Command line: [exonerate -m p2g --showtargetgff --exhaustive yes -q ./SelTryp.fa -t ./fastasubseq_Lmajor_SelTryp_1]
Hostname: [luke]

C4 Alignment:
------------
         Query:  SelTryp; hypothetical protein [Trypanosoma brucei TREU927] PARTIALLY FROM XP_844760.1
        Target: LmjF35_01_20050601_V5.2:subseq(508327,4400) [~/leish/curated/chr35/LmjF35_01_20050601_V5.2.artemis] This data was sequenced at the Sanger Institute or SBRI
         Model: protein2genome:local
     Raw score: 239
   Query range: 12 -> 249
  Target range: 1417 -> 2425

   13 : AlaLeuLeuIleAlaAlaPheLeuAlaAlaAsnAlaGlySerAlaThrAsnAlaAspAsnGl :   33
        :::|||   :::            ||||||   ......::::::......      .....
        SerLeuAlaLeuLeuLeuValSerAlaAlaCysCysAlaAsnSerAlaArgGluValGlnSe
 1418 : tcgctggcacttctcctcgtttccgctgcgtgttgtgcgaattcggcgcgtgaggtgcagtc : 1478

   34 : uAlaThrAspTyrSerSerHisArgTyrLysTyrLeuGluMetLeuLysGluAlaAspLeuL :   54
        .......:::::::::...      |||   ||||||:::||||||   |||...||||||:
        rThrValGluHisAsnLysAspProTyrAlaTyrLeuAspMetLeuAspGluValAspLeuG
 1479 : tactgtggagcacaacaaggacccgtacgcctacctcgacatgctggatgaggtagacctgc : 1541

   55 : ysGlnMetLeuHisGluLysGlyGluAla<-><-><->PheHisHisLeuArgSerLysArg :   71
        ::|||||||||:::||||||   ......                  ...|||...|||:::
        lnGlnMetLeuTyrGluLysThrHisGlyArgValGlnValSerAlaPheArgAspLysLys
 1542 : agcaaatgttatatgaaaagacgcatgggcgagtgcaagtcagtgccttccgcgacaagaag : 1601

   72 : GluLeuIleLeuAlaValLeuLysLeuGluLysArgGluGluAlaLeuArgLysAlaArgVa :   92
        ||||||:::   ||||||   |||||||||:::||||||:::|||      ...   ...  
        GluLeuValAlaAlaValArgLysLeuGluGluArgGluAspAlaGluSerSerPheAsnGl
 1602 : gagctggttgctgcagtgcgcaagcttgaggagcgcgaggacgcggagtccagcttcaacga : 1664

   93 : lThrAspThrVal{G}  >>>> Target Intron 1 >>>>  {ln}HisGluValArgV :  102
               |||...{ }            318 bp           { !}|||   :::...|
        uArgValThrAla{V}--                         ++{al}HisAlaLeuGluV
 1665 : gcgtgtgacggcg{g}cg.........................ag{tg}catgcgctggaag : 2012

  103 : alGluTyrCysSerGlyUnkGlyTyrArgArgHisTyrGluGluValAlaGluSerLeuLeu :  122
        ||   ||||||:::|||   ||||||   :::::::::|||::::::   :::...|||   
        alLeuTyrCysThrGly***GlyTyrAlaLysTyrPheGluAspMetLysGlnGlnLeuGln
 2013 : tgctgtactgtaccggatgaggatacgcgaagtattttgaagatatgaagcagcagctgcag : 2072

  123 : ArgSerLeuProProGluLeuArgGluGlnGlnLysGlyLysLysProPheIleLysPheVa :  143
        ...:::||||||         ...   |||:::                  ::::::...||
        HisThrLeuPro---------AsnAlaGlnGlu------------------ValArgIleVa
 2073 : catacactgccc---------aacgcacaagag------------------gtacgcattgt : 2108

  144 : lGlyValValTyrSerValGlyAlaPheArgGluPheIleGlyAsnIleLeuSerThrGlyP :  164
        ||||   ...|||   ...         |||   ...   ......:::   ||||||...|
        lGlyGlyThrTyrProThrProProAlaArgAlaLeuAlaAlaLysValCysSerThrAlaP
 2109 : gggcggtacctaccccaccccacctgcccgtgccctcgccgcgaaggtgtgctcgaccgcct : 2171

  165 : heLeuAlaSerIleAlaIleSerPhePheAlaProPheLeuArgGlyAlaLeuProProHis :  184
        |||||||||||:::...::::::...   ...      |||         |||||||||   
        heLeuAlaSerLeuGlyValAlaLeuAlaGlyGlnGlnLeu---ValPheLeuProProThr
 2172 : ttctggcctccctcggtgttgcccttgcaggacagcagctc---gtgtttctgccccccacc : 2228

  185 : IleAlaGluTrpIleGluGlnHisArgGlyMetValValGlyAlaGlyPheMetMetAsnMe :  205
        :::   ...:::|||   |||...|||||||||::::::||||||||||||::::::|||||
        ValLeuAsnPheIleAlaGlnGlnArgGlyMetLeuIleGlyAlaGlyPheLeuLeuAsnMe
 2229 : gttctgaactttatcgctcagcagcgcggcatgttgatcggcgctggtttcttgctcaatat : 2291

  206 : tValAlaSerSerLeuLeuGlnSerGlyAlaPheGluValTyrLeuAsnGlySerLeuIleT :  226
        |:::......:::|||   |||:::|||||||||||||||   |||:::|||...||||||:
        tIleGlyGlyAlaLeuGlyGlnThrGlyAlaPheGluValSerLeuAspGlyGluLeuIleP
 2292 : gatcggtggcgctctcgggcagaccggtgccttcgaggtgagcttggatggcgaactcatct : 2354

  227 : yrSerLysLeuGluThrGlyAlaValProThrAlaGluThrLeuAlaAspHisIleLeuArg :  246
        ::|||||||||:::...||||||||||||......      :::         :::|||:::
        heSerLysLeuGlnAlaGlyAlaValProAlaValAlaGluIleArgArgIleValLeuGln
 2355 : tctcaaagctacaggccggagctgtgccggccgttgcggaaatacgtcgtattgttctgcag : 2414

  247 : GlnIleIle :  249
        :::   :::
        LysThrLeu
 2415 : aagacgctg : 2425

vulgar:  12 249 . LmjF35_01_20050601_V5.2:subseq(508327,4400) 1417 2425 + 239 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 G 3 0 M 4 12 G 6 0 M 38 114 G 1 0 M 71 213
# --- 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(508327,4400)	exonerate:protein2genome:local	gene	1418	2425	239	+	.	gene_id 1 ; sequence  ; gene_orientation +
LmjF35_01_20050601_V5.2:subseq(508327,4400)	exonerate:protein2genome:local	cds	1418	1679	.	+	.	
LmjF35_01_20050601_V5.2:subseq(508327,4400)	exonerate:protein2genome:local	exon	1418	1679	.	+	.	insertions 9 ; deletions 0
LmjF35_01_20050601_V5.2:subseq(508327,4400)	exonerate:protein2genome:local	splice5	1680	1681	.	+	.	intron_id 1 ; splice_site "cg"
LmjF35_01_20050601_V5.2:subseq(508327,4400)	exonerate:protein2genome:local	intron	1680	1997	.	+	.	intron_id 1
LmjF35_01_20050601_V5.2:subseq(508327,4400)	exonerate:protein2genome:local	splice3	1996	1997	.	+	.	intron_id 0 ; splice_site "ag"
LmjF35_01_20050601_V5.2:subseq(508327,4400)	exonerate:protein2genome:local	cds	1998	2425	.	+	.	
LmjF35_01_20050601_V5.2:subseq(508327,4400)	exonerate:protein2genome:local	exon	1998	2425	.	+	.	insertions 0 ; deletions 10
LmjF35_01_20050601_V5.2:subseq(508327,4400)	exonerate:protein2genome:local	similarity	1418	2425	239	+	.	alignment_id 1 ; Query  ; Align 1418 13 153 ; Align 1580 64 99 ; Align 2000 98 87 ; Align 2087 130 12 ; Align 2099 140 114 ; Align 2213 179 213
# --- 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(508327,4400) [~/leish/curated/chr35/LmjF35_01_20050601_V5.2.artemis] This data was sequenced at the Sanger Institute or SBRI
         Model: protein2genome:local
     Raw score: 132
   Query range: 181 -> 249
  Target range: 2 -> 209

 182 : ProProHisIleAlaGluTrpIleGluGlnHisArgGlyMetValValGlyAlaGlyPheMetM : 203
       |||      :::         :::...   ...||||||::::::.........||||||::::
       ProGluSerValLeuAlaValLeuArgAlaArgArgGlyLeuIleThrSerThrGlyPheLeuL
   3 : ccggagtcggtgctcgctgtcctgcgcgcacgtcgtggcctcatcaccagcaccggcttcctgc :  66

 204 : etAsnMetValAlaSerSerLeuLeuGlnSerGlyAlaPheGluValTyrLeuAsnGlySerLe : 224
       ::|||:::::::::   :::   ||||||:::...||||||||||||:::|||:::|||...||
       euAsnValLeuSerArgAlaAlaLeuGlnAsnAsnAlaPheGluValPheLeuAspGlyGluLe
  67 : tcaacgtgctgagtcgagcggcgctgcagaacaatgccttcgaggtgtttttggacggcgaact : 129

 225 : uIleTyrSerLysLeuGlu<->ThrGlyAlaValProThrAlaGluThrLeuAlaAspHisIle : 244
       ||||||||||   |||...   :::|||   |||||||||||||||   |||::::::   :::
       uIleTyrSerAlaLeuAsnAlaSerGlyArgValProThrAlaGluLeuLeuSerAsnLeuLeu
 130 : catctactccgccctgaacgcgagtgggcgagtgccgacggcagagctgttgagcaacctcctc : 192

 245 : LeuArgGlnIleIle : 249
       |||...:::   :::
       LeuGluArgThrLeu
 193 : ctcgagcgaacgctc : 209

vulgar:  181 249 . LmjF35_01_20050601_V5.2:subseq(508327,4400) 2 209 + 132 M 49 147 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(508327,4400)	exonerate:protein2genome:local	gene	3	209	132	+	.	gene_id 2 ; sequence  ; gene_orientation .
LmjF35_01_20050601_V5.2:subseq(508327,4400)	exonerate:protein2genome:local	cds	3	209	.	+	.	
LmjF35_01_20050601_V5.2:subseq(508327,4400)	exonerate:protein2genome:local	exon	3	209	.	+	.	insertions 3 ; deletions 0
LmjF35_01_20050601_V5.2:subseq(508327,4400)	exonerate:protein2genome:local	similarity	3	209	132	+	.	alignment_id 2 ; Query  ; Align 3 182 147 ; Align 153 231 57
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
