Command line: [exonerate -m p2g --showtargetgff -q query_sacaromices.fa -t pallidumgenomic.fa --exhaustive]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: SPP00000077_1.0 # Protein # Selenoprotein R  (SelR) # Saccharomyces cerevisiae # Complete
        Target: gi|284795303|gb|GL291017.1|:subseq(387099,2452) Polysphondylium pallidum PN500 unplaced genomic scaffold PPL_contig20, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 305
   Query range: 38 -> 163
  Target range: 990 -> 1452

   39 : AsnAspValLysTrpAsnAspAlaLeuThrProLeuGlnLeuMetValLeuArgAspLysAl :   59
        :::!!:! !:!!|||!!.!    !|||:!!|||  !|||!!!   |||||||||.!.|||!.
        SerGluAspGluTrpLysValLysLeuSerProGluGlnPheHisValLeuArgGlnLysGl
  991 : TCAGAGGACGAATGGAAGGTGAAGCTCTCACCAGAGCAATTTCATGTGTTGCGTCAAAAGGG : 1051

   60 : aThrGluArgProAsnThrGlyAlaTyrLeuHisThrAsnGluSerGlyValTyrHisCysA :   80
        !||||||||| !!..!||||||  !|||  ! !   !::!|||..!|||||||||:!!||||
        yThrGluArgAlaGlyThrGlyGlnTyrAsnLysHisSerGluGluGlyValTyrAsnCysA
 1052 : AACAGAGAGAGCTGGTACCGGTCAGTATAATAAGCACTCTGAGGAGGGTGTATATAATTGCG : 1114

   81 : laAsnCysAspArgProLeuTyrSerSerLysAlaLysPheAspAlaArgCysGlyTrpPro :  100
        ||..!|||!!:! !|||||||||!!!||||||::!||||||:!!:!! !!||||||||||||
        laGlyCysGluThrProLeuTyrThrSerLysSerLysPheAsnSerGlyCysGlyTrpPro
 1115 : CTGGTTGCGAGACTCCACTCTACACATCGAAGAGCAAGTTCAACTCTGGCTGTGGATGGCCG : 1174

  101 : AlaPheTyrGluGluValSerProGlyAlaIleThrTyrHisArgAspAsnSerLeuMetPr :  121
        ||||||!:!|||! !:!!   |||||||||:!:|||  !  !..!|||..!|||! !     
        AlaPhePheGluAlaIle---ProGlyAlaLeuThrIlePheGluAspArgSerHisGlyMe
 1175 : GCTTTCTTCGAAGCGATA---CCCGGTGCTTTGACCATCTTTGAAGATCGTTCACACGGTAT : 1234

  122 : oAlaArgValGluIleCysCysAlaArgCysGlyGlyHisLeuGlyHisValPheGlu  >> :  141
        !!.!|||..!||||||||||||  !!.!|||||||||||||||||||||||||||:!!    
        tValArgThrGluIleCysCysLysAsnCysGlyGlyHisLeuGlyHisValPheLys++  
 1235 : GGTTAGAACAGAGATCTGTTGTAAGAACTGCGGTGGTCATTTAGGTCATGTATTTAAGgt.. : 1296

  142 : >> Target Intron 1 >>>>  GlyGluGlyTrpLysGlnLeuLeuAsnLeuProLysA :  153
                90 bp              !:!!  !! !   :!!  !! !!:!  !|||!  |
                               +-LysLys******GlyGluGlyTyrSerThrProThrA
 1297 : .......................aaAAAAAATAATAGGGCGAAGGATATAGCACACCAACTG : 1420

  154 : spThrArgHisUnkValAsnSerAlaSerLeu :  163
        ||  !||||||   |||||||||  !||||||
        spGluArgHisCysValAsnSerIleSerLeu
 1421 : ATGAAAGACATTGCGTAAACTCAATAAGTTTA : 1452

vulgar: SPP00000077_1.0 38 163 . gi|284795303|gb|GL291017.1|:subseq(387099,2452) 990 1452 + 305 M 68 204 G 1 0 M 33 99 5 0 2 I 0 86 3 0 2 M 23 69
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-03-08
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|284795303|gb|GL291017.1|:subseq(387099,2452)	exonerate:protein2genome:local	gene	991	1452	305	+	.	gene_id 1 ; sequence SPP00000077_1.0 ; gene_orientation +
gi|284795303|gb|GL291017.1|:subseq(387099,2452)	exonerate:protein2genome:local	cds	991	1293	.	+	.	
gi|284795303|gb|GL291017.1|:subseq(387099,2452)	exonerate:protein2genome:local	exon	991	1293	.	+	.	insertions 0 ; deletions 1
gi|284795303|gb|GL291017.1|:subseq(387099,2452)	exonerate:protein2genome:local	splice5	1294	1295	.	+	.	intron_id 1 ; splice_site "GT"
gi|284795303|gb|GL291017.1|:subseq(387099,2452)	exonerate:protein2genome:local	intron	1294	1383	.	+	.	intron_id 1
gi|284795303|gb|GL291017.1|:subseq(387099,2452)	exonerate:protein2genome:local	splice3	1382	1383	.	+	.	intron_id 0 ; splice_site "AA"
gi|284795303|gb|GL291017.1|:subseq(387099,2452)	exonerate:protein2genome:local	cds	1384	1452	.	+	.	
gi|284795303|gb|GL291017.1|:subseq(387099,2452)	exonerate:protein2genome:local	exon	1384	1452	.	+	.	insertions 0 ; deletions 0
gi|284795303|gb|GL291017.1|:subseq(387099,2452)	exonerate:protein2genome:local	similarity	991	1452	305	+	.	alignment_id 1 ; Query SPP00000077_1.0 ; Align 991 39 204 ; Align 1195 108 99 ; Align 1384 141 69
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis