Command line: [exonerate -m p2g --showtargetgff --exhaustive yes -q ./SelTryp.fa -t ./fastasubseq_Lmajor_SelTryp_3]
Hostname: [luke]

C4 Alignment:
------------
         Query:  SelTryp; hypothetical protein [Trypanosoma brucei TREU927] PARTIALLY FROM XP_844760.1
        Target: LmjF35_01_20050601_V5.2:subseq(507814,4400) [~/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: 1930 -> 2938

   13 : AlaLeuLeuIleAlaAlaPheLeuAlaAlaAsnAlaGlySerAlaThrAsnAlaAspAsnGl :   33
        :::|||   :::            ||||||   ......::::::......      .....
        SerLeuAlaLeuLeuLeuValSerAlaAlaCysCysAlaAsnSerAlaArgGluValGlnSe
 1931 : tcgctggcacttctcctcgtttccgctgcgtgttgtgcgaattcggcgcgtgaggtgcagtc : 1991

   34 : uAlaThrAspTyrSerSerHisArgTyrLysTyrLeuGluMetLeuLysGluAlaAspLeuL :   54
        .......:::::::::...      |||   ||||||:::||||||   |||...||||||:
        rThrValGluHisAsnLysAspProTyrAlaTyrLeuAspMetLeuAspGluValAspLeuG
 1992 : tactgtggagcacaacaaggacccgtacgcctacctcgacatgctggatgaggtagacctgc : 2054

   55 : ysGlnMetLeuHisGluLysGlyGluAla<-><-><->PheHisHisLeuArgSerLysArg :   71
        ::|||||||||:::||||||   ......                  ...|||...|||:::
        lnGlnMetLeuTyrGluLysThrHisGlyArgValGlnValSerAlaPheArgAspLysLys
 2055 : agcaaatgttatatgaaaagacgcatgggcgagtgcaagtcagtgccttccgcgacaagaag : 2114

   72 : GluLeuIleLeuAlaValLeuLysLeuGluLysArgGluGluAlaLeuArgLysAlaArgVa :   92
        ||||||:::   ||||||   |||||||||:::||||||:::|||      ...   ...  
        GluLeuValAlaAlaValArgLysLeuGluGluArgGluAspAlaGluSerSerPheAsnGl
 2115 : gagctggttgctgcagtgcgcaagcttgaggagcgcgaggacgcggagtccagcttcaacga : 2177

   93 : lThrAspThrVal{G}  >>>> Target Intron 1 >>>>  {ln}HisGluValArgV :  102
               |||...{ }            318 bp           { !}|||   :::...|
        uArgValThrAla{V}--                         ++{al}HisAlaLeuGluV
 2178 : gcgtgtgacggcg{g}cg.........................ag{tg}catgcgctggaag : 2525

  103 : alGluTyrCysSerGlyUnkGlyTyrArgArgHisTyrGluGluValAlaGluSerLeuLeu :  122
        ||   ||||||:::|||   ||||||   :::::::::|||::::::   :::...|||   
        alLeuTyrCysThrGly***GlyTyrAlaLysTyrPheGluAspMetLysGlnGlnLeuGln
 2526 : tgctgtactgtaccggatgaggatacgcgaagtattttgaagatatgaagcagcagctgcag : 2585

  123 : ArgSerLeuProProGluLeuArgGluGlnGlnLysGlyLysLysProPheIleLysPheVa :  143
        ...:::||||||         ...   |||:::                  ::::::...||
        HisThrLeuPro---------AsnAlaGlnGlu------------------ValArgIleVa
 2586 : catacactgccc---------aacgcacaagag------------------gtacgcattgt : 2621

  144 : lGlyValValTyrSerValGlyAlaPheArgGluPheIleGlyAsnIleLeuSerThrGlyP :  164
        ||||   ...|||   ...         |||   ...   ......:::   ||||||...|
        lGlyGlyThrTyrProThrProProAlaArgAlaLeuAlaAlaLysValCysSerThrAlaP
 2622 : gggcggtacctaccccaccccacctgcccgtgccctcgccgcgaaggtgtgctcgaccgcct : 2684

  165 : heLeuAlaSerIleAlaIleSerPhePheAlaProPheLeuArgGlyAlaLeuProProHis :  184
        |||||||||||:::...::::::...   ...      |||         |||||||||   
        heLeuAlaSerLeuGlyValAlaLeuAlaGlyGlnGlnLeu---ValPheLeuProProThr
 2685 : ttctggcctccctcggtgttgcccttgcaggacagcagctc---gtgtttctgccccccacc : 2741

  185 : IleAlaGluTrpIleGluGlnHisArgGlyMetValValGlyAlaGlyPheMetMetAsnMe :  205
        :::   ...:::|||   |||...|||||||||::::::||||||||||||::::::|||||
        ValLeuAsnPheIleAlaGlnGlnArgGlyMetLeuIleGlyAlaGlyPheLeuLeuAsnMe
 2742 : gttctgaactttatcgctcagcagcgcggcatgttgatcggcgctggtttcttgctcaatat : 2804

  206 : tValAlaSerSerLeuLeuGlnSerGlyAlaPheGluValTyrLeuAsnGlySerLeuIleT :  226
        |:::......:::|||   |||:::|||||||||||||||   |||:::|||...||||||:
        tIleGlyGlyAlaLeuGlyGlnThrGlyAlaPheGluValSerLeuAspGlyGluLeuIleP
 2805 : gatcggtggcgctctcgggcagaccggtgccttcgaggtgagcttggatggcgaactcatct : 2867

  227 : yrSerLysLeuGluThrGlyAlaValProThrAlaGluThrLeuAlaAspHisIleLeuArg :  246
        ::|||||||||:::...||||||||||||......      :::         :::|||:::
        heSerLysLeuGlnAlaGlyAlaValProAlaValAlaGluIleArgArgIleValLeuGln
 2868 : tctcaaagctacaggccggagctgtgccggccgttgcggaaatacgtcgtattgttctgcag : 2927

  247 : GlnIleIle :  249
        :::   :::
        LysThrLeu
 2928 : aagacgctg : 2938

vulgar:  12 249 . LmjF35_01_20050601_V5.2:subseq(507814,4400) 1930 2938 + 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(507814,4400)	exonerate:protein2genome:local	gene	1931	2938	239	+	.	gene_id 1 ; sequence  ; gene_orientation +
LmjF35_01_20050601_V5.2:subseq(507814,4400)	exonerate:protein2genome:local	cds	1931	2192	.	+	.	
LmjF35_01_20050601_V5.2:subseq(507814,4400)	exonerate:protein2genome:local	exon	1931	2192	.	+	.	insertions 9 ; deletions 0
LmjF35_01_20050601_V5.2:subseq(507814,4400)	exonerate:protein2genome:local	splice5	2193	2194	.	+	.	intron_id 1 ; splice_site "cg"
LmjF35_01_20050601_V5.2:subseq(507814,4400)	exonerate:protein2genome:local	intron	2193	2510	.	+	.	intron_id 1
LmjF35_01_20050601_V5.2:subseq(507814,4400)	exonerate:protein2genome:local	splice3	2509	2510	.	+	.	intron_id 0 ; splice_site "ag"
LmjF35_01_20050601_V5.2:subseq(507814,4400)	exonerate:protein2genome:local	cds	2511	2938	.	+	.	
LmjF35_01_20050601_V5.2:subseq(507814,4400)	exonerate:protein2genome:local	exon	2511	2938	.	+	.	insertions 0 ; deletions 10
LmjF35_01_20050601_V5.2:subseq(507814,4400)	exonerate:protein2genome:local	similarity	1931	2938	239	+	.	alignment_id 1 ; Query  ; Align 1931 13 153 ; Align 2093 64 99 ; Align 2513 98 87 ; Align 2600 130 12 ; Align 2612 140 114 ; Align 2726 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(507814,4400) [~/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: 392 -> 722

 140 : IleLysPheValGlyValValTyrSerValGlyAlaPheArgGluPheIleGlyAsnIleLeuS : 161
       ::::::...||||||   ...|||   :::...      |||   ...|||......   |||.
       LeuGlnIleValGlyGlnAlaTyrProMetSerProArgArgValLeuIleSerLysAlaLeuG
 393 : cttcaaattgttgggcaggcgtacccgatgagtcccaggcgagtcctgatcagcaaggcgttgc : 456

 162 : erThrGlyPheLeuAlaSerIleAlaIleSerPhePheAlaProPheLeuArgGlyAlaLeuPr : 182
       ..   ...|||......::::::...::::::.........      |||:::      :::||
       lnGlyAlaPhePheGlyThrLeuGlyLeuAlaLeuMetGlyAspGlnLeuLys---PheIlePr
 457 : agggggctttcttcggcacgctagggcttgcccttatgggggatcaactgaag---ttcatccc : 516

 183 : oProHisIleAlaGluTrpIleGluGlnHisArgGlyMetValValGlyAlaGlyPheMetMet : 203
       |      :::         :::...   ...||||||::::::.........||||||::::::
       oGluSerValLeuAlaValLeuArgAlaArgArgGlyLeuIleThrSerThrGlyPheLeuLeu
 517 : ggagtcggtgctcgctgtcctgcgcgcacgtcgtggcctcatcaccagcaccggcttcctgctc : 579

 204 : AsnMetValAlaSerSerLeuLeuGlnSerGlyAlaPheGluValTyrLeuAsnGlySerLeuI : 225
       |||:::::::::   :::   ||||||:::...||||||||||||:::|||:::|||...||||
       AsnValLeuSerArgAlaAlaLeuGlnAsnAsnAlaPheGluValPheLeuAspGlyGluLeuI
 580 : aacgtgctgagtcgagcggcgctgcagaacaatgccttcgaggtgtttttggacggcgaactca : 645

 226 : leTyrSerLysLeuGlu<->ThrGlyAlaValProThrAlaGluThrLeuAlaAspHisIleLe : 245
       ||||||||   |||...   :::|||   |||||||||||||||   |||::::::   :::||
       leTyrSerAlaLeuAsnAlaSerGlyArgValProThrAlaGluLeuLeuSerAsnLeuLeuLe
 646 : tctactccgccctgaacgcgagtgggcgagtgccgacggcagagctgttgagcaacctcctcct : 708

 246 : uArgGlnIleIle : 249
       |...:::   :::
       uGluArgThrLeu
 709 : cgagcgaacgctc : 722

vulgar:  139 249 . LmjF35_01_20050601_V5.2:subseq(507814,4400) 392 722 + 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(507814,4400)	exonerate:protein2genome:local	gene	393	722	150	+	.	gene_id 2 ; sequence  ; gene_orientation .
LmjF35_01_20050601_V5.2:subseq(507814,4400)	exonerate:protein2genome:local	cds	393	722	.	+	.	
LmjF35_01_20050601_V5.2:subseq(507814,4400)	exonerate:protein2genome:local	exon	393	722	.	+	.	insertions 3 ; deletions 1
LmjF35_01_20050601_V5.2:subseq(507814,4400)	exonerate:protein2genome:local	similarity	393	722	150	+	.	alignment_id 2 ; Query  ; Align 393 140 117 ; Align 510 180 153 ; Align 666 231 57
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
