Command line: [exonerate -m p2g --showtargetgff -q ../Sel.human/DI3.fa -t gi|397456552|gb|JH738948.1|subseq.fa -E]
Hostname: [ws101062]

** (process:3210): WARNING **: Exhaustively generating suboptimal alignments will be VERY SLOW

C4 Alignment:
------------
         Query: SPP00000016_2.0 # Protein # Iodothyronine deiodinase 3 (DI3) # Human (Homo sapiens)
        Target: gi|397456552|gb|JH738948.1|:subseq(10000,100000) Alligator mississippiensis unplaced genomic scaffold scaffold-13070, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 833
   Query range: 0 -> 272
  Target range: 50988 -> 51789

     1 : MetLeuArgSerLeuLeuLeuHisSerLeuArgLeuCysAlaGlnThrAlaSerCysLeu :    20
         ||||||! !.!!|||  !:!!|||!!!! !!:!! !   ||||||.!!|||:!!||||||
         MetLeuProGlyLeuGlyValHisThrTrpGlnArgLeuAlaGlnAlaAlaAlaCysLeu
 50989 : ATGCTGCCCGGGCTGGGCGTGCACACCTGGCAGCGCCTGGCCCAGGCGGCCGCCTGCCTG : 51046

    21 : ValLeuPheProArgPheLeuGlyThrAlaPheMetLeuTrpLeuLeuAspPheLeuCys :    40
         :!!||||||||||||||||||  !!:!|||   |||||||||||||||||||||||||||
         LeuLeuPheProArgPheLeuLeuSerAlaAlaMetLeuTrpLeuLeuAspPheLeuCys
 51047 : CTGCTCTTCCCCCGCTTCCTGCTCAGCGCCGCGATGCTCTGGCTGCTGGATTTCCTGTGC : 51106

    41 : IleArgLysHisPheLeuGlyArgArgArgArgGlyGlnProGluProGluValGluLeu :    60
         ||||||||| !  ! |||!.!            |||   |||! ! !!! !!.!! !  !
         IleArgLysLysValLeuAla------------GlyGlyProAlaAlaAlaAlaAlaAla
 51107 : ATCAGGAAGAAGGTGCTGGCC------------GGGGGCCCGGCGGCGGCGGCGGCGGCG : 51154

    61 : AsnSerGluGlyGluGluValProProAspAspProProIleCysValSerAspAspAsn :    80
            :!!! !||||||  !   ||||||||||||||||||:!:||||||||||||...|||
         AlaAlaAlaGlyGluPro---ProProAspAspProProLeuCysValSerAspSerAsn
 51155 : GCAGCGGCGGGGGAGCCG---CCCCCCGACGACCCGCCGCTGTGCGTGTCCGACTCGAAC : 51211

    81 : ArgLeuCysThrLeuAlaSerLeuLysAlaValTrpHisGlyGlnLysLeuAspPhePhe :   100
         ||||||! !|||! !! !||||||||||||||||||||||||!!.|||||||||!!.|||
         ArgLeuPheThrArgGluSerLeuLysAlaValTrpHisGlyHisLysLeuAspLeuPhe
 51212 : CGCCTGTTCACGCGGGAGTCGCTGAAGGCCGTGTGGCACGGCCACAAGCTGGACTTGTTC : 51271

   101 : LysGlnAlaHisGluGlyGlyProAlaProAsnSerGluValValLeuProAspGlyPhe :   120
         |||  !||||||! !|||!.!! !||||||||| !!||||||:!!! !! !||||||   
         LysAlaAlaHisValGlyAlaArgAlaProAsnProGluValIleArgLeuAspGlyGln
 51272 : AAGGCGGCGCACGTGGGCGCGCGGGCGCCCAACCCCGAGGTCATCCGGCTGGACGGGCAG : 51331

   121 : GlnSerGlnHisIleLeuAspTyrAlaGlnGlyAsnArgProLeuValLeuAsnPheGly :   140
         :!! !!! !!.!:!!||||||!:!|||!::|||!!.||||||||||||||||||||||||
         LysArgLeuArgLeuLeuAspPheAlaArgGlyLysArgProLeuValLeuAsnPheGly
 51332 : AAGCGGCTGCGCCTCCTGGACTTCGCCCGCGGCAAGCGGCCGCTCGTGCTCAACTTCGGC : 51391

   141 : SerCysThrUnkProProPheMetAlaArgMetSerAlaPheGlnArgLeuValThrLys :   160
         |||||||||   ||||||||||||||||||:!! !!|||||||||||||||!.!.!! ! 
         SerCysThr***ProProPheMetAlaArgLeuArgAlaPheGlnArgLeuAlaAlaHis
 51392 : AGCTGCACCTGACCGCCCTTCATGGCCCGCCTGCGCGCCTTCCAGCGCCTGGCCGCGCAC : 51451

   161 : TyrGlnArgAspValAspPheLeuIleIleTyrIleGluGluAlaHisProSerAspGly :   180
         !:!! !  !  !!.!|||||||||:!::!:||||||||||||||||||||||||||||||
         PheLeuAspIleAlaAspPheLeuLeuValTyrIleGluGluAlaHisProSerAspGly
 51452 : TTCCTGGACATCGCCGACTTCCTGCTGGTGTACATCGAGGAGGCGCACCCCTCCGACGGC : 51511

   181 : TrpValThrThrAspSerProTyrIleIleProGlnHisArgSerLeuGluAspArgVal :   200
         ||||||!:!:!!|||:!! !!|||!  ||||||:!!|||!:!!!!|||:!!||||||:!!
         TrpValSerSerAspAlaAlaTyrLysIleProLysHisGlnCysLeuGlnAspArgLeu
 51512 : TGGGTCAGCTCGGACGCCGCCTACAAGATCCCCAAGCACCAGTGCCTGCAGGACCGGCTG : 51571

   201 : SerAlaAlaArgValLeuGlnGlnGlyAlaProGlyCysAlaLeuValLeuAspThrMet :   220
          !!||||||!:!:!!:!!!:!:!!||||||||||||||| !!|||!.!:!!|||||||||
         ArgAlaAlaGlnLeuMetArgGluGlyAlaProGlyCysProLeuAlaValAspThrMet
 51572 : CGGGCGGCGCAGCTCATGCGGGAAGGCGCCCCCGGGTGCCCGCTGGCGGTGGACACCATG : 51631

   221 : AlaAsnSerSerSerSerAlaTyrGlyAlaTyrPheGluArgLeuTyrValIleGlnSer :   240
         ! !|||:!!||||||:!!||||||||||||||||||||||||||||||:!!:!!|||..!
         AspAsnAlaSerSerAlaAlaTyrGlyAlaTyrPheGluArgLeuTyrIleValGlnGlu
 51632 : GACAACGCCTCCAGCGCCGCCTACGGAGCCTACTTCGAGCGGCTGTACATCGTCCAGGAG : 51691

   241 : GlyThrIleMetTyrGlnGlyGlyArgGlyProAspGlyTyrGlnValSerGluLeuArg :   260
         ! !  !:!!||||||||||||||||||||||||!!:||||||:!!:!!||||||||||||
         GluArgValMetTyrGlnGlyGlyArgGlyProGluGlyTyrLysIleSerGluLeuArg
 51692 : GAGCGCGTCATGTACCAGGGCGGCCGCGGCCCCGAGGGCTACAAGATCTCGGAGCTGCGC : 51751

   261 : ThrTrpLeuGluArgTyrAspGluGlnLeuHisGly :   272
         !:!||||||!!:!:!||| !    !:!|||!..|||
         SerTrpLeuAspGlnTyrLysThrArgLeuArgGly
 51752 : AGCTGGCTCGACCAGTACAAGACCCGGCTGCGGGGC : 51789

vulgar: SPP00000016_2.0 0 272 . gi|397456552|gb|JH738948.1|:subseq(10000,100000) 50988 51789 + 833 M 47 141 G 4 0 M 15 45 G 1 0 M 205 615
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-15
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|397456552|gb|JH738948.1|:subseq(10000,100000)	exonerate:protein2genome:local	gene	50989	51789	833	+	.	gene_id 1 ; sequence SPP00000016_2.0 ; gene_orientation .
gi|397456552|gb|JH738948.1|:subseq(10000,100000)	exonerate:protein2genome:local	cds	50989	51789	.	+	.	
gi|397456552|gb|JH738948.1|:subseq(10000,100000)	exonerate:protein2genome:local	exon	50989	51789	.	+	.	insertions 0 ; deletions 5
gi|397456552|gb|JH738948.1|:subseq(10000,100000)	exonerate:protein2genome:local	similarity	50989	51789	833	+	.	alignment_id 1 ; Query SPP00000016_2.0 ; Align 50989 1 141 ; Align 51130 52 45 ; Align 51175 68 615
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis