511 bp           {||}|||||||||||||||||||||||||||||||
                               ++{sp}GlyTrpAlaPheLysAsnAsnMetAspIleA
 105403 : .....................ag{AT}GGCTGGGCTTTTAAGAACAACATGGACATCA : 103863

    173 : rgAsnHisGlnAsnLeuGlnAspArgLeuGlnAlaAlaHisLeuLeuLeuAlaArgSe :    191
          ||||||||!:!|||||||||||||||||||||||||||||||||||||||||||||||
          rgAsnHisArgAsnLeuGlnAspArgLeuGlnAlaAlaHisLeuLeuLeuAlaArgSe
 103862 : GAAATCACCGGAACCTTCAGGACCGCCTGCAGGCAGCCCATCTACTGCTGGCCAGGAG : 103806

    192 : rProGlnCysProValValValAspThrMetGlnAsnGlnSerSerGlnLeuTyrAla :    210
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          rProGlnCysProValValValAspThrMetGlnAsnGlnSerSerGlnLeuTyrAla
 103805 : CCCCCAGTGCCCTGTGGTGGTGGATACCATGCAGAACCAGAGCAGCCAGCTCTACGCA : 103749

    211 : AlaLeuProGluArgLeuTyrIleIleGlnGluGlyArgIleLeuTyrLys  >>>>  :    228
          |||||||||||||||||||||:!!|||||||||||||||||||||||||||       
          AlaLeuProGluArgLeuTyrValIleGlnGluGlyArgIleLeuTyrLys++     
 103748 : GCACTGCCTGAGAGGCTCTACGTAATCCAGGAGGGCAGGATCCTCTACAAGgt..... : 103693

    229 : Target Intron 3 >>>>  GlyLysSerGlyProTrpAsnTyrAsnProGluGlu :    239
              3630 bp           ||||||||||||||||||||||||||||||||||||
                              ++GlyLysSerGlyProTrpAsnTyrAsnProGluGlu
 103692 : ....................agGGTAAATCCGGCCCTTGGAACTACAATCCAGAGGAA : 100032

    240 : ValArgAlaValLeuGluLysLeuHisSer :    249
          ||||||||||||||||||||||||:!!|||
          ValArgAlaValLeuGluLysLeuTyrSer
 100031 : GTTCGTGCTGTTCTGGAAAAGCTCTACAGT : 100000

vulgar: SPP00000002_2.0 0 249 . gi|511782573|gb|CM001961.1|:subseq(78925275,215869) 115869 99999 - 1272 M 112 336 S 0 1 5 0 2 I 0 9978 3 0 2 S 1 2 M 47 141 S 0 1 5 0 2 I 0 1507 3 0 2 S 1 2 M 66 198 5 0 2 I 0 3626 3 0 2 M 22 66
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-21
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	gene	100000	115869	1272	-	.	gene_id 1 ; sequence SPP00000002_2.0 ; gene_orientation +
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	cds	115533	115869	.	-	.	
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	exon	115533	115869	.	-	.	insertions 0 ; deletions 0
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	splice5	115531	115532	.	-	.	intron_id 1 ; splice_site "GT"
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	intron	105551	115532	.	-	.	intron_id 1
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	splice3	105551	105552	.	-	.	intron_id 0 ; splice_site "AG"
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	cds	105407	105550	.	-	.	
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	exon	105407	105550	.	-	.	insertions 0 ; deletions 0
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	splice5	105405	105406	.	-	.	intron_id 2 ; splice_site "GT"
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	intron	103896	105406	.	-	.	intron_id 2
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	splice3	103896	103897	.	-	.	intron_id 1 ; splice_site "AG"
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	cds	103696	103895	.	-	.	
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	exon	103696	103895	.	-	.	insertions 0 ; deletions 0
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	splice5	103694	103695	.	-	.	intron_id 3 ; splice_site "GT"
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	intron	100066	103695	.	-	.	intron_id 3
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	splice3	100066	100067	.	-	.	intron_id 2 ; splice_site "AG"
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	cds	100000	100065	.	-	.	
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	exon	100000	100065	.	-	.	insertions 0 ; deletions 0
gi|511782573|gb|CM001961.1|:subseq(78925275,215869)	exonerate:protein2genome:local	similarity	100000	115869	1272	-	.	alignment_id 1 ; Query SPP00000002_2.0 ; Align 115870 1 336 ; Align 105549 114 141 ; Align 103894 162 198 ; Align 100066 228 66
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis