Command line: [exonerate -m p2g --showtargetgff -q query_celegans.fa -t paragenomic.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query: SPP00000059_1.0 # Protein # Selenoprotein R  (SelR) # Caenorhabditis elegans # Complete
        Target: gi|288565193|gb|GG744004.1|:subseq(53134,2380) Saprolegnia parasitica CBS 223.65 genomic scaffold supercont1.122, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 230
   Query range: 20 -> 149
  Target range: 1002 -> 1380

   21 : AsnProLysAspValLysGlnThrGluTrpLysSerValLeuProAsnGluValTyrArgVa :   41
        !!.|||! !  !..!!  .!.  !|||||||||:!!  !||| !!     !! !||||||||
        LysProIleProThrThrAspAspGluTrpLysAlaLysLeuThrProTrpGluTyrArgVa
 1003 : AAGCCCATACCCACGACCGACGACGAGTGGAAGGCGAAGCTGACGCCGTGGGAATACCGCGT : 1063

   42 : lAlaArgGluSerGlyThrGluThrProHisThrGlyGlyPheAsnAspHisPheGluLysG :   62
        |  !|||:!!!.!||||||||| !!|||  !!:!|||  !!!.||| ! |||||||||||||
        lLeuArgGlnLysGlyThrGluProProGlySerGlyProLeuAsnLysHisPheGluLysG
 1064 : CTTGCGGCAGAAGGGCACGGAGCCACCGGGCAGCGGGCCCTTGAACAAGCACTTTGAGAAAG : 1126

   63 : lyArgTyrValCysLeuCysCysGlySerGluLeuPheAsnSerAspAlaLysPheTrpAla :   82
        ||! !|||||||||  ! !!|||  !!!!   |||!:!:::|||!    !||||||   :!!
        lyThrTyrValCysAlaGlyCysHisThrProLeuTyrSerSerAlaHisLysPheAspSer
 1127 : GAACGTACGTGTGCGCCGGCTGCCACACGCCCTTGTACTCGTCGGCGCACAAGTTTGACTCG : 1186

   83 : GlyCysGlyTrpProAlaPheSerGluSerValGlyGlnAspAlaAsnIleValArgIleVa :  103
        |||||||||||||||||||||! !!!::!!:!!          !!!:!  !:!!  !   ||
        GlyCysGlyTrpProAlaPheTyrAspAlaLeu---------ProSerAlaIleSerTrpVa
 1187 : GGCTGCGGGTGGCCTGCGTTCTACGATGCGCTG---------CCCAGTGCCATCTCGTGGGT : 1240

  104 : lAspArgSerHisGlyMetHisArgThrGluValArgCysLysThrCysAspAlaHisLeuG :  124
        |  !  !||| !!|||   !!.|||||||||:!!  !|||   ..!||| !!!.!|||:!!|
        lProAspSerAspGly---GlnArgThrGluIleValCysAlaValCysHisGlyHisMetG
 1241 : GCCCGACAGCGACGGC---CAGCGAACCGAGATCGTCTGCGCTGTGTGCCACGGCCACATGG : 1300

  125 : lyHisValPhe<->AsnAspGlyProLysGluThrThrGlyGluArgTyrUnkIleAsnSer :  143
        |||||||||||   |||!!:|||  !     ! !!|||..!.!.|||:!!   :!!||||||
        lyHisValPheGluAsnGluGlyPheProThrProThrAsnHisArgHisCysValAsnSer
 1301 : GTCATGTCTTTGAGAACGAAGGCTTCCCTACGCCGACGAACCACCGCCACTGCGTCAATAGC : 1360

  144 : ValCysMetAlaPheGlu :  149
        :!!!  !!:  !|||:!!
        IleSerIleLysPheLys
 1361 : ATCTCGATCAAGTTCAAG : 1380

vulgar: SPP00000059_1.0 20 149 . gi|288565193|gb|GG744004.1|:subseq(53134,2380) 1002 1380 + 230 M 73 219 G 3 0 M 12 36 G 1 0 M 18 54 G 0 3 M 22 66
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-03-04
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|288565193|gb|GG744004.1|:subseq(53134,2380)	exonerate:protein2genome:local	gene	1003	1380	230	+	.	gene_id 1 ; sequence SPP00000059_1.0 ; gene_orientation .
gi|288565193|gb|GG744004.1|:subseq(53134,2380)	exonerate:protein2genome:local	cds	1003	1380	.	+	.	
gi|288565193|gb|GG744004.1|:subseq(53134,2380)	exonerate:protein2genome:local	exon	1003	1380	.	+	.	insertions 3 ; deletions 4
gi|288565193|gb|GG744004.1|:subseq(53134,2380)	exonerate:protein2genome:local	similarity	1003	1380	230	+	.	alignment_id 1 ; Query SPP00000059_1.0 ; Align 1003 21 219 ; Align 1222 97 36 ; Align 1258 110 54 ; Align 1315 128 66
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis