C4 Alignment:
------------
         Query: SPP00000123_2.0 # Protein # Selenoprotein V (SelV) # Human (Homo sapiens)
        Target: gi|397456032|gb|JH739468.1|:subseq(30000,100000) Alligator mississippiensis unplaced genomic scaffold scaffold-13950, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 114
   Query range: 4 -> 192
  Target range: 27927 -> 80470

     5 : AlaArgThrProAlaProSerSerAlaArgThrSerThrSerValArgAlaSerThrPro :    24
         ||||||  !|||! !|||!!!|||  !|||.!!..!..!:!!|||!.!::!  !:!!|||
         AlaArgAspProGluProCysSerGlnArgAlaAspValAlaValHisSerHisSerPro
 27928 : GCCAGAGATCCAGAGCCATGCAGCCAGAGGGCAGATGTGGCAGTTCATAGTCACTCCCCT : 27985

    25 : ThrArgThrProThrProLeuArgThrPro  >>>> Target Intron 1 >>>>  T :    35
         |||  !  !|||:!!  !  !!:!:!!  !           16983 bp          .
         ThrPheGlnProSerSerSerLysSerGlu-+                         +-V
 27986 : ACCTTCCAGCCCTCTAGCAGCAAGTCTGAGct.........................aaG : 45001

    36 : hrProValArgThrArgThrProIleArgThrLeuThrProValLeuThrProSerProA :    55
         .!  !  !||||||  !|||  !:!!|||! !! !  ! !!|||  !! !! !! !||| 
         alLysProArgThrAlaThrAsnLeuArgIleProGlyThrValAlaLysHisLeuProT
 45002 : TGAAACCACGAACTGCTACAAACCTACGTATTCCTGGGACTGTTGCAAAACATTTACCAT : 45061

    56 : laGlyThrSerProLeuValLeuThrProAlaProAlaGlnIleProThr  >>>> Tar :    72
          !|||  !!!!|||  !! !:!! !!! !  !|||!.!:!!! !|||  !          
         rpGly***ThrProThrAspMetProLeuIleProGlyGluSerProGlu++        
 45062 : GGGGGTGAACTCCCACAGACATGCCCCTGATTCCTGGTGAGAGTCCTGAAgt........ : 45114

    73 : get Intron 2 >>>>  LeuValProThrProAlaLeuAlaArgIleProArgLeuVa :    85
          21063 bp          |||:!!|||!.!! ! !!  !  !|||||| !!!:!  !  
                          ++LeuLeuProAsnGlnProAsnLeuArgIleThrLysAlaPr
 45115 : .................agCTCCTGCCGAACCAGCCGAATCTCCGAATCACAAAGGCCCC : 66214

    86 : lProProProAlaProAlaTrpIleProThrProValProThrProValProValArgAs :   105
         ! !!||| !!  ! !!  !|||:!:|||  !|||!.!|||..!|||! ! !!:!!!:!||
         oAlaProAlaHisSerHisTrpLeuProLeuProAlaProValProGlySerLeuLysAs
 66215 : AGCCCCTGCCCACTCTCACTGGCTGCCCCTGCCCGCCCCAGTGCCCGGCTCTTTGAAAAA : 66274

   106 : nProThrProVal<->ProThrProAlaArgThrLeuThrProProValArgValProAl :   124
         |  !!:!|||  !   |||..!|||||| !!  !  !  !||| !!:!!! !  !! !||
         nLysSerProTyrSerProValProAlaTrpTrpGlyGlyProSerLeuLeuProArgAl
 66275 : CAAAAGCCCATACTCACCGGTTCCTGCCTGGTGGGGGGGGCCATCCCTACTGCCCCGTGC : 66334

   125 : aProAlaProAlaGlnLeuLeu  >>>> Target Intron 3 >>>>  AlaGlyIle :   134
         ||||  !|||  !|||  !|||           13593 bp          ||||||! !
         aProArgProLeuGlnGluLeu++                         ++AlaGlyThr
 66335 : CCCAAGGCCTCTGCAGGAGCTGgt.........................agGCAGGCACA : 79957

   135 : ArgAlaAlaLeuProValLeuAspSerTyrLeuAlaProAlaLeuProLeuAspPro  > :   154
           !  !  !|||! !||||||   ..!  !|||  !! !..!|||||||||  !  !   
         AlaArgArgLeuGlnValLeuProGlnLeuLeuGlnLeuCysLeuProLeuProGly-+ 
 79958 : GCCAGGCGGCTGCAGGTTCTCCCGCAGCTCCTCCAACTGTGCCTGCCTCTTCCCGGGct. : 80019

   155 : >>> Target Intron 4 >>>>  ProProGluProAlaProGluLeuProLeuLeuP :   165
                  123 bp           |||  !... !!  !|||:!!! !|||! !||||
                                 ++ProGlySerThrGlnProGlnArgProGlnLeuP
 80020 : ........................agCCTGGCAGCACTCAGCCCCAGCGGCCCCAGCTCC : 80173

   166 : roGluGluAspProGluProAlaProSerLeuLysLeu{I}  >>>> Target Intro :   178
         |||||...   ! !...|||!.!  !|||! !     !{ }            214 bp 
         roGluSerMetGlnArgProValGluSerHisCysThr{S}++                 
 80174 : CAGAGAGCATGCAGCGCCCTGTCGAGTCACACTGCACA{T}gt................. : 80215

   179 : n 5 >>>>  {le}ProSerValSerSerGluAlaGlyProAlaProGlyProLeu :   192
                   { !}||| !!!.!!!!..!||||||||| !!|||  !||| !!:!!
                 ++{er}ProProAlaTrpGluGluAlaGlyThrAlaGlyGlyAlaMet
 80216 : ........ag{CT}CCCCCTGCCTGGGAAGAAGCAGGCACAGCTGGAGGAGCCATG : 80470

vulgar: SPP00000123_2.0 4 192 . gi|397456032|gb|JH739468.1|:subseq(30000,100000) 27927 80470 + 114 M 30 90 5 0 2 I 0 16979 3 0 2 M 37 111 5 0 2 I 0 21059 3 0 2 M 38 114 G 0 3 M 22 66 5 0 2 I 0 13589 3 0 2 M 22 66 5 0 2 I 0 119 3 0 2 M 24 72 S 0 1 5 0 2 I 0 210 3 0 2 S 1 2 M 14 42
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-11-15
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	gene	27928	80470	114	+	.	gene_id 1 ; sequence SPP00000123_2.0 ; gene_orientation +
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	cds	27928	28017	.	+	.	
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	exon	27928	28017	.	+	.	insertions 0 ; deletions 0
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	splice5	28018	28019	.	+	.	intron_id 1 ; splice_site "CT"
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	intron	28018	45000	.	+	.	intron_id 1
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	splice3	44999	45000	.	+	.	intron_id 0 ; splice_site "AA"
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	cds	45001	45111	.	+	.	
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	exon	45001	45111	.	+	.	insertions 0 ; deletions 0
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	splice5	45112	45113	.	+	.	intron_id 2 ; splice_site "GT"
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	intron	45112	66174	.	+	.	intron_id 2
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	splice3	66173	66174	.	+	.	intron_id 1 ; splice_site "AG"
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	cds	66175	66357	.	+	.	
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	exon	66175	66357	.	+	.	insertions 3 ; deletions 0
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	splice5	66358	66359	.	+	.	intron_id 3 ; splice_site "GT"
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	intron	66358	79950	.	+	.	intron_id 3
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	splice3	79949	79950	.	+	.	intron_id 2 ; splice_site "AG"
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	cds	79951	80016	.	+	.	
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	exon	79951	80016	.	+	.	insertions 0 ; deletions 0
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	splice5	80017	80018	.	+	.	intron_id 4 ; splice_site "CT"
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	intron	80017	80139	.	+	.	intron_id 4
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	splice3	80138	80139	.	+	.	intron_id 3 ; splice_site "AG"
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	cds	80140	80212	.	+	.	
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	exon	80140	80212	.	+	.	insertions 0 ; deletions 0
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	splice5	80213	80214	.	+	.	intron_id 5 ; splice_site "GT"
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	intron	80213	80426	.	+	.	intron_id 5
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	splice3	80425	80426	.	+	.	intron_id 4 ; splice_site "AG"
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	cds	80427	80470	.	+	.	
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	exon	80427	80470	.	+	.	insertions 0 ; deletions 0
gi|397456032|gb|JH739468.1|:subseq(30000,100000)	exonerate:protein2genome:local	similarity	27928	80470	114	+	.	alignment_id 1 ; Query SPP00000123_2.0 ; Align 27928 5 90 ; Align 45001 35 111 ; Align 66175 72 114 ; Align 66292 110 66 ; Align 79951 132 66 ; Align 80140 154 72 ; Align 80429 179 42
# --- END OF GFF DUMP ---
#