Command line: [exonerate -m p2g --showtargetgff -q TR.fa -t TR1_homo_scaffold11_seqDNA.fa]
Hostname: [localhost]

C4 Alignment:
------------
         Query: SPP00000080_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Mus musculus # Complete
        Target: scaffold_11:subseq(783554,7436) [revcomp]
         Model: protein2genome
     Raw score: 893
   Query range: 41 -> 496
  Target range: 4433 -> 2975

   42 : SerPheAspLeuLeuValIleGlyGlyGlySerGlyGlyLeuAlaCysAlaLysGluAlaAl :   62
        ...:::|||::::::|||:::|||||||||||||||||||||||||||:!!||||||..!||
        AspTyrAspValValValValGlyGlyGlySerGlyGlyLeuAlaCysSerLysGluCysAl
 4433 : gactacgacgtcgtcgtcgtcggcggcggctccggcggcCTCGCCTGCTCCAAGGAGTGCGC : 4373

   63 : aGlnLeuGlyLysLysValAlaValAlaAspTyrValGluProSerProArgGlyThrLysT :   83
        |:!!||||||   ||||||||||||  !|||!:!|||:!!|||||||||  !|||:!!! !|
        aLysLeuGlyAlaLysValAlaValLeuAspPheValLysProSerProAlaGlySerThrT
 4372 : GAAGCTCGGCGCCAAGGTCGCCGTGCTCGACTTCGTGAAGCCGTCGCCGGCGGGGTCGACGT : 4310

   84 : rpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHisGlnAla :  103
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||  !|||
        rpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHisThrAla
 4309 : GGGGCCTCGGCGGCACGTGCGTCAACGTCGGCTGCATCCCGAAGAAGCTCATGCACACGGCG : 4250

  104 : AlaLeuLeuGlyGlyMetIleArg<->AspAlaHisHisTyrGlyTrpGluValAlaGlnPr :  123
        :!!:!!:!!|||! !! !:!!!:!   ||||||  !  !!:!||||||:!!! !|||    !
        SerIleIleGlyGluThrLeuLysAspAspAlaAlaAlaPheGlyTrpLysAspAlaAlaAl
 4249 : TCCATCATCGGCGAGACGCTCAAGGACGACGCCGCCGCCTTCGGGTGGAAGGACGCCGCCGC : 4187

  124 : oValGlnHisAsnTrpLysThrMetAlaGluAlaValGlnAsnHisValLysSerLeuAsnT :  144
        !! !  !|||:!!|||:!!:!!|||  !..!.!!||||||:!!|||:!!||||||||||||!
        aGlyAlaHisAspTrpGluSerMetLysSerThrValGlnAspHisIleLysSerLeuAsnP
 4186 : GGGCGCGCACGACTGGGAGTCGATGAAGTCGACGGTGCAGGACCACATCAAGTCGCTCAACT : 4124

  145 : rpGlyHisArgValGlnLeuGlnAspArgLysValLysTyrPheAsnIleLysAlaSerPhe :  164
        ::  !:!!||||||  !|||!::!!:  !   :!!!  |||.!.|||  !   !.!..!|||
        heLysTyrArgValAlaLeuArgGluAlaGlyIleThrTyrLeuAsnArgLeuGlyGluPhe
 4123 : TCAAGTACCGCGTCGCGCTCCGCGAGGCGGGCATCACCTACCTGAACCGCCTCGGCGAGTTC : 4064

  165 : ValAspGluHisThrValArgGlyValAspLysGlyGlyLysAlaThrLeuLeuSerAlaGl :  185
        ! !|||:!!:!!|||:!!  !  !..!||||||  !|||!!.  !|||! !:!!!!!|||! 
        GluAspLysAsnThrIleSerLeuThrAspLysLysGlyAsnLysThrSerValThrAlaAl
 4063 : GAGGACAAGAACACCATCTCCCTCACGGACAAGAAGGGCAACAAGACGTCCGTCACGGCCGC : 4001

  186 : uHisIleValIleAlaThrGlyGlyArgProArgTyrProThrGlnValLysGlyAlaLeuG :  206
        !!...!!:!!:!!|||..!||||||||||||!.! ! ! !  !     !   |||      |
        aArgPheIleValAlaValGlyGlyArgProAsnLysLeuGlyCysProGlyGly------G
 4000 : GCGGTTCATCGTCGCCGTCGGCGGCCGCCCGAACAAGCTCGGCTGCCCCGGCGGC------G : 3944

  207 : luTyrGlyIleThrSerAspAspIlePheTrpLeuLysGluSerProGlyLysThrSerVal :  226
        ||:!!!.!|||  !|||||||||:!:|||!  |||   :!!:!!||||||:::..!  !  !
        luHisAlaIleAspSerAspAspLeuPheSerLeuProLysAlaProGlyArgValLeuCys
 3943 : AGCACGCCATCGACAGCGACGACCTGTTCTCCCTGCCCAAGGCGCCGGGCCGCGTGCTCTGC : 3884

  227 : ProAlaAlaGluAspValAlaLeuGluCysAlaGlyPheLeuThrGlyIleGlyLeuAspTh :  247
          !!.!!.!!   !!:!!||||||||||||!.!||||||  !.!!|||!!:|||! !   ||
        ValGlyGlyGlyTyrIleAlaLeuGluCysGlyGlyPheThrAlaGlyMetGlyTyrProTh
 3883 : GTCGGCGGCGGCTACATCGCGCTCGAGTGCGGCGGCTTCACGGCCGGCATGGGCTACCCGAC : 3821

  248 : rThrValMetMetArgSerIleProLeuArgGlyPheAspGlnGlnMetSerSerLeuValT :  268
        ||||  !|||:!:|||||||||! !|||||||||||||||!:::!!     !.!!  !:!! 
        rThrCysMetValArgSerIleLeuLeuArgGlyPheAspArgGluCysValGlyLysIleG
 3820 : GACGTGCATGGTCCGGTCCATCCTCCTCCGCGGCTTCGACCGCGAGTGCGTCGGCAAGATCG : 3758

  269 : hrGluHisMetGluSerHisGlyThrGlnPheLeuLysGlyCysValProSerHisIleLys :  288
         !!  |||!!::!!  !||||||..!|||.!!! !   |||  !..!|||:!! ! |||:!!
        luAlaHisIleLysHisHisGlyValGlnLeuGlnValGlyValThrProAlaLysIleGlu
 3757 : AGGCCCACATCAAGCACCACGGCGTCCAGCTCCAGGTCGGCGTCACGCCCGCGAAGATCGAG : 3698

  289 : LysLeuProThrAsnGlnLeuGlnValThrTrpGluAspHisAlaSerGlyLysGluAspTh :  309
        |||  ! !!.!!!..   :!!   :!!|||     !|||  !!.!.!!|||   .!.!!:  
        LysAspAlaAlaThrGlyVal---LeuThrValThrAspSerGlyGlyGlyValHisGluTy
 3697 : AAGGACGCGGCGACGGGCGTC---CTCACGGTCACGGACTCCGGCGGCGGCGTCCACGAGTA : 3638

  310 : rGlyThrPheAspThrValLeuTrpAlaIleGlyArgValProGluThrArgThrLeuAsnL :  330
        !! !||| !   !..!!.!  ! !   !  !!.!  !..! !!!    ! !!! !  !|||:
        rAspThrValLeuValAlaThrGlyArgTyrAlaAspThrAlaAlaLeuGlyIleAspAsnV
 3637 : CGACACGGTGCTCGTCGCGACGGGCCGCTACGCGGACACGGCGGCCCTCGGCATCGACAACG : 3575

  331 : euGluLysAlaGlyIleSerThrAsnProLysAsnGlnLysIleIleValAspAlaGlnGlu :  350
        !!      |||..!   !:!..!||| !!|||!..:!!|||:!!     !! !! !:!!:!!
        alProGlyAlaSerAlaAsnValAsnAlaLysThrLysLysLeuGluCysValAspGluGln
 3574 : TGCCCGGCGCGTCGGCGAACGTGAACGCGAAGACGAAGAAGCTCGAGTGCGTCGACGAGCAG : 3515

  351 : AlaThrSerValProHisIleTyrAlaIleGlyAspValAlaGluGlyArgProGluLeuTh :  371
          ! !!.!!!.!||||||:!!||||||||||||||||||!.!||||||||||||||||||||
        LeuProGlyAlaProHisValTyrAlaIleGlyAspValValGluGlyArgProGluLeuTh
 3514 : CTGCCCGGCGCGCCGCACGTCTACGCGATCGGCGACGTCGTCGAGGGCCGGCCCGAGCTCAC : 3452

  372 : rProThrAlaIleLysAlaGlyLysLeuLeuAlaGlnArgLeuPheGlyLysSerSerThrL :  392
        ||||..!||||||:!!||||||  !! !||||||!:!||||||||||||   !.!!!!  !!
        rProValAlaIleGluAlaGlyLeuArgLeuAlaArgArgLeuPheGlyGlyLysThrGluP
 3451 : GCCCGTCGCCATCGAGGCGGGCCTGCGCCTCGCGCGGCGCCTCTTCGGCGGCAAGACCGAGC : 3389

  393 : euMetAspTyrSerAsnValTyrHisAlaTyrTyrLysProLeuGluPhe{T}  >>>> Ta :  409
         !|||||||||..!  !|||      .!!  !!:!! !|||||||||!:!{ }         
        roMetAspTyrGluCysValAlaThrThrIlePheThrProLeuGluTyr{G}+-       
 3388 : CCATGGACTACGAGTGCGTCGCGACGACGATCTTCACGCCGCTCGAGTAC{G}gc....... : 3335

  410 : rget Intron 1 >>>>  {hr}ValAlaAspArgAspAlaSerGlnCysTyrIleLysMe :  422
           102 bp           { !}..!  !..!..!  !!.!..!   |||!:!  !|||:!
                          -+{lu}ThrArgSerGluArgGlyAspGlyCysPheAlaLysLe
 3334 : ..................cg{AG}ACGCGCAGCGAGCGCGGCGACGGCTGCTTCGCCAAGCT : 3197

  423 : tValCysMetArgGluProProGlnLeuValLeuGlyLeuHisPheLeuGlyProAsnAlaG :  443
        :|||  !   !:!... !!  !:!!   |||:!!|||!!!|||!:!||||||||||||||||
        uValValAspLysSerThrGlyLys---ValValGlyPheHisTyrLeuGlyProAsnAlaG
 3196 : CGTCGTCGACAAGAGCACGGGCAAG---GTCGTCGGCTTCCACTACCTCGGCCCCAACGCCG : 3137

  444 : lyGluValThrGlnGlyPheAlaLeuGlyIleLysCysGlyAlaSerTyrAlaGlnValMet :  463
        |||||:!!||||||||||||:!!:!!!.!!!::::   ||||||!!!||||||.!. !!!!:
        lyGluIleThrGlnGlyPheSerIleAlaMetArgLysGlyAlaThrTyrAlaAspPheIle
 3136 : GCGAGATCACCCAGGGCTTCTCCATCGCCATGCGCAAGGGCGCGACCTACGCCGACTTCATC : 3077

  464 : GlnThrValGlyIleHisProThrCysSerGluGluValValLysLeuHisIleSerLysAr :  484
        ...|||||||||||||||||||||  !:!!|||||| !!..!...:!!  !:!:!!!|||  
        SerThrValGlyIleHisProThrValAlaGluGluPheThrSerMetThrValThrLysSe
 3076 : TCCACCGTCGGCATCCACCCGACGGTCGCCGAGGAGTTCACGTCCATGACCGTGACCAAGTC : 3014

  485 : gSerGlyLeuGluProThrValThrGlyCysUnkGly :  496
        !||||||  !... !!.!!  !  !||||||   |||
        rSerGlyGluSerAlaAlaLysGlyGlyCys***Gly
 3013 : GAGCGGCGAGTCCGCAGCCAAGGGCGGCTGCTGAGGC : 2976

vulgar: SPP00000080_1.0 41 496 . scaffold_11:subseq(783554,7436) 4433 2975 - 893 M 70 210 G 0 3 M 92 276 G 2 0 M 90 270 G 1 0 M 112 336 S 0 1 5 0 2 I 0 98 3 0 2 S 1 2 M 21 63 G 1 0 M 65 195
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	gene	2976	4433	893	-	.	gene_id 1 ; sequence SPP00000080_1.0 ; gene_orientation +
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	3338	4433	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	3338	4433	.	-	.	insertions 3 ; deletions 3
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	splice5	3336	3337	.	-	.	intron_id 1 ; splice_site "GC"
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	intron	3236	3337	.	-	.	intron_id 1
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	splice3	3236	3237	.	-	.	intron_id 0 ; splice_site "CG"
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	2976	3235	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	2976	3235	.	-	.	insertions 0 ; deletions 1
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	similarity	2976	4433	893	-	.	alignment_id 1 ; Query SPP00000080_1.0 ; Align 4434 42 210 ; Align 4221 112 276 ; Align 3945 206 270 ; Align 3675 297 336 ; Align 3234 410 63 ; Align 3171 432 195
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000081_1.0 # Protein # Thioredoxin reductase 3 (TR3) # Mus musculus # Complete
        Target: scaffold_11:subseq(783554,7436) [revcomp]
         Model: protein2genome
     Raw score: 717
   Query range: 123 -> 374
  Target range: 4445 -> 3692

  124 : AspSerAlaHisAspTyrAspLeuIleIleIleGlyGlyGlySerGlyGlyLeuSerCysAl :  144
        :::   ...   |||||||||::::::::::::|||||||||||||||||||||:!!|||:!
        GluHisGlyPheAspTyrAspValValValValGlyGlyGlySerGlyGlyLeuAlaCysSe
 4445 : gagcacggcttcgactacgacgtcgtcgtcgtcggcggcggctccggcggcCTCGCCTGCTC : 4385

  145 : aLysGluAlaAlaAsnLeuGlyLysLysValMetValLeuAspPheValValProSerProG :  165
        !||||||..!|||!!.||||||   ||||||   |||||||||||||||  !||||||||| 
        rLysGluCysAlaLysLeuGlyAlaLysValAlaValLeuAspPheValLysProSerProA
 4384 : CAAGGAGTGCGCGAAGCTCGGCGCCAAGGTCGCCGTGCTCGACTTCGTGAAGCCGTCGCCGG : 4322

  166 : lnGlyThrThrTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeu :  185
         !|||:!!||||||||||||||||||||||||||||||||||||||||||||||||||||||
        laGlySerThrTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeu
 4321 : CGGGGTCGACGTGGGGCCTCGGCGGCACGTGCGTCAACGTCGGCTGCATCCCGAAGAAGCTC : 4262

  186 : MetHisGlnAlaAlaLeuLeuGlyHisAlaLeuGln<->AspAlaLysLysTyrGlyTrpGl :  205
        ||||||  !|||:!!:!!:!!|||.!..!!|||:!!   ||||||      !:!||||||:!
        MetHisThrAlaSerIleIleGlyGluThrLeuLysAspAspAlaAlaAlaPheGlyTrpLy
 4261 : ATGCACACGGCGTCCATCATCGGCGAGACGCTCAAGGACGACGCCGCCGCCTTCGGGTGGAA : 4199

  206 : uTyrAsnGlnGlnValLysHisAsnTrpGluAlaMetThrGluAlaIleGlnSerHisIleG :  226
        ! !!  !     !! !  !|||:!!||||||:!!|||! !..!.!!:!:|||..!|||||| 
        sAspAlaAlaAlaGlyAlaHisAspTrpGluSerMetLysSerThrValGlnAspHisIleL
 4198 : GGACGCCGCCGCGGGCGCGCACGACTGGGAGTCGATGAAGTCGACGGTGCAGGACCACATCA : 4136

  227 : lySerLeuAsnTrpGlyTyrArgValThrLeuArgGluLysGlyValThrTyrValAsnSer :  246
         !|||||||||!::  !|||||||||.!!|||||||||  !|||:!!||||||:!!||| !!
        ysSerLeuAsnPheLysTyrArgValAlaLeuArgGluAlaGlyIleThrTyrLeuAsnArg
 4135 : AGTCGCTCAACTTCAAGTACCGCGTCGCGCTCCGCGAGGCGGGCATCACCTACCTGAACCGC : 4076

  247 : PheGlyGluPheValAspLeuHisLysIleLysAlaThrAsnLysLysGlyGlnGluThrPh :  267
        .!!|||||||||! !|||  !:!!!  |||...  !|||:!!|||||||||.!.:!!|||! 
        LeuGlyGluPheGluAspLysAsnThrIleSerLeuThrAspLysLysGlyAsnLysThrSe
 4075 : CTCGGCGAGTTCGAGGACAAGAACACCATCTCCCTCACGGACAAGAAGGGCAACAAGACGTC : 4013

  268 : eTyrThrAlaSerLysPheValIleAlaThrGlyGluArgProArgTyrLeuGlyIleGlnG :  288
        !  !||||||:!!::!|||:!!:!!|||..!|||!  ||||||!.! ! ||||||  !!  |
        rValThrAlaAlaArgPheIleValAlaValGlyGlyArgProAsnLysLeuGlyCysProG
 4012 : CGTCACGGCCGCGCGGTTCATCGTCGCCGTCGGCGGCCGCCCGAACAAGCTCGGCTGCCCCG : 3950

  289 : lyAspLysGluTyrCysIleThrSerAspAspLeuPheSerLeuProTyrCysProGlyCys :  308
        ||! !   |||:!!..!|||  !|||||||||||||||||||||||| ! ...|||||| !!
        lyGly---GluHisAlaIleAspSerAspAspLeuPheSerLeuProLysAlaProGlyArg
 3949 : GCGGC---GAGCACGCCATCGACAGCGACGACCTGTTCTCCCTGCCCAAGGCGCCGGGCCGC : 3893

  309 : ThrLeuValValGlyAlaSerTyrValGlyLeuGluCysAlaGlyPheLeuAlaGlyLeuGl :  329
        ..!|||  !||||||!.!.!!|||:!!!.!|||||||||!.!||||||  !||||||:!!||
        ValLeuCysValGlyGlyGlyTyrIleAlaLeuGluCysGlyGlyPheThrAlaGlyMetGl
 3892 : GTGCTCTGCGTCGGCGGCGGCTACATCGCGCTCGAGTGCGGCGGCTTCACGGCCGGCATGGG : 3830

  330 : yLeuAspValThrValMetValArgSerValLeuLeuArgGlyPheAspGlnGluMetAlaG :  350
        |! !   ..!|||  !||||||||||||:!!||||||||||||||||||!::|||   !.!!
        yTyrProThrThrCysMetValArgSerIleLeuLeuArgGlyPheAspArgGluCysValG
 3829 : CTACCCGACGACGTGCATGGTCCGGTCCATCCTCCTCCGCGGCTTCGACCGCGAGTGCGTCG : 3767

  351 : luLysValGlySerTyrLeuGluGlnGlnGlyValLysPheGlnArgLysPheThrProIle :  370
          |||:!!! !:!!:!!:!!:!!!!.!!.||||||:!!.!!|||  !    !!||||||   
        lyLysIleGluAlaHisIleLysHisHisGlyValGlnLeuGlnValGlyValThrProAla
 3766 : GCAAGATCGAGGCCCACATCAAGCACCACGGCGTCCAGCTCCAGGTCGGCGTCACGCCCGCG : 3707

  371 : LeuValGlnGln :  374
          !:!!:!!:!!
        LysIleGluLys
 3706 : AAGATCGAGAAG : 3693

vulgar: SPP00000081_1.0 123 374 . scaffold_11:subseq(783554,7436) 4445 3692 - 717 M 74 222 G 0 3 M 92 276 G 1 0 M 84 252
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	gene	3693	4445	717	-	.	gene_id 1 ; sequence SPP00000081_1.0 ; gene_orientation .
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	3693	4445	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	3693	4445	.	-	.	insertions 3 ; deletions 1
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	similarity	3693	4445	717	-	.	alignment_id 1 ; Query SPP00000081_1.0 ; Align 4446 124 222 ; Align 4221 198 276 ; Align 3945 291 252
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000081_1.0 # Protein # Thioredoxin reductase 3 (TR3) # Mus musculus # Complete
        Target: scaffold_11:subseq(783554,7436) [revcomp]
         Model: protein2genome
     Raw score: 448
   Query range: 399 -> 615
  Target range: 3638 -> 2975

  400 : TyrAsnThrValLeuLeuAlaIleGlyArgAspSerCysThrArgLysIleGlyLeuGluLy :  420
        |||:!!|||||||||:!!|||!  |||||| !!:!!  !|||  !   :!!|||:!!!!:!!
        TyrAspThrValLeuValAlaThrGlyArgTyrAlaAspThrAlaAlaLeuGlyIleAspAs
 3638 : TACGACACGGTGCTCGTCGCGACGGGCCGCTACGCGGACACGGCGGCCCTCGGCATCGACAA : 3578

  421 : sIle<-><-><->GlyValLysIleAsnGluLysAsnGlyLysIleProValAsnAspValG :  438
        .:!:         ..!!.!!!.:!:|||! !|||!..  !|||:!!  !  !  !|||! !:
        nValProGlyAlaSerAlaAsnValAsnAlaLysThrLysLysLeuGluCysValAspGluG
 3577 : CGTGCCCGGCGCGTCGGCGAACGTGAACGCGAAGACGAAGAAGCTCGAGTGCGTCGACGAGC : 3515

  439 : luGlnThrAsnValProHisValTyrAlaIleGlyAspIleLeuAspGlyLysProGluLeu :  458
        !!! ! !!..!!.!||||||||||||||||||||||||:!!:!!!!:|||::!|||||||||
        lnLeuProGlyAlaProHisValTyrAlaIleGlyAspValValGluGlyArgProGluLeu
 3514 : AGCTGCCCGGCGCGCCGCACGTCTACGCGATCGGCGACGTCGTCGAGGGCCGGCCCGAGCTC : 3455

  459 : ThrProValAlaIleGlnAlaGlyLysLeuLeuAlaArgArgLeuPheGlyValSerLeuGl :  479
        |||||||||||||||:!!||||||  !! !|||||||||||||||||||||! !!.!  !||
        ThrProValAlaIleGluAlaGlyLeuArgLeuAlaArgArgLeuPheGlyGlyLysThrGl
 3454 : ACGCCCGTCGCCATCGAGGCGGGCCTGCGCCTCGCGCGGCGCCTCTTCGGCGGCAAGACCGA : 3392

  480 : uLysCysAspTyrIleAsnIleProThrThrValPheThrProLeuGluTyrGlyCysCysG :  500
        |      ||||||     !:!! !!||||||:!!|||||||||||||||||||||     !|
        uProMetAspTyrGluCysValAlaThrThrIlePheThrProLeuGluTyrGlyThrIleG
 3391 : GCCCATGGACTACGAGTGCGTCGCGACGACGATCTTCACGCCGCTCGAGTACGGCACGATCG : 3329

  501 : lyLeuSerGluGluLysAlaIleGluMetTyrLysLysGluAsnLeuGluValTyrHisThr :  520
        |||||||||||!!: ! |||!  !  ..!  !   :!!   |||:!!|||  !|||  !!:!
        lyLeuSerGluAspAspAlaLysAlaGlnLeuGlyGluCysAsnValGluSerTyrIleSer
 3328 : GGCTGAGCGAGGACGACGCCAAGGCCCAGCTCGGCGAGTGCAACGTCGAGTCCTACATCAGC : 3269

  521 : LeuPheTrpProLeuGluTrpThrValAla<-><-><->GlyArgAspAsnAsnThrCysTy :  538
          !|||  !|||||||||!::.!!:!!::!         .!!..!  !..!:!!  !|||!:
        GluPheAlaProLeuGluTyrAlaLeuSerGluThrArgSerGluArgGlyAspGlyCysPh
 3268 : GAGTTCGCGCCCCTCGAGTACGCCCTCAGCGAGACGCGCAGCGAGCGCGGCGACGGCTGCTT : 3206

  539 : rAlaLysIleIleCysAsnLysPheAspAsnGluArgValValGlyPheHisLeuLeuGlyP :  559
        !||||||:!!:!!  !:!!|||   ..!!..!  !:!|||||||||||||||! !|||||||
        eAlaLysLeuValValAspLys---SerThrGlyLysValValGlyPheHisTyrLeuGlyP
 3205 : CGCCAAGCTCGTCGTCGACAAG---AGCACGGGCAAGGTCGTCGGCTTCCACTACCTCGGCC : 3146

  560 : roAsnAlaGlyGluIleThrGlnGlyPheAlaAlaAlaMetLysCysGlyLeuThrLysGln :  579
        |||||||||||||||||||||||||||||:!!  !||||||:::   |||  !||| !    
        roAsnAlaGlyGluIleThrGlnGlyPheSerIleAlaMetArgLysGlyAlaThrTyrAla
 3145 : CCAACGCCGGCGAGATCACCCAGGGCTTCTCCATCGCCATGCGCAAGGGCGCGACCTACGCC : 3086

  580 : LeuLeuAspAspThrIleGlyIleHisProThrCysGlyGluValPheThrThrLeuGluIl :  600
          !!!!  !..!|||:!!|||||||||||||||  !!.!|||! !||||||:!!:!!   :!
        AspPheIleSerThrValGlyIleHisProThrValAlaGluGluPheThrSerMetThrVa
 3085 : GACTTCATCTCCACCGTCGGCATCCACCCGACGGTCGCCGAGGAGTTCACGTCCATGACCGT : 3023

  601 : eThrLysSerSerGlyLeuAspIleThrGlnLysGlyCysUnkGly :  615
        :|||||||||||||||  !..!  !.!!:!!   ||||||   |||
        lThrLysSerSerGlyGluSerAlaAlaLysGlyGlyCys***Gly
 3022 : GACCAAGTCGAGCGGCGAGTCCGCAGCCAAGGGCGGCTGCTGAGGC : 2976

vulgar: SPP00000081_1.0 399 615 . scaffold_11:subseq(783554,7436) 3638 2975 - 448 M 22 66 G 0 9 M 109 327 G 0 9 M 15 45 G 1 0 M 69 207
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	gene	2976	3638	448	-	.	gene_id 2 ; sequence SPP00000081_1.0 ; gene_orientation .
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	2976	3638	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	2976	3638	.	-	.	insertions 18 ; deletions 1
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	similarity	2976	3638	448	-	.	alignment_id 2 ; Query SPP00000081_1.0 ; Align 3639 400 66 ; Align 3564 422 327 ; Align 3228 531 45 ; Align 3183 547 207
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000091_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Drosophila melanogaster # Complete
        Target: scaffold_11:subseq(783554,7436) [revcomp]
         Model: protein2genome
     Raw score: 945
   Query range: 30 -> 514
  Target range: 4436 -> 2981

   31 : TyrAspTyrAspLeuValValLeuGlyGlyGlySerAlaGlyLeuAlaCysAlaLysGluAl :   51
        :::|||||||||:::||||||:::||||||||||||...||||||||||||:!!||||||..
        PheAspTyrAspValValValValGlyGlyGlySerGlyGlyLeuAlaCysSerLysGluCy
 4436 : ttcgactacgacgtcgtcgtcgtcggcggcggctccggcggcCTCGCCTGCTCCAAGGAGTG : 4376

   52 : aAlaGlyCysGlyAlaArgValLeuCysPheAspTyrValLysProThrProValGlyThrL :   72
        !|||  !  !||||||!:!|||  !   .!!|||!:!|||||||||:!!|||!.!|||:!!!
        sAlaLysLeuGlyAlaLysValAlaValLeuAspPheValLysProSerProAlaGlySerT
 4375 : CGCGAAGCTCGGCGCCAAGGTCGCCGTGCTCGACTTCGTGAAGCCGTCGCCGGCGGGGTCGA : 4313

   73 : ysTrpGlyIleGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHisGln :   92
         !||||||:!!||||||||||||||||||||||||||||||||||||||||||||||||  !
        hrTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHisThr
 4312 : CGTGGGGCCTCGGCGGCACGTGCGTCAACGTCGGCTGCATCCCGAAGAAGCTCATGCACACG : 4253

   93 : AlaSerLeuLeuGlyGluAlaVal<->HisGluAlaValAlaTyrGlyTrpAsnValAspAs :  112
        ||||||:!!:!!||||||.!!:!!    !!!!:|||!.!|||!:!||||||!!.   |||! 
        AlaSerIleIleGlyGluThrLeuLysAspAspAlaAlaAlaPheGlyTrpLys---AspAl
 4252 : GCGTCCATCATCGGCGAGACGCTCAAGGACGACGCCGCCGCCTTCGGGTGGAAG---GACGC : 4193

  113 : pThrAsnIleArgProAspTrpArgLysLeuValArgSerValGlnAsnHisIleLysSerV :  133
        !.!!     !  !! !||||||..!..!:!!  !  !!!!||||||:!!||||||||||||:
        aAlaAlaGlyAlaHisAspTrpGluSerMetLysSerThrValGlnAspHisIleLysSerL
 4192 : CGCCGCGGGCGCGCACGACTGGGAGTCGATGAAGTCGACGGTGCAGGACCACATCAAGTCGC : 4130

  134 : alAsnTrpValThrArgValAspLeuArgAspLysLysValGluTyrValAsnSerMetAla :  153
        !!|||!::  !  !||||||!  ||||||!!:  !   :!!   |||:!!||| !!:!:!.!
        euAsnPheLysTyrArgValAlaLeuArgGluAlaGlyIleThrTyrLeuAsnArgLeuGly
 4129 : TCAACTTCAAGTACCGCGTCGCGCTCCGCGAGGCGGGCATCACCTACCTGAACCGCCTCGGC : 4070

  154 : ThrPheArgAspSerHisThrIleGluTyrValAlaMetProGlyAlaGluHisArgGlnVa :  174
          !|||..!|||!.!:!!||||||...  !..!! !! !  !|||   .!. ! ! !...||
        GluPheGluAspLysAsnThrIleSerLeuThrAspLysLysGly---AsnLysThrSerVa
 4069 : GAGTTCGAGGACAAGAACACCATCTCCCTCACGGACAAGAAGGGC---AACAAGACGTCCGT : 4010

  175 : lThrSerGluTyrValValValAlaValGlyGlyArgProArgTyrProAspIleProGlyA :  195
        ||||:!!! !    !!:!!|||||||||||||||||||||!.! ! ! !! !  !||||||!
        lThrAlaAlaArgPheIleValAlaValGlyGlyArgProAsnLysLeuGlyCysProGlyG
 4009 : CACGGCCGCGCGGTTCATCGTCGCCGTCGGCGGCCGCCCGAACAAGCTCGGCTGCCCCGGCG : 3947

  196 : laValGluLeuGlyIleThrSerAspAspIlePheSerTyrGluArgGluProGlyArgThr :  215
        .!   |||! !!.!|||  !|||||||||:!:||||||      !:!! !|||||||||..!
        ly---GluHisAlaIleAspSerAspAspLeuPheSerLeuProLysAlaProGlyArgVal
 3946 : GC---GAGCACGCCATCGACAGCGACGACCTGTTCTCCCTGCCCAAGGCGCCGGGCCGCGTG : 3890

  216 : LeuValValGlyAlaGlyTyrValGlyLeuGluCysAlaCysPheLeuLysGlyLeuGlyTy :  236
        |||  !||||||!.!||||||:!!!.!|||||||||!.! !!|||  !   |||:!!|||||
        LeuCysValGlyGlyGlyTyrIleAlaLeuGluCysGlyGlyPheThrAlaGlyMetGlyTy
 3889 : CTCTGCGTCGGCGGCGGCTACATCGCGCTCGAGTGCGGCGGCTTCACGGCCGGCATGGGCTA : 3827

  237 : rGluProThrValMetValArgSerIleValLeuArgGlyPheAspArgGlnMetSerGluL :  257
        |  ! !!|||  !|||||||||||||||:!!||||||||||||||||||:!!     !!   
        rProThrThrCysMetValArgSerIleLeuLeuArgGlyPheAspArgGluCysValGlyL
 3826 : CCCGACGACGTGCATGGTCCGGTCCATCCTCCTCCGCGGCTTCGACCGCGAGTGCGTCGGCA : 3764

  258 : euLeuAlaAlaMetMetThrGluArgGlyIleProPhe<->LeuGlyThrThrIleProLys :  276
         !:!!! !|||   !!:! !.!.!.!|||:!!! !.!!   :!!|||..!|||  ! !!|||
        ysIleGluAlaHisIleLysHisHisGlyValGlnLeuGlnValGlyValThrProAlaLys
 3763 : AGATCGAGGCCCACATCAAGCACCACGGCGTCCAGCTCCAGGTCGGCGTCACGCCCGCGAAG : 3704

  277 : AlaValGluArgGlnAlaAspGlyArgLeuLeuValArgTyrArgAsnThrThrThrGlnMe :  297
          !! !:!!  !  !|||   |||  !|||  !|||! ! !!  !..!  !  !..!!!.  
        IleGluLysAspAlaAlaThrGlyValLeuThrValThrAspSerGlyGlyGlyValHisGl
 3703 : ATCGAGAAGGACGCGGCGACGGGCGTCCTCACGGTCACGGACTCCGGCGGCGGCGTCCACGA : 3641

  298 : tAspGlySerAspValPheAspThrValLeuTrpAlaIleGlyArgLysGlyLeuIleGluA :  318
        ! !!! !!!!!  :!! !!!  |||! !! !!::|||  !  !  !     !  !|||!!::
        uTyrAspThrValLeuValAlaThrGlyArgTyrAlaAspThrAlaAlaLeuGlyIleAspA
 3640 : GTACGACACGGTGCTCGTCGCGACGGGCCGCTACGCGGACACGGCGGCCCTCGGCATCGACA : 3578

  319 : spLeuAsnLeuAspAlaAlaGlyValLysThrHisAspAspLysIleValValAspAlaAla :  338
        !!:!!  !  !!  :!!|||..!|||!!..!! !     ! |||:!!! !  !! !! !! !
        snValProGlyAlaSerAlaAsnValAsnAlaLysThrLysLysLeuGluCysValAspGlu
 3577 : ACGTGCCCGGCGCGTCGGCGAACGTGAACGCGAAGACGAAGAAGCTCGAGTGCGTCGACGAG : 3518

  339 : GluAlaThrSerValProHisIlePheAlaValGlyAspIleIleTyrGlyArgProGluLe :  359
        :!!  ! !!.!!!.!||||||:!!!:!|||:!!||||||:!!:!! ! ||||||||||||||
        GlnLeuProGlyAlaProHisValTyrAlaIleGlyAspValValGluGlyArgProGluLe
 3517 : CAGCTGCCCGGCGCGCCGCACGTCTACGCGATCGGCGACGTCGTCGAGGGCCGGCCCGAGCT : 3455

  360 : uThrProValAlaIleLeuSerGlyArgLeuLeuAlaArgArgLeuPheAlaGlySerThrG :  380
        ||||||||||||||||  !:!!|||! !! !||||||||||||||||||!.!|||!.!|||:
        uThrProValAlaIleGluAlaGlyLeuArgLeuAlaArgArgLeuPheGlyGlyLysThrG
 3454 : CACGCCCGTCGCCATCGAGGCGGGCCTGCGCCTCGCGCGGCGCCTCTTCGGCGGCAAGACCG : 3392

  381 : lnLeuMetAspTyrAlaAspValAlaThrThrValPheThrProLeuGluTyrSerCysVal :  400
        !!! !|||||||||! !  !||||||||||||:!!||||||||||||||||||.!!   :!!
        luProMetAspTyrGluCysValAlaThrThrIlePheThrProLeuGluTyrGlyThrIle
 3391 : AGCCCATGGACTACGAGTGCGTCGCGACGACGATCTTCACGCCGCTCGAGTACGGCACGATC : 3332

  401 : GlyMetSerGluGluThrAlaIleGluLeuArgGlyAlaAspAsnIleGluValPheHisGl :  421
        |||:!!||||||!!:  !|||!  !  ! !! !|||! !  !|||:!!|||  !!:!  !.!
        GlyLeuSerGluAspAspAlaLysAlaGlnLeuGlyGluCysAsnValGluSerTyrIleSe
 3331 : GGGCTGAGCGAGGACGACGCCAAGGCCCAGCTCGGCGAGTGCAACGTCGAGTCCTACATCAG : 3269

  422 : yTyrTyrLysProThrGluPhePheIleProGln<->LysSerValArg<-><->HisCysT :  439
        ! ! !:!  !|||  !|||!:!  !:!!  !:!!   :::|||! !|||        !|||!
        rGluPheAlaProLeuGluTyrAlaLeuSerGluThrArgSerGluArgGlyAspGlyCysP
 3268 : CGAGTTCGCGCCCCTCGAGTACGCCCTCAGCGAGACGCGCAGCGAGCGCGGCGACGGCTGCT : 3206

  440 : yrLeuLysAlaValAlaGluValSerGlyAspGlnLysIleLeuGlyLeuHisTyrIleGly :  459
        :!  !|||  !|||!.!!!:  !|||         |||:!!:!!|||!!!||||||:!!|||
        heAlaLysLeuValValAspLysSer---ThrGlyLysValValGlyPheHisTyrLeuGly
 3205 : TCGCCAAGCTCGTCGTCGACAAGAGC---ACGGGCAAGGTCGTCGGCTTCCACTACCTCGGC : 3149

  460 : ProValAlaGlyGluValIleGlnGlyPheAlaAlaAlaLeuLysThrGlyLeuThrValLy :  480
        |||  !|||||||||:!!! !|||||||||:!!  !|||:!!:::! !|||  !|||  !  
        ProAsnAlaGlyGluIleThrGlnGlyPheSerIleAlaMetArgLysGlyAlaThrTyrAl
 3148 : CCCAACGCCGGCGAGATCACCCAGGGCTTCTCCATCGCCATGCGCAAGGGCGCGACCTACGC : 3086

  481 : sThrLeuLeuAsnThrValGlyIleHisProThrThrAlaGluGluPheThrArgLeuSerI :  501
           !!!!:!!::!|||||||||||||||||||||..!|||||||||||||||  !:!!!!!:
        aAspPheIleSerThrValGlyIleHisProThrValAlaGluGluPheThrSerMetThrV
 3085 : CGACTTCATCTCCACCGTCGGCATCCACCCGACGGTCGCCGAGGAGTTCACGTCCATGACCG : 3023

  502 : leThrLysArgSerGlyArgAspProThrProAlaSerCys :  514
        !:||||||  !||||||..!..! !!.!!  !!.!.!!|||
        alThrLysSerSerGlyGluSerAlaAlaLysGlyGlyCys
 3022 : TGACCAAGTCGAGCGGCGAGTCCGCAGCCAAGGGCGGCTGC : 2982

vulgar: SPP00000091_1.0 30 514 . scaffold_11:subseq(783554,7436) 4436 2981 - 945 M 70 210 G 0 3 M 9 27 G 1 0 M 58 174 G 1 0 M 26 78 G 1 0 M 73 219 G 0 3 M 163 489 G 0 3 M 4 12 G 0 6 M 11 33 G 1 0 M 66 198
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	gene	2982	4436	945	-	.	gene_id 1 ; sequence SPP00000091_1.0 ; gene_orientation .
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	2982	4436	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	2982	4436	.	-	.	insertions 15 ; deletions 4
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	similarity	2982	4436	945	-	.	alignment_id 1 ; Query SPP00000091_1.0 ; Align 4437 31 210 ; Align 4224 101 27 ; Align 4197 111 174 ; Align 4023 170 78 ; Align 3945 197 219 ; Align 3723 270 489 ; Align 3231 433 12 ; Align 3213 437 33 ; Align 3180 449 198
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000063_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Caenorhabditis elegans # Complete
        Target: scaffold_11:subseq(783554,7436) [revcomp]
         Model: protein2genome
     Raw score: 660
   Query range: 172 -> 418
  Target range: 4430 -> 3692

  173 : TyrAspLeuIleValIleGlyGlyGlySerGlyGlyLeuAlaAlaAlaLysGluAlaSerAr :  193
        ||||||::::::|||:::||||||||||||||||||||||||..!:!!||||||..!:!!!:
        TyrAspValValValValGlyGlyGlySerGlyGlyLeuAlaCysSerLysGluCysAlaLy
 4430 : tacgacgtcgtcgtcgtcggcggcggctccggcggcCTCGCCTGCTCCAAGGAGTGCGCGAA : 4370

  194 : gLeuGlyLysLysValAlaCysLeuAspPheValLysProSerProGlnGlyThrSerTrpG :  214
        !||||||   |||||||||   ||||||||||||||||||||||||  !|||:!!!!!||||
        sLeuGlyAlaLysValAlaValLeuAspPheValLysProSerProAlaGlySerThrTrpG
 4369 : GCTCGGCGCCAAGGTCGCCGTGCTCGACTTCGTGAAGCCGTCGCCGGCGGGGTCGACGTGGG : 4307

  215 : lyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHisGlnAlaSer :  234
        |||||||||||||||||||||||||||||||||||||||||||||||||||||  !||||||
        lyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHisThrAlaSer
 4306 : GCCTCGGCGGCACGTGCGTCAACGTCGGCTGCATCCCGAAGAAGCTCATGCACACGGCGTCC : 4247

  235 : LeuLeuGlyHisSerIle<->HisAspAlaLysLysTyrGlyTrpLysLeuProGluGlyLy :  254
        :!!:!!|||.!.!!!:!!    !!||||||      !:!|||||||||     !!  !.!  
        IleIleGlyGluThrLeuLysAspAspAlaAlaAlaPheGlyTrpLys---AspAlaAlaAl
 4246 : ATCATCGGCGAGACGCTCAAGGACGACGCCGCCGCCTTCGGGTGGAAG---GACGCCGCCGC : 4187

  255 : sValGluHisGlnTrpAsnHisLeuArgAspSerValGlnAspHisIleAlaSerLeuAsnT :  275
        !! !! !|||.!.|||.!.   :!!!:!...!!!|||||||||||||||  !|||||||||!
        aGlyAlaHisAspTrpGluSerMetLysSerThrValGlnAspHisIleLysSerLeuAsnP
 4186 : GGGCGCGCACGACTGGGAGTCGATGAAGTCGACGGTGCAGGACCACATCAAGTCGCTCAACT : 4124

  276 : rpGlyTyrArgValGlnLeuArgGluLysThrValThrTyrIleAsnSerTyrGlyGluPhe :  295
        ::  !|||||||||  !|||||||||  !  !:!!||||||:!:||| !!  !|||||||||
        heLysTyrArgValAlaLeuArgGluAlaGlyIleThrTyrLeuAsnArgLeuGlyGluPhe
 4123 : TCAAGTACCGCGTCGCGCTCCGCGAGGCGGGCATCACCTACCTGAACCGCCTCGGCGAGTTC : 4064

  296 : ThrGlyProPheGluIleSerAlaThrAsnLysLysLysLysValGluLysLeuThrAlaAs :  316
          !! !  !  !   ||||||  !|||:!!||||||   !!.  !  !...:!!||||||! 
        GluAspLysAsnThrIleSerLeuThrAspLysLysGlyAsnLysThrSerValThrAlaAl
 4063 : GAGGACAAGAACACCATCTCCCTCACGGACAAGAAGGGCAACAAGACGTCCGTCACGGCCGC : 4001

  317 : pArgPheLeuIleSerThrGlyLeuArgProLysTyrProGluIleProGlyValLysGluT :  337
         ||||||:!!:!!:!!..!|||  !||||||!!. ! ! !!    !||||||      |||:
        aArgPheIleValAlaValGlyGlyArgProAsnLysLeuGlyCysProGly---GlyGluH
 4000 : GCGGTTCATCGTCGCCGTCGGCGGCCGCCCGAACAAGCTCGGCTGCCCCGGC---GGCGAGC : 3941

  338 : yrThrIleThrSerAspAspLeuPheGlnLeuProTyrSerProGlyLysThrLeuCysVal :  357
        !!.!!|||  !|||||||||||||||...|||||| ! :!!||||||:::..!|||||||||
        isAlaIleAspSerAspAspLeuPheSerLeuProLysAlaProGlyArgValLeuCysVal
 3940 : ACGCCATCGACAGCGACGACCTGTTCTCCCTGCCCAAGGCGCCGGGCCGCGTGCTCTGCGTC : 3881

  358 : GlyAlaSerTyrValSerLeuGluCysAlaGlyPheLeuHisGlyPheGlyPheAspValTh :  378
        |||!.!.!!|||:!!:!!|||||||||!.!||||||  !  !|||.!.|||!:!   ..!||
        GlyGlyGlyTyrIleAlaLeuGluCysGlyGlyPheThrAlaGlyMetGlyTyrProThrTh
 3880 : GGCGGCGGCTACATCGCGCTCGAGTGCGGCGGCTTCACGGCCGGCATGGGCTACCCGACGAC : 3818

  379 : rValMetValArgSerIleLeuLeuArgGlyPheAspGlnAspMetAlaGluArgIleArgL :  399
        |  !|||||||||||||||||||||||||||||||||!::!!:   !.!!  !:!|||..! 
        rCysMetValArgSerIleLeuLeuArgGlyPheAspArgGluCysValGlyLysIleGluA
 3817 : GTGCATGGTCCGGTCCATCCTCCTCCGCGGCTTCGACCGCGAGTGCGTCGGCAAGATCGAGG : 3755

  400 : ysHisMetIleAlaTyrGlyMetLysPheGluAlaGlyVal<->ProThrArgIleGluGln :  418
          |||!!:!    !:!!|||:!::!!.!!:!!!.!||||||   |||.!!!:!||||||:!!
        laHisIleLysHisHisGlyValGlnLeuGlnValGlyValThrProAlaLysIleGluLys
 3754 : CCCACATCAAGCACCACGGCGTCCAGCTCCAGGTCGGCGTCACGCCCGCGAAGATCGAGAAG : 3695

vulgar: SPP00000063_1.0 172 418 . scaffold_11:subseq(783554,7436) 4430 3692 - 660 M 68 204 G 0 3 M 9 27 G 1 0 M 83 249 G 1 0 M 78 234 G 0 3 M 6 18
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	gene	3693	4430	660	-	.	gene_id 1 ; sequence SPP00000063_1.0 ; gene_orientation .
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	3693	4430	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	3693	4430	.	-	.	insertions 6 ; deletions 2
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	similarity	3693	4430	660	-	.	alignment_id 1 ; Query SPP00000063_1.0 ; Align 4431 173 204 ; Align 4224 241 27 ; Align 4197 251 249 ; Align 3948 335 234 ; Align 3711 413 18
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000063_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Caenorhabditis elegans # Complete
        Target: scaffold_11:subseq(783554,7436) [revcomp]
         Model: protein2genome
     Raw score: 442
   Query range: 475 -> 657
  Target range: 3551 -> 3002

  476 : ArgAlaLysSerLysLysValLeuGlyArgArgGluGlnSerThrThrIleProTrpValTy :  496
        !.!||||||!!!||||||:!!  ! !!  !  !||||||  ! !!  !   |||   |||||
        AsnAlaLysThrLysLysLeuGluCysValAspGluGlnLeuProGlyAlaProHisValTy
 3551 : AACGCGAAGACGAAGAAGCTCGAGTGCGTCGACGAGCAGCTGCCCGGCGCGCCGCACGTCTA : 3491

  497 : rAlaIleGlyAspValLeuGluGlyThrProGluLeuThrProValAlaIleGlnAlaGlyA :  517
        ||||||||||||||||:!!||||||  !||||||||||||||||||||||||:!!||||||!
        rAlaIleGlyAspValValGluGlyArgProGluLeuThrProValAlaIleGluAlaGlyL
 3490 : CGCGATCGGCGACGTCGTCGAGGGCCGGCCCGAGCTCACGCCCGTCGCCATCGAGGCGGGCC : 3428

  518 : rgValLeuMetArgArgIlePheAspGlyAlaAsnGluLeuThrGluTyrAspGlnIlePro :  537
         !  !|||  !||||||:!!|||! !|||  !!.!|||! !! !!!:|||!!:   :!! !!
        euArgLeuAlaArgArgLeuPheGlyGlyLysThrGluProMetAspTyrGluCysValAla
 3427 : TGCGCCTCGCGCGGCGCCTCTTCGGCGGCAAGACCGAGCCCATGGACTACGAGTGCGTCGCG : 3368

  538 : ThrThrValPheThrProLeuGluTyrGlyCysCysGlyLeuSerGluGluAspAlaMetMe :  558
        ||||||:!!|||||||||||||||||||||     !||||||||||||!!:||||||! !  
        ThrThrIlePheThrProLeuGluTyrGlyThrIleGlyLeuSerGluAspAspAlaLysAl
 3367 : ACGACGATCTTCACGCCGCTCGAGTACGGCACGATCGGGCTGAGCGAGGACGACGCCAAGGC : 3305

  559 : tLysTyrGlyLysAspAsnIleIleIleTyrHisAsnValPheAsnProLeuGluTyrThrI :  579
         :!!  !|||:!!  !|||:!!     !|||  !!:!! !|||   ||||||||||||.!!:
        aGlnLeuGlyGluCysAsnValGluSerTyrIleSerGluPheAlaProLeuGluTyrAlaL
 3304 : CCAGCTCGGCGAGTGCAACGTCGAGTCCTACATCAGCGAGTTCGCGCCCCTCGAGTACGCCC : 3242

  580 : leSerGlu<->ArgMetAspLysAspHisCysTyrLeuLysMetIleCysLeuArgAsnGlu :  598
        !!||||||   |||!  !!::::! ! !! !!! !!!!   ! !:!!  !:!!  !!!....
        euSerGluThrArgSerGluArgGlyAspGlyCysPheAlaLysLeuValValAspLysSer
 3241 : TCAGCGAGACGCGCAGCGAGCGCGGCGACGGCTGCTTCGCCAAGCTCGTCGTCGACAAGAGC : 3182

  599 : GluGluLysValValGlyPheHisIleLeuThrProAsnAlaGlyGluValThrGlnGlyPh :  619
          !!  ||||||||||||||||||  !|||  !|||||||||||||||:!!|||||||||||
        ThrGlyLysValValGlyPheHisTyrLeuGlyProAsnAlaGlyGluIleThrGlnGlyPh
 3181 : ACGGGCAAGGTCGTCGGCTTCCACTACCTCGGCCCCAACGCCGGCGAGATCACCCAGGGCTT : 3119

  620 : eGlyIleAlaLeuLysLeuAlaAlaLysLysAlaAspPheAspArgLeuIleGlyIleHisP :  640
        |..!||||||:!!:::  !!.!|||!   ! |||||||||  !  !  !:!!||||||||||
        eSerIleAlaMetArgLysGlyAlaThrTyrAlaAspPheIleSerThrValGlyIleHisP
 3118 : CTCCATCGCCATGCGCAAGGGCGCGACCTACGCCGACTTCATCTCCACCGTCGGCATCCACC : 3056

  641 : roThrValAlaGluAsnPheThrThrLeuThrLeuGluLysLysGluGlyAsp :  657
        ||||||||||||||.!.||||||:!!:!!|||:!!   |||..!...|||!!:
        roThrValAlaGluGluPheThrSerMetThrValThrLysSerSerGlyGlu
 3055 : CGACGGTCGCCGAGGAGTTCACGTCCATGACCGTGACCAAGTCGAGCGGCGAG : 3003

vulgar: SPP00000063_1.0 475 657 . scaffold_11:subseq(783554,7436) 3551 3002 - 442 M 106 318 G 0 3 M 76 228
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	gene	3003	3551	442	-	.	gene_id 2 ; sequence SPP00000063_1.0 ; gene_orientation .
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	3003	3551	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	3003	3551	.	-	.	insertions 3 ; deletions 0
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	similarity	3003	3551	442	-	.	alignment_id 2 ; Query SPP00000063_1.0 ; Align 3552 476 318 ; Align 3231 582 228
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000090_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Drosophila melanogaster # Complete
        Target: scaffold_11:subseq(783554,7436) [revcomp]
         Model: protein2genome
     Raw score: 1013
   Query range: 95 -> 594
  Target range: 4487 -> 2981

   96 : AlaAlaMetTyrAlaGlnProValArgLysMetSerThrLysGlyGlySerTyrAspTyrAs :  116
        ||||||      :::...   |||            ||||||      ...:::||||||||
        AlaAlaAlaAlaSerSerMetValAspAspGlyPheThrLysGluHisGlyPheAspTyrAs
 4487 : gccgcggcggcgtcgtcgatggtcgacgacggcttcacgaaggagcacggcttcgactacga : 4427

  117 : pLeuIleValIleGlyGlyGlySerAlaGlyLeuAlaCysAlaLysGluAlaValLeuAsnG :  137
        |::::::|||:::||||||||||||...||||||||||||:!!||||||..!!.!  !  !|
        pValValValValGlyGlyGlySerGlyGlyLeuAlaCysSerLysGluCysAlaLysLeuG
 4426 : cgtcgtcgtcgtcggcggcggctccggcggcCTCGCCTGCTCCAAGGAGTGCGCGAAGCTCG : 4364

  138 : lyAlaArgValAlaCysLeuAspPheValLysProThrProThrLeuGlyThrLysTrpGly :  157
        |||||!:!||||||   ||||||||||||||||||:!!|||.!!   |||:!!! !||||||
        lyAlaLysValAlaValLeuAspPheValLysProSerProAla---GlySerThrTrpGly
 4363 : GCGCCAAGGTCGCCGTGCTCGACTTCGTGAAGCCGTCGCCGGCG---GGGTCGACGTGGGGC : 4307

  158 : ValGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHisGlnAlaSerLe :  178
        :!!||||||||||||||||||||||||||||||||||||||||||||||||  !||||||:!
        LeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHisThrAlaSerIl
 4306 : CTCGGCGGCACGTGCGTCAACGTCGGCTGCATCCCGAAGAAGCTCATGCACACGGCGTCCAT : 4244

  179 : uLeuGlyGluAlaVal<->HisGluAlaAlaAlaTyrGlyTrpAsnValAspGluLysIleL :  198
        !:!!||||||.!!:!!    !!!!:|||||||||!:!||||||!!.! !! !!    !  ! 
        eIleGlyGluThrLeuLysAspAspAlaAlaAlaPheGlyTrpLysAspAlaAlaAlaGlyA
 4243 : CATCGGCGAGACGCTCAAGGACGACGCCGCCGCCTTCGGGTGGAAGGACGCCGCCGCGGGCG : 4181

  199 : ysProAspTrpHisLysLeuValGlnSerValGlnAsnHisIleLysSerValAsnTrpVal :  218
         !! !||||||.!...!:!!  !..!!!!||||||:!!||||||||||||:!!|||!::  !
        laHisAspTrpGluSerMetLysSerThrValGlnAspHisIleLysSerLeuAsnPheLys
 4180 : CGCACGACTGGGAGTCGATGAAGTCGACGGTGCAGGACCACATCAAGTCGCTCAACTTCAAG : 4121

  219 : ThrArgValAspLeuArgAspLysLysValGluTyrIleAsnGlyLeuGlySerPheValAs :  239
          !||||||!  ||||||!!:  !   :!!   |||:!:||| !!||||||..!|||! !||
        TyrArgValAlaLeuArgGluAlaGlyIleThrTyrLeuAsnArgLeuGlyGluPheGluAs
 4120 : TACCGCGTCGCGCTCCGCGAGGCGGGCATCACCTACCTGAACCGCCTCGGCGAGTTCGAGGA : 4058

  240 : pSerHisThrLeuLeuAlaLysLeuLysSerGlyGluArgThr<->IleThrAlaGlnThrP :  259
        |!.!:!!|||:!!! !  !! !  !|||!.!|||.!.!:!|||   :!!||||||  !  !|
        pLysAsnThrIleSerLeuThrAspLysLysGlyAsnLysThrSerValThrAlaAlaArgP
 4057 : CAAGAACACCATCTCCCTCACGGACAAGAAGGGCAACAAGACGTCCGTCACGGCCGCGCGGT : 3995

  260 : heValIleAlaValGlyGlyArgProArgTyrProAspIleProGlyAlaValGluTyrGly :  279
        ||:!!:!!||||||||||||||||||!.! ! ! !! !  !||||||!.!   |||:!!!.!
        heIleValAlaValGlyGlyArgProAsnLysLeuGlyCysProGlyGly---GluHisAla
 3994 : TCATCGTCGCCGTCGGCGGCCGCCCGAACAAGCTCGGCTGCCCCGGCGGC---GAGCACGCC : 3938

  280 : IleThrSerAspAspLeuPheSerLeuAspArgGluProGlyLysThrLeuValValGlyAl :  300
        |||  !|||||||||||||||||||||  !!:!! !||||||:::..!|||  !||||||!.
        IleAspSerAspAspLeuPheSerLeuProLysAlaProGlyArgValLeuCysValGlyGl
 3937 : ATCGACAGCGACGACCTGTTCTCCCTGCCCAAGGCGCCGGGCCGCGTGCTCTGCGTCGGCGG : 3875

  301 : aGlyTyrIleGlyLeuGluCysAlaGlyPheLeuLysGlyLeuGlyTyrGluProThrValM :  321
        !|||||||||!.!|||||||||!.!||||||  !   |||:!!||||||  ! !!|||  !|
        yGlyTyrIleAlaLeuGluCysGlyGlyPheThrAlaGlyMetGlyTyrProThrThrCysM
 3874 : CGGCTACATCGCGCTCGAGTGCGGCGGCTTCACGGCCGGCATGGGCTACCCGACGACGTGCA : 3812

  322 : etValArgSerIleValLeuArgGlyPheAspGlnGlnMetAlaGluLeuValAlaAlaSer :  341
        ||||||||||||||:!!|||||||||||||||!:::!!   !.!!    !:!!! !|||  !
        etValArgSerIleLeuLeuArgGlyPheAspArgGluCysValGlyLysIleGluAlaHis
 3811 : TGGTCCGGTCCATCCTCCTCCGCGGCTTCGACCGCGAGTGCGTCGGCAAGATCGAGGCCCAC : 3752

  342 : MetGluGluArgGlyIleProPheLeuArgLysThrValProLeuSerValGluLysGln<- :  362
        !!::!!.!.!.!|||:!!! !.!!! !  !   ..!..!|||  !!.!:!!||||||.!.  
        IleLysHisHisGlyValGlnLeuGlnValGlyValThrProAlaLysIleGluLysAspAl
 3751 : ATCAAGCACCACGGCGTCCAGCTCCAGGTCGGCGTCACGCCCGCGAAGATCGAGAAGGACGC : 3689

  363 : >AspAspGlyLysLeuLeuValLysTyrLysAsnValGluThrGlyGluGluAlaGluAspV :  382
         !     |||   |||  !|||! ! !!.....!! !!  ..!  !||| ! ! !  !!  :
        aAlaThrGlyValLeuThrValThrAspSerGlyGlyGlyValHisGluTyrAspThrValL
 3688 : GGCGACGGGCGTCCTCACGGTCACGGACTCCGGCGGCGGCGTCCACGAGTACGACACGGTGC : 3626

  383 : alTyrAspThrValLeuTrpAlaIleGlyArgLysGlyLeuValAspAspLeuAsnLeuPro :  402
        !!  !!  |||! !! !!::|||  !  !  !     !  !:!!|||:!!:!!  !  ! !!
        euValAlaThrGlyArgTyrAlaAspThrAlaAlaLeuGlyIleAspAsnValProGlyAla
 3625 : TCGTCGCGACGGGCCGCTACGCGGACACGGCGGCCCTCGGCATCGACAACGTGCCCGGCGCG : 3566

  403 : AsnAlaGlyValThrValGlnLysAspLysIleProValAspSerGlnGluAlaThrAsnVa :  423
        :::|||..!|||!.!!.!:!!! ! ! |||:!!  !  !! !..!:!!:!!  ! !!..!!.
        SerAlaAsnValAsnAlaLysThrLysLysLeuGluCysValAspGluGlnLeuProGlyAl
 3565 : TCGGCGAACGTGAACGCGAAGACGAAGAAGCTCGAGTGCGTCGACGAGCAGCTGCCCGGCGC : 3503

  424 : lAlaAsnIleTyrAlaValGlyAspIleIleTyrGlyLysProGluLeuThrProValAlaV :  444
        ! !!:!!:!!||||||:!!||||||:!!:!! ! |||::!|||||||||||||||||||||:
        aProHisValTyrAlaIleGlyAspValValGluGlyArgProGluLeuThrProValAlaI
 3502 : GCCGCACGTCTACGCGATCGGCGACGTCGTCGAGGGCCGGCCCGAGCTCACGCCCGTCGCCA : 3440

  445 : alLeuAlaGlyArgLeuLeuAlaArgArgLeuTyrGlyGlySerThrGlnArgMetAspTyr :  464
        !!  !||||||! !! !|||||||||||||||!:!||||||!.!|||:!!! !|||||||||
        leGluAlaGlyLeuArgLeuAlaArgArgLeuPheGlyGlyLysThrGluProMetAspTyr
 3439 : TCGAGGCGGGCCTGCGCCTCGCGCGGCGCCTCTTCGGCGGCAAGACCGAGCCCATGGACTAC : 3380

  465 : LysAspValAlaThrThrValPheThrProLeuGluTyrAlaCysValGlyLeuSerGluGl :  485
        :!!  !||||||||||||:!!||||||||||||||||||!.!   :!!||||||||||||!!
        GluCysValAlaThrThrIlePheThrProLeuGluTyrGlyThrIleGlyLeuSerGluAs
 3379 : GAGTGCGTCGCGACGACGATCTTCACGCCGCTCGAGTACGGCACGATCGGGCTGAGCGAGGA : 3317

  486 : uAspAlaValLysGlnPheGlyAlaAspGluIleGluValPheHisGlyTyrTyrLysProT :  506
        :||||||  !   |||.!!|||! !  !.!.:!!|||  !!:!  !.!! ! !:!  !||| 
        pAspAlaLysAlaGlnLeuGlyGluCysAsnValGluSerTyrIleSerGluPheAlaProL
 3316 : CGACGCCAAGGCCCAGCTCGGCGAGTGCAACGTCGAGTCCTACATCAGCGAGTTCGCGCCCC : 3254

  507 : hrGluPhePheIleProGln<->LysSerValArg<-><->TyrCysTyrLeuLysAlaVal :  523
         !|||!:!  !:!!  !:!!   :::|||! !|||        !|||!:!  !|||  !|||
        euGluTyrAlaLeuSerGluThrArgSerGluArgGlyAspGlyCysPheAlaLysLeuVal
 3253 : TCGAGTACGCCCTCAGCGAGACGCGCAGCGAGCGCGGCGACGGCTGCTTCGCCAAGCTCGTC : 3194

  524 : AlaGluArgHisGlyAspGlnArgValTyrGlyLeuHisTyrIleGlyProValAlaGlyGl :  544
        !.!!!:!:!   .!!      !:!|||  !|||!!!||||||:!!||||||  !||||||||
        ValAspLys---SerThrGlyLysValValGlyPheHisTyrLeuGlyProAsnAlaGlyGl
 3193 : GTCGACAAG---AGCACGGGCAAGGTCGTCGGCTTCCACTACCTCGGCCCCAACGCCGGCGA : 3134

  545 : uValIleGlnGlyPheAlaAlaAlaLeuLysSerGlyLeuThrIleAsnThrLeuIleAsnT :  565
        |:!!! !|||||||||:!!  !|||:!!:::!.!|||  !|||  !  !  !!!!|||::!|
        uIleThrGlnGlyPheSerIleAlaMetArgLysGlyAlaThrTyrAlaAspPheIleSerT
 3133 : GATCACCCAGGGCTTCTCCATCGCCATGCGCAAGGGCGCGACCTACGCCGACTTCATCTCCA : 3071

  566 : hrValGlyIleHisProThrThrAlaGluGluPheThrArgLeuAlaIleThrLysArgSer :  585
        ||||||||||||||||||||..!|||||||||||||||  !:!!.!!:!:||||||  !|||
        hrValGlyIleHisProThrValAlaGluGluPheThrSerMetThrValThrLysSerSer
 3070 : CCGTCGGCATCCACCCGACGGTCGCCGAGGAGTTCACGTCCATGACCGTGACCAAGTCGAGC : 3011

  586 : GlyLeuAspProThrProAlaSerCys :  594
        |||  !..! !!.!!  !!.!.!!|||
        GlyGluSerAlaAlaLysGlyGlyCys
 3010 : GGCGAGTCCGCAGCCAAGGGCGGCTGC : 2982

vulgar: SPP00000090_1.0 95 594 . scaffold_11:subseq(783554,7436) 4487 2981 - 1013 M 56 168 G 1 0 M 31 93 G 0 3 M 70 210 G 0 3 M 22 66 G 1 0 M 85 255 G 0 3 M 151 453 G 0 3 M 4 12 G 0 6 M 10 30 G 1 0 M 67 201
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	gene	2982	4487	1013	-	.	gene_id 1 ; sequence SPP00000090_1.0 ; gene_orientation .
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	2982	4487	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	2982	4487	.	-	.	insertions 18 ; deletions 3
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	similarity	2982	4487	1013	-	.	alignment_id 1 ; Query SPP00000090_1.0 ; Align 4488 96 168 ; Align 4320 153 93 ; Align 4224 184 210 ; Align 4011 254 66 ; Align 3945 277 255 ; Align 3687 362 453 ; Align 3231 513 12 ; Align 3213 517 30 ; Align 3183 528 201
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000035_1.0 # Protein # Thioredoxin reductase 2 (TR2) # Homo sapiens # Complete
        Target: scaffold_11:subseq(783554,7436) [revcomp]
         Model: protein2genome
     Raw score: 1026
   Query range: 38 -> 524
  Target range: 4433 -> 2975

   39 : AspTyrAspLeuLeuValValGlyGlyGlySerGlyGlyLeuAlaCysAlaLysGluAlaAl :   59
        |||||||||::::::|||||||||||||||||||||||||||||||||:!!||||||..!||
        AspTyrAspValValValValGlyGlyGlySerGlyGlyLeuAlaCysSerLysGluCysAl
 4433 : gactacgacgtcgtcgtcgtcggcggcggctccggcggcCTCGCCTGCTCCAAGGAGTGCGC : 4373

   60 : aGlnLeuGlyArgLysValAlaValValAspTyrValGluProSerProGlnGlyThrArgT :   80
        |:!!||||||  !||||||||||||:!!|||!:!|||:!!|||||||||  !|||:!!! !|
        aLysLeuGlyAlaLysValAlaValLeuAspPheValLysProSerProAlaGlySerThrT
 4372 : GAAGCTCGGCGCCAAGGTCGCCGTGCTCGACTTCGTGAAGCCGTCGCCGGCGGGGTCGACGT : 4310

   81 : rpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHisGlnAla :  100
        ||||||||||||||||||||||||||||||||||||||||||||||||||||||||  !|||
        rpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHisThrAla
 4309 : GGGGCCTCGGCGGCACGTGCGTCAACGTCGGCTGCATCCCGAAGAAGCTCATGCACACGGCG : 4250

  101 : AlaLeuLeuGlyGlyLeuIleGln<->AspAlaProAsnTyrGlyTrpGluValAlaGlnPr :  120
        :!!:!!:!!|||! !  !:!!:!!   |||||| !!  !!:!||||||:!!! !|||    !
        SerIleIleGlyGluThrLeuLysAspAspAlaAlaAlaPheGlyTrpLysAspAlaAlaAl
 4249 : TCCATCATCGGCGAGACGCTCAAGGACGACGCCGCCGCCTTCGGGTGGAAGGACGCCGCCGC : 4187

  121 : oValProHisAspTrpArgLysMetAlaGluAlaValGlnAsnHisValLysSerLeuAsnT :  141
        !! ! !!|||||||||..!..!|||  !..!.!!||||||:!!|||:!!||||||||||||!
        aGlyAlaHisAspTrpGluSerMetLysSerThrValGlnAspHisIleLysSerLeuAsnP
 4186 : GGGCGCGCACGACTGGGAGTCGATGAAGTCGACGGTGCAGGACCACATCAAGTCGCTCAACT : 4124

  142 : rpGlyHisArgValGlnLeuGlnAspArgLysValLysTyrPheAsnIleLysAlaSerPhe :  161
        ::  !:!!||||||  !|||!::!!:  !   :!!!  |||.!.|||  !   !.!..!|||
        heLysTyrArgValAlaLeuArgGluAlaGlyIleThrTyrLeuAsnArgLeuGlyGluPhe
 4123 : TCAAGTACCGCGTCGCGCTCCGCGAGGCGGGCATCACCTACCTGAACCGCCTCGGCGAGTTC : 4064

  162 : ValAspGluHisThrValCysGlyValAlaLysGlyGlyLysGluIleLeuLeuSerAlaAs :  182
        ! !|||:!!:!!|||:!!! !  !..!! !|||  !|||!!.:!!!  ! !:!!!!!|||! 
        GluAspLysAsnThrIleSerLeuThrAspLysLysGlyAsnLysThrSerValThrAlaAl
 4063 : GAGGACAAGAACACCATCTCCCTCACGGACAAGAAGGGCAACAAGACGTCCGTCACGGCCGC : 4001

  183 : pHisIleIleIleAlaThrGlyGlyArgProArgTyrProThrHisIleGluGlyAlaLeuG :  203
         !...!!|||:!!|||..!||||||||||||!.! ! ! !  !  !  !!  |||      |
        aArgPheIleValAlaValGlyGlyArgProAsnLysLeuGlyCysProGlyGly------G
 4000 : GCGGTTCATCGTCGCCGTCGGCGGCCGCCCGAACAAGCTCGGCTGCCCCGGCGGC------G : 3944

  204 : luTyrGlyIleThrSerAspAspIlePheTrpLeuLysGluSerProGlyLysThrLeuVal :  223
        ||:!!!.!|||  !|||||||||:!:|||!  |||   :!!:!!||||||:::..!|||  !
        luHisAlaIleAspSerAspAspLeuPheSerLeuProLysAlaProGlyArgValLeuCys
 3943 : AGCACGCCATCGACAGCGACGACCTGTTCTCCCTGCCCAAGGCGCCGGGCCGCGTGCTCTGC : 3884

  224 : ValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuThrGlyIleGlyLeuAspTh :  244
        ||||||!.!.!!|||:!!||||||||||||!.!||||||  !.!!|||!!:|||! !   ||
        ValGlyGlyGlyTyrIleAlaLeuGluCysGlyGlyPheThrAlaGlyMetGlyTyrProTh
 3883 : GTCGGCGGCGGCTACATCGCGCTCGAGTGCGGCGGCTTCACGGCCGGCATGGGCTACCCGAC : 3821

  245 : rThrIleMetMetArgSerIleProLeuArgGlyPheAspGlnGlnMetSerSerMetValI :  265
        ||||  !|||:!:|||||||||! !|||||||||||||||!:::!!     !.!!! !:!! 
        rThrCysMetValArgSerIleLeuLeuArgGlyPheAspArgGluCysValGlyLysIleG
 3820 : GACGTGCATGGTCCGGTCCATCCTCCTCCGCGGCTTCGACCGCGAGTGCGTCGGCAAGATCG : 3758

  266 : leGluHisMetAlaSerHisGlyThrArgPheLeuArgGlyCysAlaProSerArgValArg :  285
          !  |||!!:  !  !||||||..!!:!.!!! !  !|||  !.!!|||:!!!:!:!!..!
        luAlaHisIleLysHisHisGlyValGlnLeuGlnValGlyValThrProAlaLysIleGlu
 3757 : AGGCCCACATCAAGCACCACGGCGTCCAGCTCCAGGTCGGCGTCACGCCCGCGAAGATCGAG : 3698

  286 : ArgLeuProAspGlyGlnLeuGlnValThrTrpGluAspSerThrThrGlyLysGluAspTh :  306
        !:!     !!  !.!  !  !   :!!|||     !||||||  !  !|||   .!.!!:  
        Lys---AspAlaAlaThrGlyValLeuThrValThrAspSerGlyGlyGlyValHisGluTy
 3697 : AAG---GACGCGGCGACGGGCGTCCTCACGGTCACGGACTCCGGCGGCGGCGTCCACGAGTA : 3638

  307 : rGlyThrPheAspThrValLeuTrpAlaIleGlyArgValProAspThrArgSerLeuAsnL :  327
        !! !||| !   !..!!.!  ! !   !  !!.!  !..! !!! !  ! !!! !  !|||:
        rAspThrValLeuValAlaThrGlyArgTyrAlaAspThrAlaAlaLeuGlyIleAspAsnV
 3637 : CGACACGGTGCTCGTCGCGACGGGCCGCTACGCGGACACGGCGGCCCTCGGCATCGACAACG : 3575

  328 : euGluLysAlaGlyValAspThrSerProAspThrGlnLysIleLeuValAspSerArgGlu :  347
        !!      |||..!!.!:!!..!!:! !! ! |||:!!|||:!!  !  !! !..!..!:!!
        alProGlyAlaSerAlaAsnValAsnAlaLysThrLysLysLeuGluCysValAspGluGln
 3574 : TGCCCGGCGCGTCGGCGAACGTGAACGCGAAGACGAAGAAGCTCGAGTGCGTCGACGAGCAG : 3515

  348 : AlaThrSerValProHisIleTyrAlaIleGlyAspValValGluGlyArgProGluLeuTh :  368
          ! !!.!!!.!||||||:!!|||||||||||||||||||||||||||||||||||||||||
        LeuProGlyAlaProHisValTyrAlaIleGlyAspValValGluGlyArgProGluLeuTh
 3514 : CTGCCCGGCGCGCCGCACGTCTACGCGATCGGCGACGTCGTCGAGGGCCGGCCCGAGCTCAC : 3452

  369 : rProIleAlaIleMetAlaGlyArgLeuLeuValGlnArgLeuPheGlyGlySerSerAspL :  389
        ||||:!!||||||  !||||||! !! !|||!.!!:!|||||||||||||||!.!!!!!!:!
        rProValAlaIleGluAlaGlyLeuArgLeuAlaArgArgLeuPheGlyGlyLysThrGluP
 3451 : GCCCGTCGCCATCGAGGCGGGCCTGCGCCTCGCGCGGCGCCTCTTCGGCGGCAAGACCGAGC : 3389

  390 : euMetAspTyrAspAsnValProThrThrValPheThrProLeuGluTyrGlyCysValGly :  409
         !|||||||||!!:  !||| !!||||||:!!|||||||||||||||||||||   :!!|||
        roMetAspTyrGluCysValAlaThrThrIlePheThrProLeuGluTyrGlyThrIleGly
 3388 : CCATGGACTACGAGTGCGTCGCGACGACGATCTTCACGCCGCTCGAGTACGGCACGATCGGG : 3329

  410 : LeuSerGluGluGluAlaValAlaArgHisGlyGlnGluHisValGluValTyrHisAlaHi :  430
        |||||||||!!:!!:|||  !|||!:!! !|||:!!   :!!||||||  !|||  !::!.!
        LeuSerGluAspAspAlaLysAlaGlnLeuGlyGluCysAsnValGluSerTyrIleSerGl
 3328 : CTGAGCGAGGACGACGCCAAGGCCCAGCTCGGCGAGTGCAACGTCGAGTCCTACATCAGCGA : 3266

  431 : sTyrLysProLeuGluPheThrValAlaGlyArgAspAlaSerGln<-><-><->CysTyrV :  448
        .!:!  !|||||||||!:!.!!:!!::!! !! !  !::!..!!::         |||!:!!
        uPheAlaProLeuGluTyrAlaLeuSerGluThrArgSerGluArgGlyAspGlyCysPheA
 3265 : GTTCGCGCCCCTCGAGTACGCCCTCAGCGAGACGCGCAGCGAGCGCGGCGACGGCTGCTTCG : 3203

  449 : alLysMetValCysLeuArgGluProProGlnLeuValLeuGlyLeuHisPheLeuGlyPro :  468
        .!|||:!:|||  !  !!:!... !!  !:!!   |||:!!|||!!!|||!:!|||||||||
        laLysLeuValValAspLysSerThrGlyLys---ValValGlyPheHisTyrLeuGlyPro
 3202 : CCAAGCTCGTCGTCGACAAGAGCACGGGCAAG---GTCGTCGGCTTCCACTACCTCGGCCCC : 3146

  469 : AsnAlaGlyGluValThrGlnGlyPheAlaLeuGlyIleLysCysGlyAlaSerTyrAlaGl :  489
        ||||||||||||:!!||||||||||||:!!:!!!.!!!::::   ||||||!!!||||||.!
        AsnAlaGlyGluIleThrGlnGlyPheSerIleAlaMetArgLysGlyAlaThrTyrAlaAs
 3145 : AACGCCGGCGAGATCACCCAGGGCTTCTCCATCGCCATGCGCAAGGGCGCGACCTACGCCGA : 3083

  490 : nValMetArgThrValGlyIleHisProThrCysSerGluGluValValLysLeuArgIleS :  510
        . !!!!:  !|||||||||||||||||||||  !:!!|||||| !!..!...:!!! !:!:!
        pPheIleSerThrValGlyIleHisProThrValAlaGluGluPheThrSerMetThrValT
 3082 : CTTCATCTCCACCGTCGGCATCCACCCGACGGTCGCCGAGGAGTTCACGTCCATGACCGTGA : 3020

  511 : erLysArgSerGlyLeuAspProThrValThrGlyCysUnkGly :  524
        !!|||  !||||||  !..! !!.!!  !  !||||||   |||
        hrLysSerSerGlyGluSerAlaAlaLysGlyGlyCys***Gly
 3019 : CCAAGTCGAGCGGCGAGTCCGCAGCCAAGGGCGGCTGCTGAGGC : 2976

vulgar: SPP00000035_1.0 38 524 . scaffold_11:subseq(783554,7436) 4433 2975 - 1026 M 70 210 G 0 3 M 92 276 G 2 0 M 84 252 G 1 0 M 158 474 G 0 9 M 13 39 G 1 0 M 65 195
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	gene	2976	4433	1026	-	.	gene_id 1 ; sequence SPP00000035_1.0 ; gene_orientation .
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	2976	4433	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	2976	4433	.	-	.	insertions 12 ; deletions 4
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	similarity	2976	4433	1026	-	.	alignment_id 1 ; Query SPP00000035_1.0 ; Align 4434 39 210 ; Align 4221 109 276 ; Align 3945 203 252 ; Align 3693 288 474 ; Align 3210 446 39 ; Align 3171 460 195
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000079_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Mus musculus # Complete
        Target: scaffold_11:subseq(783554,7436) [revcomp]
         Model: protein2genome
     Raw score: 654
   Query range: 123 -> 375
  Target range: 4439 -> 3692

  124 : SerTyrAspPheAspLeuIleIleIleGlyGlyGlySerGlyGlyLeuAlaAlaAlaLysAl :  144
        ...:::|||:::|||::::::::::::||||||||||||||||||||||||..!:!!|||  
        GlyPheAspTyrAspValValValValGlyGlyGlySerGlyGlyLeuAlaCysSerLys--
 4439 : ggcttcgactacgacgtcgtcgtcgtcggcggcggctccggcggcCTCGCCTGCTCCAAG-- : 4379

  145 : aArgLeuSerAlaAlaLysPheAspLysLysValLeuValLeuAspPheValThrProThrP :  165
               ..!..!||||||.!!! !   ||||||  !|||||||||||||||! !|||:!!|
        -------GluCysAlaLysLeuGlyAlaLysValAlaValLeuAspPheValLysProSerP
 4378 : -------GAGTGCGCGAAGCTCGGCGCCAAGGTCGCCGTGCTCGACTTCGTGAAGCCGTCGC : 4325

  166 : roLeuGlyThrArgTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLys :  185
        ||  !|||:!!! !||||||||||||||||||||||||||||||||||||||||||||||||
        roAlaGlySerThrTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLys
 4324 : CGGCGGGGTCGACGTGGGGCCTCGGCGGCACGTGCGTCAACGTCGGCTGCATCCCGAAGAAG : 4265

  186 : LeuMetHisGlnAlaAlaLeuLeuGlyGlnAlaLeuLys<->AspSerArgAsnTyrGlyTr :  205
        |||||||||  !|||:!!:!!:!!|||:!!.!!||||||   |||:!!  !  !!:!|||||
        LeuMetHisThrAlaSerIleIleGlyGluThrLeuLysAspAspAlaAlaAlaPheGlyTr
 4264 : CTCATGCACACGGCGTCCATCATCGGCGAGACGCTCAAGGACGACGCCGCCGCCTTCGGGTG : 4202

  206 : pLysValGluAspThrValLysHisAspTrpGluLysMetThrGluSerValGlnSerHisI :  226
        ||||! !!  ! !.!!! !  !||||||||||||..!|||! !..!!!!||||||..!||||
        pLysAspAlaAlaAlaGlyAlaHisAspTrpGluSerMetLysSerThrValGlnAspHisI
 4201 : GAAGGACGCCGCCGCGGGCGCGCACGACTGGGAGTCGATGAAGTCGACGGTGCAGGACCACA : 4139

  227 : leGlySerLeuAsnTrpGlyTyrArgValAlaLeuArgGluLysLysValValTyrGluAsn :  246
        ||  !|||||||||!::  !|||||||||||||||||||||  !   :!!..!|||  !|||
        leLysSerLeuAsnPheLysTyrArgValAlaLeuArgGluAlaGlyIleThrTyrLeuAsn
 4138 : TCAAGTCGCTCAACTTCAAGTACCGCGTCGCGCTCCGCGAGGCGGGCATCACCTACCTGAAC : 4079

  247 : AlaTyrGlyArgPheIleGlyProHisArgIleValAlaThrAsnAsnLysGlyLysGluLy :  267
          !  !|||..!|||   ! !  !:!!! !|||  !  !|||:!!!!.||||||!!.:!!! 
        ArgLeuGlyGluPheGluAspLysAsnThrIleSerLeuThrAspLysLysGlyAsnLysTh
 4078 : CGCCTCGGCGAGTTCGAGGACAAGAACACCATCTCCCTCACGGACAAGAAGGGCAACAAGAC : 4016

  268 : sIleTyrSerAlaGluArgPheLeuIleAlaThrGlyGluArgProArgTyrLeuGlyIleP :  288
        !  !  !!!!|||! !||||||:!!:!!|||..!|||!  ||||||!.! ! ||||||  !|
        rSerValThrAlaAlaArgPheIleValAlaValGlyGlyArgProAsnLysLeuGlyCysP
 4015 : GTCCGTCACGGCCGCGCGGTTCATCGTCGCCGTCGGCGGCCGCCCGAACAAGCTCGGCTGCC : 3953

  289 : roGlyAspLysGluTyrCysIleSerSerAspAspLeuPheSerLeuProTyrCysProGly :  308
        |||||! !   |||:!!..!|||..!|||||||||||||||||||||||| ! ...||||||
        roGlyGly---GluHisAlaIleAspSerAspAspLeuPheSerLeuProLysAlaProGly
 3952 : CCGGCGGC---GAGCACGCCATCGACAGCGACGACCTGTTCTCCCTGCCCAAGGCGCCGGGC : 3896

  309 : LysThrLeuValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuAlaGlyIl :  329
        :::..!|||  !||||||!.!.!!|||:!!||||||||||||!.!||||||  !||||||!!
        ArgValLeuCysValGlyGlyGlyTyrIleAlaLeuGluCysGlyGlyPheThrAlaGlyMe
 3895 : CGCGTGCTCTGCGTCGGCGGCGGCTACATCGCGCTCGAGTGCGGCGGCTTCACGGCCGGCAT : 3833

  330 : eGlyLeuAspValThrValMetValArgSerIleLeuLeuArgGlyPheAspGlnAspMetA :  350
        :|||! !   ..!|||  !|||||||||||||||||||||||||||||||||!::!!:   !
        tGlyTyrProThrThrCysMetValArgSerIleLeuLeuArgGlyPheAspArgGluCysV
 3832 : GGGCTACCCGACGACGTGCATGGTCCGGTCCATCCTCCTCCGCGGCTTCGACCGCGAGTGCG : 3770

  351 : laAsnLysIleGlyGluHisMetGluGluHisGlyIleLysPheIleArgGlnPheValPro :  370
        .!..!||||||! !!  |||!!::!!.!.||||||:!!:!!.!!     !    !!..!|||
        alGlyLysIleGluAlaHisIleLysHisHisGlyValGlnLeuGlnValGlyValThrPro
 3769 : TCGGCAAGATCGAGGCCCACATCAAGCACCACGGCGTCCAGCTCCAGGTCGGCGTCACGCCC : 3710

  371 : ThrLysIleGluGln :  375
        .!!|||||||||:!!
        AlaLysIleGluLys
 3709 : GCGAAGATCGAGAAG : 3693

vulgar: SPP00000079_1.0 123 375 . scaffold_11:subseq(783554,7436) 4439 3692 - 654 M 20 60 G 3 0 M 52 156 G 0 3 M 92 276 G 1 0 M 84 252
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	gene	3693	4439	654	-	.	gene_id 1 ; sequence SPP00000079_1.0 ; gene_orientation .
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	3693	4439	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	3693	4439	.	-	.	insertions 3 ; deletions 4
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	similarity	3693	4439	654	-	.	alignment_id 1 ; Query SPP00000079_1.0 ; Align 4440 124 60 ; Align 4380 147 156 ; Align 4221 199 276 ; Align 3945 292 252
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000079_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Mus musculus # Complete
        Target: scaffold_11:subseq(783554,7436) [revcomp]
         Model: protein2genome
     Raw score: 478
   Query range: 399 -> 616
  Target range: 3641 -> 2975

  400 : GluPheAsnThrValLeuLeuAlaValGlyArgAspSerCysThrArgThrIleGlyLeuGl :  420
        |||!:!:!!|||||||||:!!|||..!|||||| !!:!!  !|||  !.!!:!!|||:!!!!
        GluTyrAspThrValLeuValAlaThrGlyArgTyrAlaAspThrAlaAlaLeuGlyIleAs
 3641 : GAGTACGACACGGTGCTCGTCGCGACGGGCCGCTACGCGGACACGGCGGCCCTCGGCATCGA : 3581

  421 : uThrVal<-><-><->GlyValLysIleAsnGluLysThrGlyLysIleProValThrAspG :  438
        :!.!|||         ..!!.!!!.:!:|||! !||||||  !|||:!!  !  !..!||||
        pAsnValProGlyAlaSerAlaAsnValAsnAlaLysThrLysLysLeuGluCysValAspG
 3580 : CAACGTGCCCGGCGCGTCGGCGAACGTGAACGCGAAGACGAAGAAGCTCGAGTGCGTCGACG : 3518

  439 : luGluGlnThrAsnValProTyrIleTyrAlaIleGlyAspIleLeuGluGlyLysLeuGlu :  458
        ||:!!! ! !!..!!.!|||:!!:!!|||||||||||||||:!!:!!||||||::!! !|||
        luGlnLeuProGlyAlaProHisValTyrAlaIleGlyAspValValGluGlyArgProGlu
 3517 : AGCAGCTGCCCGGCGCGCCGCACGTCTACGCGATCGGCGACGTCGTCGAGGGCCGGCCCGAG : 3458

  459 : LeuThrProValAlaIleGlnAlaGlyArgLeuLeuAlaGlnArgLeuTyrGlyGlySerAs :  479
        ||||||||||||||||||:!!||||||! !! !||||||!:!||||||!:!||||||!.!!.
        LeuThrProValAlaIleGluAlaGlyLeuArgLeuAlaArgArgLeuPheGlyGlyLysTh
 3457 : CTCACGCCCGTCGCCATCGAGGCGGGCCTGCGCCTCGCGCGGCGCCTCTTCGGCGGCAAGAC : 3395

  480 : nValLysCysAspTyrAspAsnValProThrThrValPheThrProLeuGluTyrGlyCysC :  500
        !! !      ||||||!!:  !||| !!||||||:!!|||||||||||||||||||||    
        rGluProMetAspTyrGluCysValAlaThrThrIlePheThrProLeuGluTyrGlyThrI
 3394 : CGAGCCCATGGACTACGAGTGCGTCGCGACGACGATCTTCACGCCGCTCGAGTACGGCACGA : 3332

  501 : ysGlyLeuSerGluGluLysAlaValGluLysPheGlyGluGluAsnIleGluValTyrHis :  520
         !||||||||||||!!: ! |||  !!  :!!.!!||||||   |||:!!|||  !|||  !
        leGlyLeuSerGluAspAspAlaLysAlaGlnLeuGlyGluCysAsnValGluSerTyrIle
 3331 : TCGGGCTGAGCGAGGACGACGCCAAGGCCCAGCTCGGCGAGTGCAACGTCGAGTCCTACATC : 3272

  521 : SerPhePheTrpProLeuGluTrpThrValPro<-><-><->SerArgAspAsnAsnLysCy :  538
        |||   |||  !|||||||||!::.!!:!!  !         |||..!  !..!:!!   ||
        SerGluPheAlaProLeuGluTyrAlaLeuSerGluThrArgSerGluArgGlyAspGlyCy
 3271 : AGCGAGTTCGCGCCCCTCGAGTACGCCCTCAGCGAGACGCGCAGCGAGCGCGGCGACGGCTG : 3209

  539 : sTyrAlaLysIleIleCysAsnLeuLysAspAspGluArgValValGlyPheHisValLeuG :  559
        |!:!||||||:!!:!!  !:!!   |||..!   !  !:!|||||||||||||||  !||||
        sPheAlaLysLeuValValAsp---LysSerThrGlyLysValValGlyPheHisTyrLeuG
 3208 : CTTCGCCAAGCTCGTCGTCGAC---AAGAGCACGGGCAAGGTCGTCGGCTTCCACTACCTCG : 3149

  560 : lyProAsnAlaGlyGluValThrGlnGlyPheAlaAlaAlaLeuLysCysGlyLeuThrLys :  579
        |||||||||||||||||:!!||||||||||||:!!  !|||:!!:::   |||  !||| ! 
        lyProAsnAlaGlyGluIleThrGlnGlyPheSerIleAlaMetArgLysGlyAlaThrTyr
 3148 : GCCCCAACGCCGGCGAGATCACCCAGGGCTTCTCCATCGCCATGCGCAAGGGCGCGACCTAC : 3089

  580 : GlnGlnLeuAspSerThrIleGlyIleHisProValCysAlaGluIlePheThrThrLeuSe :  600
           .!.!!!  !||||||:!!||||||||||||..!  !||||||   ||||||:!!:!!!!
        AlaAspPheIleSerThrValGlyIleHisProThrValAlaGluGluPheThrSerMetTh
 3088 : GCCGACTTCATCTCCACCGTCGGCATCCACCCGACGGTCGCCGAGGAGTTCACGTCCATGAC : 3026

  601 : rValThrLysArgSerGlyGlyAspIleLeuGlnSerGlyCysUnkGly :  616
        !|||||||||  !||||||! !..!  !  !:!!.!!||||||   |||
        rValThrLysSerSerGlyGluSerAlaAlaLysGlyGlyCys***Gly
 3025 : CGTGACCAAGTCGAGCGGCGAGTCCGCAGCCAAGGGCGGCTGCTGAGGC : 2976

vulgar: SPP00000079_1.0 399 616 . scaffold_11:subseq(783554,7436) 3641 2975 - 478 M 23 69 G 0 9 M 109 327 G 0 9 M 14 42 G 1 0 M 70 210
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	gene	2976	3641	478	-	.	gene_id 2 ; sequence SPP00000079_1.0 ; gene_orientation .
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	2976	3641	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	2976	3641	.	-	.	insertions 18 ; deletions 1
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	similarity	2976	3641	478	-	.	alignment_id 2 ; Query SPP00000079_1.0 ; Align 3642 400 69 ; Align 3564 423 327 ; Align 3228 532 42 ; Align 3186 547 210
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000036_1.0 # Protein # Thioredoxin reductase 3 (TR3) # Homo sapiens # Complete
        Target: scaffold_11:subseq(783554,7436) [revcomp]
         Model: protein2genome
     Raw score: 705
   Query range: 249 -> 513
  Target range: 4484 -> 3692

  250 : AlaTyrGlnSerGlyLeuLeuGlnLysLeuLeuGlnGluAspLeuAlaTyrAspTyrAspLe :  270
        |||      |||...::::::...      ...   ::::::   ...:::|||||||||::
        AlaAlaAlaSerSerMetValAspAspGlyPheThrLysGluHisGlyPheAspTyrAspVa
 4484 : gcggcggcgtcgtcgatggtcgacgacggcttcacgaaggagcacggcttcgactacgacgt : 4424

  271 : uIleIleIleGlyGlyGlySerGlyGlyLeuSerCysAlaLysGluAlaAlaIleLeuGlyL :  291
        ::::::::::|||||||||||||||||||||:!!|||:!!||||||..!|||!  |||||| 
        lValValValGlyGlyGlySerGlyGlyLeuAlaCysSerLysGluCysAlaLysLeuGlyA
 4423 : cgtcgtcgtcggcggcggctccggcggcCTCGCCTGCTCCAAGGAGTGCGCGAAGCTCGGCG : 4361

  292 : ysLysValMetValLeuAspPheValValProSerProGlnGlyThrSerTrpGlyLeuGly :  311
          ||||||   |||||||||||||||  !|||||||||  !|||:!!!!!||||||||||||
        laLysValAlaValLeuAspPheValLysProSerProAlaGlySerThrTrpGlyLeuGly
 4360 : CCAAGGTCGCCGTGCTCGACTTCGTGAAGCCGTCGCCGGCGGGGTCGACGTGGGGCCTCGGC : 4301

  312 : GlyThrCysValAsnValGlyCysIleProLysLysLeuMetHisGlnAlaAlaLeuLeuGl :  332
        |||||||||||||||||||||||||||||||||||||||||||||  !|||:!!:!!:!!||
        GlyThrCysValAsnValGlyCysIleProLysLysLeuMetHisThrAlaSerIleIleGl
 4300 : GGCACGTGCGTCAACGTCGGCTGCATCCCGAAGAAGCTCATGCACACGGCGTCCATCATCGG : 4238

  333 : yGlnAlaLeu<->CysAspSerArgLysPheGlyTrpGluTyrAsnGlnGlnValArgHisA :  352
        |:!!.!!|||     !|||:!!  !   |||||||||:!! !!  !     !! !  !|||:
        yGluThrLeuLysAspAspAlaAlaAlaPheGlyTrpLysAspAlaAlaAlaGlyAlaHisA
 4237 : CGAGACGCTCAAGGACGACGCCGCCGCCTTCGGGTGGAAGGACGCCGCCGCGGGCGCGCACG : 4175

  353 : snTrpGluThrMetThrLysAlaIleGlnAsnHisIleSerSerLeuAsnTrpGlyTyrArg :  372
        !!||||||:!!|||! !..!.!!:!:|||:!!||||||!.!|||||||||!::  !||||||
        spTrpGluSerMetLysSerThrValGlnAspHisIleLysSerLeuAsnPheLysTyrArg
 4174 : ACTGGGAGTCGATGAAGTCGACGGTGCAGGACCACATCAAGTCGCTCAACTTCAAGTACCGC : 4115

  373 : LeuSerLeuArgGluLysAlaValAlaTyrValAsnSerTyrGlyGluPheValGluHisHi :  393
        :!!:!!|||||||||  !!.!:!!.!!|||:!!||| !!  !|||||||||! !!!: ! :!
        ValAlaLeuArgGluAlaGlyIleThrTyrLeuAsnArgLeuGlyGluPheGluAspLysAs
 4114 : GTCGCGCTCCGCGAGGCGGGCATCACCTACCTGAACCGCCTCGGCGAGTTCGAGGACAAGAA : 4052

  394 : sLysIleLysAlaThrAsnLysLysGlyGlnGluThrTyrTyrThrAlaAlaGlnPheValI :  414
        !!  |||...  !|||:!!|||||||||.!.:!!|||! !  !|||||||||!:!|||:!!:
        nThrIleSerLeuThrAspLysLysGlyAsnLysThrSerValThrAlaAlaArgPheIleV
 4051 : CACCATCTCCCTCACGGACAAGAAGGGCAACAAGACGTCCGTCACGGCCGCGCGGTTCATCG : 3989

  415 : leAlaThrGlyGluArgProArgTyrLeuGlyIleGlnGlyAspLysGluTyrCysIleThr :  434
        !!|||..!|||!  ||||||!.! ! ||||||  !!  |||! !   |||:!!..!|||  !
        alAlaValGlyGlyArgProAsnLysLeuGlyCysProGlyGly---GluHisAlaIleAsp
 3988 : TCGCCGTCGGCGGCCGCCCGAACAAGCTCGGCTGCCCCGGCGGC---GAGCACGCCATCGAC : 3932

  435 : SerAspAspLeuPheSerLeuProTyrCysProGlyLysThrLeuValValGlyAlaSerTy :  455
        |||||||||||||||||||||||| ! ...||||||:::..!|||  !||||||!.!.!!||
        SerAspAspLeuPheSerLeuProLysAlaProGlyArgValLeuCysValGlyGlyGlyTy
 3931 : AGCGACGACCTGTTCTCCCTGCCCAAGGCGCCGGGCCGCGTGCTCTGCGTCGGCGGCGGCTA : 3869

  456 : rValAlaLeuGluCysAlaGlyPheLeuAlaGlyPheGlyLeuAspValThrValMetValA :  476
        |:!!||||||||||||!.!||||||  !||||||.!.|||! !   ..!|||  !|||||||
        rIleAlaLeuGluCysGlyGlyPheThrAlaGlyMetGlyTyrProThrThrCysMetValA
 3868 : CATCGCGCTCGAGTGCGGCGGCTTCACGGCCGGCATGGGCTACCCGACGACGTGCATGGTCC : 3806

  477 : rgSerIleLeuLeuArgGlyPheAspGlnGluMetAlaGluLysValGlySerTyrMetGlu :  496
        ||||||||||||||||||||||||||!::|||   !.!!  |||:!!! !:!!:!!!!::!!
        rgSerIleLeuLeuArgGlyPheAspArgGluCysValGlyLysIleGluAlaHisIleLys
 3805 : GGTCCATCCTCCTCCGCGGCTTCGACCGCGAGTGCGTCGGCAAGATCGAGGCCCACATCAAG : 3746

  497 : GlnHisGlyValLysPheLeuArgLysPheIleProValMetValGlnGln :  513
        !!.|||||||||:!!.!!! !  !    !!!  |||!.!! !:!!:!!:!!
        HisHisGlyValGlnLeuGlnValGlyValThrProAlaLysIleGluLys
 3745 : CACCACGGCGTCCAGCTCCAGGTCGGCGTCACGCCCGCGAAGATCGAGAAG : 3693

vulgar: SPP00000036_1.0 249 513 . scaffold_11:subseq(783554,7436) 4484 3692 - 705 M 86 258 G 0 3 M 93 279 G 1 0 M 84 252
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	gene	3693	4484	705	-	.	gene_id 1 ; sequence SPP00000036_1.0 ; gene_orientation .
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	3693	4484	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	3693	4484	.	-	.	insertions 3 ; deletions 1
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	similarity	3693	4484	705	-	.	alignment_id 1 ; Query SPP00000036_1.0 ; Align 4485 250 258 ; Align 4224 336 279 ; Align 3945 430 252
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000036_1.0 # Protein # Thioredoxin reductase 3 (TR3) # Homo sapiens # Complete
        Target: scaffold_11:subseq(783554,7436) [revcomp]
         Model: protein2genome
     Raw score: 432
   Query range: 538 -> 754
  Target range: 3638 -> 2975

  539 : TyrAsnThrValLeuLeuAlaIleGlyArgAspSerCysThrArgLysIleGlyLeuGluLy :  559
        |||:!!|||||||||:!!|||!  |||||| !!:!!  !|||  !   :!!|||:!!!!:!!
        TyrAspThrValLeuValAlaThrGlyArgTyrAlaAspThrAlaAlaLeuGlyIleAspAs
 3638 : TACGACACGGTGCTCGTCGCGACGGGCCGCTACGCGGACACGGCGGCCCTCGGCATCGACAA : 3578

  560 : sIle<-><-><->GlyValLysIleAsnGluLysSerGlyLysIleProValAsnAspValG :  577
        .:!:         ..!!.!!!.:!:|||! !|||!!!  !|||:!!  !  !  !|||! !:
        nValProGlyAlaSerAlaAsnValAsnAlaLysThrLysLysLeuGluCysValAspGluG
 3577 : CGTGCCCGGCGCGTCGGCGAACGTGAACGCGAAGACGAAGAAGCTCGAGTGCGTCGACGAGC : 3515

  578 : luGlnThrAsnValProTyrValTyrAlaValGlyAspIleLeuGluAspLysProGluLeu :  597
        !!! ! !!..!!.!|||:!!|||||||||:!!||||||:!!:!!|||! !::!|||||||||
        lnLeuProGlyAlaProHisValTyrAlaIleGlyAspValValGluGlyArgProGluLeu
 3514 : AGCTGCCCGGCGCGCCGCACGTCTACGCGATCGGCGACGTCGTCGAGGGCCGGCCCGAGCTC : 3455

  598 : ThrProValAlaIleGlnSerGlyLysLeuLeuAlaGlnArgLeuPheGlyAlaSerLeuGl :  618
        |||||||||||||||:!!:!!|||  !! !||||||!:!||||||||||||!.!!.!  !||
        ThrProValAlaIleGluAlaGlyLeuArgLeuAlaArgArgLeuPheGlyGlyLysThrGl
 3454 : ACGCCCGTCGCCATCGAGGCGGGCCTGCGCCTCGCGCGGCGCCTCTTCGGCGGCAAGACCGA : 3392

  619 : uLysCysAspTyrIleAsnValProThrThrValPheThrProLeuGluTyrGlyCysCysG :  639
        |      ||||||     !||| !!||||||:!!|||||||||||||||||||||     !|
        uProMetAspTyrGluCysValAlaThrThrIlePheThrProLeuGluTyrGlyThrIleG
 3391 : GCCCATGGACTACGAGTGCGTCGCGACGACGATCTTCACGCCGCTCGAGTACGGCACGATCG : 3329

  640 : lyLeuSerGluGluLysAlaIleGluValTyrLysLysGluAsnLeuGluIleTyrHisThr :  659
        |||||||||||!!: ! |||!  !    !  !   :!!   |||:!!|||  !|||  !!:!
        lyLeuSerGluAspAspAlaLysAlaGlnLeuGlyGluCysAsnValGluSerTyrIleSer
 3328 : GGCTGAGCGAGGACGACGCCAAGGCCCAGCTCGGCGAGTGCAACGTCGAGTCCTACATCAGC : 3269

  660 : LeuPheTrpProLeuGluTrpThrValAla<-><-><->GlyArgGluAsnAsnThrCysTy :  677
          !|||  !|||||||||!::.!!:!!::!         .!!..!.....!:!!  !|||!:
        GluPheAlaProLeuGluTyrAlaLeuSerGluThrArgSerGluArgGlyAspGlyCysPh
 3268 : GAGTTCGCGCCCCTCGAGTACGCCCTCAGCGAGACGCGCAGCGAGCGCGGCGACGGCTGCTT : 3206

  678 : rAlaLysIleIleCysAsnLysPheAspHisAspArgValIleGlyPheHisIleLeuGlyP :  698
        !||||||:!!:!!  !:!!|||   ..!   ! !!:!|||:!!|||||||||  !|||||||
        eAlaLysLeuValValAspLys---SerThrGlyLysValValGlyPheHisTyrLeuGlyP
 3205 : CGCCAAGCTCGTCGTCGACAAG---AGCACGGGCAAGGTCGTCGGCTTCCACTACCTCGGCC : 3146

  699 : roAsnAlaGlyGluValThrGlnGlyPheAlaAlaAlaMetLysCysGlyLeuThrLysGln :  718
        ||||||||||||||:!!||||||||||||:!!  !||||||:::   |||  !||| !    
        roAsnAlaGlyGluIleThrGlnGlyPheSerIleAlaMetArgLysGlyAlaThrTyrAla
 3145 : CCAACGCCGGCGAGATCACCCAGGGCTTCTCCATCGCCATGCGCAAGGGCGCGACCTACGCC : 3086

  719 : LeuLeuAspAspThrIleGlyIleHisProThrCysGlyGluValPheThrThrLeuGluIl :  739
          !!!!  !..!|||:!!|||||||||||||||  !!.!|||! !||||||:!!:!!   :!
        AspPheIleSerThrValGlyIleHisProThrValAlaGluGluPheThrSerMetThrVa
 3085 : GACTTCATCTCCACCGTCGGCATCCACCCGACGGTCGCCGAGGAGTTCACGTCCATGACCGT : 3023

  740 : eThrLysSerSerGlyLeuAspIleThrGlnLysGlyCysUnkGly :  754
        :|||||||||||||||  !..!  !.!!:!!   ||||||   |||
        lThrLysSerSerGlyGluSerAlaAlaLysGlyGlyCys***Gly
 3022 : GACCAAGTCGAGCGGCGAGTCCGCAGCCAAGGGCGGCTGCTGAGGC : 2976

vulgar: SPP00000036_1.0 538 754 . scaffold_11:subseq(783554,7436) 3638 2975 - 432 M 22 66 G 0 9 M 109 327 G 0 9 M 15 45 G 1 0 M 69 207
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	gene	2976	3638	432	-	.	gene_id 2 ; sequence SPP00000036_1.0 ; gene_orientation .
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	2976	3638	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	2976	3638	.	-	.	insertions 18 ; deletions 1
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	similarity	2976	3638	432	-	.	alignment_id 2 ; Query SPP00000036_1.0 ; Align 3639 539 66 ; Align 3564 561 327 ; Align 3228 670 45 ; Align 3183 686 207
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000034_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Homo sapiens # Complete
        Target: scaffold_11:subseq(783554,7436) [revcomp]
         Model: protein2genome
     Raw score: 692
   Query range: 9 -> 258
  Target range: 4439 -> 3692

   10 : SerTyrAspTyrAspLeuIleIleIleGlyGlyGlySerGlyGlyLeuAlaAlaAlaLysGl :   30
        ...:::|||||||||::::::::::::||||||||||||||||||||||||..!:!!|||||
        GlyPheAspTyrAspValValValValGlyGlyGlySerGlyGlyLeuAlaCysSerLysGl
 4439 : ggcttcgactacgacgtcgtcgtcgtcggcggcggctccggcggcCTCGCCTGCTCCAAGGA : 4379

   31 : uAlaAlaGlnTyrGlyLysLysValMetValLeuAspPheValThrProThrProLeuGlyT :   51
        |..!|||:!!  !|||   ||||||   |||||||||||||||! !|||:!!|||  !|||:
        uCysAlaLysLeuGlyAlaLysValAlaValLeuAspPheValLysProSerProAlaGlyS
 4378 : GTGCGCGAAGCTCGGCGCCAAGGTCGCCGTGCTCGACTTCGTGAAGCCGTCGCCGGCGGGGT : 4316

   52 : hrArgTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHis :   71
        !!! !|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        erThrTrpGlyLeuGlyGlyThrCysValAsnValGlyCysIleProLysLysLeuMetHis
 4315 : CGACGTGGGGCCTCGGCGGCACGTGCGTCAACGTCGGCTGCATCCCGAAGAAGCTCATGCAC : 4256

   72 : GlnAlaAlaLeuLeuGlyGlnAlaLeuGln<->AspSerArgAsnTyrGlyTrpLysValGl :   91
          !|||:!!:!!:!!|||:!!.!!|||:!!   |||:!!  !  !!:!|||||||||! !! 
        ThrAlaSerIleIleGlyGluThrLeuLysAspAspAlaAlaAlaPheGlyTrpLysAspAl
 4255 : ACGGCGTCCATCATCGGCGAGACGCTCAAGGACGACGCCGCCGCCTTCGGGTGGAAGGACGC : 4193

   92 : uGluThrValLysHisAspTrpAspArgMetIleGluAlaValGlnAsnHisIleGlySerL :  112
         !  .!!! !  !|||||||||!!:  !|||!  ..!.!!||||||:!!||||||  !||||
        aAlaAlaGlyAlaHisAspTrpGluSerMetLysSerThrValGlnAspHisIleLysSerL
 4192 : CGCCGCGGGCGCGCACGACTGGGAGTCGATGAAGTCGACGGTGCAGGACCACATCAAGTCGC : 4130

  113 : euAsnTrpGlyTyrArgValAlaLeuArgGluLysLysValValTyrGluAsnAlaTyrGly :  132
        |||||!::  !|||||||||||||||||||||  !   :!!..!|||  !|||  !  !|||
        euAsnPheLysTyrArgValAlaLeuArgGluAlaGlyIleThrTyrLeuAsnArgLeuGly
 4129 : TCAACTTCAAGTACCGCGTCGCGCTCCGCGAGGCGGGCATCACCTACCTGAACCGCCTCGGC : 4070

  133 : GlnPheIleGlyProHisArgIleLysAlaThrAsnAsnLysGlyLysGluLysIleTyrSe :  153
        :!!|||   ! !  !:!!! !|||...  !|||:!!!!.||||||!!.:!!! !  !  !!!
        GluPheGluAspLysAsnThrIleSerLeuThrAspLysLysGlyAsnLysThrSerValTh
 4069 : GAGTTCGAGGACAAGAACACCATCTCCCTCACGGACAAGAAGGGCAACAAGACGTCCGTCAC : 4007

  154 : rAlaGluArgPheLeuIleAlaThrGlyGluArgProArgTyrLeuGlyIleProGlyAspL :  174
        !|||! !||||||:!!:!!|||..!|||!  ||||||!.! ! ||||||  !||||||! ! 
        rAlaAlaArgPheIleValAlaValGlyGlyArgProAsnLysLeuGlyCysProGlyGly-
 4006 : GGCCGCGCGGTTCATCGTCGCCGTCGGCGGCCGCCCGAACAAGCTCGGCTGCCCCGGCGGC- : 3944

  175 : ysGluTyrCysIleSerSerAspAspLeuPheSerLeuProTyrCysProGlyLysThrLeu :  194
          |||:!!..!|||..!|||||||||||||||||||||||| ! ...||||||:::..!|||
        --GluHisAlaIleAspSerAspAspLeuPheSerLeuProLysAlaProGlyArgValLeu
 3943 : --GAGCACGCCATCGACAGCGACGACCTGTTCTCCCTGCCCAAGGCGCCGGGCCGCGTGCTC : 3887

  195 : ValValGlyAlaSerTyrValAlaLeuGluCysAlaGlyPheLeuAlaGlyIleGlyLeuAs :  215
          !||||||!.!.!!|||:!!||||||||||||!.!||||||  !||||||!!:|||! !  
        CysValGlyGlyGlyTyrIleAlaLeuGluCysGlyGlyPheThrAlaGlyMetGlyTyrPr
 3886 : TGCGTCGGCGGCGGCTACATCGCGCTCGAGTGCGGCGGCTTCACGGCCGGCATGGGCTACCC : 3824

  216 : pValThrValMetValArgSerIleLeuLeuArgGlyPheAspGlnAspMetAlaAsnLysI :  236
         ..!|||  !|||||||||||||||||||||||||||||||||!::!!:   !.!..!||||
        oThrThrCysMetValArgSerIleLeuLeuArgGlyPheAspArgGluCysValGlyLysI
 3823 : GACGACGTGCATGGTCCGGTCCATCCTCCTCCGCGGCTTCGACCGCGAGTGCGTCGGCAAGA : 3761

  237 : leGlyGluHisMetGluGluHisGlyIleLysPheIleArgGlnPheValProIleLysVal :  256
        ||! !!  |||!!::!!.!.||||||:!!:!!.!!     !    !!..!|||   |||:!!
        leGluAlaHisIleLysHisHisGlyValGlnLeuGlnValGlyValThrProAlaLysIle
 3760 : TCGAGGCCCACATCAAGCACCACGGCGTCCAGCTCCAGGTCGGCGTCACGCCCGCGAAGATC : 3701

  257 : GluGln :  258
        |||:!!
        GluLys
 3700 : GAGAAG : 3693

vulgar: SPP00000034_1.0 9 258 . scaffold_11:subseq(783554,7436) 4439 3692 - 692 M 72 216 G 0 3 M 92 276 G 1 0 M 84 252
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	gene	3693	4439	692	-	.	gene_id 1 ; sequence SPP00000034_1.0 ; gene_orientation .
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	3693	4439	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	3693	4439	.	-	.	insertions 3 ; deletions 1
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	similarity	3693	4439	692	-	.	alignment_id 1 ; Query SPP00000034_1.0 ; Align 4440 10 216 ; Align 4221 82 276 ; Align 3945 175 252
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000034_1.0 # Protein # Thioredoxin reductase 1 (TR1) # Homo sapiens # Complete
        Target: scaffold_11:subseq(783554,7436) [revcomp]
         Model: protein2genome
     Raw score: 487
   Query range: 282 -> 499
  Target range: 3641 -> 2975

  283 : GluTyrAsnThrValMetLeuAlaIleGlyArgAspAlaCysThrArgLysIleGlyLeuGl :  303
        ||||||:!!||||||:!::!!|||!  |||||| !!|||  !|||  !   :!!|||:!!!!
        GluTyrAspThrValLeuValAlaThrGlyArgTyrAlaAspThrAlaAlaLeuGlyIleAs
 3641 : GAGTACGACACGGTGCTCGTCGCGACGGGCCGCTACGCGGACACGGCGGCCCTCGGCATCGA : 3581

  304 : uThrVal<-><-><->GlyValLysIleAsnGluLysThrGlyLysIleProValThrAspG :  321
        :!.!|||         ..!!.!!!.:!:|||! !||||||  !|||:!!  !  !..!||||
        pAsnValProGlyAlaSerAlaAsnValAsnAlaLysThrLysLysLeuGluCysValAspG
 3580 : CAACGTGCCCGGCGCGTCGGCGAACGTGAACGCGAAGACGAAGAAGCTCGAGTGCGTCGACG : 3518

  322 : luGluGlnThrAsnValProTyrIleTyrAlaIleGlyAspIleLeuGluAspLysValGlu :  341
        ||:!!! ! !!..!!.!|||:!!:!!|||||||||||||||:!!:!!|||! !::!  !|||
        luGlnLeuProGlyAlaProHisValTyrAlaIleGlyAspValValGluGlyArgProGlu
 3517 : AGCAGCTGCCCGGCGCGCCGCACGTCTACGCGATCGGCGACGTCGTCGAGGGCCGGCCCGAG : 3458

  342 : LeuThrProValAlaIleGlnAlaGlyArgLeuLeuAlaGlnArgLeuTyrAlaGlySerTh :  362
        ||||||||||||||||||:!!||||||! !! !||||||!:!||||||!:!!.!|||!.!||
        LeuThrProValAlaIleGluAlaGlyLeuArgLeuAlaArgArgLeuPheGlyGlyLysTh
 3457 : CTCACGCCCGTCGCCATCGAGGCGGGCCTGCGCCTCGCGCGGCGCCTCTTCGGCGGCAAGAC : 3395

  363 : rValLysCysAspTyrGluAsnValProThrThrValPheThrProLeuGluTyrGlyAlaC :  383
        |! !      |||||||||  !||| !!||||||:!!|||||||||||||||||||||.!! 
        rGluProMetAspTyrGluCysValAlaThrThrIlePheThrProLeuGluTyrGlyThrI
 3394 : CGAGCCCATGGACTACGAGTGCGTCGCGACGACGATCTTCACGCCGCTCGAGTACGGCACGA : 3332

  384 : ysGlyLeuSerGluGluLysAlaValGluLysPheGlyGluGluAsnIleGluValTyrHis :  403
         !||||||||||||!!: ! |||  !!  :!!.!!||||||   |||:!!|||  !|||  !
        leGlyLeuSerGluAspAspAlaLysAlaGlnLeuGlyGluCysAsnValGluSerTyrIle
 3331 : TCGGGCTGAGCGAGGACGACGCCAAGGCCCAGCTCGGCGAGTGCAACGTCGAGTCCTACATC : 3272

  404 : SerTyrPheTrpProLeuGluTrpThrIlePro<-><-><->SerArgAspAsnAsnLysCy :  421
        ||| ! |||  !|||||||||!::.!!:!!  !         |||..!  !..!:!!   ||
        SerGluPheAlaProLeuGluTyrAlaLeuSerGluThrArgSerGluArgGlyAspGlyCy
 3271 : AGCGAGTTCGCGCCCCTCGAGTACGCCCTCAGCGAGACGCGCAGCGAGCGCGGCGACGGCTG : 3209

  422 : sTyrAlaLysIleIleCysAsnThrLysAspAsnGluArgValValGlyPheHisValLeuG :  442
        |!:!||||||:!!:!!  !:!!   |||..!!..!  !:!|||||||||||||||  !||||
        sPheAlaLysLeuValValAsp---LysSerThrGlyLysValValGlyPheHisTyrLeuG
 3208 : CTTCGCCAAGCTCGTCGTCGAC---AAGAGCACGGGCAAGGTCGTCGGCTTCCACTACCTCG : 3149

  443 : lyProAsnAlaGlyGluValThrGlnGlyPheAlaAlaAlaLeuLysCysGlyLeuThrLys :  462
        |||||||||||||||||:!!||||||||||||:!!  !|||:!!:::   |||  !||| ! 
        lyProAsnAlaGlyGluIleThrGlnGlyPheSerIleAlaMetArgLysGlyAlaThrTyr
 3148 : GCCCCAACGCCGGCGAGATCACCCAGGGCTTCTCCATCGCCATGCGCAAGGGCGCGACCTAC : 3089

  463 : LysGlnLeuAspSerThrIleGlyIleHisProValCysAlaGluValPheThrThrLeuSe :  483
           .!.!!!  !||||||:!!||||||||||||..!  !||||||! !||||||:!!:!!!!
        AlaAspPheIleSerThrValGlyIleHisProThrValAlaGluGluPheThrSerMetTh
 3088 : GCCGACTTCATCTCCACCGTCGGCATCCACCCGACGGTCGCCGAGGAGTTCACGTCCATGAC : 3026

  484 : rValThrLysArgSerGlyAlaSerIleLeuGlnAlaGlyCysUnkGly :  499
        !|||||||||  !||||||! !|||  !  !:!!!.!||||||   |||
        rValThrLysSerSerGlyGluSerAlaAlaLysGlyGlyCys***Gly
 3025 : CGTGACCAAGTCGAGCGGCGAGTCCGCAGCCAAGGGCGGCTGCTGAGGC : 2976

vulgar: SPP00000034_1.0 282 499 . scaffold_11:subseq(783554,7436) 3641 2975 - 487 M 23 69 G 0 9 M 109 327 G 0 9 M 14 42 G 1 0 M 70 210
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-02-27
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	gene	2976	3641	487	-	.	gene_id 2 ; sequence SPP00000034_1.0 ; gene_orientation .
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	cds	2976	3641	.	-	.	
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	exon	2976	3641	.	-	.	insertions 18 ; deletions 1
scaffold_11:subseq(783554,7436)	exonerate:protein2genome	similarity	2976	3641	487	-	.	alignment_id 2 ; Query SPP00000034_1.0 ; Align 3642 283 69 ; Align 3564 306 327 ; Align 3228 415 42 ; Align 3186 430 210
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
