Command line: [exonerate -m p2g --showtargetgff -q ./proteins/SPP00000001_1.0.fa -t ./exonerate/SPP00000001_1.0_1_genomic.fa_exonerate.fa]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00000001_1.0 # Protein # Iodothyronine deiodinase 1 (DI1) # Homo sapiens # Complete
        Target: gi|357434255|gb|JH378108.1|:subseq(31482165,318886) Saimiri boliviensis boliviensis unplaced genomic scaffold scaffold00004, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 1244
   Query range: 0 -> 249
  Target range: 168886 -> 149999

      1 : MetGlyLeuProGlnProGlyLeuTrpLeuLysArgLeuTrpValLeuLeuGluValA :     20
          ||||||||||||  !|||||||||||||||||||||||||||||||||||||||||||
          MetGlyLeuProGlyProGlyLeuTrpLeuLysArgLeuTrpValLeuLeuGluValA
 168886 : ATGGGGCTGCCCGGGCCAGGGCTATGGCTGAAGAGGCTCTGGGTGCTCTTGGAGGTGG : 168829

     21 : laValHisValValValGlyLysValLeuLeuIleLeuPheProAspArgValLysAr :     39
          |||||||||||!.!|||||||||:!!||||||! !|||||||||||||||||||||!:
          laValHisValAlaValGlyLysLeuLeuLeuThrLeuPheProAspArgValLysLy
 168828 : CTGTGCATGTGGCTGTGGGCAAACTGCTTCTGACATTGTTTCCAGACAGAGTCAAGAA : 168772

     40 : gAsnIleLeuAlaMetGlyGluLysThrGlyMetThrArgAsnProHisPheSerHis :     58
          !||||||||||||||||||!!:||||||||||||||||||||||||:!!|||||||||
          sAsnIleLeuAlaMetGlyAspLysThrGlyMetThrArgAsnProAsnPheSerHis
 168771 : GAACATACTAGCCATGGGCGACAAGACGGGTATGACCAGGAACCCTAACTTCAGCCAC : 168715

     59 : AspAsnTrpIleProThrPhePheSerThrGlnTyrPheTrpPheValLeuLysValA :     78
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          AspAsnTrpIleProThrPhePheSerThrGlnTyrPheTrpPheValLeuLysValA
 168714 : GACAACTGGATCCCGACCTTTTTCAGCACCCAGTATTTCTGGTTCGTCCTGAAGGTCC : 168655

     79 : rgTrpGlnArgLeuGluAspThrThrGluLeuGlyGlyLeuAlaProAsnCysProVa :     97
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          rgTrpGlnArgLeuGluAspThrThrGluLeuGlyGlyLeuAlaProAsnCysProVa
 168654 : GTTGGCAGCGACTAGAGGACACGACTGAGCTAGGGGGTCTGGCCCCAAACTGCCCAGT : 168598

     98 : lValArgLeuSerGlyGlnArgCysAsnIleTrpGluPheMetGln{G}  >>>> Ta :    113
          ||||!.!|||||||||||||||||||||||||||!!:|||||||||{|}         
          lValHisLeuSerGlyGlnArgCysAsnIleTrpAspPheMetGln{G}++       
 168597 : GGTCCACCTCTCAGGACAGAGGTGCAACATTTGGGACTTTATGCAA{G}gt....... : 168547

    114 : rget Intron 1 >>>>  {ly}AsnArgProLeuValLeuAsnPheGlySerCysT :    125
            9987 bp           {||}||||||||||||||||||||||||||||||||||
                            ++{ly}AsnArgProLeuValLeuAsnPheGlySerCysT
 168546 : ..................ag{GC}AACAGGCCCCTGGTGCTGAATTTTGGAAGTTGTA : 158527

    126 : hrUnkProSerPheMetPheLysPheAspGlnPheLysArgLeuIleGluAspPheSe :    144
          ||   |||||||||||||||||||||||||||||||||||||||! !|||||||||||
          hr***ProSerPheMetPheLysPheAspGlnPheLysArgLeuThrGluAspPheSe
 158526 : CCTGACCTTCATTTATGTTCAAATTTGACCAATTCAAGAGACTTACTGAAGACTTTAG : 158470

    145 : rSerIleAlaAspPheLeuValIleTyrIleGluGluAlaHisAlaSer{A}  >>>> :    161
          ||||:!!||||||||||||:!!|||||||||||||||||||||||||||{|}      
          rSerValAlaAspPheLeuIleIleTyrIleGluGluAlaHisAlaSer{A}++    
 158469 : TTCCGTAGCAGATTTTCTCATCATTTACATTGAAGAAGCACATGCATCA{G}gt.... : 158416

    162 :  Target Intron 2 >>>>  {sp}GlyTrpAlaPheLysAsnAsnMetAspIleA :    172
               5189 bp           {||}|||||||||||||||||||||:!!|||||||
                               ++{sp}GlyTrpAlaPheLysAsnAsnValAspIleA
 158415 : .....................ag{AT}GGCTGGGCTTTCAAGAACAACGTGGACATCA : 153197

    173 : rgAsnHisGlnAsnLeuGlnAspArgLeuGlnAlaAlaHisLeuLeuLeuAlaArgSe :    191
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
          rgAsnHisGlnAsnLeuGlnAspArgLeuGlnAlaAlaHisLeuLeuLeuAlaArgSe
 153196 : GGAATCACCAGAACCTTCAGGACCGCCTGCAGGCAGCCCATCTGCTGCTGGCCAGGAG : 153140

    192 : rProGlnCysProValValValAspThrMetGlnAsnGlnSerSerGlnLeuTyrAla :    210
          ||||||||||||||||||||||||||||||||||||||||||||||:!!|||||||||
          rProGlnCysProValValValAspThrMetGlnAsnGlnSerSerGluLeuTyrAla
 153139 : CCCCCAGTGCCCTGTGGTAGTGGACACGATGCAGAACCAGAGCAGCGAGCTCTACGCA : 153083

    211 : AlaLeuProGluArgLeuTyrIleIleGlnGluGlyArgIleLeuTyrLys  >>>>  :    228
          |||||||||||||||||||||||||||||||||||||||||||||||||||       
          AlaLeuProGluArgLeuTyrIleIleGlnGluGlyArgIleLeuTyrLys++     
 153082 : GCACTGCCTGAGAGGCTCTACATAATCCAGGAAGGCAGGATCCTCTACAAGgt..... : 153027

    229 : Target Intron 3 >>>>  GlyLysSerGlyProTrpAsnTyrAsnProGluGlu :    239
              2964 bp           ||||||||||||||||||||||||||||||||||||
                              ++GlyLysSerGlyProTrpAsnTyrAsnProGluGlu
 153026 : ....................agGGTAAATCCGGCCCTTGGAACTACAATCCAGAGGAA : 150032

    240 : ValArgAlaValLeuGluLysLeuHisSer :    249
          ||||||! !|||||||||||||||||||||
          ValArgAspValLeuGluLysLeuHisSer
 150031 : GTTCGTGATGTTCTGGAAAAACTCCACAGT : 150000

vulgar: SPP00000001_1.0 0 249 . gi|357434255|gb|JH378108.1|:subseq(31482165,318886) 168886 149999 - 1244 M 112 336 S 0 1 5 0 2 I 0 9983 3 0 2 S 1 2 M 47 141 S 0 1 5 0 2 I 0 5185 3 0 2 S 1 2 M 66 198 5 0 2 I 0 2960 3 0 2 M 22 66
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2012-11-14
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	gene	150000	168886	1244	-	.	gene_id 1 ; sequence SPP00000001_1.0 ; gene_orientation +
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	cds	168550	168886	.	-	.	
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	exon	168550	168886	.	-	.	insertions 0 ; deletions 0
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	splice5	168548	168549	.	-	.	intron_id 1 ; splice_site "GT"
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	intron	158563	168549	.	-	.	intron_id 1
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	splice3	158563	158564	.	-	.	intron_id 0 ; splice_site "AG"
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	cds	158419	158562	.	-	.	
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	exon	158419	158562	.	-	.	insertions 0 ; deletions 0
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	splice5	158417	158418	.	-	.	intron_id 2 ; splice_site "GT"
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	intron	153230	158418	.	-	.	intron_id 2
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	splice3	153230	153231	.	-	.	intron_id 1 ; splice_site "AG"
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	cds	153030	153229	.	-	.	
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	exon	153030	153229	.	-	.	insertions 0 ; deletions 0
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	splice5	153028	153029	.	-	.	intron_id 3 ; splice_site "GT"
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	intron	150066	153029	.	-	.	intron_id 3
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	splice3	150066	150067	.	-	.	intron_id 2 ; splice_site "AG"
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	cds	150000	150065	.	-	.	
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	exon	150000	150065	.	-	.	insertions 0 ; deletions 0
gi|357434255|gb|JH378108.1|:subseq(31482165,318886)	exonerate:protein2genome:local	similarity	150000	168886	1244	-	.	alignment_id 1 ; Query SPP00000001_1.0 ; Align 168887 1 336 ; Align 158561 114 141 ; Align 153228 162 198 ; Align 150066 228 66
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis