Command line: [exonerate -m p2g --showtargetgff --exhaustive yes -q ./SelTryp.fa -t ./fastasubseq_Linfantum_SelTryp_3]
Hostname: [luke]

C4 Alignment:
------------
         Query:  SelTryp; hypothetical protein [Trypanosoma brucei TREU927] PARTIALLY FROM XP_844760.1
        Target: gi|146102387|ref|NC_009419.1|:subseq(515756,4500) Leishmania infantum JPCM5 chromosome 35, complete sequence
         Model: protein2genome:local
     Raw score: 246
   Query range: 12 -> 249
  Target range: 1912 -> 2917

   13 : AlaLeuLeuIleAlaAlaPheLeuAlaAlaAsnAlaGlySerAlaThrAsnAlaAspAsnGl :   33
        :!!|||  !:!!  !  ! !!! !||||||  !..!!.!!:!:!!.!!..!! !!  .!.  
        SerLeuAlaLeuLeuPheValSerAlaAlaCysCysAlaAsnSerAlaArgGluValGlnPr
 1913 : TCACTGGCGCTTCTCTTCGTTTCCGCTGCGTGTTGTGCGAATTCGGCGCGTGAAGTGCAGCC : 1973

   34 : uAlaThrAspTyrSerSerHisArgTyrLysTyrLeuGluMetLeuLysGluAlaAspLeuL :   54
         .!!..!!!: ! !:!!.! !!! !|||   ||||||!!:|||||| ! |||!.!||||||:
        oThrValGluGlnAsnLysAspProTyrAlaTyrLeuAspMetLeuAspGluValAspLeuG
 1974 : TACTGTTGAGCAGAACAAGGACCCGTACGCCTACCTCGACATGCTGGATGAGGTGGACCTAC : 2036

   55 : ysGlnMetLeuHisGluLysGlyGluAla<-><-><->PheHisHisLeuArgSerLysArg :   71
        !!|||||||||:!!||||||  !.!.!.!          !!  !  !!!!|||..!|||!:!
        lnGlnMetLeuTyrGluLysThrHisGlyGlnValProValSerAlaPheArgAspLysLys
 2037 : AGCAAATGCTATATGAAAAGACGCATGGGCAGGTGCCGGTCAGCGCTTTCCGCGACAAGAAG : 2096

   72 : GluLeuIleLeuAlaValLeuLysLeuGluLysArgGluGluAlaLeuArgLysAlaArgVa :   92
        ||||||:!!  !||||||! !|||||||||:!!||||||!!:! !  !  !!..  !!.!!.
        GluLeuValAlaAlaValArgLysLeuGluGluArgGluAspGluGluAlaSerPheAsnAl
 2097 : GAGCTGGTTGCCGCAGTGCGCAAGCTCGAGGAGCGCGAGGACGAGGAGGCCAGCTTCAACGC : 2159

   93 : lThr  >>>> Target Intron 1 >>>>  AspThrValGlnHisGluValArgValGl :  103
        !  !            315 bp             !:!!!.!..!||||||:!!..!|||  
        aArg++                         +-LeuSerAlaMetHisGluLeuGluValLe
 2160 : GCGTgt.........................aaCTCTCTGCAATGCATGAGTTGGAAGTGCT : 2507

  104 : uTyrCysSerGlyUnkGlyTyrArgArgHisTyrGluGluValAlaGluSerLeuLeuArgS :  124
        !||||||!!!|||   ||||||  !!:!:!!!:!|||!!::!!  !:!!..!|||! !|||!
        uTyrCysThrGly***GlyTyrAlaLysTyrPheGluAspMetLysGlnGlnLeuGlnArgT
 2508 : GTACTGTACCGGATGAGGATACGCGAAGTATTTTGAAGATATGAAGCAGCAGCTGCAACGTA : 2570

  125 : erLeuProProGluLeuArgGluGlnGlnLysGlyLysLysProPheIleLysPheValGly :  144
        !!||||||         !.!! !|||:!!                  :!!:::.!!||||||
        hrLeuPro---------AsnAlaGlnGlu------------------ValArgIleValGly
 2571 : CGCTGCCC---------AACGCACAAGAG------------------GTACGCATTGTGGGC : 2603

  145 : ValValTyrSerValGlyAlaPheArgGluPheIleGlyAsnIleLeuSerThrGlyPheLe :  165
        ! !..!||| !!..!  ! !!  !|||!  .!!  !!.!!!.   ! !||||||!.!|||||
        GlyThrTyrProThrProProAlaArgAlaLeuAlaAlaLysAlaCysSerThrAlaPheLe
 2604 : GGTACCTACCCCACCCCACCTGCCCGCGCCCTCGCCGCGAAGGCGTGCTCGACCGCCTTTCT : 2666

  166 : uAlaSerIleAlaIleSerPhePheAlaProPheLeuArgGlyAlaLeuProProHisIleA :  186
        |||||||:!!!.!:!!:!!.!!   !.!! !   |||   ! !  !|||||||||  !:!! 
        uAlaSerLeuGlyValAlaLeuAlaGlyGlnGlnLeu---ValPheLeuProProThrValL
 2667 : GGCCTCCCTCGGTGTCGCCCTTGCAGGACAGCAACTC---GTGTTTCTGCCCCCCACCGTTC : 2726

  187 : laGluTrpIleGluGlnHisArgGlyMetValValGlyAlaGlyPheMetMetAsnMetVal :  206
         !.!.!::|||!  |||!!.|||||||||:!!:!!||||||||||||:!!:!:|||||||||
        euAsnPheIleAlaGlnGlnArgGlyMetLeuIleGlyAlaGlyPheLeuLeuAsnMetVal
 2727 : TGAACTTCATCGCTCAGCAGCGCGGCATGTTGATCGGCGCTGGTTTCTTGCTCAATATGGTC : 2786

  207 : AlaSerSerLeuLeuGlnSerGlyAlaPheGluValTyrLeuAsnGlySerLeuIleTyrSe :  227
        !.!.!!:!!|||  !|||!!!|||||||||||||||  !|||:!!|||..!||||||!:!||
        GlyGlyAlaLeuGlyGlnThrGlyAlaPheGluValSerLeuAspGlyGluLeuIlePheSe
 2787 : GGCGGCGCCCTCGGGCAGACCGGTGCCTTCGAGGTGAGCTTGGACGGCGAACTTATCTTCTC : 2849

  228 : rLysLeuGluThrGlyAlaValProThrAlaGluThrLeuAlaAspHisIleLeuArgGlnI :  248
        |||||||:!!.!!|||||||||||||||!.!! !  !:!!  !  !  !:!!|||!:!:!!!
        rLysLeuGlnAlaGlyAlaValProThrValAlaGluIleArgArgIleValLeuGlnLysT
 2850 : AAAACTGCAGGCTGGGGCTGTACCGACCGTGGCGGAAATACGTCGTATTGTCCTGCAGAAGA : 2912

  249 : leIle :  249
          :!:
        hrLeu
 2913 : CGCTG : 2917

vulgar:  12 249 . gi|146102387|ref|NC_009419.1|:subseq(515756,4500) 1912 2917 + 246 M 51 153 G 0 9 M 30 90 5 0 2 I 0 311 3 0 2 M 33 99 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
#
gi|146102387|ref|NC_009419.1|:subseq(515756,4500)	exonerate:protein2genome:local	gene	1913	2917	246	+	.	gene_id 1 ; sequence  ; gene_orientation +
gi|146102387|ref|NC_009419.1|:subseq(515756,4500)	exonerate:protein2genome:local	cds	1913	2164	.	+	.	
gi|146102387|ref|NC_009419.1|:subseq(515756,4500)	exonerate:protein2genome:local	exon	1913	2164	.	+	.	insertions 9 ; deletions 0
gi|146102387|ref|NC_009419.1|:subseq(515756,4500)	exonerate:protein2genome:local	splice5	2165	2166	.	+	.	intron_id 1 ; splice_site "GT"
gi|146102387|ref|NC_009419.1|:subseq(515756,4500)	exonerate:protein2genome:local	intron	2165	2479	.	+	.	intron_id 1
gi|146102387|ref|NC_009419.1|:subseq(515756,4500)	exonerate:protein2genome:local	splice3	2478	2479	.	+	.	intron_id 0 ; splice_site "AA"
gi|146102387|ref|NC_009419.1|:subseq(515756,4500)	exonerate:protein2genome:local	cds	2480	2917	.	+	.	
gi|146102387|ref|NC_009419.1|:subseq(515756,4500)	exonerate:protein2genome:local	exon	2480	2917	.	+	.	insertions 0 ; deletions 10
gi|146102387|ref|NC_009419.1|:subseq(515756,4500)	exonerate:protein2genome:local	similarity	1913	2917	246	+	.	alignment_id 1 ; Query  ; Align 1913 13 153 ; Align 2075 64 90 ; Align 2480 94 99 ; Align 2579 130 12 ; Align 2591 140 114 ; Align 2705 179 213
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query:  SelTryp; hypothetical protein [Trypanosoma brucei TREU927] PARTIALLY FROM XP_844760.1
        Target: gi|146102387|ref|NC_009419.1|:subseq(515756,4500) Leishmania infantum JPCM5 chromosome 35, complete sequence
         Model: protein2genome:local
     Raw score: 154
   Query range: 139 -> 249
  Target range: 258 -> 588

 140 : IleLysPheValGlyValValTyrSerValGlyAlaPheArgGluPheIleGlyAsnIleLeuS : 161
       .!!|||.!!:!!|||  !!.!||| !!:!!.!! !!   |||!  .!.|||.!!!!.   |||.
       PheLysIleIleGlyGlnAlaTyrProMetSerProArgArgValLeuIleSerLysAlaLeuG
 259 : TTTAAAATCATTGGGCAGGCGTACCCGATGAGTCCCAGGCGAGTCCTGATCAGCAAGGCGTTAC : 322

 162 : erThrGlyPheLeuAlaSerIleAlaIleSerPhePheAlaProPheLeuArgGlyAlaLeuPr : 182
       .!  !!.!|||!!!!.!!!!:!!!.!:!!:!!.!!.!.!.!  !   |||!:!     !:!!||
       lnGlyAlaPhePheGlyThrLeuGlyLeuAlaLeuMetGlyAspGlnLeuLys---PheIlePr
 323 : AGGGGGCTTTCTTCGGCACGCTAGGGCTTGCCCTTATGGGGGATCAGCTGAAG---TTCATCCC : 382

 183 : oProHisIleAlaGluTrpIleGluGlnHisArgGlyMetValValGlyAlaGlyPheMetMet : 203
       |  !   :!:  !!     :!:...  !!.!||||||:!::!!..!.!!.!!|||||||||:!:
       oGluSerValLeuAlaValLeuArgAlaArgArgGlyLeuIleThrSerThrGlyPheMetLeu
 383 : GGAGTCGGTGCTCGCTGTTCTGCGCGCACGTCGTGGCCTCATCACCAGCACCGGCTTCATGCTC : 445

 204 : AsnMetValAlaSerSerLeuLeuGlnSerGlyAlaPheGluValTyrLeuAsnGlySerLeuI : 225
       |||:!!:!!::! !!:!!  !||||||!:!..!||||||||||||!:!|||:!!|||..!||||
       AsnValLeuSerArgAlaAlaLeuGlnAsnAsnAlaPheGluValPheLeuAspGlyGluLeuI
 446 : AACGTGCTGAGTCGAGCGGCGCTGCAGAACAATGCCTTCGAGGTGTTTTTGGACGGCGAACTCA : 511

 226 : leTyrSerLysLeuGlu<->ThrGlyAlaValProThrAlaGluThrLeuAlaAspHisIleLe : 245
       ||||||||   |||.!.   !:!|||  !|||||||||||||||  !|||::!:!!! !:!!||
       leTyrSerAlaLeuAsnAlaSerGlyArgValProThrAlaGluLeuLeuSerAsnLeuLeuLe
 512 : TCTACTCCGCCCTGAACGCGAGTGGGCGAGTGCCGACAGCAGAGCTGTTGAGCAACCTCCTCCT : 574

 246 : uArgGlnIleIle : 249
       |..!!:!!  :!!
       uGluArgThrLeu
 575 : CGAGCGAACGCTC : 588

vulgar:  139 249 . gi|146102387|ref|NC_009419.1|:subseq(515756,4500) 258 588 + 154 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
#
gi|146102387|ref|NC_009419.1|:subseq(515756,4500)	exonerate:protein2genome:local	gene	259	588	154	+	.	gene_id 2 ; sequence  ; gene_orientation .
gi|146102387|ref|NC_009419.1|:subseq(515756,4500)	exonerate:protein2genome:local	cds	259	588	.	+	.	
gi|146102387|ref|NC_009419.1|:subseq(515756,4500)	exonerate:protein2genome:local	exon	259	588	.	+	.	insertions 3 ; deletions 1
gi|146102387|ref|NC_009419.1|:subseq(515756,4500)	exonerate:protein2genome:local	similarity	259	588	154	+	.	alignment_id 2 ; Query  ; Align 259 140 117 ; Align 376 180 153 ; Align 532 231 57
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
