Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/E.DI1.1.fa.x.fa -t 3B.fastasub.dir/2.E.DI1.1.fa.x.fa]
Hostname: [ws116063]

C4 Alignment:
------------
         Query: SPP00000849_2.0 # Protein # Iodothyronine deiodinase 1 (DI1) # Horse (Equus caballus)
        Target: gi|398921711|gb|JH767796.1|:subseq(6226177,115432) Ceratotherium simum simum unplaced genomic scaffold scaffold00074, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 1184
   Query range: 0 -> 244
  Target range: 49999 -> 65432

     1 : MetGlyLeuProArgAlaGlyLeuTrpLeuLysArgLeuTrpValLeuLeuGlnValAla :    20
         |||||||||||| !!|||||||||||||||!:!|||||||||||||||||||||||||||
         MetGlyLeuProTrpAlaGlyLeuTrpLeuArgArgLeuTrpValLeuLeuGlnValAla
 50000 : ATGGGGCTGCCCTGGGCCGGGCTGTGGCTGAGGAGGCTCTGGGTGCTCCTGCAGGTGGCT : 50057

    21 : LeuGlnValAlaValGlyLysValLeuLeuThrLeuPheProAspArgValLysGlnHis :    40
         ||||||||||||||||||||||||||||||! !|||||||||!!:|||||||||:!!|||
         LeuGlnValAlaValGlyLysValLeuLeuIleLeuPheProGluArgValLysLysHis
 50058 : CTGCAAGTGGCTGTGGGCAAAGTGCTACTGATACTCTTTCCTGAGAGAGTCAAGAAGCAC : 50117

    41 : IleValAlaMetAsnGlnLysAsnProHisPheSerTyrAspAsnTrpValProThrLeu :    60
         ||||||||||||||||||||||||||||||||||||||||||||||||!.!|||||||||
         IleValAlaMetAsnGlnLysAsnProHisPheSerTyrAspAsnTrpAlaProThrLeu
 50118 : ATCGTGGCCATGAACCAGAAGAACCCCCACTTCTCCTATGACAACTGGGCCCCGACCCTC : 50177

    61 : TyrSerThrGlnTyrPheTrpPheValLeuLysValHisTrpGlnArgLeuGluAspThr :    80
         |||||||||||||||||| !!|||:!!|||||||||||||||||||||||||||||||||
         TyrSerThrGlnTyrPheArgPheIleLeuLysValHisTrpGlnArgLeuGluAspThr
 50178 : TACAGCACCCAGTATTTCCGGTTCATCCTGAAGGTCCACTGGCAGCGACTAGAGGACACG : 50237

    81 : ThrLysArgGlyGlyLeuAlaProAsnSerProValValArgLeuSerGlyGlnArgCys :   100
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         ThrLysArgGlyGlyLeuAlaProAsnSerProValValArgLeuSerGlyGlnArgCys
 50238 : ACTAAGCGAGGGGGTCTGGCCCCAAACAGCCCCGTGGTCCGCCTCTCAGGACAGAGGTGC : 50297

   101 : AsnIleTrpAspPheMetGln{G}  >>>> Target Intron 1 >>>>  {ly}Asn :   109
         |||||||||||||||||||||{|}           7650 bp           {||}|||
         AsnIleTrpAspPheMetGln{G}++                         ++{ly}Asn
 50298 : AACATCTGGGACTTCATGCAA{G}gt.........................ag{GC}AAC : 57974

   110 : ArgProLeuValLeuAsnPheGlySerCysThrUnkProSerPheLeuPheLysPheAsp :   129
         |||||||||||||||||||||||||||||||||   ||||||||||||||||||||||||
         ArgProLeuValLeuAsnPheGlySerCysThr***ProSerPheLeuPheLysPheAsp
 57975 : AGGCCATTGGTGCTGAATTTCGGAAGTTGTACCTGACCTTCGTTTCTTTTCAAATTTGAC : 58034

   130 : GlnPheLysArgLeuIleGluAspPheSerSerIleAlaAspPheLeuIleIleTyrIle :   149
         |||||||||||||||||||||||||||!!!||||||||||||||||||||||||||||||
         GlnPheLysArgLeuIleGluAspPheThrSerIleAlaAspPheLeuIleIleTyrIle
 58035 : CAATTCAAGAGACTTATTGAAGACTTTACTTCCATCGCGGATTTTCTCATCATCTACATA : 58094

   150 : GluGluAlaHisAlaSer{A}  >>>> Target Intron 2 >>>>  {sp}GlyTrp :   158
         ||||||||||||||||||{|}           5033 bp           {||}||||||
         GluGluAlaHisAlaSer{A}++                         ++{sp}GlyTrp
 58095 : GAAGAAGCACACGCATCA{G}gt.........................ag{AT}GGCTGG : 63154

   159 : AlaPheLysAsnAsnValValIleArgAsnHisArgAsnLeuGlnAspArgLeuArgAla :   178
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         AlaPheLysAsnAsnValValIleArgAsnHisArgAsnLeuGlnAspArgLeuArgAla
 63155 : GCTTTTAAGAACAACGTGGTCATCAGGAATCACCGGAATCTCCAGGACCGCCTGCGGGCA : 63214

   179 : AlaArgLeuLeuLeuAspArgSerProProCysProValValValAspSerMetGluAsn :   198
         |||||||||||||||||||||||||||! !||||||||||||||||||!!!|||:!!|||
         AlaArgLeuLeuLeuAspArgSerProGlnCysProValValValAspThrMetLysAsn
 63215 : GCCCGCCTGCTGCTGGACAGGAGCCCCCAGTGCCCGGTGGTGGTGGACACGATGAAGAAC : 63274

   199 : ArgSerSerGlnLeuTyrAlaAlaLeuProAspArgLeuTyrValLeuGlnAlaArgArg :   218
         !:!|||||||||||||||||||||||||||!!:|||||||||||||||!:!! ! !!|||
         GlnSerSerGlnLeuTyrAlaAlaLeuProGluArgLeuTyrValLeuArgGluGlyArg
 63275 : CAGAGCAGCCAGCTCTACGCGGCACTGCCCGAGAGGCTCTATGTGCTCCGGGAGGGCAGG : 63334

   219 : IleLeuTyrLys  >>>> Target Intron 3 >>>>  GlyLysProGlyProTrpA :   229
         ||||||||||||           2018 bp           |||||||||||||||||||
         IleLeuTyrLys++                         ++GlyLysProGlyProTrpA
 63335 : ATCCTCTACAAGgt.........................agGGTAAACCTGGCCCTTGGA : 65385

   230 : snTyrHisProGluGluValArgAlaValLeuGluLysLeuHisSer :   244
         |||||||||||||||||||||||||||||||||||||||||||||||
         snTyrHisProGluGluValArgAlaValLeuGluLysLeuHisSer
 65386 : ACTACCATCCAGAGGAAGTCCGTGCTGTTCTGGAAAAGCTCCACAGT : 65432

vulgar: SPP00000849_2.0 0 244 . gi|398921711|gb|JH767796.1|:subseq(6226177,115432) 49999 65432 + 1184 M 107 321 S 0 1 5 0 2 I 0 7646 3 0 2 S 1 2 M 47 141 S 0 1 5 0 2 I 0 5029 3 0 2 S 1 2 M 66 198 5 0 2 I 0 2014 3 0 2 M 22 66
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-25
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	gene	50000	65432	1184	+	.	gene_id 1 ; sequence SPP00000849_2.0 ; gene_orientation +
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	cds	50000	50321	.	+	.	
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	exon	50000	50321	.	+	.	insertions 0 ; deletions 0
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	splice5	50322	50323	.	+	.	intron_id 1 ; splice_site "GT"
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	intron	50322	57971	.	+	.	intron_id 1
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	splice3	57970	57971	.	+	.	intron_id 0 ; splice_site "AG"
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	cds	57972	58115	.	+	.	
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	exon	57972	58115	.	+	.	insertions 0 ; deletions 0
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	splice5	58116	58117	.	+	.	intron_id 2 ; splice_site "GT"
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	intron	58116	63148	.	+	.	intron_id 2
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	splice3	63147	63148	.	+	.	intron_id 1 ; splice_site "AG"
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	cds	63149	63348	.	+	.	
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	exon	63149	63348	.	+	.	insertions 0 ; deletions 0
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	splice5	63349	63350	.	+	.	intron_id 3 ; splice_site "GT"
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	intron	63349	65366	.	+	.	intron_id 3
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	splice3	65365	65366	.	+	.	intron_id 2 ; splice_site "AG"
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	cds	65367	65432	.	+	.	
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	exon	65367	65432	.	+	.	insertions 0 ; deletions 0
gi|398921711|gb|JH767796.1|:subseq(6226177,115432)	exonerate:protein2genome:local	similarity	50000	65432	1184	+	.	alignment_id 1 ; Query SPP00000849_2.0 ; Align 50000 1 321 ; Align 57974 109 141 ; Align 63151 157 198 ; Align 65367 223 66
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
