Command line: [exonerate -m p2g --showtargetgff -q 1B.query.dir/SP.TR1.1.fa.x.fa -t 3B.fastasub.dir/3.SP.TR1.1.fa.x.fa]
Hostname: [ws116055]

C4 Alignment:
------------
         Query: SPP00000034_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Homo sapiens # Complete
        Target: gi|398923323|gb|JH767749.1|:subseq(20079275,104102) Ceratotherium simum simum unplaced genomic scaffold scaffold00027, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 122
   Query range: 432 -> 482
  Target range: 50149 -> 49999

   433 : GluArgValValGlyPheHisValLeuGlyProAsnAlaGlyGluValThrGlnGlyPhe :   452
         ...!:!|||||||||.!!|||:!!! !|||  !.....!! !|||:!!  !|||||||||
         SerGlnValValGlyIleHisMetGlnGlyIleGlyCysAspGluMetLeuGlnGlyPhe
 50149 : TCCCAGGTGGTTGGGATCCATATGCAGGGCATTGGGTGTGATGAAATGCTGCAGGGTTTT : 50092

   453 : AlaAlaAlaLeuLysCysGlyLeuThrLysLysGlnLeuAspSerThrIleGlyIleHis :   472
         |||!.!|||:!!|||   |||  !||||||   .!.!!!|||!:!|||:!!!.!||||||
         AlaValAlaValLysMetGlyAlaThrLysAlaAspPheAspAsnThrValAlaIleHis
 50091 : GCTGTGGCAGTGAAAATGGGAGCAACAAAAGCCGACTTTGATAATACGGTTGCTATTCAC : 50032

   473 : ProValCysAlaGluValPheThrThrLeu :   482
         |||..!! !||||||! !!!...!||||||
         ProThrSerAlaGluGluLeuValThrLeu
 50031 : CCTACCTCTGCAGAAGAATTGGTCACGCTT : 50000

vulgar: SPP00000034_1.0 432 482 . gi|398923323|gb|JH767749.1|:subseq(20079275,104102) 50149 49999 - 122 M 50 150
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-25
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|398923323|gb|JH767749.1|:subseq(20079275,104102)	exonerate:protein2genome:local	gene	50000	50149	122	-	.	gene_id 1 ; sequence SPP00000034_1.0 ; gene_orientation .
gi|398923323|gb|JH767749.1|:subseq(20079275,104102)	exonerate:protein2genome:local	cds	50000	50149	.	-	.	
gi|398923323|gb|JH767749.1|:subseq(20079275,104102)	exonerate:protein2genome:local	exon	50000	50149	.	-	.	insertions 0 ; deletions 0
gi|398923323|gb|JH767749.1|:subseq(20079275,104102)	exonerate:protein2genome:local	similarity	50000	50149	122	-	.	alignment_id 1 ; Query SPP00000034_1.0 ; Align 50150 433 150
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000034_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Homo sapiens # Complete
        Target: gi|398923323|gb|JH767749.1|:subseq(20079275,104102) Ceratotherium simum simum unplaced genomic scaffold scaffold00027, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 119
   Query range: 309 -> 387
  Target range: 56215 -> 53970

   310 : AsnGluLysThrGlyLysIleProValThrAspGluGluGlnThrAsnValProTyrIle :   329
         !.!!!: ! ! !||| ! |||  !|||  !!!:   :!!.!.|||||||||  !  !:!!
         ThrAspAspArgGlyHisIleIleValAspGluPheGlnAsnThrAsnValLysGlyVal
 56215 : ACTGATGACAGAGGTCATATCATAGTAGATGAATTCCAGAATACTAATGTAAAAGGTGTC : 56158

   330 : TyrAlaIleGlyAspIleLeuGluAspLysValGluLeuThrPro{V}  >>>> Targe :   345
         ||||||:!!||||||:!:! !   !  |||!.!   |||||||||{|}           2
         TyrAlaValGlyAspValCys---GlyLysAlaLeuLeuThrPro{V}++          
 56157 : TACGCAGTTGGGGACGTGTGT---GGAAAAGCTCTCCTTACTCCA{G}gt.......... : 56110

   346 : t Intron 1 >>>>  {al}AlaIleGlnAlaGlyArgLeuLeuAlaGlnArgLeuTyr :   358
         011 bp           {||}||||||   |||||||||  !||||||!!.||||||!:!
                        ++{al}AlaIleAlaAlaGlyArgLysLeuAlaHisArgLeuPhe
 56109 : ...............ag{TT}GCAATAGCTGCTGGCCGAAAACTTGCCCATAGACTTTTT : 54063

   359 : <->AlaGlySerThrValLysCysAspTyrGluAsnValProThrThrValPheThrPro :   377
            ..!  !..!  !  !|||!  ||||||!!:|||:!!||||||..!||||||!:!! !
         GluCysLysGluAspSerLysLeuAspTyrAspAsnIleProThrValValPheSerHis
 54062 : GAATGCAAAGAAGATTCCAAATTAGACTATGACAACATCCCCACAGTGGTCTTCAGCCAC : 54003

   378 : LeuGluTyrGlyAlaCysGlyLeuSerGlu :   387
         ! !     !|||.!!   ||||||!!!|||
         ProProIleGlyThrValGlyLeuThrGlu
 54002 : CCACCTATTGGGACAGTGGGACTCACGGAA : 53971

vulgar: SPP00000034_1.0 309 387 . gi|398923323|gb|JH767749.1|:subseq(20079275,104102) 56215 53970 - 119 M 27 81 G 1 0 M 7 21 S 0 1 5 0 2 I 0 2007 3 0 2 S 1 2 M 13 39 G 0 3 M 29 87
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2014-11-25
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|398923323|gb|JH767749.1|:subseq(20079275,104102)	exonerate:protein2genome:local	gene	53971	56215	119	-	.	gene_id 2 ; sequence SPP00000034_1.0 ; gene_orientation +
gi|398923323|gb|JH767749.1|:subseq(20079275,104102)	exonerate:protein2genome:local	cds	56113	56215	.	-	.	
gi|398923323|gb|JH767749.1|:subseq(20079275,104102)	exonerate:protein2genome:local	exon	56113	56215	.	-	.	insertions 0 ; deletions 1
gi|398923323|gb|JH767749.1|:subseq(20079275,104102)	exonerate:protein2genome:local	splice5	56111	56112	.	-	.	intron_id 1 ; splice_site "GT"
gi|398923323|gb|JH767749.1|:subseq(20079275,104102)	exonerate:protein2genome:local	intron	54102	56112	.	-	.	intron_id 1
gi|398923323|gb|JH767749.1|:subseq(20079275,104102)	exonerate:protein2genome:local	splice3	54102	54103	.	-	.	intron_id 0 ; splice_site "AG"
gi|398923323|gb|JH767749.1|:subseq(20079275,104102)	exonerate:protein2genome:local	cds	53971	54101	.	-	.	
gi|398923323|gb|JH767749.1|:subseq(20079275,104102)	exonerate:protein2genome:local	exon	53971	54101	.	-	.	insertions 3 ; deletions 0
gi|398923323|gb|JH767749.1|:subseq(20079275,104102)	exonerate:protein2genome:local	similarity	53971	56215	119	-	.	alignment_id 2 ; Query SPP00000034_1.0 ; Align 56216 310 81 ; Align 56135 338 21 ; Align 54100 346 39 ; Align 54058 359 87
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
