Command line: [exonerate -m p2g --showtargetgff -q query.MSP.D.discoideum_AX4.fa -t MSP.D.discoideum.fastasubseq.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: MSP, [Se user]; [Dictyostelium discoideum AX4 (Eukaryota/Dictyosteliida)]
        Target: gi|256541943|gb|CM000151.3|:subseq(7223000,4000) Dictyostelium discoideum AX4 chromosome 2, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 1107
   Query range: 0 -> 227
  Target range: 2967 -> 2157

    1 : MetSerLeuPheAsnLeuProLysValAspLeuGlyGluAspCysGlu{G}  >>>> Targ :   17
        ||||||||||||||||||||||||||||||||||||||||||||||||{!}           
        MetSerLeuPheAsnLeuProLysValAspLeuGlyGluAspCysGlu{A}++         
 2967 : ATGTCATTATTTAATTTACCAAAAGTGGATTTAGGTGAAGATTGTGAA{G}gt......... : 2916

   18 : et Intron 1 >>>>  {ly}GlyValUnkAlaArgProAspGluSerThrProLeuIleS :   31
         33 bp            {.!}..!:!!     !  !  !||||||||||||||||||||||
                        +-{la}SerIleAsnAsnAlaSerAspGluSerThrProLeuIleS
 2915 : ................at{CA}TCTATCAATAATGCTAGTGATGAGTCTACACCATTAATTT : 2844

   32 : erLysThrAsnAspGluGluLysAlaAsnIleGlyIleSerSerThrSerAsnSerProGln :   51
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        erLysThrAsnAspGluGluLysAlaAsnIleGlyIleSerSerThrSerAsnSerProGln
 2843 : CAAAGACAAACGATGAAGAAAAAGCAAACATTGGTATCTCCTCAACCTCAAACTCCCCACAA : 2784

   52 : GluGluGlnThrLysLysProLeuPheIleSerIleLeuThrLeuLeuIleSerIleProAl :   72
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        GluGluGlnThrLysLysProLeuPheIleSerIleLeuThrLeuLeuIleSerIleProAl
 2783 : GAAGAACAAACTAAAAAACCATTATTCATTTCAATTCTTACACTTTTAATTAGTATTCCAGC : 2721

   73 : aLeuVal{G}  >>>> Target Intron 2 >>>>  {ly}SerUnkCysTrpProValL :   82
        |||||||{|}            96 bp            {||}|||   |||||||||||||
        aLeuVal{G}++                         ++{ly}Ser***CysTrpProValL
 2720 : TTTAGTT{G}gt.........................ag{GT}TCTTGATGTTGGCCTGTGC : 2595

   83 : euIleAlaSerLeuSerGlyValAlaValSerAlaGlySerValGluLeuAlaHisSerLeu :  102
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        euIleAlaSerLeuSerGlyValAlaValSerAlaGlySerValGluLeuAlaHisSerLeu
 2594 : TCATTGCAAGCCTTTCTGGTGTTGCAGTTAGTGCAGGATCCGTTGAACTAGCTCATTCTTTA : 2535

  103 : ThrPheAlaIleThrLeuSerIleLeuSerAsnLeuAlaGlnTyrHisPheHisLysCysLy :  123
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        ThrPheAlaIleThrLeuSerIleLeuSerAsnLeuAlaGlnTyrHisPheHisLysCysLy
 2534 : ACATTCGCCATTACACTTAGTATACTTTCAAACCTTGCTCAATATCATTTCCATAAATGTAA : 2472

  124 : sLysArgProSerAspArgGlyHisTrpIleLysPheGlyProPheTyrLeuThrAlaIleA :  144
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        sLysArgProSerAspArgGlyHisTrpIleLysPheGlyProPheTyrLeuThrAlaIleA
 2471 : AAAGAGACCATCGGATAGAGGTCATTGGATTAAATTTGGACCTTTTTATCTTACAGCTATCG : 2409

  145 : laValProLeuAlaThrPheAspIleLeuArgHisIleLeuValAspAsnSerIleTrpThr :  164
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        laValProLeuAlaThrPheAspIleLeuArgHisIleLeuValAspAsnSerIleTrpThr
 2408 : CTGTTCCATTGGCAACCTTTGATATTCTAAGACATATTCTAGTTGATAATAGTATTTGGACC : 2349

  165 : IleHisSerPheIleSerProAlaAlaTyrArgProGlyCysGluAsnGluAsnIleThrCy :  185
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        IleHisSerPheIleSerProAlaAlaTyrArgProGlyCysGluAsnGluAsnIleThrCy
 2348 : ATCCACTCTTTCATTTCACCTGCTGCCTATAGACCTGGTTGCGAGAATGAAAATATAACTTG : 2286

  186 : sLeuSerValMetGlyTrpPheSerAlaIleValPheThrTyrThrGlyTyrAlaCysLeuL :  206
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        sLeuSerValMetGlyTrpPheSerAlaIleValPheThrTyrThrGlyTyrAlaCysLeuL
 2285 : CTTGTCTGTTATGGGTTGGTTCTCTGCTATAGTTTTCACTTATACAGGTTATGCTTGTCTTT : 2223

  207 : euValGlyThrIleTrpAlaAlaAspLeuIleProLysIleLysLysValTrpThrGlnLeu :  226
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        euValGlyThrIleTrpAlaAlaAspLeuIleProLysIleLysLysValTrpThrGlnLeu
 2222 : TAGTTGGTACAATTTGGGCTGCCGATTTAATTCCAAAAATTAAAAAGGTTTGGACACAATTA : 2163

  227 : Arg :  227
        |||
        Arg
 2162 : CGT : 2158

vulgar: MSP, 0 227 . gi|256541943|gb|CM000151.3|:subseq(7223000,4000) 2967 2157 - 1107 M 16 48 S 0 1 5 0 2 I 0 29 3 0 2 S 1 2 M 57 171 S 0 1 5 0 2 I 0 92 3 0 2 S 1 2 M 152 456
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-11-30
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|256541943|gb|CM000151.3|:subseq(7223000,4000)	exonerate:protein2genome:local	gene	2158	2967	1107	-	.	gene_id 1 ; sequence MSP, ; gene_orientation +
gi|256541943|gb|CM000151.3|:subseq(7223000,4000)	exonerate:protein2genome:local	cds	2919	2967	.	-	.	
gi|256541943|gb|CM000151.3|:subseq(7223000,4000)	exonerate:protein2genome:local	exon	2919	2967	.	-	.	insertions 0 ; deletions 0
gi|256541943|gb|CM000151.3|:subseq(7223000,4000)	exonerate:protein2genome:local	splice5	2917	2918	.	-	.	intron_id 1 ; splice_site "GT"
gi|256541943|gb|CM000151.3|:subseq(7223000,4000)	exonerate:protein2genome:local	intron	2886	2918	.	-	.	intron_id 1
gi|256541943|gb|CM000151.3|:subseq(7223000,4000)	exonerate:protein2genome:local	splice3	2886	2887	.	-	.	intron_id 0 ; splice_site "AT"
gi|256541943|gb|CM000151.3|:subseq(7223000,4000)	exonerate:protein2genome:local	cds	2712	2885	.	-	.	
gi|256541943|gb|CM000151.3|:subseq(7223000,4000)	exonerate:protein2genome:local	exon	2712	2885	.	-	.	insertions 0 ; deletions 0
gi|256541943|gb|CM000151.3|:subseq(7223000,4000)	exonerate:protein2genome:local	splice5	2710	2711	.	-	.	intron_id 2 ; splice_site "GT"
gi|256541943|gb|CM000151.3|:subseq(7223000,4000)	exonerate:protein2genome:local	intron	2616	2711	.	-	.	intron_id 2
gi|256541943|gb|CM000151.3|:subseq(7223000,4000)	exonerate:protein2genome:local	splice3	2616	2617	.	-	.	intron_id 1 ; splice_site "AG"
gi|256541943|gb|CM000151.3|:subseq(7223000,4000)	exonerate:protein2genome:local	cds	2158	2615	.	-	.	
gi|256541943|gb|CM000151.3|:subseq(7223000,4000)	exonerate:protein2genome:local	exon	2158	2615	.	-	.	insertions 0 ; deletions 0
gi|256541943|gb|CM000151.3|:subseq(7223000,4000)	exonerate:protein2genome:local	similarity	2158	2967	1107	-	.	alignment_id 1 ; Query MSP, ; Align 2968 1 48 ; Align 2884 18 171 ; Align 2614 76 456
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
