Command line: [exonerate -m p2g --showtargetgff --exhaustive yes -q ./SelTryp.fa -t ./fastasubseq_Linfantum_SelTryp_1]
Hostname: [luke]

C4 Alignment:
------------
         Query:  SelTryp; hypothetical protein [Trypanosoma brucei TREU927] PARTIALLY FROM XP_844760.1
        Target: gi|146102387|ref|NC_009419.1|:subseq(516239,4300) Leishmania infantum JPCM5 chromosome 35, complete sequence
         Model: protein2genome:local
     Raw score: 246
   Query range: 12 -> 249
  Target range: 1429 -> 2434

   13 : AlaLeuLeuIleAlaAlaPheLeuAlaAlaAsnAlaGlySerAlaThrAsnAlaAspAsnGl :   33
        :!!|||  !:!!  !  ! !!! !||||||  !..!!.!!:!:!!.!!..!! !!  .!.  
        SerLeuAlaLeuLeuPheValSerAlaAlaCysCysAlaAsnSerAlaArgGluValGlnPr
 1430 : TCACTGGCGCTTCTCTTCGTTTCCGCTGCGTGTTGTGCGAATTCGGCGCGTGAAGTGCAGCC : 1490

   34 : uAlaThrAspTyrSerSerHisArgTyrLysTyrLeuGluMetLeuLysGluAlaAspLeuL :   54
         .!!..!!!: ! !:!!.! !!! !|||   ||||||!!:|||||| ! |||!.!||||||:
        oThrValGluGlnAsnLysAspProTyrAlaTyrLeuAspMetLeuAspGluValAspLeuG
 1491 : TACTGTTGAGCAGAACAAGGACCCGTACGCCTACCTCGACATGCTGGATGAGGTGGACCTAC : 1553

   55 : ysGlnMetLeuHisGluLysGlyGluAla<-><-><->PheHisHisLeuArgSerLysArg :   71
        !!|||||||||:!!||||||  !.!.!.!          !!  !  !!!!|||..!|||!:!
        lnGlnMetLeuTyrGluLysThrHisGlyGlnValProValSerAlaPheArgAspLysLys
 1554 : AGCAAATGCTATATGAAAAGACGCATGGGCAGGTGCCGGTCAGCGCTTTCCGCGACAAGAAG : 1613

   72 : GluLeuIleLeuAlaValLeuLysLeuGluLysArgGluGluAlaLeuArgLysAlaArgVa :   92
        ||||||:!!  !||||||! !|||||||||:!!||||||!!:! !  !  !!..  !!.!!.
        GluLeuValAlaAlaValArgLysLeuGluGluArgGluAspGluGluAlaSerPheAsnAl
 1614 : GAGCTGGTTGCCGCAGTGCGCAAGCTCGAGGAGCGCGAGGACGAGGAGGCCAGCTTCAACGC : 1676

   93 : lThr  >>>> Target Intron 1 >>>>  AspThrValGlnHisGluValArgValGl :  103
        !  !            315 bp             !:!!!.!..!||||||:!!..!|||  
        aArg++                         +-LeuSerAlaMetHisGluLeuGluValLe
 1677 : GCGTgt.........................aaCTCTCTGCAATGCATGAGTTGGAAGTGCT : 2024

  104 : uTyrCysSerGlyUnkGlyTyrArgArgHisTyrGluGluValAlaGluSerLeuLeuArgS :  124
        !||||||!!!|||   ||||||  !!:!:!!!:!|||!!::!!  !:!!..!|||! !|||!
        uTyrCysThrGly***GlyTyrAlaLysTyrPheGluAspMetLysGlnGlnLeuGlnArgT
 2025 : GTACTGTACCGGATGAGGATACGCGAAGTATTTTGAAGATATGAAGCAGCAGCTGCAACGTA : 2087

  125 : erLeuProProGluLeuArgGluGlnGlnLysGlyLysLysProPheIleLysPheValGly :  144
        !!||||||         !.!! !|||:!!                  :!!:::.!!||||||
        hrLeuPro---------AsnAlaGlnGlu------------------ValArgIleValGly
 2088 : CGCTGCCC---------AACGCACAAGAG------------------GTACGCATTGTGGGC : 2120

  145 : ValValTyrSerValGlyAlaPheArgGluPheIleGlyAsnIleLeuSerThrGlyPheLe :  165
        ! !..!||| !!..!  ! !!  !|||!  .!!  !!.!!!.   ! !||||||!.!|||||
        GlyThrTyrProThrProProAlaArgAlaLeuAlaAlaLysAlaCysSerThrAlaPheLe
 2121 : GGTACCTACCCCACCCCACCTGCCCGCGCCCTCGCCGCGAAGGCGTGCTCGACCGCCTTTCT : 2183

  166 : uAlaSerIleAlaIleSerPhePheAlaProPheLeuArgGlyAlaLeuProProHisIleA :  186
        |||||||:!!!.!:!!:!!.!!   !.!! !   |||   ! !  !|||||||||  !:!! 
        uAlaSerLeuGlyValAlaLeuAlaGlyGlnGlnLeu---ValPheLeuProProThrValL
 2184 : GGCCTCCCTCGGTGTCGCCCTTGCAGGACAGCAACTC---GTGTTTCTGCCCCCCACCGTTC : 2243

  187 : laGluTrpIleGluGlnHisArgGlyMetValValGlyAlaGlyPheMetMetAsnMetVal :  206
         !.!.!::|||!  |||!!.|||||||||:!!:!!||||||||||||:!!:!:|||||||||
        euAsnPheIleAlaGlnGlnArgGlyMetLeuIleGlyAlaGlyPheLeuLeuAsnMetVal
 2244 : TGAACTTCATCGCTCAGCAGCGCGGCATGTTGATCGGCGCTGGTTTCTTGCTCAATATGGTC : 2303

  207 : AlaSerSerLeuLeuGlnSerGlyAlaPheGluValTyrLeuAsnGlySerLeuIleTyrSe :  227
        !.!.!!:!!|||  !|||!!!|||||||||||||||  !|||:!!|||..!||||||!:!||
        GlyGlyAlaLeuGlyGlnThrGlyAlaPheGluValSerLeuAspGlyGluLeuIlePheSe
 2304 : GGCGGCGCCCTCGGGCAGACCGGTGCCTTCGAGGTGAGCTTGGACGGCGAACTTATCTTCTC : 2366

  228 : rLysLeuGluThrGlyAlaValProThrAlaGluThrLeuAlaAspHisIleLeuArgGlnI :  248
        |||||||:!!.!!|||||||||||||||!.!! !  !:!!  !  !  !:!!|||!:!:!!!
        rLysLeuGlnAlaGlyAlaValProThrValAlaGluIleArgArgIleValLeuGlnLysT
 2367 : AAAACTGCAGGCTGGGGCTGTACCGACCGTGGCGGAAATACGTCGTATTGTCCTGCAGAAGA : 2429

  249 : leIle :  249
          :!:
        hrLeu
 2430 : CGCTG : 2434

vulgar:  12 249 . gi|146102387|ref|NC_009419.1|:subseq(516239,4300) 1429 2434 + 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(516239,4300)	exonerate:protein2genome:local	gene	1430	2434	246	+	.	gene_id 1 ; sequence  ; gene_orientation +
gi|146102387|ref|NC_009419.1|:subseq(516239,4300)	exonerate:protein2genome:local	cds	1430	1681	.	+	.	
gi|146102387|ref|NC_009419.1|:subseq(516239,4300)	exonerate:protein2genome:local	exon	1430	1681	.	+	.	insertions 9 ; deletions 0
gi|146102387|ref|NC_009419.1|:subseq(516239,4300)	exonerate:protein2genome:local	splice5	1682	1683	.	+	.	intron_id 1 ; splice_site "GT"
gi|146102387|ref|NC_009419.1|:subseq(516239,4300)	exonerate:protein2genome:local	intron	1682	1996	.	+	.	intron_id 1
gi|146102387|ref|NC_009419.1|:subseq(516239,4300)	exonerate:protein2genome:local	splice3	1995	1996	.	+	.	intron_id 0 ; splice_site "AA"
gi|146102387|ref|NC_009419.1|:subseq(516239,4300)	exonerate:protein2genome:local	cds	1997	2434	.	+	.	
gi|146102387|ref|NC_009419.1|:subseq(516239,4300)	exonerate:protein2genome:local	exon	1997	2434	.	+	.	insertions 0 ; deletions 10
gi|146102387|ref|NC_009419.1|:subseq(516239,4300)	exonerate:protein2genome:local	similarity	1430	2434	246	+	.	alignment_id 1 ; Query  ; Align 1430 13 153 ; Align 1592 64 90 ; Align 1997 94 99 ; Align 2096 130 12 ; Align 2108 140 114 ; Align 2222 179 213
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
