Command line: [exonerate -m p2g --showtargetgff -q dio3a_zf.aa.fa.canviat -t genomedio3a_JXSJ01000029.1.fa]
Hostname: [ws116069U]

C4 Alignment:
------------
         Query: SPP00000612_2.0DIO3a # Protein # Iodothyronine deiodinase 3a (DIO3a) # Zebrafish 
        Target: JXSJ01000029.1:subseq(1601922,100791) Miichthys miiuy scaffold29, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 941
   Query range: 0 -> 265
  Target range: 49999 -> 50791

     1 : GlyMetGluMetLeuGlnGlySerAlaGlyValGln<-><->SerAlaLeuLysAsnAla :    18
         |||   ||||||  !!!.! !|||!.!|||||||||      !!!|||||||||:!!|||
         GlyGluGluMetThrHisAspSerGlyGlyValGlnMetAlaArgAlaLeuLysHisAla
 50000 : GGGGAAGAGATGACGCACGACTCTGGCGGTGTCCAAATGGCGAGGGCGCTGAAACATGCA : 50057

    19 : AlaValCysValLeuLeuLeuProArgPheLeuLeuAlaAlaLeuMetLeuCysLeuLeu :    38
         |||:!!|||::::::|||||||||||||||||||||||||||:!!||||||!! ||||||
         AlaLeuCysLeuMetLeuLeuProArgPheLeuLeuAlaAlaValMetLeuTrpLeuLeu
 50058 : GCCCTGTgcctgatgctgctgccccGGTTCCTCCTGGCCGCCGTTATGCTTTGGCTCCTG : 50117

    39 : AspPheLeuCysIleArgArgLysLeuLeuLeuLysMetGlnGluGlyAlaPheSerSer :    58
         ||||||||||||||||||!:!|||:!!||||||||||||  !||| !!  !   ..!|||
         AspPheLeuCysIleArgLysLysValLeuLeuLysMetGlyGluArgGln---AspSer
 50118 : GATTTCTTGTGCATTAGGAAAAAAGTGCTGCTGAAAATGGGAGAGAGGCAG---GACAGC : 50174

    59 : ProAspAspProProLeuArgValSerAspSerAsnLysMetPheThrLeuGluSerLeu :    78
         |||||||||||||||:!! !!|||||||||||||||||||||||||||||||||||||||
         ProAspAspProProValCysValSerAspSerAsnLysMetPheThrLeuGluSerLeu
 50175 : CCGGACGACCCGCCGGTGTGCGTCTCTGACTCTAATAAGATGTTCACCTTGGAGTCCCTC : 50234

    79 : ArgAlaValTrpTyrGlyGlnLysLeuAspPhePheLysSerAlaArgLeuGlyGlyAla :    98
         |||||||||||||||||||||||||||||||||.!!|||||||||!.!|||||| !!|||
         ArgAlaValTrpTyrGlyGlnLysLeuAspPheLeuLysSerAlaHisLeuGlyArgAla
 50235 : AGGGCCGTTTGGTACGGCCAGAAATTGGACTTTCTCAAATCTGCGCACCTCGGGCGCGCT : 50294

    99 : AlaProAsnThrGluValPheProLeuAspGlyAspAlaArgAlaAlaGluArgIleLeu :   118
         ||||||||||||||||||.!.! !:!!.!.! !      |||  !  !!  |||||||||
         AlaProAsnThrGluValMetLeuValGlnAsp------ArgArgGlnValArgIleLeu
 50295 : GCGCCCAACACTGAGGTGATGCTGGTCCAGGAC------CGGAGGCAGGTCCGGATCCTG : 50348

   119 : AspTyrAlaArgGlyArgArgProLeuIleLeuAsnPheGlySerCysSerUnkProPro :   138
         |||! !  !!:!|||!:!|||||||||||||||||||||||||||||||||   ||||||
         AspCysMetLysGlyLysArgProLeuIleLeuAsnPheGlySerCysSer***ProPro
 50349 : GACTGCATGAAAGGGAAGAGACCGCTCATCCTTAACTTTGGCAGCTGCTCCTGACCGCCA : 50408

   139 : PheMetThrArgLeuSerAlaPheGlnArgValAlaArgGlnTyrAlaAspIleAlaAsp :   158
         |||||||||||||||:!!||||||!!.||||||!.!!!!|||||||||||||||||||||
         PheMetThrArgLeuAlaAlaPheHisArgValValSerGlnTyrAlaAspIleAlaAsp
 50409 : TTCATGACGCGCCTGGCGGCGTTTCACCGCGTCGTGAGCCAGTACGCAGACATTGCGGAC : 50468

   159 : SerLeuLeuValTyrIleGluGluAlaHisProSerAspGlyTrpValSerSerAspAla :   178
         ! !|||:!!|||||||||||||||||||||||||||||||||||||||||||||||||||
         PheLeuValValTyrIleGluGluAlaHisProSerAspGlyTrpValSerSerAspAla
 50469 : TTTTTAGTTGTATATATCGAGGAGGCGCATCCGTCGGACGGCTGGGTGAGCTCGGACGCT : 50528

   179 : ProValGlnIleProArgHisArgCysLeuGluAspArgLeuArgAlaAlaGlnMetLeu :   198
         |||  !|||||||||!:!||||||||||||||||||||||||||||||||||||:!!:!!
         ProTyrGlnIleProLysHisArgCysLeuGluAspArgLeuArgAlaAlaGlnLeuMet
 50529 : CCGTATCAGATCCCGAAGCACCGCTGTTTGGAGGACAGACTGAGAGCAGCTCAGCTGATG : 50588

   199 : HisArgGluAlaAlaGlySerAlaValValValAspSerMetGlnAsnSerCysAsnAla :   218
         ! !! !|||!.! !!|||!!!  !||||||||||||!:!|||.!.||||||! !||||||
         LeuThrGluValProGlyThrAsnValValValAspAsnMetAspAsnSerSerAsnAla
 50589 : CTCACCGAGGTGCCGGGGACCAACGTGGTGGTGGATAATATGGACAACTCATCCAACGCC : 50648

   219 : AlaTyrGlyAlaTyrPheGluArgLeuTyrIleValLysAspAlaThrValValTyrGln :   238
         ||||||||||||||||||||||||||||||||||||!:!|||! !! !||||||||||||
         AlaTyrGlyAlaTyrPheGluArgLeuTyrIleValArgAspGluArgValValTyrGln
 50649 : GCGTACGGAGCCTACTTTGAGAGACTTTACATCGTGAGGGATGAGAGAGTGGTGTACCAG : 50708

   239 : GlyGlyArgGlyProGluGlyTyrArgIleAlaGluLeuArgAspTrpLeuGluArgTyr :   258
         ||||||||||||||||||||||||||||||:!!|||||||||:!!|||||||||!:!|||
         GlyGlyArgGlyProGluGlyTyrArgIleSerGluLeuArgAsnTrpLeuGluGlnTyr
 50709 : GGGGGCAGAGGTCCAGAGGGATACCGGATTTCCGAGCTTAGAAACTGGCTGGAGCAATAC : 50768

   259 : ArgSerGlyLeuGlnGluSer :   265
         |||!:!! !|||..!.!.|||
         ArgAsnAspLeuMetAsnSer
 50769 : AGGAACGATCTGATGAATTCC : 50791

vulgar: SPP00000612_2.0DIO3a 0 265 . JXSJ01000029.1:subseq(1601922,100791) 49999 50791 + 941 M 12 36 G 0 6 M 43 129 G 1 0 M 53 159 G 2 0 M 154 462
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2016-11-18
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
JXSJ01000029.1:subseq(1601922,100791)	exonerate:protein2genome:local	gene	50000	50791	941	+	.	gene_id 1 ; sequence SPP00000612_2.0DIO3a ; gene_orientation .
JXSJ01000029.1:subseq(1601922,100791)	exonerate:protein2genome:local	cds	50000	50791	.	+	.	
JXSJ01000029.1:subseq(1601922,100791)	exonerate:protein2genome:local	exon	50000	50791	.	+	.	insertions 6 ; deletions 3
JXSJ01000029.1:subseq(1601922,100791)	exonerate:protein2genome:local	similarity	50000	50791	941	+	.	alignment_id 1 ; Query SPP00000612_2.0DIO3a ; Align 50000 1 36 ; Align 50042 13 129 ; Align 50171 57 159 ; Align 50330 112 462
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis