Command line: [exonerate -m p2g --showtargetgff -q query_celegans.fa -t parasitica2genomic.fa]
Hostname: [localhost.localdomain]

C4 Alignment:
------------
         Query:  query_Caenorhabditis elegans SPP00000059_1.0 # Protein # Selenoprotein R  (SelR) #  # Complete
        Target: gi|288565236|gb|GG743961.1|:subseq(175973,3500) Saprolegnia parasitica CBS 223.65 genomic scaffold supercont1.79, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 229
   Query range: 23 -> 148
  Target range: 2081 -> 2447

   24 : AspValLysGlnThrGluTrpLysSerValLeuProAsnGluValTyrArgValAlaArgGl :   44
        :!!:!!!..:!!  !||||||::!!!!  !||| !!!!.|||  !!:!||||||  !|||||
        AsnLeuSerGluGlyGluTrpArgThrLysLeuSerLysGluGlnPheArgValLeuArgGl
 2082 : AACCTCAGCGAAGGCGAGTGGCGGACCAAGCTCTCCAAGGAGCAGTTCCGCGTGCTGCGCGA : 2142

   45 : uSerGlyThrGluThrProHisThrGlyGlyPheAsnAspHisPheGluLysGlyArgTyrV :   65
        |!.!|||||||||  ! !!  !||||||! !!:!||| ! |||!:!|||:!!|||  !||| 
        uLysGlyThrGluArgAlaGlyThrGlyGluTyrAsnLysHisTyrGluGluGlyValTyrH
 2143 : GAAAGGCACGGAGCGCGCTGGCACGGGCGAGTACAACAAGCACTACGAAGAGGGCGTCTACC : 2205

   66 : alCysLeuCysCysGlySerGluLeuPheAsnSerAspAlaLysPheTrpAlaGlyCysGly :   85
         !|||  ! !!|||! !:!!   |||!:!!!.|||..!  !||||||   :!!|||||||||
        isCysAlaGlyCysAspAlaProLeuTyrLysSerSerHisLysPheAspSerGlyCysGly
 2206 : ACTGCGCCGGCTGCGACGCGCCCTTGTACAAGTCGAGCCACAAGTTCGACTCGGGCTGCGGC : 2265

   86 : TrpProAlaPheSerGluSerValGlyGlnAspAlaAsnIleValArgIleValAspArgSe :  106
        ||||||||||||! !!!::!!:!!        !!.!   |||..!  !|||  !|||..!..
        TrpProAlaPhePheAspAlaLeu------ProGlyAlaIleThrAlaIleProAspGluAs
 2266 : TGGCCCGCGTTCTTCGACGCGCTT------CCCGGTGCGATCACGGCCATCCCGGACGAAGA : 2322

  107 : rHisGlyMetHisArgThrGluValArgCysLysThrCysAspAlaHisLeuGlyHisValP :  127
        !  !      :!!|||..!|||:!!  !|||  !.!!|||! !!.!|||:!!||||||||||
        pGly------TyrArgValGluIleValCysAlaAlaCysGlyGlyHisMetGlyHisValP
 2323 : TGGC------TACCGCGTCGAGATTGTCTGCGCGGCTTGCGGCGGCCACATGGGTCACGTCT : 2379

  128 : he<->AsnAspGlyProLysGluThrThrGlyGluArgTyrUnkIleAsnSerValCysMet :  146
        ||   |||!!:|||  !|||.!. !!|||..!||||||:!!   :!!|||||||||!  !!:
        heLysAsnGluGlyPheLysAsnProThrAsnGluArgHisCysValAsnSerValSerIle
 2380 : TCAAGAACGAAGGCTTCAAGAACCCGACGAACGAGCGTCACTGCGTCAACAGCGTGTCGATC : 2439

  147 : AlaPhe :  148
          !|||
        ArgPhe
 2440 : CGCTTT : 2447

vulgar:  23 148 . gi|288565236|gb|GG743961.1|:subseq(175973,3500) 2081 2447 + 229 M 70 210 G 2 0 M 12 36 G 2 0 M 18 54 G 0 3 M 21 63
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-03-14
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|288565236|gb|GG743961.1|:subseq(175973,3500)	exonerate:protein2genome:local	gene	2082	2447	229	+	.	gene_id 1 ; sequence  ; gene_orientation .
gi|288565236|gb|GG743961.1|:subseq(175973,3500)	exonerate:protein2genome:local	cds	2082	2447	.	+	.	
gi|288565236|gb|GG743961.1|:subseq(175973,3500)	exonerate:protein2genome:local	exon	2082	2447	.	+	.	insertions 3 ; deletions 4
gi|288565236|gb|GG743961.1|:subseq(175973,3500)	exonerate:protein2genome:local	similarity	2082	2447	229	+	.	alignment_id 1 ; Query  ; Align 2082 24 210 ; Align 2292 96 36 ; Align 2328 110 54 ; Align 2385 128 63
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query:  query_Caenorhabditis elegans SPP00000059_1.0 # Protein # Selenoprotein R  (SelR) #  # Complete
        Target: gi|288565236|gb|GG743961.1|:subseq(175973,3500) Saprolegnia parasitica CBS 223.65 genomic scaffold supercont1.79, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 216
   Query range: 23 -> 148
  Target range: 1365 -> 999

   24 : AspValLysGlnThrGluTrpLysSerValLeuProAsnGluValTyrArgValAlaArgGl :   44
        |||:!!!  ! !  !||||||:!!  !  !||| !!!!.|||  !!:!|||:!!  !|||||
        AspLeuThrProGlyGluTrpGlnValLysLeuSerLysGluGlnPheArgIleLeuArgGl
 1365 : GACCTGACCCCAGGCGAGTGGCAAGTGAAGCTCTCCAAGGAGCAATTCCGCATCCTGCGCGA : 1305

   45 : uSerGlyThrGluThrProHisThrGlyGlyPheAsnAspHisPheGluLysGlyArgTyrV :   65
        |!.!|||||||||.!!  !  !||||||! !!:!||| ! |||!:!|||! !|||  !||| 
        uLysGlyThrGluAlaLysGlyThrGlyGluTyrAsnLysHisTyrGluThrGlyValTyrH
 1304 : GAAGGGCACGGAAGCCAAGGGCACTGGCGAGTACAACAAGCACTACGAGACGGGTGTCTACC : 1242

   66 : alCysLeuCysCysGlySerGluLeuPheAsnSerAspAlaLysPheTrpAlaGlyCysGly :   85
         !|||  ! !!|||! !:!!   |||!:!!!.|||!!:.!!||||||   :!!|||||||||
        isCysAlaGlyCysAspAlaProLeuTyrLysSerGluThrLysPheAspSerGlyCysGly
 1241 : ACTGCGCGGGCTGCGACGCGCCCTTGTACAAGTCCGAGACCAAGTTTGACTCGGGCTGCGGC : 1182

   86 : TrpProAlaPheSerGluSerValGlyGlnAspAlaAsnIleValArgIleValAspArgSe :  106
        ||||||||||||! !!!::!!:!!   !  ||||||   ||||||  !     !|||  !..
        TrpProAlaPhePheAspAlaLeu---ProAspAla---IleValSerGlnProAspValAs
 1181 : TGGCCTGCTTTTTTTGACGCGCTA---CCTGATGCA---ATTGTTTCGCAGCCCGACGTCGA : 1125

  107 : rHisGlyMetHisArgThrGluValArgCysLysThrCysAspAlaHisLeuGlyHisValP :  127
        !         !..|||||||||:!!! !|||   !.!|||! !!.!|||:!!||||||||||
        pGly------ArgArgThrGluIleIleCysAlaAsnCysGlyGlyHisMetGlyHisValP
 1124 : CGGG------CGACGCACCGAGATCATCTGCGCCAACTGCGGCGGCCACATGGGCCACGTCT : 1068

  128 : he<->AsnAspGlyProLysGluThrThrGlyGluArgTyrUnkIleAsnSerValCysMet :  146
        ||   ..!!!:|||  !|||  ! !!|||! !:!!|||:!!   :!!|||||||||! !:!!
        heThrGlyGluGlyPheLysThrProThrAspGlnArgHisCysValAsnSerValSerVal
 1067 : TCACGGGCGAAGGGTTCAAGACGCCGACGGACCAGCGTCACTGCGTCAACAGCGTCTCCGTG : 1008

  147 : AlaPhe :  148
          !|||
        ArgPhe
 1007 : CGCTTC : 1000

vulgar:  23 148 . gi|288565236|gb|GG743961.1|:subseq(175973,3500) 1365 999 - 216 M 70 210 G 1 0 M 3 9 G 1 0 M 9 27 G 2 0 M 18 54 G 0 3 M 21 63
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2011-03-14
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|288565236|gb|GG743961.1|:subseq(175973,3500)	exonerate:protein2genome:local	gene	1000	1365	216	-	.	gene_id 1 ; sequence  ; gene_orientation .
gi|288565236|gb|GG743961.1|:subseq(175973,3500)	exonerate:protein2genome:local	cds	1000	1365	.	-	.	
gi|288565236|gb|GG743961.1|:subseq(175973,3500)	exonerate:protein2genome:local	exon	1000	1365	.	-	.	insertions 3 ; deletions 4
gi|288565236|gb|GG743961.1|:subseq(175973,3500)	exonerate:protein2genome:local	similarity	1000	1365	216	-	.	alignment_id 1 ; Query  ; Align 1366 24 210 ; Align 1156 95 9 ; Align 1147 99 27 ; Align 1120 110 54 ; Align 1063 128 63
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis