Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/MM.GPx5.1.fa.x.fa -t 3B.fastasub.dir/9.MM.GPx5.1.fa.x.fa]
Hostname: [ws101159]

C4 Alignment:
------------
         Query: SPP00001549_2.0 # Protein # Glutathione peroxidase 5 (GPx5) # Mouse (Mus musculus)
        Target: gi|398920810|gb|JH767833.1|:subseq(2505864,139500) Ceratotherium simum simum unplaced genomic scaffold scaffold00111, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 806
   Query range: 27 -> 220
  Target range: 82509 -> 89500

    28 : MetLysMetAspCysTyrLysAspValLysGlyThrIleTyrAspTyrGluAlaLeuSer :    47
         .!.:!!|||||||||||||||!  |||! !||||||||||||!!:|||! !||||||!!!
         PheGlnMetAspCysTyrLysGlyValThrGlyThrIleTyrGluTyrGlyAlaLeuThr
 82510 : TTTCAGATGGATTGCTATAAGGGGGTGACAGGCACCATCTATGAGTATGGAGCCCTCACC : 82567

    48 : LeuAsnGlyLysGluHisIleProPheLysGlnTyrAlaGlyLysHisValLeuPheVal :    67
         |||||||||:!!|||:!!|||! !|||||||||||||||||||||||||||||||||:!!
         LeuAsnGlyGluGluTyrIleGlnPheLysGlnTyrAlaGlyLysHisValLeuPheIle
 82568 : CTCAATGGCGAGGAGTATATCCAGTTCAAGCAGTATGCGGGCAAGCACGTCCTCTTTATC : 82627

    68 : AsnValAlaThrTyrCysGlyLeuThrIleGlnTyrPro{G}  >>>> Target Intr :    81
         |||||||||||||||!! |||||||||  !|||||||||{|}           4440 bp
         AsnValAlaThrTyr***GlyLeuThrAlaGlnTyrPro{G}++                
 82628 : AATGTGGCCACCTATTGAGGCTTGACAGCTCAGTATCCT{G}gt................ : 82672

    82 : on 1 >>>>  {lu}LeuAsnAlaLeuGlnGluAspLeuLysProPheGlyLeuValIle :    96
                    {||}||||||||||||||||||!!:|||||||||||||||:!!|||:!:
                  ++{lu}LeuAsnAlaLeuGlnGluGluLeuLysProPheGlyValValLeu
 82673 : .........ag{AA}CTGAATGCACTACAGGAGGAGCTGAAGCCTTTTGGTGTAGTTTTG : 87154

    97 : LeuGlyPheProCysAsnGlnPheGlyLysGlnGluProGlyAspAsnLeuGluIleLeu :   116
         |||||||||||||||||||||||||||||||||||||||||| ! |||! !|||||||||
         LeuGlyPheProCysAsnGlnPheGlyLysGlnGluProGlyLysAsnSerGluIleLeu
 87155 : TTGGGCTTTCCCTGCAACCAGTTTGGAAAACAAGAACCAGGAAAAAACTCAGAGATCCTT : 87214

   117 : ProGlyLeu{Ly}  >>>> Target Intron 2 >>>>  {s}TyrValArgProGly :   125
           !||||||{||}            487 bp           {|}|||||||||||||||
         PheGlyLeu{Ly}++                         ++{s}TyrValArgProGly
 87215 : TTTGGGCTC{AA}gt.........................ag{G}TATGTGCGTCCAGGT : 87728

   126 : LysGlyPheLeuProAsnPheGlnLeuPheAlaLysGlyAspValAsnGlyGluAsnGlu :   145
            ||||||:!!||||||||||||||||||! !|||||||||||||||||||||!!.|||
         GlyGlyPheValProAsnPheGlnLeuPheGluLysGlyAspValAsnGlyGluLysGlu
 87729 : GGTGGCTTTGTCCCCAACTTTCAGCTCTTTGAGAAAGGGGATGTGAATGGAGAAAAAGAA : 87788

   146 : GlnLysIlePheThrPheLeuLys  >>>> Target Intron 3 >>>>  ArgSerC :   156
         ||||||:!!|||||||||||||||           1485 bp           !.!||||
         GlnLysValPheThrPheLeuLys++                         ++AsnSerC
 87789 : CAGAAGGTCTTTACCTTCCTGAAGgt.........................agAACTCCT : 89306

   157 : ysProHisProSerGluThrValValMetSerLysHisThrPheTrpGluProIleLysV :   176
         |||||!   !!|||!!:  !:!!! !   |||!!.!!.  !||||||! !|||!!:||||
         ysProProThrSerAspLeuLeuGlySerSerAsnGlnLeuPheTrpAlaProMetLysV
 89307 : GCCCTCCAACCTCTGATCTTTTGGGCTCATCAAACCAACTCTTCTGGGCGCCCATGAAGG : 89366

   177 : alHisAspIleArgTrpAsnPheGluLysPheLeuValGlyProAspGlyIleProValM :   196
         ||||||||||||||||||||||||||||||||||||||||||||||||||:!!|||||||
         alHisAspIleArgTrpAsnPheGluLysPheLeuValGlyProAspGlyValProValM
 89367 : TCCATGACATCCGCTGGAACTTTGAGAAGTTCCTGGTGGGACCTGATGGGGTCCCTGTCA : 89426

   197 : etArgTrpPheHisGlnAlaProValSerThrValLysSerAspIleMetAlaTyrLeuS :   216
         ||||||||||||||!:!||| !!||||||||||||||||||||||||:!!! !||||||!
         etArgTrpPheHisArgAlaSerValSerThrValLysSerAspIleLeuGluTyrLeuL
 89427 : TGCGCTGGTTCCACCGGGCTTCAGTTAGCACAGTCAAGTCAGACATCCTGGAGTACCTGA : 89486

   217 : erHisPheLysThr :   220
         .!!!.||||||:!!
         ysGlnPheLysSer
 89487 : AGCAGTTCAAATCC : 89500

vulgar: SPP00001549_2.0 27 220 . gi|398920810|gb|JH767833.1|:subseq(2505864,139500) 82509 89500 + 806 M 53 159 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 67 201
# --- 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(2505864,139500)	exonerate:protein2genome:local	gene	82510	89500	806	+	.	gene_id 1 ; sequence SPP00001549_2.0 ; gene_orientation +
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	cds	82510	82669	.	+	.	
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	exon	82510	82669	.	+	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	splice5	82670	82671	.	+	.	intron_id 1 ; splice_site "GT"
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	intron	82670	87109	.	+	.	intron_id 1
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	splice3	87108	87109	.	+	.	intron_id 0 ; splice_site "AG"
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	cds	87110	87227	.	+	.	
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	exon	87110	87227	.	+	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	splice5	87228	87229	.	+	.	intron_id 2 ; splice_site "GT"
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	intron	87228	87714	.	+	.	intron_id 2
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	splice3	87713	87714	.	+	.	intron_id 1 ; splice_site "AG"
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	cds	87715	87814	.	+	.	
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	exon	87715	87814	.	+	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	splice5	87815	87816	.	+	.	intron_id 3 ; splice_site "GT"
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	intron	87815	89299	.	+	.	intron_id 3
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	splice3	89298	89299	.	+	.	intron_id 2 ; splice_site "AG"
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	cds	89300	89500	.	+	.	
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	exon	89300	89500	.	+	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	similarity	82510	89500	806	+	.	alignment_id 1 ; Query SPP00001549_2.0 ; Align 82510 28 159 ; Align 87112 82 114 ; Align 87716 121 99 ; Align 89300 154 201
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00001549_2.0 # Protein # Glutathione peroxidase 5 (GPx5) # Mouse (Mus musculus)
        Target: gi|398920810|gb|JH767833.1|:subseq(2505864,139500) Ceratotherium simum simum unplaced genomic scaffold scaffold00111, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 949
   Query range: 0 -> 220
  Target range: 57608 -> 49999

     1 : MetValThrGluLeuArgValPheTyrLeuValProLeuLeuLeuAlaSerTyrValGln :    20
         |||..!.!!:!!||||||!.!! !|||||| !!||||||!!!||||||.!!!:!||||||
         MetThrAlaGlnLeuArgAlaSerTyrLeuPheProLeuPheLeuAlaGlyPheValGln
 57608 : ATGACTGCACAGTTAAGGGCCTCCTATCTCTTCCCCCTTTTCCTAGCTGGCTTTGTGCAG : 57551

    21 : ThrThrProArgProGluLysMetLys  >>>> Target Intron 1 >>>>  MetA :    31
         |||  !|||!:!|||||||||||||||           2556 bp           ! !|
         ThrAspProLysProGluLysMetLys++                         ++ThrA
 57550 : ACAGATCCCAAGCCAGAGAAGATGAAGgt.........................agACGG : 54962

    32 : spCysTyrLysAspValLysGlyThrIleTyrAspTyrGluAlaLeuSerLeuAsnGlyL :    51
         ||||||||||||||||||||||||||||||||!!:|||!!:|||:!!!!!|||!!.|||!
         spCysTyrLysAspValLysGlyThrIleTyrGluTyrAspAlaIleThrLeuLysGlyA
 54961 : ATTGCTACAAAGATGTGAAAGGCACCATCTATGAATATGACGCCATCACTCTTAAAGGAA : 54902

    52 : ysGluHisIleProPheLysGlnTyrAlaGlyLysHisValLeuPheValAsnValAlaT :    71
         :!|||||||||! !||||||!:!|||||||||||||||||||||||||||||||||||||
         rgGluHisIleGlnPheLysArgTyrAlaGlyLysHisValLeuPheValAsnValAlaT
 54901 : GGGAACACATTCAGTTCAAGCGGTATGCGGGCAAGCATGTCCTTTTTGTCAATGTGGCCA : 54842

    72 : hrTyrCysGlyLeuThrIleGlnTyrPro{G}  >>>> Target Intron 2 >>>>  :    81
         |||||||||||||||||  !|||||||||{|}           2832 bp          
         hrTyrCysGlyLeuThrAlaGlnTyrPro{G}++                         +
 54841 : CCTATTGTGGTCTGACGGCTCAATATCCT{G}gt.........................a : 51981

    82 :  {lu}LeuAsnAlaLeuGlnGluAspLeuLysProPheGlyLeuValIleLeuGlyPheP :   100
          {||}||||||.!!|||||||||!!:|||||| !!||||||||||||:!:||||||||||
         +{lu}LeuAsnThrLeuGlnGluGluLeuLysSerPheGlyLeuValValLeuGlyPheP
 51980 : g{AA}CTGAATACACTTCAGGAGGAGCTGAAGTCCTTTGGCTTAGTTGTGTTGGGTTTCC : 51923

   101 : roCysAsnGlnPheGlyLysGlnGluProGlyAspAsnLeuGluIleLeuProGlyLeu{ :   120
         ||||||||||||||||||||||||||||||||!!:|||! !||||||||||||||||||{
         roCysAsnGlnPheGlyLysGlnGluProGlyGluAsnSerGluIleLeuProGlyLeu{
 51922 : CCTGTAACCAATTTGGAAAGCAAGAACCAGGAGAGAACTCGGAGATCCTTCCAGGGCTG{ : 51863

   121 : Ly}  >>>> Target Intron 3 >>>>  {s}TyrValArgProGlyLysGlyPheL :   129
         ||}            460 bp           {|}|||||||||||||||  !|||!:!:
         Ly}++                         ++{s}TyrValArgProGlyGlyGlyTyrV
 51862 : AA}gt.........................ag{G}TATGTCCGTCCAGGGGGAGGATATG : 51376

   130 : euProAsnPheGlnLeuPheAlaLysGlyAspValAsnGlyGluAsnGluGlnLysIleP :   149
         !!||||||||||||||||||! !|||||||||||||||||||||!!.|||||||||:!!|
         alProAsnPheGlnLeuPheGluLysGlyAspValAsnGlyGluLysGluGlnLysValP
 51375 : TACCTAATTTCCAGCTTTTTGAGAAAGGAGATGTGAATGGGGAAAAAGAACAGAAAGTCT : 51316

   150 : heThrPheLeuLys  >>>> Target Intron 4 >>>>  ArgSerCysProHisPr :   159
         ||||||||||||||           1101 bp           !.!||||||||||||||
         heThrPheLeuLys++                         ++HisSerCysProHisPr
 51315 : TCACCTTCTTGAAGgt.........................agCACTCCTGTCCTCACCC : 50185

   160 : oSerGluThrValValMetSerLysHisThrPheTrpGluProIleLysValHisAspIl :   179
         |||||||! !:!!! !   ! !||||||! !! !||||||||||||||||||||||||||
         oSerGluIleLeuGlySerLeuLysHisIleSerTrpGluProIleLysValHisAspIl
 50184 : CTCTGAGATTTTAGGCTCATTAAAACATATATCCTGGGAACCTATAAAGGTCCATGACAT : 50125

   180 : eArgTrpAsnPheGluLysPheLeuValGlyProAspGlyIleProValMetArgTrpPh :   199
         ||||||||||||||||||||||||||||||||||:!!|||:!!|||||||||||||||||
         eArgTrpAsnPheGluLysPheLeuValGlyProAsnGlyValProValMetArgTrpPh
 50124 : CCGCTGGAATTTTGAAAAGTTCCTGGTGGGGCCTAATGGAGTCCCCGTCATGCGCTGGTT : 50065

   200 : eHisGlnAlaProValSerThrValLysSerAspIleMetAlaTyrLeuSerHisPheLy :   219
         ||||!:!||||||||||||.!!|||||||||||||||:!!|||||||||..!!!.|||||
         eHisArgAlaProValSerAlaValLysSerAspIleLeuAlaTyrLeuGlnGlnPheLy
 50064 : CCATCGGGCCCCAGTCAGTGCGGTCAAGTCGGATATCCTGGCATACCTGCAGCAGTTCAA : 50005

   220 : sThr :   220
         ||||
         sThr
 50004 : AACT : 50000

vulgar: SPP00001549_2.0 0 220 . gi|398920810|gb|JH767833.1|:subseq(2505864,139500) 57608 49999 - 949 M 29 87 5 0 2 I 0 2552 3 0 2 M 51 153 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 67 201
# --- 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(2505864,139500)	exonerate:protein2genome:local	gene	50000	57608	949	-	.	gene_id 1 ; sequence SPP00001549_2.0 ; gene_orientation +
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	cds	57522	57608	.	-	.	
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	exon	57522	57608	.	-	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	splice5	57520	57521	.	-	.	intron_id 1 ; splice_site "GT"
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	intron	54966	57521	.	-	.	intron_id 1
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	splice3	54966	54967	.	-	.	intron_id 0 ; splice_site "AG"
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	cds	54812	54965	.	-	.	
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	exon	54812	54965	.	-	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	splice5	54810	54811	.	-	.	intron_id 2 ; splice_site "GT"
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	intron	51980	54811	.	-	.	intron_id 2
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	splice3	51980	51981	.	-	.	intron_id 1 ; splice_site "AG"
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	cds	51862	51979	.	-	.	
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	exon	51862	51979	.	-	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	splice5	51860	51861	.	-	.	intron_id 3 ; splice_site "GT"
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	intron	51402	51861	.	-	.	intron_id 3
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	splice3	51402	51403	.	-	.	intron_id 2 ; splice_site "AG"
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	cds	51302	51401	.	-	.	
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	exon	51302	51401	.	-	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	splice5	51300	51301	.	-	.	intron_id 4 ; splice_site "GT"
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	intron	50201	51301	.	-	.	intron_id 4
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	splice3	50201	50202	.	-	.	intron_id 3 ; splice_site "AG"
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	cds	50000	50200	.	-	.	
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	exon	50000	50200	.	-	.	insertions 0 ; deletions 0
gi|398920810|gb|JH767833.1|:subseq(2505864,139500)	exonerate:protein2genome:local	similarity	50000	57608	949	-	.	alignment_id 1 ; Query SPP00001549_2.0 ; Align 57609 1 87 ; Align 54966 30 153 ; Align 51978 82 114 ; Align 51401 121 99 ; Align 50201 154 201
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
