Command line: [exonerate -m p2g --showtargetgff --exhaustive yes -q ./SelTryp.fa -t ./fastasubseq_Linfantum_SelTryp_2]
Hostname: [luke]

C4 Alignment:
------------
         Query:  SelTryp; hypothetical protein [Trypanosoma brucei TREU927] PARTIALLY FROM XP_844760.1
        Target: gi|146102387|ref|NC_009419.1|:subseq(513853,4500) Leishmania infantum JPCM5 chromosome 35, complete sequence
         Model: protein2genome:local
     Raw score: 154
   Query range: 139 -> 249
  Target range: 2161 -> 2491

  140 : IleLysPheValGlyValValTyrSerValGlyAlaPheArgGluPheIleGlyAsnIleLe :  160
        .!!|||.!!:!!|||  !!.!||| !!:!!.!! !!   |||!  .!.|||.!!!!.   ||
        PheLysIleIleGlyGlnAlaTyrProMetSerProArgArgValLeuIleSerLysAlaLe
 2162 : TTTAAAATCATTGGGCAGGCGTACCCGATGAGTCCCAGGCGAGTCCTGATCAGCAAGGCGTT : 2222

  161 : uSerThrGlyPheLeuAlaSerIleAlaIleSerPhePheAlaProPheLeuArgGlyAlaL :  181
        |..!  !!.!|||!!!!.!!!!:!!!.!:!!:!!.!!.!.!.!  !   |||!:!     !:
        uGlnGlyAlaPhePheGlyThrLeuGlyLeuAlaLeuMetGlyAspGlnLeuLys---PheI
 2223 : ACAGGGGGCTTTCTTCGGCACGCTAGGGCTTGCCCTTATGGGGGATCAGCTGAAG---TTCA : 2282

  182 : euProProHisIleAlaGluTrpIleGluGlnHisArgGlyMetValValGlyAlaGlyPhe :  201
        !!|||  !   :!:  !!     :!:...  !!.!||||||:!::!!..!.!!.!!||||||
        leProGluSerValLeuAlaValLeuArgAlaArgArgGlyLeuIleThrSerThrGlyPhe
 2283 : TCCCGGAGTCGGTGCTCGCTGTTCTGCGCGCACGTCGTGGCCTCATCACCAGCACCGGCTTC : 2342

  202 : MetMetAsnMetValAlaSerSerLeuLeuGlnSerGlyAlaPheGluValTyrLeuAsnGl :  222
        |||:!:|||:!!:!!::! !!:!!  !||||||!:!..!||||||||||||!:!|||:!!||
        MetLeuAsnValLeuSerArgAlaAlaLeuGlnAsnAsnAlaPheGluValPheLeuAspGl
 2343 : ATGCTCAACGTGCTGAGTCGAGCGGCGCTGCAGAACAATGCCTTCGAGGTGTTTTTGGACGG : 2405

  223 : ySerLeuIleTyrSerLysLeuGlu<->ThrGlyAlaValProThrAlaGluThrLeuAlaA :  242
        |..!||||||||||||   |||.!.   !:!|||  !|||||||||||||||  !|||::!:
        yGluLeuIleTyrSerAlaLeuAsnAlaSerGlyArgValProThrAlaGluLeuLeuSerA
 2406 : CGAACTCATCTACTCCGCCCTGAACGCGAGTGGGCGAGTGCCGACAGCAGAGCTGTTGAGCA : 2468

  243 : spHisIleLeuArgGlnIleIle :  249
        !!! !:!!|||..!!:!!  :!!
        snLeuLeuLeuGluArgThrLeu
 2469 : ACCTCCTCCTCGAGCGAACGCTC : 2491

vulgar:  139 249 . gi|146102387|ref|NC_009419.1|:subseq(513853,4500) 2161 2491 + 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(513853,4500)	exonerate:protein2genome:local	gene	2162	2491	154	+	.	gene_id 1 ; sequence  ; gene_orientation .
gi|146102387|ref|NC_009419.1|:subseq(513853,4500)	exonerate:protein2genome:local	cds	2162	2491	.	+	.	
gi|146102387|ref|NC_009419.1|:subseq(513853,4500)	exonerate:protein2genome:local	exon	2162	2491	.	+	.	insertions 3 ; deletions 1
gi|146102387|ref|NC_009419.1|:subseq(513853,4500)	exonerate:protein2genome:local	similarity	2162	2491	154	+	.	alignment_id 1 ; Query  ; Align 2162 140 117 ; Align 2279 180 153 ; Align 2435 231 57
# --- 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(513853,4500) Leishmania infantum JPCM5 chromosome 35, complete sequence
         Model: protein2genome:local
     Raw score: 125
   Query range: 12 -> 126
  Target range: 3815 -> 4481

   13 : AlaLeuLeuIleAlaAlaPheLeuAlaAlaAsnAlaGlySerAlaThrAsnAlaAspAsnGl :   33
        :!!|||  !:!!  !  ! !!! !||||||  !..!!.!!:!:!!.!!..!! !!  .!.  
        SerLeuAlaLeuLeuPheValSerAlaAlaCysCysAlaAsnSerAlaArgGluValGlnPr
 3816 : TCACTGGCGCTTCTCTTCGTTTCCGCTGCGTGTTGTGCGAATTCGGCGCGTGAAGTGCAGCC : 3876

   34 : uAlaThrAspTyrSerSerHisArgTyrLysTyrLeuGluMetLeuLysGluAlaAspLeuL :   54
         .!!..!!!: ! !:!!.! !!! !|||   ||||||!!:|||||| ! |||!.!||||||:
        oThrValGluGlnAsnLysAspProTyrAlaTyrLeuAspMetLeuAspGluValAspLeuG
 3877 : TACTGTTGAGCAGAACAAGGACCCGTACGCCTACCTCGACATGCTGGATGAGGTGGACCTAC : 3939

   55 : ysGlnMetLeuHisGluLysGlyGluAla<-><-><->PheHisHisLeuArgSerLysArg :   71
        !!|||||||||:!!||||||  !.!.!.!          !!  !  !!!!|||..!|||!:!
        lnGlnMetLeuTyrGluLysThrHisGlyGlnValProValSerAlaPheArgAspLysLys
 3940 : AGCAAATGCTATATGAAAAGACGCATGGGCAGGTGCCGGTCAGCGCTTTCCGCGACAAGAAG : 3999

   72 : GluLeuIleLeuAlaValLeuLysLeuGluLysArgGluGluAlaLeuArgLysAlaArgVa :   92
        ||||||:!!  !||||||! !|||||||||:!!||||||!!:! !  !  !!..  !!.!!.
        GluLeuValAlaAlaValArgLysLeuGluGluArgGluAspGluGluAlaSerPheAsnAl
 4000 : GAGCTGGTTGCCGCAGTGCGCAAGCTCGAGGAGCGCGAGGACGAGGAGGCCAGCTTCAACGC : 4062

   93 : lThr  >>>> Target Intron 1 >>>>  AspThrValGlnHisGluValArgValGl :  103
        !  !            315 bp             !:!!!.!..!||||||:!!..!|||  
        aArg++                         +-LeuSerAlaMetHisGluLeuGluValLe
 4063 : GCGTgt.........................aaCTCTCTGCAATGCATGAGTTGGAAGTGCT : 4410

  104 : uTyrCysSerGlyUnkGlyTyrArgArgHisTyrGluGluValAlaGluSerLeuLeuArgS :  124
        !||||||!!!|||   ||||||  !!:!:!!!:!|||!!::!!  !:!!..!|||! !|||!
        uTyrCysThrGly***GlyTyrAlaLysTyrPheGluAspMetLysGlnGlnLeuGlnArgT
 4411 : GTACTGTACCGGATGAGGATACGCGAAGTATTTTGAAGATATGAAGCAGCAGCTGCAACGTA : 4473

  125 : erLeuPro :  126
        !!||||||
        hrLeuPro
 4474 : CGCTGCCC : 4481

vulgar:  12 126 . gi|146102387|ref|NC_009419.1|:subseq(513853,4500) 3815 4481 + 125 M 51 153 G 0 9 M 30 90 5 0 2 I 0 311 3 0 2 M 33 99
# --- 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(513853,4500)	exonerate:protein2genome:local	gene	3816	4481	125	+	.	gene_id 2 ; sequence  ; gene_orientation +
gi|146102387|ref|NC_009419.1|:subseq(513853,4500)	exonerate:protein2genome:local	cds	3816	4067	.	+	.	
gi|146102387|ref|NC_009419.1|:subseq(513853,4500)	exonerate:protein2genome:local	exon	3816	4067	.	+	.	insertions 9 ; deletions 0
gi|146102387|ref|NC_009419.1|:subseq(513853,4500)	exonerate:protein2genome:local	splice5	4068	4069	.	+	.	intron_id 1 ; splice_site "GT"
gi|146102387|ref|NC_009419.1|:subseq(513853,4500)	exonerate:protein2genome:local	intron	4068	4382	.	+	.	intron_id 1
gi|146102387|ref|NC_009419.1|:subseq(513853,4500)	exonerate:protein2genome:local	splice3	4381	4382	.	+	.	intron_id 0 ; splice_site "AA"
gi|146102387|ref|NC_009419.1|:subseq(513853,4500)	exonerate:protein2genome:local	cds	4383	4481	.	+	.	
gi|146102387|ref|NC_009419.1|:subseq(513853,4500)	exonerate:protein2genome:local	exon	4383	4481	.	+	.	insertions 0 ; deletions 0
gi|146102387|ref|NC_009419.1|:subseq(513853,4500)	exonerate:protein2genome:local	similarity	3816	4481	125	+	.	alignment_id 2 ; Query  ; Align 3816 13 153 ; Align 3978 64 90 ; Align 4383 94 99
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
