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

C4 Alignment:
------------
         Query: MSP, [Se user]; [Dictyostelium discoideum AX4 (Eukaryota/Dictyosteliida)]
        Target: supercont1.1087:subseq(16000,5000) of Sphaeroforma arctica JP610:[revcomp]
         Model: protein2genome:local
     Raw score: 144
   Query range: 130 -> 219
  Target range: 3465 -> 2386

  131 : HisTrpIleLysPheGlyProPheTyrLeuThrAlaIleAlaValProLeuAlaThrPheAs :  151
        |||  !! !::!|||||||||||||||||||||  !!!:||||||||||||!.!! !  !||
        HisMetAsnArgPheGlyProPheTyrLeuThrLeuMetAlaValProLeuValMetAlaAs
 3465 : CATATGAATCGGTTCGGTCCGTTCTATCTCACACTGATGGCTGTGCCGCTGGTGATGGCTGA : 3405

  152 : pIleLeuArgHisIleLeuValAspAsn{S}  >>>> Target Intron 1 >>>>  {e :  161
        |:!!  !||||||||||||  !|||:::{ }            815 bp           { 
        pLeuThrArgHisIleLeuGlnAspSer{V}++                         +-{a
 3404 : CCTCACTCGACACATCCTACAAGATTCG{G}gt.........................ac{T : 2559

  162 : r}IleTrpThrIleHisSerPheIleSerProAlaAlaTyrArgProGlyCysGluAsnGlu :  181
        !}  !   :!!:!!   ..!.!.  !||| !!  !|||  !  !  !!.!  !  !! !  !
        l}ArgHisSerValIleAspMetAspSerThrAsnAlaLeuAlaValAlaAspLeuIleLeu
 2558 : T}CGCCACTCAGTCATAGACATGGATTCAACAAATGCTCTCGCTGTGGCTGATTTAATTTTG : 2500

  182 : AsnIleThrCysLeuSerValMetGlyTrpPheSerAlaIleValPheThrTyrThrGlyTy :  202
           .!!..!!  :!!..!|||  !  !||||||!!!   |||||||||||||||!:!|||!:
        LeuPheValSerIleGlnValGlyPheTrpPheThr---IleValPheThrTyrSerGlyPh
 2499 : TTGTTTGTTTCAATACAGGTCGGGTTCTGGTTCACA---ATAGTATTCACGTACAGCGGGTT : 2440

  203 : rAlaCysLeuLeuValGlyThrIleTrpAlaAlaAspLeuIleProLysIle :  219
        !|||!  |||:!!|||||||||:!!||||||:!!:!!:!!:!!||||||:!!
        eAlaLeuLeuValValGlyThrValTrpAlaSerAsnValValProLysVal
 2439 : TGCCTTGCTGGTGGTGGGTACTGTATGGGCCTCGAATGTTGTACCCAAGGTA : 2387

vulgar: MSP, 130 219 . supercont1.1087:subseq(16000,5000) 3465 2386 - 144 M 30 90 S 0 1 5 0 2 I 0 811 3 0 2 S 1 2 M 32 96 G 1 0 M 25 75
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-11-24
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
supercont1.1087:subseq(16000,5000)	exonerate:protein2genome:local	gene	2387	3465	144	-	.	gene_id 1 ; sequence MSP, ; gene_orientation +
supercont1.1087:subseq(16000,5000)	exonerate:protein2genome:local	cds	3375	3465	.	-	.	
supercont1.1087:subseq(16000,5000)	exonerate:protein2genome:local	exon	3375	3465	.	-	.	insertions 0 ; deletions 0
supercont1.1087:subseq(16000,5000)	exonerate:protein2genome:local	splice5	3373	3374	.	-	.	intron_id 1 ; splice_site "GT"
supercont1.1087:subseq(16000,5000)	exonerate:protein2genome:local	intron	2560	3374	.	-	.	intron_id 1
supercont1.1087:subseq(16000,5000)	exonerate:protein2genome:local	splice3	2560	2561	.	-	.	intron_id 0 ; splice_site "AC"
supercont1.1087:subseq(16000,5000)	exonerate:protein2genome:local	cds	2387	2559	.	-	.	
supercont1.1087:subseq(16000,5000)	exonerate:protein2genome:local	exon	2387	2559	.	-	.	insertions 0 ; deletions 1
supercont1.1087:subseq(16000,5000)	exonerate:protein2genome:local	similarity	2387	3465	144	-	.	alignment_id 1 ; Query MSP, ; Align 3466 131 90 ; Align 2558 162 96 ; Align 2462 195 75
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
