Command line: [exonerate -m p2g --showtargetgff -q ./sps.fa -t Sps_scaffold6_seqDNA.fa]
Hostname: [localhost]

C4 Alignment:
------------
         Query: SPP00000108_1.0 # Protein # Selenophosphate synthetase 2 (SPS2) # Mus musculus # Complete
        Target: scaffold_6:subseq(1815585,6626) [revcomp]
         Model: protein2genome
     Raw score: 133
   Query range: 127 -> 259
  Target range: 3626 -> 3233

  128 : ProLeuArgHisGlyGlyLeuSerLeuValGlnThrThrAspPhePheTyrProLeuValGl :  148
        |||  !!:! !!  ! !!  !..!:!!|||!!.|||..!|||||||||    !!!!!|||..
        ProGluLysAspGlnArgThrGlnValValHisThrValAspPhePheArgSerPheValSe
 3626 : CCCGAGAAGGACCAGCGGACCCAGGTCGTCCATACCGTCGACTTCTTCCGGTCGTTCGTGTC : 3566

  149 : uAspProTyrMetMetGlyArgIleAlaCysAlaAsnValLeuSerAspLeuTyrAlaMetG :  169
        !|||||||||:!:.!.|||!:!||||||...  !:!!!.!|||||||||! ! !!|||||||
        rAspProTyrValPheGlyGlnIleAlaAlaAsnHisAlaLeuSerAspCysAspAlaMetG
 3565 : GGACCCCTACGTCTTTGGGCAGATCGCCGCGAACCACGCGCTCTCGGACTGCGACGCCATGG : 3503

  170 : lyIleThrGluCysAspAsnMetLeuMetLeuLeuSerValSerGlnSerMetSerGluLys :  189
        ||     !   ...   :::  !|||  !|||:!!  !||| !! ! .!!  !!:!..!   
        lyAlaLeuProAla---SerAlaLeuAlaLeuValValValProTyrGlySerAsnArgCys
 3502 : GCGCGCTGCCCGCG---TCGGCGCTGGCGCTCGTCGTCGTGCCCTACGGGTCGAACCGGTGC : 3446

  190 : GluArgGluLysValThrProLeuMetIleLysGlyPheArgAspAlaAlaGluGluGlyGl :  210
        !  ..!!!:! !:!!  !! !||||||   ...|||   |||! !|||  !!!:!  !.!||
        ValGluAspThrLeuPheGlnLeuMet---SerGlyAlaArgValAlaLeuAspAlaAlaGl
 3445 : GTCGAGGACACGCTCTTCCAGCTCATG---TCCGGCGCGCGCGTCGCGCTGGACGCCGCGGG : 3386

  211 : yThrAlaValThrGlyGlyGlnThrValValAsnProTrpIleIleIleGly<->GlyValA :  230
        |  !.!!:!!..!||||||!!.|||  !! !..! !!  !:!!   :!:|||   !.!||| 
        yCysThrLeuValGlyGlyHisThrCysGluGlyAlaGluLeuGlyLeuGlyPheAlaValA
 3385 : CTGCACTTTGGTCGGCGGCCACACGTGCGAGGGCGCGGAGCTCGGGCTGGGCTTCGCCGTCA : 3323

  231 : laThrValValCysGlnGlnAsnGluPheIleMetProAspSerAlaValValGlyAspVal :  250
         !  !|||  !  !         !  |||:!:     !!!:.!!  !|||!.!||||||!.!
        snGlyValProAspGlyGlyAlaAlaPheLeuSerLysGluGlyMetValAlaGlyAspAla
 3322 : ACGGCGTGCCGGACGGCGGCGCGGCCTTCCTGTCCAAGGAGGGCATGGTCGCGGGCGACGCG : 3263

  251 : LeuValLeuThrLysProLeuGlyThr :  259
        |||:!!|||||||||||||||||||||
        LeuIleLeuThrLysProLeuGlyThr
 3262 : CTGATCCTCACGAAGCCGCTCGGCACG : 3234

vulgar: SPP00000108_1.0 127 259 . scaffold_6:subseq(1815585,6626) 3626 3233 - 133 M 46 138 G 1 0 M 24 72 G 1 0 M 28 84 G 0 3 M 32 96
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-03-05
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	gene	3234	3626	133	-	.	gene_id 1 ; sequence SPP00000108_1.0 ; gene_orientation .
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	cds	3234	3626	.	-	.	
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	exon	3234	3626	.	-	.	insertions 3 ; deletions 2
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	similarity	3234	3626	133	-	.	alignment_id 1 ; Query SPP00000108_1.0 ; Align 3627 128 138 ; Align 3489 175 72 ; Align 3417 200 84 ; Align 3330 228 96
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000056_1.0 # Protein # Selenophosphate synthetase 2 (SPS2) # Anopheles gambiae # Complete
        Target: scaffold_6:subseq(1815585,6626) [revcomp]
         Model: protein2genome
     Raw score: 100
   Query range: 233 -> 299
  Target range: 3182 -> 2981

  234 : ArgIleAlaLeuGluSerMetSerArgLeuAsnLysThrGlyAlaGluLeuMetLysLysTy :  254
        |||   ..!|||! !||||||!!!!:!  !|||:::.!!!.!|||  !  !:!:|||:!!:!
        ArgGluCysLeuAlaSerMetThrGlnSerAsnArgAlaAlaAlaThrGluLeuLysGluHi
 3182 : CGCGAGTGCCTCGCGTCCATGACCCAGAGCAACCGCGCGGCGGCGACGGAGCTCAAGGAGCA : 3122

  255 : rGlyAlaHisAlaAlaThrAspValThrGlyPheGlyLeuTyrGlyHis<->AlaGluAsnL :  274
        !|||..!   :!!..!||||||||||||||||||||||||  !||||||   ||||||!  !
        sGlyCysThrSerCysThrAspValThrGlyPheGlyLeuLeuGlyHisLeuAlaGluMetC
 3121 : CGGCTGCACGTCCTGCACGGACGTCACGGGCTTCGGGCTCCTCGGGCATCTGGCGGAGATGT : 3059

  275 : euAlaSerHisGlnThrAlaAspValAspPheHisLeuAspThrLeuProIleIleLysAsn :  294
         !  !:!!        !|||  !|||!!:.!!   |||!  .!!  !|||:!!.!!   ..!
        ysArgAlaSerGlyGlyAlaArgValGluLeuSerLeuAlaAlaThrProValPheAlaGly
 3058 : GCCGCGCGTCGGGCGGCGCGCGCGTGGAGCTCTCGCTGGCGGCGACGCCCGTCTTCGCCGGC : 2999

  295 : ValArgGluIleAla :  299
        !.!!:!...:!:|||
        AlaLysArgLeuAla
 2998 : GCGAAGCGCCTGGCG : 2982

vulgar: SPP00000056_1.0 233 299 . scaffold_6:subseq(1815585,6626) 3182 2981 - 100 M 37 111 G 0 3 M 29 87
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-03-05
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	gene	2982	3182	100	-	.	gene_id 1 ; sequence SPP00000056_1.0 ; gene_orientation .
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	cds	2982	3182	.	-	.	
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	exon	2982	3182	.	-	.	insertions 3 ; deletions 0
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	similarity	2982	3182	100	-	.	alignment_id 1 ; Query SPP00000056_1.0 ; Align 3183 234 111 ; Align 3069 271 87
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000047_1.0 # Protein # Selenophosphate synthetase 1 (SPS1) # Drosophila melanogaster # Complete
        Target: scaffold_6:subseq(1815585,6626) [revcomp]
         Model: protein2genome
     Raw score: 127
   Query range: 103 -> 227
  Target range: 3602 -> 3233

  104 : LeuValGlnThrThrAspPhePheTyrProIleValAspAspProTyrMetMetGlyLysIl :  124
        :!!|||!!.|||..!|||||||||    !!.!!|||...|||||||||:!:.!.|||:!!||
        ValValHisThrValAspPhePheArgSerPheValSerAspProTyrValPheGlyGlnIl
 3602 : GTCGTCCATACCGTCGACTTCTTCCGGTCGTTCGTGTCGGACCCCTACGTCTTTGGGCAGAT : 3542

  125 : eAlaCysAlaAsnValLeuSerAspLeuTyrAlaMetGlyValThrAspCysAspAsnMetL :  145
        ||||...  !:!!!.!|||||||||! ! !!|||||||||!.!  !  !...   :::  !|
        eAlaAlaAsnHisAlaLeuSerAspCysAspAlaMetGlyAlaLeuProAla---SerAlaL
 3541 : CGCCGCGAACCACGCGCTCTCGGACTGCGACGCCATGGGCGCGCTGCCCGCG---TCGGCGC : 3482

  146 : euMetLeuLeuAlaValSerThrLysMetThrGluLysGluArgAspValValIleProLeu :  165
        ||  !|||:!!!.!||| !!  !  !  !!.!..!   !  ..!|||..!:!!.!!! !|||
        euAlaLeuValValValProTyrGlySerAsnArgCysValGluAspThrLeuPheGlnLeu
 3481 : TGGCGCTCGTCGTCGTGCCCTACGGGTCGAACCGGTGCGTCGAGGACACGCTCTTCCAGCTC : 3422

  166 : IleMetArgGlyPheLysAspSerAlaLeuGluAlaGlyThrThrValThrGlyGlyGlnSe :  186
           |||  !|||   :::! !:!!  !  !!  ||||||  !|||:!!..!||||||!!.!!
        ---MetSerGlyAlaArgValAlaLeuAspAlaAlaGlyCysThrLeuValGlyGlyHisTh
 3421 : ---ATGTCCGGCGCGCGCGTCGCGCTGGACGCCGCGGGCTGCACTTTGGTCGGCGGCCACAC : 3362

  187 : rValValAsnProTrpCysThrIleGlyGlyValAlaSerThrIleCysGlnProAsn<->G :  206
        !  !! !..! !!  !  !  !:!:|||  !!.!!.!!:!  !:!:   .!.  !..!   !
        rCysGluGlyAlaGluLeuGlyLeuGlyPheAlaValAsnGlyValProAspGlyGlyAlaA
 3361 : GTGCGAGGGCGCGGAGCTCGGGCTGGGCTTCGCCGTCAACGGCGTGCCGGACGGCGGCGCGG : 3299

  207 : luTyrIleValProAspAsnAlaValValGlyAspValLeuValLeuThrLysProLeuGly :  226
          !:!:!:  !  !!!:..!  !|||!.!||||||!.!|||:!!||||||||||||||||||
        laPheLeuSerLysGluGlyMetValAlaGlyAspAlaLeuIleLeuThrLysProLeuGly
 3298 : CCTTCCTGTCCAAGGAGGGCATGGTCGCGGGCGACGCGCTGATCCTCACGAAGCCGCTCGGC : 3239

  227 : Thr :  227
        |||
        Thr
 3238 : ACG : 3234

vulgar: SPP00000047_1.0 103 227 . scaffold_6:subseq(1815585,6626) 3602 3233 - 127 M 38 114 G 1 0 M 23 69 G 1 0 M 39 117 G 0 3 M 22 66
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-03-05
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	gene	3234	3602	127	-	.	gene_id 1 ; sequence SPP00000047_1.0 ; gene_orientation .
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	cds	3234	3602	.	-	.	
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	exon	3234	3602	.	-	.	insertions 3 ; deletions 2
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	similarity	3234	3602	127	-	.	alignment_id 1 ; Query SPP00000047_1.0 ; Align 3603 104 114 ; Align 3489 143 69 ; Align 3420 167 117 ; Align 3300 206 66
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000107_1.0 # Protein # Selenophosphate synthetase 1 (SPS1) # Mus musculus # Complete
        Target: scaffold_6:subseq(1815585,6626) [revcomp]
         Model: protein2genome
     Raw score: 126
   Query range: 73 -> 210
  Target range: 3626 -> 3218

   74 : ProLeuArgHisGlyGlyLeuSerLeuValGlnThrThrAspTyrIleTyrProIleValAs :   94
        |||  !!:! !!  ! !!  !..!:!!|||!!.|||..!|||!:!.!!    !!.!!|||..
        ProGluLysAspGlnArgThrGlnValValHisThrValAspPhePheArgSerPheValSe
 3626 : CCCGAGAAGGACCAGCGGACCCAGGTCGTCCATACCGTCGACTTCTTCCGGTCGTTCGTGTC : 3566

   95 : pAspProTyrMetMetGlyArgIleAlaCysAlaAsnValLeuSerAspLeuTyrAlaMetG :  115
        .|||||||||:!:.!.|||!:!||||||...  !:!!!.!|||||||||! ! !!|||||||
        rAspProTyrValPheGlyGlnIleAlaAlaAsnHisAlaLeuSerAspCysAspAlaMetG
 3565 : GGACCCCTACGTCTTTGGGCAGATCGCCGCGAACCACGCGCTCTCGGACTGCGACGCCATGG : 3503

  116 : lyValThrGluCysAspAsnMetLeuMetLeuLeuGlyValSerAsnLysMetThrAspArg :  135
        ||!.!  !   ......   :!!  !:!::!!      |||  !  ! !   !:!!:!!|||
        lyAlaLeuProAlaSerAlaLeuAlaLeuVal------ValValProTyrGlySerAsnArg
 3502 : GCGCGCTGCCCGCGTCGGCGCTGGCGCTCGTC------GTCGTGCCCTACGGGTCGAACCGG : 3449

  136 : GluArgAspLysValIleProLeuIleIleGlnGlyPheLysAspAlaAlaGluGluAlaGl :  156
             !!!: ! ..!:!!  !! !:!!!!:...|||   :::! !|||  !!!:!  |||||
        CysValGluAspThrLeuPheGlnLeuMetSerGlyAlaArgValAlaLeuAspAlaAlaGl
 3448 : TGCGTCGAGGACACGCTCTTCCAGCTCATGTCCGGCGCGCGCGTCGCGCTGGACGCCGCGGG : 3386

  157 : yThrSerValThrGlyGlyGlnThrValLeuAsnProTrpIleValLeuGlyGlyValAlaT :  177
        |  !!!!:!!..!||||||!!.|||  !  !..! !!  !:!!! !||||||  !!.!!.!!
        yCysThrLeuValGlyGlyHisThrCysGluGlyAlaGluLeuGlyLeuGlyPheAlaValA
 3385 : CTGCACTTTGGTCGGCGGCCACACGTGCGAGGGCGCGGAGCTCGGGCTGGGCTTCGCCGTCA : 3323

  178 : hrThrValCysGlnProAsn<->GluPheIleMetProAspAsnAlaValProGlyAspVal :  196
        .!  !|||   .!.  !..!   !  |||:!:     !!!:..!  !||| !!||||||!.!
        snGlyValProAspGlyGlyAlaAlaPheLeuSerLysGluGlyMetValAlaGlyAspAla
 3322 : ACGGCGTGCCGGACGGCGGCGCGGCCTTCCTGTCCAAGGAGGGCATGGTCGCGGGCGACGCG : 3263

  197 : LeuValLeuThrLysProLeuGlyThrGlnValAlaValAla :  210
        |||:!!|||||||||||||||||||||   !.!!.! !!|||
        LeuIleLeuThrLysProLeuGlyThrGlyAlaValPheAla
 3262 : CTGATCCTCACGAAGCCGCTCGGCACGGGCGCGGTCTTCGCG : 3219

vulgar: SPP00000107_1.0 73 210 . scaffold_6:subseq(1815585,6626) 3626 3218 - 126 M 52 156 G 2 0 M 56 168 G 0 3 M 27 81
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-03-05
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	gene	3219	3626	126	-	.	gene_id 1 ; sequence SPP00000107_1.0 ; gene_orientation .
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	cds	3219	3626	.	-	.	
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	exon	3219	3626	.	-	.	insertions 3 ; deletions 2
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	similarity	3219	3626	126	-	.	alignment_id 1 ; Query SPP00000107_1.0 ; Align 3627 74 156 ; Align 3471 128 168 ; Align 3300 184 81
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000073_1.0 # Protein # Selenophosphate synthetase 2 (SPS2) # Pan troglodytes # Complete
        Target: scaffold_6:subseq(1815585,6626) [revcomp]
         Model: protein2genome
     Raw score: 133
   Query range: 84 -> 256
  Target range: 3746 -> 3233

   85 : LeuGlyArgGlyLeuValGlyGlyGlnGluGluAlaSerGlnGluAlaGlyLeuProAlaGl :  105
        |||  !|||!.!|||!.!..!  !! !:!!..!  !!!!   !!:  !|||  !||| !!  
        LeuThrArgAlaLeuAlaAsnLeuProLysSerLeuThrPheAspAsnGlyThrProProPr
 3746 : CTCACGCGCGCGCTGGCGAACCTGCCGAAGTCGCTGACCTTCGACAACGGCACGCCGCCGCC : 3686

  106 : yAlaAspProSerProThrPheProAlaLeuGlyIleGlyMetAspSerCysValIleProL :  126
        !..!|||  !  !  !  ! !!  !|||! !! !  !|||   ! !  !..!  !  !||| 
        oCysAspValValValGlyValAspAlaProAspAspGlyAlaValValAlaTyrGlyProG
 3685 : CTGCGACGTCGTCGTCGGCGTCGACGCGCCCGACGACGGCGCCGTCGTCGCCTACGGCCCCG : 3623

  127 : euArgHisGlyGlyLeuSerLeuValGlnThrThrAspPhePheTyrProLeuValGluAsp :  146
         !!:! !!  ! !!  !..!:!!|||!!.|||..!|||||||||    !!!!!|||..!|||
        luLysAspGlnArgThrGlnValValHisThrValAspPhePheArgSerPheValSerAsp
 3622 : AGAAGGACCAGCGGACCCAGGTCGTCCATACCGTCGACTTCTTCCGGTCGTTCGTGTCGGAC : 3563

  147 : ProTyrMetMetGlyArgIleAlaCysAlaAsnValLeuSerAspLeuTyrAlaMetGlyIl :  167
        ||||||:!:.!.|||!:!||||||...  !:!!!.!|||||||||! ! !!|||||||||  
        ProTyrValPheGlyGlnIleAlaAlaAsnHisAlaLeuSerAspCysAspAlaMetGlyAl
 3562 : CCCTACGTCTTTGGGCAGATCGCCGCGAACCACGCGCTCTCGGACTGCGACGCCATGGGCGC : 3500

  168 : eThrGluCysAspAsnMetLeuMetLeuLeuSerValSerGlnSerMetSerGluGluGluA :  188
           !   ...   :::  !|||  !|||:!!  !||| !! ! .!!  !!:!..!   !  .
        aLeuProAla---SerAlaLeuAlaLeuValValValProTyrGlySerAsnArgCysValG
 3499 : GCTGCCCGCG---TCGGCGCTGGCGCTCGTCGTCGTGCCCTACGGGTCGAACCGGTGCGTCG : 3440

  189 : rgGluLysValThrProLeuMetValLysGlyPheArgAspAlaAlaGluGluGlyGlyThr :  208
        .!!!:! !:!!  !! !||||||   ...|||   |||! !|||  !!!:!  !.!|||  !
        luAspThrLeuPheGlnLeuMet---SerGlyAlaArgValAlaLeuAspAlaAlaGlyCys
 3439 : AGGACACGCTCTTCCAGCTCATG---TCCGGCGCGCGCGTCGCGCTGGACGCCGCGGGCTGC : 3383

  209 : AlaValThrGlyGlyGlnThrValValAsnProTrpIleIleIleGly<->GlyValAlaTh :  228
        .!!:!!..!||||||!!.|||  !! !..! !!  !:!!   :!:|||   !.!|||  !  
        ThrLeuValGlyGlyHisThrCysGluGlyAlaGluLeuGlyLeuGlyPheAlaValAsnGl
 3382 : ACTTTGGTCGGCGGCCACACGTGCGAGGGCGCGGAGCTCGGGCTGGGCTTCGCCGTCAACGG : 3320

  229 : rValValCysGlnProAsnGluPheIleMetProAspSerAlaValValGlyAspValLeuV :  249
        !|||  !  !     !   !  |||:!:     !!!:.!!  !|||!.!||||||!.!|||:
        yValProAspGlyGlyAlaAlaPheLeuSerLysGluGlyMetValAlaGlyAspAlaLeuI
 3319 : CGTGCCGGACGGCGGCGCGGCCTTCCTGTCCAAGGAGGGCATGGTCGCGGGCGACGCGCTGA : 3257

  250 : alLeuThrLysProLeuGlyThr :  256
        !!|||||||||||||||||||||
        leLeuThrLysProLeuGlyThr
 3256 : TCCTCACGAAGCCGCTCGGCACG : 3234

vulgar: SPP00000073_1.0 84 256 . scaffold_6:subseq(1815585,6626) 3746 3233 - 133 M 86 258 G 1 0 M 24 72 G 1 0 M 28 84 G 0 3 M 32 96
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-03-05
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	gene	3234	3746	133	-	.	gene_id 1 ; sequence SPP00000073_1.0 ; gene_orientation .
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	cds	3234	3746	.	-	.	
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	exon	3234	3746	.	-	.	insertions 3 ; deletions 2
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	similarity	3234	3746	133	-	.	alignment_id 1 ; Query SPP00000073_1.0 ; Align 3747 85 258 ; Align 3489 172 72 ; Align 3417 197 84 ; Align 3330 225 96
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000072_1.0 # Protein # Selenophosphate synthetase 1 (SPS1) # Pan troglodytes # Complete
        Target: scaffold_6:subseq(1815585,6626) [revcomp]
         Model: protein2genome
     Raw score: 126
   Query range: 72 -> 209
  Target range: 3626 -> 3218

   73 : ProLeuArgHisGlyGlyLeuSerLeuValGlnThrThrAspTyrIleTyrProIleValAs :   93
        |||  !!:! !!  ! !!  !..!:!!|||!!.|||..!|||!:!.!!    !!.!!|||..
        ProGluLysAspGlnArgThrGlnValValHisThrValAspPhePheArgSerPheValSe
 3626 : CCCGAGAAGGACCAGCGGACCCAGGTCGTCCATACCGTCGACTTCTTCCGGTCGTTCGTGTC : 3566

   94 : pAspProTyrMetMetGlyArgIleAlaCysAlaAsnValLeuSerAspLeuTyrAlaMetG :  114
        .|||||||||:!:.!.|||!:!||||||...  !:!!!.!|||||||||! ! !!|||||||
        rAspProTyrValPheGlyGlnIleAlaAlaAsnHisAlaLeuSerAspCysAspAlaMetG
 3565 : GGACCCCTACGTCTTTGGGCAGATCGCCGCGAACCACGCGCTCTCGGACTGCGACGCCATGG : 3503

  115 : lyValThrGluCysAspAsnMetLeuMetLeuLeuGlyValSerAsnLysMetThrAspArg :  134
        ||!.!  !   ......   :!!  !:!::!!      |||  !  ! !   !:!!:!!|||
        lyAlaLeuProAlaSerAlaLeuAlaLeuVal------ValValProTyrGlySerAsnArg
 3502 : GCGCGCTGCCCGCGTCGGCGCTGGCGCTCGTC------GTCGTGCCCTACGGGTCGAACCGG : 3449

  135 : GluArgAspLysValMetProLeuIleIleGlnGlyPheLysAspAlaAlaGluGluAlaGl :  155
             !!!: ! ..!:!:  !! !:!!!!:...|||   :::! !|||  !!!:!  |||||
        CysValGluAspThrLeuPheGlnLeuMetSerGlyAlaArgValAlaLeuAspAlaAlaGl
 3448 : TGCGTCGAGGACACGCTCTTCCAGCTCATGTCCGGCGCGCGCGTCGCGCTGGACGCCGCGGG : 3386

  156 : yThrSerValThrGlyGlyGlnThrValLeuAsnProTrpIleValLeuGlyGlyValAlaT :  176
        |  !!!!:!!..!||||||!!.|||  !  !..! !!  !:!!! !||||||  !!.!!.!!
        yCysThrLeuValGlyGlyHisThrCysGluGlyAlaGluLeuGlyLeuGlyPheAlaValA
 3385 : CTGCACTTTGGTCGGCGGCCACACGTGCGAGGGCGCGGAGCTCGGGCTGGGCTTCGCCGTCA : 3323

  177 : hrThrValCysGlnProAsn<->GluPheIleMetProAspAsnAlaValProGlyAspVal :  195
        .!  !|||   .!.  !..!   !  |||:!:     !!!:..!  !||| !!||||||!.!
        snGlyValProAspGlyGlyAlaAlaPheLeuSerLysGluGlyMetValAlaGlyAspAla
 3322 : ACGGCGTGCCGGACGGCGGCGCGGCCTTCCTGTCCAAGGAGGGCATGGTCGCGGGCGACGCG : 3263

  196 : LeuValLeuThrLysProLeuGlyThrGlnValAlaValAla :  209
        |||:!!|||||||||||||||||||||   !.!!.! !!|||
        LeuIleLeuThrLysProLeuGlyThrGlyAlaValPheAla
 3262 : CTGATCCTCACGAAGCCGCTCGGCACGGGCGCGGTCTTCGCG : 3219

vulgar: SPP00000072_1.0 72 209 . scaffold_6:subseq(1815585,6626) 3626 3218 - 126 M 52 156 G 2 0 M 56 168 G 0 3 M 27 81
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-03-05
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	gene	3219	3626	126	-	.	gene_id 1 ; sequence SPP00000072_1.0 ; gene_orientation .
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	cds	3219	3626	.	-	.	
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	exon	3219	3626	.	-	.	insertions 3 ; deletions 2
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	similarity	3219	3626	126	-	.	alignment_id 1 ; Query SPP00000072_1.0 ; Align 3627 73 156 ; Align 3471 127 168 ; Align 3300 183 81
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000033_1.0 # Protein # Selenophosphate synthetase 2 (SPS2) # Homo sapiens # Complete
        Target: scaffold_6:subseq(1815585,6626) [revcomp]
         Model: protein2genome
     Raw score: 132
   Query range: 124 -> 256
  Target range: 3626 -> 3233

  125 : ProLeuArgHisGlyGlyLeuSerLeuValGlnThrThrAspPhePheTyrProLeuValGl :  145
        |||  !!:! !!  ! !!  !..!:!!|||!!.|||..!|||||||||    !!!!!|||..
        ProGluLysAspGlnArgThrGlnValValHisThrValAspPhePheArgSerPheValSe
 3626 : CCCGAGAAGGACCAGCGGACCCAGGTCGTCCATACCGTCGACTTCTTCCGGTCGTTCGTGTC : 3566

  146 : uAspProTyrMetMetGlyArgIleAlaCysAlaAsnValLeuSerAspLeuTyrAlaMetG :  166
        !|||||||||:!:.!.|||!:!||||||...  !:!!!.!|||||||||! ! !!|||||||
        rAspProTyrValPheGlyGlnIleAlaAlaAsnHisAlaLeuSerAspCysAspAlaMetG
 3565 : GGACCCCTACGTCTTTGGGCAGATCGCCGCGAACCACGCGCTCTCGGACTGCGACGCCATGG : 3503

  167 : lyIleThrGluCysAspAsnMetLeuMetLeuLeuSerValSerGlnSerMetSerGluGlu :  186
        ||     !   ...   :::  !|||  !|||:!!  !||| !! ! .!!  !!:!..!   
        lyAlaLeuProAla---SerAlaLeuAlaLeuValValValProTyrGlySerAsnArgCys
 3502 : GCGCGCTGCCCGCG---TCGGCGCTGGCGCTCGTCGTCGTGCCCTACGGGTCGAACCGGTGC : 3446

  187 : GluArgGluLysValThrProLeuMetValLysGlyPheArgAspAlaAlaGluGluGlyGl :  207
        !  ..!!!:! !:!!  !! !||||||   ...|||   |||! !|||  !!!:!  !.!||
        ValGluAspThrLeuPheGlnLeuMet---SerGlyAlaArgValAlaLeuAspAlaAlaGl
 3445 : GTCGAGGACACGCTCTTCCAGCTCATG---TCCGGCGCGCGCGTCGCGCTGGACGCCGCGGG : 3386

  208 : yThrAlaValThrGlyGlyGlnThrValValAsnProTrpIleIleIleGly<->GlyValA :  227
        |  !.!!:!!..!||||||!!.|||  !! !..! !!  !:!!   :!:|||   !.!||| 
        yCysThrLeuValGlyGlyHisThrCysGluGlyAlaGluLeuGlyLeuGlyPheAlaValA
 3385 : CTGCACTTTGGTCGGCGGCCACACGTGCGAGGGCGCGGAGCTCGGGCTGGGCTTCGCCGTCA : 3323

  228 : laThrValValCysGlnProAsnGluPheIleMetProAspSerAlaValValGlyAspVal :  247
         !  !|||  !  !     !   !  |||:!:     !!!:.!!  !|||!.!||||||!.!
        snGlyValProAspGlyGlyAlaAlaPheLeuSerLysGluGlyMetValAlaGlyAspAla
 3322 : ACGGCGTGCCGGACGGCGGCGCGGCCTTCCTGTCCAAGGAGGGCATGGTCGCGGGCGACGCG : 3263

  248 : LeuValLeuThrLysProLeuGlyThr :  256
        |||:!!|||||||||||||||||||||
        LeuIleLeuThrLysProLeuGlyThr
 3262 : CTGATCCTCACGAAGCCGCTCGGCACG : 3234

vulgar: SPP00000033_1.0 124 256 . scaffold_6:subseq(1815585,6626) 3626 3233 - 132 M 46 138 G 1 0 M 24 72 G 1 0 M 28 84 G 0 3 M 32 96
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-03-05
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	gene	3234	3626	132	-	.	gene_id 1 ; sequence SPP00000033_1.0 ; gene_orientation .
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	cds	3234	3626	.	-	.	
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	exon	3234	3626	.	-	.	insertions 3 ; deletions 2
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	similarity	3234	3626	132	-	.	alignment_id 1 ; Query SPP00000033_1.0 ; Align 3627 125 138 ; Align 3489 172 72 ; Align 3417 197 84 ; Align 3330 225 96
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00000032_1.0 # Protein # Selenophosphate synthetase 1 (SPS1) # Homo sapiens # Complete
        Target: scaffold_6:subseq(1815585,6626) [revcomp]
         Model: protein2genome
     Raw score: 126
   Query range: 73 -> 210
  Target range: 3626 -> 3218

   74 : ProLeuArgHisGlyGlyLeuSerLeuValGlnThrThrAspTyrIleTyrProIleValAs :   94
        |||  !!:! !!  ! !!  !..!:!!|||!!.|||..!|||!:!.!!    !!.!!|||..
        ProGluLysAspGlnArgThrGlnValValHisThrValAspPhePheArgSerPheValSe
 3626 : CCCGAGAAGGACCAGCGGACCCAGGTCGTCCATACCGTCGACTTCTTCCGGTCGTTCGTGTC : 3566

   95 : pAspProTyrMetMetGlyArgIleAlaCysAlaAsnValLeuSerAspLeuTyrAlaMetG :  115
        .|||||||||:!:.!.|||!:!||||||...  !:!!!.!|||||||||! ! !!|||||||
        rAspProTyrValPheGlyGlnIleAlaAlaAsnHisAlaLeuSerAspCysAspAlaMetG
 3565 : GGACCCCTACGTCTTTGGGCAGATCGCCGCGAACCACGCGCTCTCGGACTGCGACGCCATGG : 3503

  116 : lyValThrGluCysAspAsnMetLeuMetLeuLeuGlyValSerAsnLysMetThrAspArg :  135
        ||!.!  !   ......   :!!  !:!::!!      |||  !  ! !   !:!!:!!|||
        lyAlaLeuProAlaSerAlaLeuAlaLeuVal------ValValProTyrGlySerAsnArg
 3502 : GCGCGCTGCCCGCGTCGGCGCTGGCGCTCGTC------GTCGTGCCCTACGGGTCGAACCGG : 3449

  136 : GluArgAspLysValMetProLeuIleIleGlnGlyPheLysAspAlaAlaGluGluAlaGl :  156
             !!!: ! ..!:!:  !! !:!!!!:...|||   :::! !|||  !!!:!  |||||
        CysValGluAspThrLeuPheGlnLeuMetSerGlyAlaArgValAlaLeuAspAlaAlaGl
 3448 : TGCGTCGAGGACACGCTCTTCCAGCTCATGTCCGGCGCGCGCGTCGCGCTGGACGCCGCGGG : 3386

  157 : yThrSerValThrGlyGlyGlnThrValLeuAsnProTrpIleValLeuGlyGlyValAlaT :  177
        |  !!!!:!!..!||||||!!.|||  !  !..! !!  !:!!! !||||||  !!.!!.!!
        yCysThrLeuValGlyGlyHisThrCysGluGlyAlaGluLeuGlyLeuGlyPheAlaValA
 3385 : CTGCACTTTGGTCGGCGGCCACACGTGCGAGGGCGCGGAGCTCGGGCTGGGCTTCGCCGTCA : 3323

  178 : hrThrValCysGlnProAsn<->GluPheIleMetProAspAsnAlaValProGlyAspVal :  196
        .!  !|||   .!.  !..!   !  |||:!:     !!!:..!  !||| !!||||||!.!
        snGlyValProAspGlyGlyAlaAlaPheLeuSerLysGluGlyMetValAlaGlyAspAla
 3322 : ACGGCGTGCCGGACGGCGGCGCGGCCTTCCTGTCCAAGGAGGGCATGGTCGCGGGCGACGCG : 3263

  197 : LeuValLeuThrLysProLeuGlyThrGlnValAlaValAla :  210
        |||:!!|||||||||||||||||||||   !.!!.! !!|||
        LeuIleLeuThrLysProLeuGlyThrGlyAlaValPheAla
 3262 : CTGATCCTCACGAAGCCGCTCGGCACGGGCGCGGTCTTCGCG : 3219

vulgar: SPP00000032_1.0 73 210 . scaffold_6:subseq(1815585,6626) 3626 3218 - 126 M 52 156 G 2 0 M 56 168 G 0 3 M 27 81
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome 1.4.0
##date 2009-03-05
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	gene	3219	3626	126	-	.	gene_id 1 ; sequence SPP00000032_1.0 ; gene_orientation .
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	cds	3219	3626	.	-	.	
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	exon	3219	3626	.	-	.	insertions 3 ; deletions 2
scaffold_6:subseq(1815585,6626)	exonerate:protein2genome	similarity	3219	3626	126	-	.	alignment_id 1 ; Query SPP00000032_1.0 ; Align 3627 74 156 ; Align 3471 128 168 ; Align 3300 184 81
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
