Command line: [exonerate -m p2g --showtargetgff --exhaustive yes -q ./SelTryp.fa -t ./fastasubseq_Lmajor_SelTryp_2]
Hostname: [luke]

C4 Alignment:
------------
         Query:  SelTryp; hypothetical protein [Trypanosoma brucei TREU927] PARTIALLY FROM XP_844760.1
        Target: LmjF35_01_20050601_V5.2:subseq(506084,4400) [~/leish/curated/chr35/LmjF35_01_20050601_V5.2.artemis] This data was sequenced at the Sanger Institute or SBRI
         Model: protein2genome:local
     Raw score: 150
   Query range: 139 -> 249
  Target range: 2122 -> 2452

  140 : IleLysPheValGlyValValTyrSerValGlyAlaPheArgGluPheIleGlyAsnIleLe :  160
        ::::::...||||||   ...|||   :::...      |||   ...|||......   ||
        LeuGlnIleValGlyGlnAlaTyrProMetSerProArgArgValLeuIleSerLysAlaLe
 2123 : cttcaaattgttgggcaggcgtacccgatgagtcccaggcgagtcctgatcagcaaggcgtt : 2183

  161 : uSerThrGlyPheLeuAlaSerIleAlaIleSerPhePheAlaProPheLeuArgGlyAlaL :  181
        |...   ...|||......::::::...::::::.........      |||:::      :
        uGlnGlyAlaPhePheGlyThrLeuGlyLeuAlaLeuMetGlyAspGlnLeuLys---PheI
 2184 : gcagggggctttcttcggcacgctagggcttgcccttatgggggatcaactgaag---ttca : 2243

  182 : euProProHisIleAlaGluTrpIleGluGlnHisArgGlyMetValValGlyAlaGlyPhe :  201
        ::|||      :::         :::...   ...||||||::::::.........||||||
        leProGluSerValLeuAlaValLeuArgAlaArgArgGlyLeuIleThrSerThrGlyPhe
 2244 : tcccggagtcggtgctcgctgtcctgcgcgcacgtcgtggcctcatcaccagcaccggcttc : 2303

  202 : MetMetAsnMetValAlaSerSerLeuLeuGlnSerGlyAlaPheGluValTyrLeuAsnGl :  222
        ::::::|||:::::::::   :::   ||||||:::...||||||||||||:::|||:::||
        LeuLeuAsnValLeuSerArgAlaAlaLeuGlnAsnAsnAlaPheGluValPheLeuAspGl
 2304 : ctgctcaacgtgctgagtcgagcggcgctgcagaacaatgccttcgaggtgtttttggacgg : 2366

  223 : ySerLeuIleTyrSerLysLeuGlu<->ThrGlyAlaValProThrAlaGluThrLeuAlaA :  242
        |...||||||||||||   |||...   :::|||   |||||||||||||||   |||::::
        yGluLeuIleTyrSerAlaLeuAsnAlaSerGlyArgValProThrAlaGluLeuLeuSerA
 2367 : cgaactcatctactccgccctgaacgcgagtgggcgagtgccgacggcagagctgttgagca : 2429

  243 : spHisIleLeuArgGlnIleIle :  249
        ::   :::|||...:::   :::
        snLeuLeuLeuGluArgThrLeu
 2430 : acctcctcctcgagcgaacgctc : 2452

vulgar:  139 249 . LmjF35_01_20050601_V5.2:subseq(506084,4400) 2122 2452 + 150 M 39 117 G 1 0 M 51 153 G 0 3 M 19 57
# --- 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
#
LmjF35_01_20050601_V5.2:subseq(506084,4400)	exonerate:protein2genome:local	gene	2123	2452	150	+	.	gene_id 1 ; sequence  ; gene_orientation .
LmjF35_01_20050601_V5.2:subseq(506084,4400)	exonerate:protein2genome:local	cds	2123	2452	.	+	.	
LmjF35_01_20050601_V5.2:subseq(506084,4400)	exonerate:protein2genome:local	exon	2123	2452	.	+	.	insertions 3 ; deletions 1
LmjF35_01_20050601_V5.2:subseq(506084,4400)	exonerate:protein2genome:local	similarity	2123	2452	150	+	.	alignment_id 1 ; Query  ; Align 2123 140 117 ; Align 2240 180 153 ; Align 2396 231 57
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query:  SelTryp; hypothetical protein [Trypanosoma brucei TREU927] PARTIALLY FROM XP_844760.1
        Target: LmjF35_01_20050601_V5.2:subseq(506084,4400) [~/leish/curated/chr35/LmjF35_01_20050601_V5.2.artemis] This data was sequenced at the Sanger Institute or SBRI
         Model: protein2genome:local
     Raw score: 120
   Query range: 12 -> 126
  Target range: 3660 -> 4329

   13 : AlaLeuLeuIleAlaAlaPheLeuAlaAlaAsnAlaGlySerAlaThrAsnAlaAspAsnGl :   33
        :::|||   :::            ||||||   ......::::::......      .....
        SerLeuAlaLeuLeuLeuValSerAlaAlaCysCysAlaAsnSerAlaArgGluValGlnSe
 3661 : tcgctggcacttctcctcgtttccgctgcgtgttgtgcgaattcggcgcgtgaggtgcagtc : 3721

   34 : uAlaThrAspTyrSerSerHisArgTyrLysTyrLeuGluMetLeuLysGluAlaAspLeuL :   54
        .......:::::::::...      |||   ||||||:::||||||   |||...||||||:
        rThrValGluHisAsnLysAspProTyrAlaTyrLeuAspMetLeuAspGluValAspLeuG
 3722 : tactgtggagcacaacaaggacccgtacgcctacctcgacatgctggatgaggtagacctgc : 3784

   55 : ysGlnMetLeuHisGluLysGlyGluAla<-><-><->PheHisHisLeuArgSerLysArg :   71
        ::|||||||||:::||||||   ......                  ...|||...|||:::
        lnGlnMetLeuTyrGluLysThrHisGlyArgValGlnValSerAlaPheArgAspLysLys
 3785 : agcaaatgttatatgaaaagacgcatgggcgagtgcaagtcagtgccttccgcgacaagaag : 3844

   72 : GluLeuIleLeuAlaValLeuLysLeuGluLysArgGluGluAlaLeuArgLysAlaArgVa :   92
        ||||||:::   ||||||   |||||||||:::||||||:::|||      ...   ...  
        GluLeuValAlaAlaValArgLysLeuGluGluArgGluAspAlaGluSerSerPheAsnGl
 3845 : gagctggttgctgcagtgcgcaagcttgaggagcgcgaggacgcggagtccagcttcaacga : 3907

   93 : lThrAspThrVal{G}  >>>> Target Intron 1 >>>>  {ln}HisGluValArgV :  102
               |||...{ }            318 bp           { !}|||   :::...|
        uArgValThrAla{V}--                         ++{al}HisAlaLeuGluV
 3908 : gcgtgtgacggcg{g}cg.........................ag{tg}catgcgctggaag : 4255

  103 : alGluTyrCysSerGlyUnkGlyTyrArgArgHisTyrGluGluValAlaGluSerLeuLeu :  122
        ||   ||||||:::|||   ||||||   :::::::::|||::::::   :::...|||   
        alLeuTyrCysThrGly***GlyTyrAlaLysTyrPheGluAspMetLysGlnGlnLeuGln
 4256 : tgctgtactgtaccggatgaggatacgcgaagtattttgaagatatgaagcagcagctgcag : 4315

  123 : ArgSerLeuPro :  126
        ...:::||||||
        HisThrLeuPro
 4316 : catacactgccc : 4329

vulgar:  12 126 . LmjF35_01_20050601_V5.2:subseq(506084,4400) 3660 4329 + 120 M 51 153 G 0 9 M 33 99 S 0 1 5 0 2 I 0 314 3 0 2 S 1 2 M 29 87
# --- 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
#
LmjF35_01_20050601_V5.2:subseq(506084,4400)	exonerate:protein2genome:local	gene	3661	4329	120	+	.	gene_id 2 ; sequence  ; gene_orientation +
LmjF35_01_20050601_V5.2:subseq(506084,4400)	exonerate:protein2genome:local	cds	3661	3922	.	+	.	
LmjF35_01_20050601_V5.2:subseq(506084,4400)	exonerate:protein2genome:local	exon	3661	3922	.	+	.	insertions 9 ; deletions 0
LmjF35_01_20050601_V5.2:subseq(506084,4400)	exonerate:protein2genome:local	splice5	3923	3924	.	+	.	intron_id 1 ; splice_site "cg"
LmjF35_01_20050601_V5.2:subseq(506084,4400)	exonerate:protein2genome:local	intron	3923	4240	.	+	.	intron_id 1
LmjF35_01_20050601_V5.2:subseq(506084,4400)	exonerate:protein2genome:local	splice3	4239	4240	.	+	.	intron_id 0 ; splice_site "ag"
LmjF35_01_20050601_V5.2:subseq(506084,4400)	exonerate:protein2genome:local	cds	4241	4329	.	+	.	
LmjF35_01_20050601_V5.2:subseq(506084,4400)	exonerate:protein2genome:local	exon	4241	4329	.	+	.	insertions 0 ; deletions 0
LmjF35_01_20050601_V5.2:subseq(506084,4400)	exonerate:protein2genome:local	similarity	3661	4329	120	+	.	alignment_id 2 ; Query  ; Align 3661 13 153 ; Align 3823 64 99 ; Align 4243 98 87
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
