Command line: [exonerate -m p2g --showtargetgff --exhaustive yes -q ./SelJ.fa -t ./fastasubseq_Lmajor_SelJ_1]
Hostname: [luke]

C4 Alignment:
------------
         Query: SelJ_tetraodon_nigroviridis 
        Target: LmjF28_01_20050601_V5.2:subseq(1005616,4500) [~/leish/curated/chr28/LmjF28_01_20050601_V5.2.artemis] This data was sequenced at the Sanger Institute or SBRI
         Model: protein2genome:local
     Raw score: 105
   Query range: 111 -> 184
  Target range: 993 -> 2167

  112 : LeuProGlyAlaPheGlnAlaAlaLeuHisGlyValLeuThrAla{T}  >>>> Target  :  127
        ||||||      ...|||||||||   ||||||...      |||{!}            95
        LeuProGluGlnLeuGlnAlaAlaGlnHisGlyAlaAlaGluAla{I}++            
  994 : ctaccagaacagcttcaagcagctcagcatggtgcagcagaagca{a}gt............ : 1042

  128 : Intron 1 >>>>  {hr}AsnTyrValGlnAlaValArgAspThrMetSerCysGlyGlyC :  142
        5 bp           { !}...:::...|||...|||   ......:::      |||||| 
                     -+{le}ThrPheAlaGlnGlyValAlaGlnAlaIleArgLeuGlyGlyP
 1043 : .............cg{tt}acgtttgcgcagggagtcgcgcaggcgatccggctcggcggtc : 2039

  143 : ysThrCysSerArgGlySerPheIleGlyAlaCysLeuGlyAlaGlnValGlyLeuGluGly :  162
          ||||||...|||...   ...:::||||||   |||||||||::::::|||:::...   
        roThrCysGlnArgAlaMetLeuValGlyAlaLeuLeuGlyAlaLysLeuGlyValArgHis
 2040 : caacgtgccagcgagctatgctggttggcgcgctgctgggggcgaagcttggggtgcggcac : 2099

  163 : IleProAlaSerTrpSerSerArgThrGlnArgTyrGluSerValLeuGluHisAlaLysLy :  183
        ||||||   ...|||   |||   |||      ::::::   |||         |||   ::
        IleProMetGluTrpLeuSerAlaThrAlaAspHisLysProValSerThrMetAlaLeuGl
 2100 : attccgatggaatggctgagcgccacggccgaccacaagcccgtgtccacgatggcgctgga : 2162

  184 : sIle :  184
        ::::
        uVal
 2163 : ggtg : 2167

vulgar: SelJ_tetraodon_nigroviridis 111 184 . LmjF28_01_20050601_V5.2:subseq(1005616,4500) 993 2167 + 105 M 15 45 S 0 1 5 0 2 I 0 951 3 0 2 S 1 2 M 57 171
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-03-07
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
LmjF28_01_20050601_V5.2:subseq(1005616,4500)	exonerate:protein2genome:local	gene	994	2167	105	+	.	gene_id 1 ; sequence SelJ_tetraodon_nigroviridis ; gene_orientation +
LmjF28_01_20050601_V5.2:subseq(1005616,4500)	exonerate:protein2genome:local	cds	994	1039	.	+	.	
LmjF28_01_20050601_V5.2:subseq(1005616,4500)	exonerate:protein2genome:local	exon	994	1039	.	+	.	insertions 0 ; deletions 0
LmjF28_01_20050601_V5.2:subseq(1005616,4500)	exonerate:protein2genome:local	splice5	1040	1041	.	+	.	intron_id 1 ; splice_site "gt"
LmjF28_01_20050601_V5.2:subseq(1005616,4500)	exonerate:protein2genome:local	intron	1040	1994	.	+	.	intron_id 1
LmjF28_01_20050601_V5.2:subseq(1005616,4500)	exonerate:protein2genome:local	splice3	1993	1994	.	+	.	intron_id 0 ; splice_site "cg"
LmjF28_01_20050601_V5.2:subseq(1005616,4500)	exonerate:protein2genome:local	cds	1995	2167	.	+	.	
LmjF28_01_20050601_V5.2:subseq(1005616,4500)	exonerate:protein2genome:local	exon	1995	2167	.	+	.	insertions 0 ; deletions 0
LmjF28_01_20050601_V5.2:subseq(1005616,4500)	exonerate:protein2genome:local	similarity	994	2167	105	+	.	alignment_id 1 ; Query SelJ_tetraodon_nigroviridis ; Align 994 112 45 ; Align 1997 128 171
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
