Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/MM.DI3.1.fa.x.fa -t 3B.fastasub.dir/1.MM.DI3.1.fa.x.fa]
Hostname: [ws116061]

C4 Alignment:
------------
         Query: SPP00001545_2.0 # Protein # Iodothyronine deiodinase 3 (DI3) # Mouse (Mus musculus)
        Target: gi|398922406|gb|JH767771.1|:subseq(13476903,100788) Ceratotherium simum simum unplaced genomic scaffold scaffold00049, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 1339
   Query range: 0 -> 275
  Target range: 49963 -> 50788

     1 : MetLeuArgSerLeuLeuLeuHisSerLeuArgLeuCysAlaGlnThrAlaSerCysLeu :    20
         ||||||||||||||||||||||||:!!|||||||||||||||||||||||||||||||||
         MetLeuArgSerLeuLeuLeuHisAlaLeuArgLeuCysAlaGlnThrAlaSerCysLeu
 49964 : ATGCTCCGCTCCCTACTGCTTCACGCCCTGAGGCTCTGCGCCCAGACCGCCTCGTGCCTC : 50021

    21 : ValLeuPheProArgPheLeuGlyThrAlaPheMetLeuTrpLeuLeuAspPheLeuCys :    40
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         ValLeuPheProArgPheLeuGlyThrAlaPheMetLeuTrpLeuLeuAspPheLeuCys
 50022 : GTGCTCTTCCCGCGCTTCCTCGGCACGGCCTTCATGCTCTGGCTCCTCGACTTCCTGTGC : 50081

    41 : IleArgLysHisPheLeuArgArgArgHisProAspHisProGluProGluValGluLeu :    60
         ||||||||||||||||||!!!|||!:!!.!! !!  !!.||||||||||||! !|||!!!
         IleArgLysHisPheLeuSerArgGlnArgArgGlyGlnProGluProGluGlyGluPhe
 50082 : ATCCGCAAGCATTTCCTGAGCCGCCAGCGCCGGGGGCAGCCAGAACCTGAAGGGGAGTTC : 50141

    61 : AsnSerGluGlyGluGluMetProProAspAspProProIleCysValSerAspAspAsn :    80
         |||!!!!!:|||||||||:!!|||||||||||||||||||||||||||||||||||||||
         AsnCysAspGlyGluGluValProProAspAspProProIleCysValSerAspAspAsn
 50142 : AACTGTGATGGCGAGGAGGTGCCCCCCGACGACCCGCCCATCTGCGTGTCCGACGACAAC : 50201

    81 : ArgLeuCysThrLeuAlaSerLeuLysAlaValTrpHisGlyGlnLysLeuAspPhePhe :   100
         ||||||||||||||||||||||||||||||||||||:!!|||||||||||||||||||||
         ArgLeuCysThrLeuAlaSerLeuLysAlaValTrpTyrGlyGlnLysLeuAspPhePhe
 50202 : CGCCTGTGCACCCTGGCGTCGCTGAAGGCGGTGTGGTACGGCCAGAAGTTGGATTTCTTC : 50261

   101 : LysGlnAlaHisGluGlyGlyProAlaProAsnSerGluValValArgProAspGlyPhe :   120
         |||||||||||||||||||||||||||||||||||||||||||||! !||||||||||||
         LysGlnAlaHisGluGlyGlyProAlaProAsnSerGluValValLeuProAspGlyPhe
 50262 : AAGCAGGCGCACGAGGGTGGTCCGGCGCCCAACTCCGAGGTGGTCCTACCCGACGGCTTC : 50321

   121 : GlnSerGlnArgIleLeuAspTyrAlaGlnGlyThrArgProLeuValLeuAsnPheGly :   140
         |||!:!|||!.!|||||||||||||||!:!|||!.!||||||||||||||||||||||||
         GlnAsnGlnHisIleLeuAspTyrAlaArgGlyAsnArgProLeuValLeuAsnPheGly
 50322 : CAGAACCAGCATATCCTCGACTACGCGCGAGGAAACCGCCCGCTGGTGCTCAATTTCGGC : 50381

   141 : SerCysThrUnkProProPheMetAlaArgMetSerAlaPheGlnArgLeuValThrLys :   160
         |||||||||   ||||||||||||||||||||||||||||||!:!|||||||||||||||
         SerCysThr***ProProPheMetAlaArgMetSerAlaPheArgArgLeuValThrLys
 50382 : AGCTGCACCTGACCACCGTTCATGGCGCGCATGAGCGCCTTCCGGCGCCTGGTCACTAAG : 50441

   161 : TyrGlnArgAspValAspPheLeuIleIleTyrIleGluGluAlaHisProSerAspGly :   180
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         TyrGlnArgAspValAspPheLeuIleIleTyrIleGluGluAlaHisProSerAspGly
 50442 : TACCAGCGCGACGTCGACTTCCTCATCATCTACATCGAGGAAGCGCATCCCTCCGACGGC : 50501

   181 : TrpValThrThrAspSerProTyrValIleProGlnHisArgSerLeuGluAspArgVal :   200
         ||||||||||||||||||||||||:!!|||||||||||||||||||||||||||||||||
         TrpValThrThrAspSerProTyrIleIleProGlnHisArgSerLeuGluAspArgVal
 50502 : TGGGTCACCACAGACTCCCCCTACATCATCCCGCAGCACCGAAGCCTGGAGGACCGGGTC : 50561

   201 : SerAlaAlaArgValLeuGlnGlnGlyAlaProGlyCysAlaLeuValLeuAspThrMet :   220
         |||||||||||||||||||||||||||!.!|||||||||:!!||||||||||||||||||
         SerAlaAlaArgValLeuGlnGlnGlyValProGlyCysSerLeuValLeuAspThrMet
 50562 : AGCGCGGCTCGCGTGCTGCAGCAAGGAGTGCCTGGCTGCTCTCTTGTCCTCGACACCATG : 50621

   221 : AlaAsnSerSerSerSerAlaTyrGlyAlaTyrPheGluArgLeuTyrValIleGlnSer :   240
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         AlaAsnSerSerSerSerAlaTyrGlyAlaTyrPheGluArgLeuTyrValIleGlnSer
 50622 : GCCAACTCCAGCAGCTCGGCCTATGGCGCCTACTTCGAGCGCCTCTACGTCATCCAAAGT : 50681

   241 : GlyThrIleMetTyrGlnGlyGlyArgGlyProAspGlyTyrGlnValSerGluLeuArg :   260
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         GlyThrIleMetTyrGlnGlyGlyArgGlyProAspGlyTyrGlnValSerGluLeuArg
 50682 : GGCACCATTATGTACCAGGGTGGCCGTGGCCCAGACGGCTACCAGGTCTCCGAGCTGCGA : 50741

   261 : ThrTrpLeuGluArgTyrAspGluGlnLeuHisGlyThrArgPro :   275
         ||||||||||||!.!|||||||||||||||||||||..!!:!|||
         ThrTrpLeuGluHisTyrAspGluGlnLeuHisGlyValGlnPro
 50742 : ACCTGGCTGGAGCACTACGACGAGCAGCTGCACGGAGTTCAGCCC : 50788

vulgar: SPP00001545_2.0 0 275 . gi|398922406|gb|JH767771.1|:subseq(13476903,100788) 49963 50788 + 1339 M 275 825
# --- 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|398922406|gb|JH767771.1|:subseq(13476903,100788)	exonerate:protein2genome:local	gene	49964	50788	1339	+	.	gene_id 1 ; sequence SPP00001545_2.0 ; gene_orientation .
gi|398922406|gb|JH767771.1|:subseq(13476903,100788)	exonerate:protein2genome:local	cds	49964	50788	.	+	.	
gi|398922406|gb|JH767771.1|:subseq(13476903,100788)	exonerate:protein2genome:local	exon	49964	50788	.	+	.	insertions 0 ; deletions 0
gi|398922406|gb|JH767771.1|:subseq(13476903,100788)	exonerate:protein2genome:local	similarity	49964	50788	1339	+	.	alignment_id 1 ; Query SPP00001545_2.0 ; Align 49964 1 825
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
