Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/MM.DI2.1.fa.x.fa -t 3B.fastasub.dir/3.MM.DI2.1.fa.x.fa]
Hostname: [ws116061]

C4 Alignment:
------------
         Query: SPP00001544_2.0 # Protein # Iodothyronine deiodinase 2 (DI2) # Mouse (Mus musculus)
        Target: gi|398923836|gb|JH767740.1|:subseq(25520801,108458) Ceratotherium simum simum unplaced genomic scaffold scaffold00018, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 1216
   Query range: 0 -> 262
  Target range: 58458 -> 49999

     1 : MetGlyLeuLeuSerValAspLeuLeuIleThrLeuGlnIleLeuProValPhePheSer :    20
         ||||||:!!|||||||||||||||||||||||||||||||||||||||||||||||||||
         MetGlyIleLeuSerValAspLeuLeuIleThrLeuGlnIleLeuProValPhePheSer
 58458 : ATGGGCATCCTCAGCGTAGACTTGCTGATCACACTGCAAATTCTGCCAGTTTTTTTCTCC : 58401

    21 : AsnCysLeuPheLeuAlaLeuTyrAspSerValIleLeuLeuLysHisValAlaLeuLeu :    40
         |||||||||||||||||||||||||||||||||||||||||||||||||||!.!||||||
         AsnCysLeuPheLeuAlaLeuTyrAspSerValIleLeuLeuLysHisValValLeuLeu
 58400 : AACTGCCTCTTCCTGGCACTCTATGACTCGGTCATTCTCCTCAAGCACGTGGTGCTCCTG : 58341

    41 : LeuSerArgSerLysSerThrArgGlyGluTrpArgArgMetLeuThrSerGluGlyLeu :    60
         |||||||||||||||||||||||||||||||||||||||||||||||||||||||||:!!
         LeuSerArgSerLysSerThrArgGlyGluTrpArgArgMetLeuThrSerGluGlyMet
 58340 : TTGAGCCGCTCCAAGTCCACTCGCGGGGAGTGGAGGCGCATGCTGACCTCAGAGGGAATG : 58281

    61 : ArgCysValTrpAsnSerPheLeuLeuAspAlaTyrLysGln  >>>> Target Intr :    75
         ||||||:!!|||!!.|||||||||||||||||||||||||||           7664 bp
         ArgCysIleTrpLysSerPheLeuLeuAspAlaTyrLysGln++                
 58280 : CGCTGCATCTGGAAGAGCTTCCTGCTCGATGCCTACAAACAGgt................ : 58234

    76 : on 1 >>>>  ValLysLeuGlyGluAspAlaProAsnSerSerValValHisValSerA :    91
                    ||||||||||||||||||||||||||||||!!!|||||||||:!!||||
                  ++ValLysLeuGlyGluAspAlaProAsnSerArgValValHisIleSerA
 58233 : .........agGTGAAATTGGGTGAAGATGCCCCTAATTCCAGAGTGGTGCATATCTCCA : 50524

    92 : snProGluSerGlyAsn<-><-><->AsnTyrAlaSerGluLysThrAlaAspGlyAlaG :   108
         ||||||||.!!|||:!!         |||  !|||..!!!:||||||!.!||||||||||
         snProGluGlyGlyAspAsnAspGlyAsnGlyAlaGlnAspLysThrValAspGlyAlaG
 50523 : ATCCCGAAGGAGGTGACAACGATGGAAATGGTGCCCAGGATAAGACAGTTGATGGAGCCG : 50464

   109 : luCysHisLeuLeuAspPheAlaSerAlaGluArgProLeuValValAsnPheGlySerA :   128
         ||||||||||||||||||||||||||:!!|||||||||||||||||||||||||||||||
         luCysHisLeuLeuAspPheAlaSerSerGluArgProLeuValValAsnPheGlySerA
 50463 : AGTGCCATCTTCTTGACTTTGCCAGCTCTGAGCGCCCACTGGTGGTCAACTTTGGCTCAG : 50404

   129 : laThrUnkProProPheThrArgGlnLeuProAlaPheArgGlnLeuValGluGluPheS :   148
         |||||   |||||||||! !!.!|||||||||||||||!!!:!!||||||||||||||||
         laThr***ProProPheIleAsnGlnLeuProAlaPheSerLysLeuValGluGluPheS
 50403 : CCACTTGACCTCCATTTATTAACCAGCTGCCAGCCTTCAGCAAACTGGTGGAAGAGTTCT : 50344

   149 : erSerValAlaAspPheLeuLeuValTyrIleAspGluAlaHisProSerAspGlyTrpA :   168
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         erSerValAlaAspPheLeuLeuValTyrIleAspGluAlaHisProSerAspGlyTrpA
 50343 : CATCAGTGGCTGACTTCCTGTTGGTCTACATTGATGAGGCTCATCCTTCAGATGGTTGGG : 50284

   169 : laValProGlyAspSerSerLeuSerPheGluValLysLysHisArgAsnGlnGluAspA :   188
         ||||||||||||||||||||||||||||||||||||||!:!|||!:!|||||||||||||
         laValProGlyAspSerSerLeuSerPheGluValLysArgHisGlnAsnGlnGluAspA
 50283 : CGGTGCCTGGTGATTCTTCTTTGTCTTTCGAGGTGAAGAGGCACCAGAACCAGGAAGACC : 50224

   189 : rgCysAlaAlaAlaHisGlnLeuLeuGluArgPheSerLeuProProGlnCysGlnValV :   208
         |||||||||||||||||||||||||||||||||||||||||||||||||||||!:!||||
         rgCysAlaAlaAlaHisGlnLeuLeuGluArgPheSerLeuProProGlnCysArgValV
 50223 : GATGTGCAGCAGCCCACCAGCTTCTGGAGCGTTTCTCCTTGCCGCCCCAGTGCCGAGTTG : 50164

   209 : alAlaAspArgMetAspAsnAsnAlaAsnValAlaTyrGlyValAlaPheGluArgValC :   228
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         alAlaAspArgMetAspAsnAsnAlaAsnValAlaTyrGlyValAlaPheGluArgValC
 50163 : TGGCTGACCGTATGGACAATAATGCCAATGTAGCTTATGGGGTAGCCTTTGAACGCGTGT : 50104

   229 : ysIleValGlnArgArgLysIleAlaTyrLeuGlyGlyLysGlyProPheSerTyrAsnL :   248
         ||||||||||||||!:!|||||||||||||||||||||||||||||||||! !|||||||
         ysIleValGlnArgGlnLysIleAlaTyrLeuGlyGlyLysGlyProPheTyrTyrAsnL
 50103 : GTATTGTGCAGAGACAGAAAATTGCTTATCTGGGAGGAAAGGGCCCTTTCTACTACAACC : 50044

   249 : euGlnGluValArgSerTrpLeuGluLysAsnPheSerLysArg :   262
         ||||||||||||||  !|||||||||||||||||||||||||||
         euGlnGluValArgHisTrpLeuGluLysAsnPheSerLysArg
 50043 : TTCAAGAAGTCCGGCATTGGCTGGAGAAGAATTTCAGCAAGAGA : 50000

vulgar: SPP00001544_2.0 0 262 . gi|398923836|gb|JH767740.1|:subseq(25520801,108458) 58458 49999 - 1216 M 74 222 5 0 2 I 0 7660 3 0 2 M 22 66 G 0 9 M 166 498
# --- 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|398923836|gb|JH767740.1|:subseq(25520801,108458)	exonerate:protein2genome:local	gene	50000	58458	1216	-	.	gene_id 1 ; sequence SPP00001544_2.0 ; gene_orientation +
gi|398923836|gb|JH767740.1|:subseq(25520801,108458)	exonerate:protein2genome:local	cds	58237	58458	.	-	.	
gi|398923836|gb|JH767740.1|:subseq(25520801,108458)	exonerate:protein2genome:local	exon	58237	58458	.	-	.	insertions 0 ; deletions 0
gi|398923836|gb|JH767740.1|:subseq(25520801,108458)	exonerate:protein2genome:local	splice5	58235	58236	.	-	.	intron_id 1 ; splice_site "GT"
gi|398923836|gb|JH767740.1|:subseq(25520801,108458)	exonerate:protein2genome:local	intron	50573	58236	.	-	.	intron_id 1
gi|398923836|gb|JH767740.1|:subseq(25520801,108458)	exonerate:protein2genome:local	splice3	50573	50574	.	-	.	intron_id 0 ; splice_site "AG"
gi|398923836|gb|JH767740.1|:subseq(25520801,108458)	exonerate:protein2genome:local	cds	50000	50572	.	-	.	
gi|398923836|gb|JH767740.1|:subseq(25520801,108458)	exonerate:protein2genome:local	exon	50000	50572	.	-	.	insertions 9 ; deletions 0
gi|398923836|gb|JH767740.1|:subseq(25520801,108458)	exonerate:protein2genome:local	similarity	50000	58458	1216	-	.	alignment_id 1 ; Query SPP00001544_2.0 ; Align 58459 1 222 ; Align 50573 75 66 ; Align 50498 97 498
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
