Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/MM.GPx6.1.fa.x.fa -t 3B.fastasub.dir/9.MM.GPx6.1.fa.x.fa]
Hostname: [ws101153]

C4 Alignment:
------------
         Query: SPP00001550_2.0 # Protein # Glutathione peroxidase 6 (GPx6) # Mouse (Mus musculus)
        Target: gi|398920810|gb|JH767833.1|:subseq(2505861,139506) Ceratotherium simum simum unplaced genomic scaffold scaffold00111, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 828
   Query range: 28 -> 221
  Target range: 82515 -> 89506

    29 : LysValAspCysAsnLysGlyValThrGlyThrValTyrGluTyrGlyAlaAsnThrIle :    48
         :!!:!!|||||| !!||||||||||||||||||:!!|||||||||||||||  !|||:!!
         GlnMetAspCysTyrLysGlyValThrGlyThrIleTyrGluTyrGlyAlaLeuThrLeu
 82516 : CAGATGGATTGCTATAAGGGGGTGACAGGCACCATCTATGAGTATGGAGCCCTCACCCTC : 82573

    49 : AspGlyGlyGluPheValAsnPheGlnGlnTyrAlaGlyLysHisIleLeuPheValAsn :    68
         :!!|||! !|||!:!:!!.!.|||:!!||||||||||||||||||:!!||||||:!!|||
         AsnGlyGluGluTyrIleGlnPheLysGlnTyrAlaGlyLysHisValLeuPheIleAsn
 82574 : AATGGCGAGGAGTATATCCAGTTCAAGCAGTATGCGGGCAAGCACGTCCTCTTTATCAAT : 82633

    69 : ValAlaSerPheCysGlyLeuThrAlaThrTyrPro{G}  >>>> Target Intron  :    81
         ||||||!!!!:!!! ||||||||||||  !||||||{|}           4440 bp   
         ValAlaThrTyr***GlyLeuThrAlaGlnTyrPro{G}++                   
 82634 : GTGGCCACCTATTGAGGCTTGACAGCTCAGTATCCT{G}gt................... : 82675

    82 : 1 >>>>  {lu}LeuAsnThrLeuGlnGluGluLeuLysProPheAsnValThrValLeu :    97
                 {||}||||||.!!||||||||||||||||||||||||..!|||..!:!!|||
               ++{lu}LeuAsnAlaLeuGlnGluGluLeuLysProPheGlyValValLeuLeu
 82676 : ......ag{AA}CTGAATGCACTACAGGAGGAGCTGAAGCCTTTTGGTGTAGTTTTGTTG : 87160

    98 : GlyPheProCysAsnGlnPheGlyLysGlnGluProGlyLysAsnSerGluIleLeuLeu :   117
         |||||||||||||||||||||||||||||||||||||||||||||||||||||||||!!!
         GlyPheProCysAsnGlnPheGlyLysGlnGluProGlyLysAsnSerGluIleLeuPhe
 87161 : GGCTTTCCCTGCAACCAGTTTGGAAAACAAGAACCAGGAAAAAACTCAGAGATCCTTTTT : 87220

   118 : GlyLeu{Ly}  >>>> Target Intron 2 >>>>  {s}TyrValArgProGlyGly :   126
         ||||||{||}            487 bp           {|}||||||||||||||||||
         GlyLeu{Ly}++                         ++{s}TyrValArgProGlyGly
 87221 : GGGCTC{AA}gt.........................ag{G}TATGTGCGTCCAGGTGGT : 87734

   127 : GlyTyrValProAsnPheGlnLeuPheGluLysGlyAspValAsnGlyAspAsnGluGln :   146
         |||!:!||||||||||||||||||||||||||||||||||||||||||!!:!!.||||||
         GlyPheValProAsnPheGlnLeuPheGluLysGlyAspValAsnGlyGluLysGluGln
 87735 : GGCTTTGTCCCCAACTTTCAGCTCTTTGAGAAAGGGGATGTGAATGGAGAAAAAGAACAG : 87794

   147 : LysValPheSerPheLeuLys  >>>> Target Intron 3 >>>>  AsnSerCysP :   157
         |||||||||!!!|||||||||           1485 bp           ||||||||||
         LysValPheThrPheLeuLys++                         ++AsnSerCysP
 87795 : AAGGTCTTTACCTTCCTGAAGgt.........................agAACTCCTGCC : 89312

   158 : roProThrSerGluLeuPheGlySerProGluHisLeuPheTrpAspProMetLysValH :   177
         |||||||||||!!:|||!!.|||||| !!.!.!!.|||||||||!  |||||||||||||
         roProThrSerAspLeuLeuGlySerSerAsnGlnLeuPheTrpAlaProMetLysValH
 89313 : CTCCAACCTCTGATCTTTTGGGCTCATCAAACCAACTCTTCTGGGCGCCCATGAAGGTCC : 89372

   178 : isAspIleArgTrpAsnPheGluLysPheLeuValGlyProAspGlyValProValMetA :   197
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
         isAspIleArgTrpAsnPheGluLysPheLeuValGlyProAspGlyValProValMetA
 89373 : ATGACATCCGCTGGAACTTTGAGAAGTTCCTGGTGGGACCTGATGGGGTCCCTGTCATGC : 89432

   198 : rgTrpPheHisHisThrProValArgIleValGlnSerAspIleMetGluTyrLeuAsnG :   217
         |||||||||||!...!! !!|||!!!! !|||:!!|||||||||:!!|||||||||!!.|
         rgTrpPheHisArgAlaSerValSerThrValLysSerAspIleLeuGluTyrLeuLysG
 89433 : GCTGGTTCCACCGGGCTTCAGTTAGCACAGTCAAGTCAGACATCCTGGAGTACCTGAAGC : 89492

   218 : lnThrSerThrGln :   221
         ||  !!.!:!!:!!
         lnPheLysSerGlu
 89493 : AGTTCAAATCCGAA : 89506

vulgar: SPP00001550_2.0 28 221 . gi|398920810|gb|JH767833.1|:subseq(2505861,139506) 82515 89506 + 828 M 52 156 S 0 1 5 0 2 I 0 4436 3 0 2 S 1 2 M 38 114 S 0 2 5 0 2 I 0 483 3 0 2 S 1 1 M 33 99 5 0 2 I 0 1481 3 0 2 M 68 204
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-28
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	gene	82516	89506	828	+	.	gene_id 1 ; sequence SPP00001550_2.0 ; gene_orientation +
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	cds	82516	82672	.	+	.	
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	exon	82516	82672	.	+	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	splice5	82673	82674	.	+	.	intron_id 1 ; splice_site "GT"
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	intron	82673	87112	.	+	.	intron_id 1
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	splice3	87111	87112	.	+	.	intron_id 0 ; splice_site "AG"
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	cds	87113	87230	.	+	.	
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	exon	87113	87230	.	+	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	splice5	87231	87232	.	+	.	intron_id 2 ; splice_site "GT"
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	intron	87231	87717	.	+	.	intron_id 2
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	splice3	87716	87717	.	+	.	intron_id 1 ; splice_site "AG"
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	cds	87718	87817	.	+	.	
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	exon	87718	87817	.	+	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	splice5	87818	87819	.	+	.	intron_id 3 ; splice_site "GT"
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	intron	87818	89302	.	+	.	intron_id 3
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	splice3	89301	89302	.	+	.	intron_id 2 ; splice_site "AG"
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	cds	89303	89506	.	+	.	
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	exon	89303	89506	.	+	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	similarity	82516	89506	828	+	.	alignment_id 1 ; Query SPP00001550_2.0 ; Align 82516 29 156 ; Align 87115 82 114 ; Align 87719 121 99 ; Align 89303 154 204
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00001550_2.0 # Protein # Glutathione peroxidase 6 (GPx6) # Mouse (Mus musculus)
        Target: gi|398920810|gb|JH767833.1|:subseq(2505861,139506) Ceratotherium simum simum unplaced genomic scaffold scaffold00111, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 778
   Query range: 28 -> 221
  Target range: 54971 -> 49999

    29 : LysValAspCysAsnLysGlyValThrGlyThrValTyrGluTyrGlyAlaAsnThrIle :    48
         :!!..!|||||| !!|||! !|||! !||||||:!!|||||||||! !|||! !|||:!!
         GlnThrAspCysTyrLysAspValLysGlyThrIleTyrGluTyrAspAlaIleThrLeu
 54971 : CAGACGGATTGCTACAAAGATGTGAAAGGCACCATCTATGAATATGACGCCATCACTCTT : 54914

    49 : AspGlyGlyGluPheValAsnPheGlnGlnTyrAlaGlyLysHisIleLeuPheValAsn :    68
          ! ||| !!|||  !:!!.!.|||:!!!:!|||||||||||||||:!!||||||||||||
         LysGlyArgGluHisIleGlnPheLysArgTyrAlaGlyLysHisValLeuPheValAsn
 54913 : AAAGGAAGGGAACACATTCAGTTCAAGCGGTATGCGGGCAAGCATGTCCTTTTTGTCAAT : 54854

    69 : ValAlaSerPheCysGlyLeuThrAlaThrTyrPro{G}  >>>> Target Intron  :    81
         ||||||!!!!:!|||||||||||||||  !||||||{|}           2832 bp   
         ValAlaThrTyrCysGlyLeuThrAlaGlnTyrPro{G}++                   
 54853 : GTGGCCACCTATTGTGGTCTGACGGCTCAATATCCT{G}gt................... : 54812

    82 : 1 >>>>  {lu}LeuAsnThrLeuGlnGluGluLeuLysProPheAsnValThrValLeu :    97
                 {||}||||||||||||||||||||||||||| !!|||..!:!!..!||||||
               ++{lu}LeuAsnThrLeuGlnGluGluLeuLysSerPheGlyLeuValValLeu
 54811 : ......ag{AA}CTGAATACACTTCAGGAGGAGCTGAAGTCCTTTGGCTTAGTTGTGTTG : 51935

    98 : GlyPheProCysAsnGlnPheGlyLysGlnGluProGlyLysAsnSerGluIleLeuLeu :   117
         |||||||||||||||||||||||||||||||||||||||:!!|||||||||||||||! !
         GlyPheProCysAsnGlnPheGlyLysGlnGluProGlyGluAsnSerGluIleLeuPro
 51934 : GGTTTCCCCTGTAACCAATTTGGAAAGCAAGAACCAGGAGAGAACTCGGAGATCCTTCCA : 51875

   118 : GlyLeu{Ly}  >>>> Target Intron 2 >>>>  {s}TyrValArgProGlyGly :   126
         ||||||{||}            460 bp           {|}||||||||||||||||||
         GlyLeu{Ly}++                         ++{s}TyrValArgProGlyGly
 51874 : GGGCTG{AA}gt.........................ag{G}TATGTCCGTCCAGGGGGA : 51388

   127 : GlyTyrValProAsnPheGlnLeuPheGluLysGlyAspValAsnGlyAspAsnGluGln :   146
         ||||||||||||||||||||||||||||||||||||||||||||||||!!:!!.||||||
         GlyTyrValProAsnPheGlnLeuPheGluLysGlyAspValAsnGlyGluLysGluGln
 51387 : GGATATGTACCTAATTTCCAGCTTTTTGAGAAAGGAGATGTGAATGGGGAAAAAGAACAG : 51328

   147 : LysValPheSerPheLeuLys  >>>> Target Intron 3 >>>>  AsnSerCysP :   157
         |||||||||!!!|||||||||           1101 bp           :!!|||||||
         LysValPheThrPheLeuLys++                         ++HisSerCysP
 51327 : AAAGTCTTCACCTTCTTGAAGgt.........................agCACTCCTGTC : 50194

   158 : roProThrSerGluLeuPheGlySerProGluHisLeuPheTrpAspProMetLysValH :   177
         ||! ! !!||||||:!!!!.||||||  !:!!|||:!!! !|||!!:|||!!:|||||||
         roHisProSerGluIleLeuGlySerLeuLysHisIleSerTrpGluProIleLysValH
 50193 : CTCACCCCTCTGAGATTTTAGGCTCATTAAAACATATATCCTGGGAACCTATAAAGGTCC : 50134

   178 : isAspIleArgTrpAsnPheGluLysPheLeuValGlyProAspGlyValProValMetA :   197
         |||||||||||||||||||||||||||||||||||||||||:!!||||||||||||||||
         isAspIleArgTrpAsnPheGluLysPheLeuValGlyProAsnGlyValProValMetA
 50133 : ATGACATCCGCTGGAATTTTGAAAAGTTCCTGGTGGGGCCTAATGGAGTCCCCGTCATGC : 50074

   198 : rgTrpPheHisHisThrProValArgIleValGlnSerAspIleMetGluTyrLeuAsnG :   217
         |||||||||||!...!!||||||!!!   |||:!!|||||||||:!!! !||||||.!.|
         rgTrpPheHisArgAlaProValSerAlaValLysSerAspIleLeuAlaTyrLeuGlnG
 50073 : GCTGGTTCCATCGGGCCCCAGTCAGTGCGGTCAAGTCGGATATCCTGGCATACCTGCAGC : 50014

   218 : lnThrSerThrGln :   221
         ||  !!.!|||:!!
         lnPheLysThrLys
 50013 : AGTTCAAAACTAAA : 50000

vulgar: SPP00001550_2.0 28 221 . gi|398920810|gb|JH767833.1|:subseq(2505861,139506) 54971 49999 - 778 M 52 156 S 0 1 5 0 2 I 0 2828 3 0 2 S 1 2 M 38 114 S 0 2 5 0 2 I 0 456 3 0 2 S 1 1 M 33 99 5 0 2 I 0 1097 3 0 2 M 68 204
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-28
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	gene	50000	54971	778	-	.	gene_id 1 ; sequence SPP00001550_2.0 ; gene_orientation +
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	cds	54815	54971	.	-	.	
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	exon	54815	54971	.	-	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	splice5	54813	54814	.	-	.	intron_id 1 ; splice_site "GT"
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	intron	51983	54814	.	-	.	intron_id 1
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	splice3	51983	51984	.	-	.	intron_id 0 ; splice_site "AG"
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	cds	51865	51982	.	-	.	
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	exon	51865	51982	.	-	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	splice5	51863	51864	.	-	.	intron_id 2 ; splice_site "GT"
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	intron	51405	51864	.	-	.	intron_id 2
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	splice3	51405	51406	.	-	.	intron_id 1 ; splice_site "AG"
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	cds	51305	51404	.	-	.	
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	exon	51305	51404	.	-	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	splice5	51303	51304	.	-	.	intron_id 3 ; splice_site "GT"
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	intron	50204	51304	.	-	.	intron_id 3
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	splice3	50204	50205	.	-	.	intron_id 2 ; splice_site "AG"
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	cds	50000	50203	.	-	.	
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	exon	50000	50203	.	-	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505861,139506)	exonerate:protein2genome:local	similarity	50000	54971	778	-	.	alignment_id 1 ; Query SPP00001550_2.0 ; Align 54972 29 156 ; Align 51981 82 114 ; Align 51404 121 99 ; Align 50204 154 204
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
