Command line: [exonerate -m p2g --showtargetgff -q ./queriescanviades_vampir/Sel
O2v.fa -t ./fastasubseq_vampir/SelO2v.1.genome.fa -E]
Hostname: [luke]

C4 Alignment:
------------
         Query: SPP00002307_2.0 # Protein # Selenoprotein O (SelO) # Megabat (Pt
eropus vampyrus)
        Target: gi|431899529|gb|KB030957.1|:subseq(464225,100000) Pteropus alect
o unplaced genomic scaffold scaffold118, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 109
   Query range: 20 -> 196
  Target range: 2048 -> 95050

    21 : ProLeuGlyCysArgPro  >>>> Target Intron 1 >>>>  LeuProAlaLeuC :    31
         |||:!!||||||||||||            314 bp             ! !!|||! ! 
         ProValGlyCysArgPro++                         ++GlyAlaAlaTrpL
  2049 : CCTGTCGGGTGCAGACCTgt.........................agGGAGCAGCGTGGA :  2393

    32 : ysSerAlaSerAlaAlaAlaArg{G}  >>>> Target Intron 2 >>>>  {ly}A :    40
           :!!|||.!! !!||||||  !{!}           3134 bp           {.!}|
         ysAlaAlaGlyProAlaAlaAla{A}++                         ++{la}A
  2394 : AGGCAGCGGGGCCGGCAGCAGCG{G}gt.........................ag{CA}G :  5554

    41 : laAlaMetAspProAlaProArgTrpLeuAla{G}  >>>> Target Intron 3 >> :    51
         ||..!     !|||:!! !!  !|||  !  !{|}           1344 bp       
         laCysAlaArgProSerSerAlaTrpThrArg{G}++                       
  5555 : CGTGCGCTCGTCCATCTTCAGCATGGACACGC{G}gt....................... :  5590

    52 : >>  {ly}LeuArgPheAspAsnArgAlaLeuArgGluLeuProValGluThrPro  >> :    68
             {||}||||||  !! !::!|||  !! !  !! !  !|||! !||||||! !    
           +-{ly}LeuArgGlyGlySerArgGlnHisSerValArgProGluGluThrGln++  
  5591 : ..at{GG}CTGCGTGGCGGCTCCCGGCAGCACTCAGTGAGGCCTGAGGAGACACAGgt.. :  6984

    69 : >> Target Intron 4 >>>>  ProProGlyPro{Gl}  >>>> Target Intro :    72
                 131 bp           ||||||||||||{  }           12614 bp
                                ++ProProGlyPro{Il}++                 
  6985 : .......................agCCACCGGGTCCT{AT}gt................. :  7129

    73 : n 5 >>>>  {u}GlyAlaProSerThrProArgLeuValProGlyAlaCysPhe{S}   :    87
                   { }  !  !|||||| !!|||||||||  !  !|||..!   .!!{:}  
                 ++{e}ThrTyrProSerProProArgLeuCysGluGlyCysMetLeu{A}++
  7130 : ........ag{C}ACCTACCCCTCCCCGCCTCGGCTCTGCGAAGGCTGCATGCTT{G}gt : 19785

    88 : >>>> Target Intron 6 >>>>  {er}ArgValArgProAlaProLeuArgGlnPr :    97
                  18116 bp          {!!}! !:!!! !|||||||||||||||  !||
                                  ++{la}ProLeuMetProAlaProLeuArgTrpPr
 19786 : .........................ag{CT}CCTCTGATGCCAGCGCCTCTGCGGTGGCC : 37930

    98 : oArgLeuValAlaLeuSerGluProAlaLeuAlaLeuLeuGly{L}  >>>> Target  :   112
         ||||  !!.! !!|||  !  !  !.!!|||:!!:!!||| !!{:}           165
         oArgGluAlaProLeuLeuProTyrThrLeuSerIleLeuTrp{V}++            
 37931 : CCGGGAGGCCCCCCTCCTCCCATACACACTATCTATTCTCTGG{G}gt............ : 37978

   113 : Intron 7 >>>>  {eu}GlyProProProAspAspHisAlaAlaArgAspAlaArgGl :   126
         2 bp           {!!}..!  !  !|||!  |||||||||! !!.!  !!.!  !..
                      +-{al}AsnGlySerProGlyAspHisAlaGluHisLeuGlyAlaAr
 37979 : .............ac{TC}AACGGGAGCCCAGGGGACCATGCAGAGCACCTCGGGGCACG : 39669

   127 : uAlaGluAlaAlaLeuPhePheSerGlyAsnAlaLeu{Le}  >>>> Target Intro :   139
         !|||!    !|||:!!!       !..!  !|||! !{! }            381 bp 
         gAlaAlaLeuAlaMetSerAlaLeuSerProAlaSer{Cy}++                 
 39670 : GGCAGCCCTTGCCATGTCAGCACTGTCCCCCGCCTCC{TG}gt................. : 39712

   140 : n 8 >>>>  {u}ProGlyAlaGluProAlaAla{Hi}  >>>> Target Intron 9 :   147
                   {!}|||.!!  !  !||||||.!!{  }           12121 bp   
                 ++{s}ProSerIleProProAlaThr{Gl}++                    
 39713 : ........ag{C}CCCAGCATCCCACCTGCCACA{GG}gt.................... : 40117

   148 :  >>>>  {s}CysTyrCysGlyHisGlnPheGlyGlnPheAlaGlyGlnLeuGlyAspGl :   164
                { }  !!:!   ||||||::!  !|||   ! !|||..!!:!  !|||   ..
              ++{y}AsnPheMetGlyHisArgHisGlyAlaCysAlaSerArgAlaGlyArgAs
 40118 : .....ag{G}AACTTTATGGGCCACAGACACGGGGCCTGCGCCTCACGAGCCGGCAGGAA : 52285

   165 : yAlaAlaMetTyrLeuGlyGluValCysThrAlaAlaGly{Gl}  >>>> Target In :   178
         !  !|||:!!     ! !!...  ! !!||| !!::!|||{! }           13960
         nTrpAlaLeuGlyAlaArgSerCysArgThrProSerGly{Gl}++              
 52286 : CTGGGCGCTGGGGGCCCGGAGCTGTCGCACGCCCAGCGGC{GG}gt.............. : 52331

   179 : tron 10 >>>>  {u}ArgTrpGluLeuGlnLeuLysGlyAlaGlyPro{T}  >>>>  :   190
          bp           {!}!:!|||!  !!!   |||.....!|||||| !!{:}       
                     ++{y}LysTrpGlyPheThrLeuSerSerAlaGlyThr{S}++     
 52332 : ............ag{A}AAATGGGGCTTCACTCTCTCCTCGGCAGGGACC{T}gt..... : 66326

   191 : Target Intron 11 >>>>  {hr}ProPheSerArgTrpAla :   196
             28707 bp           {!!}||| !  !! !!||||||
                              ++{er}ProValProGlyTrpAla
 66327 : .....................ag{CC}CCAGTGCCCGGCTGGGCG : 95050

vulgar: SPP00002307_2.0 20 196 . gi|431899529|gb|KB030957.1|:subseq(464225,100000) 2048 95050 + 109 M 6 18 5 0 2 I 0 310 3 0 2 M 12 36 S 0 1 5 0 2 I 0 3130 3 0 2 S 1 2 M 11 33 S 0 1
 5 0 2 I 0 1340 3 0 2 S 1 2 M 16 48 5 0 2 I 0 127 3 0 2 M 4 12 S 0 2 5 0 2 I 0 12610 3 0 2 S 1 1 M 14 42 S 0 1 5 0 2 I 0 18112 3 0 2 S 1 2 M 24 72 S 0 1 5 0 2 I 0 1648 3 0 2 S 1 2 M
 26 78 S 0 2 5 0 2 I 0 377 3 0 2 S 1 1 M 7 21 S 0 2 5 0 2 I 0 12117 3 0 2 S 1 1 M 30 90 S 0 2 5 0 2 I 0 13956 3 0 2 S 1 1 M 11 33 S 0 1 5 0 2 I 0 28703 3 0 2 S 1 2 M 6 18
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-12-01
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	gene	2049	95050	109	+	.	gene_id 1 ; sequence SPP00002307_2.0 ; gene_o
rientation +
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	2049	2066	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	2049	2066	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	2067	2068	.	+	.	intron_id 1 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	2067	2380	.	+	.	intron_id 1
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	2379	2380	.	+	.	intron_id 0 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	2381	2417	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	2381	2417	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	2418	2419	.	+	.	intron_id 2 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	2418	5551	.	+	.	intron_id 2
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	5550	5551	.	+	.	intron_id 1 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	5552	5587	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	5552	5587	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	5588	5589	.	+	.	intron_id 3 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	5588	6931	.	+	.	intron_id 3
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	6930	6931	.	+	.	intron_id 2 ; splice_site "AT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	6932	6981	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	6932	6981	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	6982	6983	.	+	.	intron_id 4 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	6982	7112	.	+	.	intron_id 4
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	7111	7112	.	+	.	intron_id 3 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	7113	7126	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	7113	7126	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	7127	7128	.	+	.	intron_id 5 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	7127	19740	.	+	.	intron_id 5
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	19739	19740	.	+	.	intron_id 4 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	19741	19784	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	19741	19784	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	19785	19786	.	+	.	intron_id 6 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	19785	37900	.	+	.	intron_id 6
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	37899	37900	.	+	.	intron_id 5 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	37901	37975	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	37901	37975	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	37976	37977	.	+	.	intron_id 7 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	37976	39627	.	+	.	intron_id 7
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	39626	39627	.	+	.	intron_id 6 ; splice_site "AC"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	39628	39709	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	39628	39709	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	39710	39711	.	+	.	intron_id 8 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	39710	40090	.	+	.	intron_id 8
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	40089	40090	.	+	.	intron_id 7 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	40091	40114	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	40091	40114	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	40115	40116	.	+	.	intron_id 9 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	40115	52235	.	+	.	intron_id 9
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	52234	52235	.	+	.	intron_id 8 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	52236	52328	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	52236	52328	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	52329	52330	.	+	.	intron_id 10 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	52329	66288	.	+	.	intron_id 10
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	66287	66288	.	+	.	intron_id 9 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	66289	66323	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	66289	66323	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	66324	66325	.	+	.	intron_id 11 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	66324	95030	.	+	.	intron_id 11
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	95029	95030	.	+	.	intron_id 10 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	95031	95050	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	95031	95050	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	similarity	2049	95050	109	+	.	alignment_id 1 ; Query SPP00002307_2.
0 ; Align 2049 21 18 ; Align 2381 27 36 ; Align 5554 40 33 ; Align 6934 52 48 ; Align 7113 68 12 ; Align 19742 73 42 ; Align 37903 88 72 ; Align 39630 113 78 ; Align 40092 140 21 ; 
Align 52237 148 90 ; Align 66290 179 33 ; Align 95033 191 18
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00002307_2.0 # Protein # Selenoprotein O (SelO) # Megabat (Pteropus vampyrus)
        Target: gi|431899529|gb|KB030957.1|:subseq(464225,100000) Pteropus alecto unplaced genomic scaffold scaffold118, whole genome shotgun sequence
         Model: protein2genome:local
     Raw score: 106
   Query range: 8 -> 191
  Target range: 5771 -> 98131

     9 : GlyAlaSerLeuAlaAlaAlaArgThrLeuSerProProLeuGlyCysArgProLeuPro :    28
         |||!.!!!!  !||||||!.! !!! !  !  !  !|||! !.!!   ||||||  !  !
         GlyGlyArgAlaAlaAlaGlyGlyArgAlaValGlyProArgSerLeuArgProAlaGlu
  5772 : GGCGGCAGGGCTGCGGCGGGAGGCAGGGCTGTGGGGCCACGGAGCCTGCGCCCTGCCGAG :  5829

    29 : AlaLeuCysSerAlaSerAlaAlaAlaArgGlyAlaAlaMetAspPro  >>>> Targe :    45
           !||| ! !!!  !..!||||||||||||!.!  !|||:!!  !  !           9
         GlnLeuGlyCysArgGluAlaAlaAlaArgAlaMetAlaLeuProGly++          
  5830 : CAGCTCGGGTGTCGGGAGGCGGCGGCAAGGGCCATGGCCCTGCCCGGGgt.......... :  5882

    46 : t Intron 1 >>>>  AlaProArgTrpLeuAlaGlyLeuArg  >>>> Target In :    54
         408 bp           !.!  !  !||||||  !|||:!!!:!            386 
                        -+GlySerSerTrpLeuLeuGlyValGln++              
  5883 : ...............tgGGCAGCTCGTGGCTGCTCGGGGTGCAGgt.............. : 15317

    55 : tron 2 >>>>  PheAspAsn{A}  >>>> Target Intron 3 >>>>  {rg}Al :    58
         bp              ..!.!.{ }           1765 bp           {!!}!.
                    ++AlaSerGlu{G}+-                         ++{ly}Va
 15318 : ...........agGCATCTGAA{G}ga.........................ag{GG}GT : 17478

    59 : aLeuArgGluLeuProValGluThrProProProGlyProGluGlyAlaProSer<->Th :    77
         !! !!:!!  |||||||||!  |||||| !!  !.!!|||   ||||||||||||    !
         lHisLysAlaLeuProValValThrProAlaIleSerProProGlyAlaProSerLeuPr
 17479 : CCACAAGGCTCTGCCCGTGGTCACCCCTGCAATCAGCCCACCTGGCGCCCCCTCACTTCC : 17538

    78 : rProArgLeuValProGlyAlaCysPheSerArg{V}  >>>> Target Intron 4  :    89
         !||| !!  ! !!|||||| !!!! |||.!!..!{|}           2085 bp     
         oProGlyArgPheProGlyProTrpPheGlyGlu{V}++                     
 17539 : ACCAGGCAGGTTCCCAGGACCCTGGTTTGGGGAG{G}gt..................... : 17577

    90 : >>>>  {al}ArgProAlaProLeuArgGlnProArgLeuValAlaLeu{S}  >>>> T :   103
               {||} !! !!! !|||:!!|||  !|||..!! !:!!:!!  !{.}        
             ++{al}GlySerGluProValArgAlaProGluCysLeuSerThr{G}++      
 17578 : ....ag{TC}GGGTCTGAGCCTGTGCGGGCGCCGGAGTGCCTGTCCACA{G}gt...... : 19704

   104 : arget Intron 5 >>>>  {er}GluProAlaLeuAlaLeuLeuGlyLeuGlyProPr :   115
            6760 bp           {.!}   |||::!|||!.!|||  !  !|||..!||| !
                            ++{lu}ThrProSerLeuValLeuAlaProLeuSerProSe
 19705 : ...................ag{AG}ACCCCCAGCTTGGTCCTCGCTCCCTTGTCCCCCTC : 26497

   116 : oProAspAspHis  >>>> Target Intron 6 >>>>  AlaAlaArg  >>>> Ta :   123
         !|||!!:!!:              11720 bp          ||| !!!:!         
         rProGluGluGly+-                         ++AlaProGln++       
 26498 : CCCAGAAGAAGGGgg.........................agGCACCTCAGgt....... : 38243

   124 : rget Intron 7 >>>>  AspAlaArgGluAlaGluAlaAlaLeuPhePheSerGlyA :   136
           6664 bp           |||:!!!.!.!.  !   |||  !||||||  !! !  !!
                           ++AspSerAsnHisArgCysAlaArgLeuPheSerPheProT
 38244 : ..................agGACTCCAATCACAGGTGTGCGAGGCTGTTCAGCTTTCCCA : 44944

   137 : snAlaLeu{Le}  >>>> Target Intron 8 >>>>  {u}ProGly{A}  >>>>  :   142
         ..|||! !{  }           13656 bp          {!}||||||{!}       
         hrAlaGln{Ar}-+                         ++{g}ProGly{G}++     
 44945 : CAGCTCAA{AG}at.........................ag{A}CCAGGC{G}gt..... : 58621

   143 : Target Intron 9 >>>>  {la}GluProAlaAlaHisCysTyrCysGlyHisGlnP :   154
             27512 bp          {.!}.!.|||.!!|||:!!! !|||   ..!!!.   !
                             ++{ly}HisProThrAlaAsnSerTyrValSerGlnAlaL
 58622 : ....................ag{GG}CACCCCACAGCTAATTCTTACGTGTCCCAGGCTT : 86166

   155 : heGlyGlnPheAlaGlyGlnLeuGlyAsp{Gl}  >>>> Target Intron 10 >>> :   164
         !.|||   !    !..!.!.|||! !  !{||}            9505 bp        
         euGlyPheSerIleAsnAspLeuGluPhe{Gl}-+                         
 86167 : TAGGATTCTCAATTAATGACCTGGAATTC{GG}tt......................... : 86200

   165 : >  {y}AlaAlaMetTyrLeuGlyGluValCysThrAlaAlaGlyGlu{Ar}  >>>> T :   179
            {|}:!!|||.!.!:!! !||||||!.!|||.!!:!!  !|||!!:{||}        
          +-{y}SerAlaPhePheSerGlyGluAlaCysAlaSer***GlyAsp{Ar}++      
 86201 : .ac{G}TCTGCATTCTTCTCTGGAGAAGCCTGTGCCTCGTGAGGTGAC{AG}gt...... : 95750

   180 : arget Intron 11 >>>>  {g}Trp  >>>> Target Intron 12 >>>>  Gl :   181
             145 bp            {|}  !            2202 bp             
                             ++{g}Thr++                          ++Th
 95751 : ....................ag{A}ACGgt..........................agAC : 98099

   182 : uLeuGlnLeuLysGlyAlaGlyProThrPro :   191
         !|||   |||  !||||||||||||  !|||
         rLeuAlaLeuProGlyAlaGlyProArgPro
 98100 : GCTGGCCCTGCCAGGCGCCGGCCCGCGGCCC : 98131

vulgar: SPP00002307_2.0 8 191 . gi|431899529|gb|KB030957.1|:subseq(464225,100000) 5771 98131 + 106 M 36 108 5 0 2 I 0 9404 3 0 2 M 9 27 5 0 2 I 0 382 3 0 2 M 3 9 S 0 1 5 0 2 I 0 176
1 3 0 2 S 1 2 M 19 57 G 0 3 M 12 36 S 0 1 5 0 2 I 0 2081 3 0 2 S 1 2 M 13 39 S 0 1 5 0 2 I 0 6756 3 0 2 S 1 2 M 16 48 5 0 2 I 0 11716 3 0 2 M 3 9 5 0 2 I 0 6660 3 0 2 M 16 48 S 0 2 
5 0 2 I 0 13652 3 0 2 S 1 1 M 2 6 S 0 1 5 0 2 I 0 27508 3 0 2 S 1 2 M 21 63 S 0 2 5 0 2 I 0 9501 3 0 2 S 1 1 M 14 42 S 0 2 5 0 2 I 0 141 3 0 2 S 1 1 M 1 3 5 0 2 I 0 2198 3 0 2 M 11 
33
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-12-01
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	gene	5772	98131	106	+	.	gene_id 2 ; sequence SPP00002307_2.0 ; gene_o
rientation +
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	5772	5879	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	5772	5879	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	5880	5881	.	+	.	intron_id 1 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	5880	15287	.	+	.	intron_id 1
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	15286	15287	.	+	.	intron_id 0 ; splice_site "TG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	15288	15314	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	15288	15314	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	15315	15316	.	+	.	intron_id 2 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	15315	15700	.	+	.	intron_id 2
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	15699	15700	.	+	.	intron_id 1 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	15701	15710	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	15701	15710	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	15711	15712	.	+	.	intron_id 3 ; splice_site "GA"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	15711	17475	.	+	.	intron_id 3
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	17474	17475	.	+	.	intron_id 2 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	17476	17574	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	17476	17574	.	+	.	insertions 3 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	17575	17576	.	+	.	intron_id 4 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	17575	19659	.	+	.	intron_id 4
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	19658	19659	.	+	.	intron_id 3 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	19660	19701	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	19660	19701	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	19702	19703	.	+	.	intron_id 5 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	19702	26461	.	+	.	intron_id 5
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	26460	26461	.	+	.	intron_id 4 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	26462	26511	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	26462	26511	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	26512	26513	.	+	.	intron_id 6 ; splice_site "GG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	26512	38231	.	+	.	intron_id 6
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	38230	38231	.	+	.	intron_id 5 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	38232	38240	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	38232	38240	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	38241	38242	.	+	.	intron_id 7 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	38241	44904	.	+	.	intron_id 7
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	44903	44904	.	+	.	intron_id 6 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	44905	44954	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	44905	44954	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	44955	44956	.	+	.	intron_id 8 ; splice_site "AT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	44955	58610	.	+	.	intron_id 8
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	58609	58610	.	+	.	intron_id 7 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	58611	58618	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	58611	58618	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	58619	58620	.	+	.	intron_id 9 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	58619	86130	.	+	.	intron_id 9
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	86129	86130	.	+	.	intron_id 8 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	86131	86197	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	86131	86197	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	86198	86199	.	+	.	intron_id 10 ; splice_site "TT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	86198	95702	.	+	.	intron_id 10
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	95701	95702	.	+	.	intron_id 9 ; splice_site "AC"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	95703	95747	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	95703	95747	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	95748	95749	.	+	.	intron_id 11 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	95748	95892	.	+	.	intron_id 11
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	95891	95892	.	+	.	intron_id 10 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	95893	95896	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	95893	95896	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	95897	95898	.	+	.	intron_id 12 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	95897	98098	.	+	.	intron_id 12
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	98097	98098	.	+	.	intron_id 11 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	98099	98131	.	+	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	98099	98131	.	+	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	similarity	5772	98131	106	+	.	alignment_id 2 ; Query SPP00002307_2.
0 ; Align 5772 9 108 ; Align 15288 45 27 ; Align 15701 54 9 ; Align 17478 58 57 ; Align 17538 77 36 ; Align 19662 90 39 ; Align 26464 104 48 ; Align 38232 120 9 ; Align 44905 123 48
 ; Align 58612 140 6 ; Align 86133 143 63 ; Align 95704 165 42 ; Align 95894 180 3 ; Align 98099 181 33
# --- END OF GFF DUMP ---
#

C4 Alignment:
------------
         Query: SPP00002307_2.0 # Protein # Selenoprotein O (SelO) # Megabat (Pteropus vampyrus)
        Target: gi|431899529|gb|KB030957.1|:subseq(464225,100000) Pteropus alecto unplaced genomic scaffold scaffold118, whole genome shotgun sequence:[revcomp]
         Model: protein2genome:local
     Raw score: 101
   Query range: 7 -> 191
  Target range: 96548 -> 35621

     8 : LeuGlyAlaSerLeuAlaAlaAlaArgThrLeuSerProProLeuGlyCysArgProLeu :    27
         :!!|||.!!..!  ! !!|||!.! !!  !|||  !  !  !  !||||||  !  !:!!
         IleGlyThrGlnGlyProAlaGlyGlyGlnLeuValAspSerAlaGlyCysSerTyrVal
 96548 : ATAGGCACGCAGGGGCCCGCGGGCGGCCAGCTTGTGGACAGCGCTGGCTGCTCATATGTC : 96491

    28 : ProAlaLeuCysSerAlaSerAlaAlaAlaArgGlyAlaAlaMetAspProAlaProArg :    47
         ||| !!  ! !!  !.!!  !!.!:!!|||!:!! !||||||   !  |||  !  ! !!
         ProProAsnSerHisThrHisGlySerAlaLysGluAlaAla---GlyPro***ArgGly
 96490 : CCCCCCAACAGCCACACGCACGGGTCAGCCAAGGAAGCCGCC---GGGCCATGAAGGGGG : 96434

    48 : TrpLeuAlaGlyLeu{Ar}  >>>> Target Intron 1 >>>>  {g}PheAspAsn :    56
         |||! !||||||! !{||}           2303 bp           {|}!:!||||||
         TrpCysAlaGlyGln{Ar}++                         ++{g}TyrAspAsn
 96433 : TGGTGCGCAGGGCAG{AG}gt.........................ag{G}TATGACAAC : 94104

    57 : ArgAlaLeuArg{Gl}  >>>> Target Intron 2 >>>>  {u}LeuProValGlu :    65
          !!|||:!! !!{! }           4697 bp           {!}! !|||!.!..!
         GlyAlaIleGly{Va}++                         ++{l}GlnProAlaArg
 94103 : GGGGCTATAGGT{GT}gt.........................ag{A}CAGCCGGCCCGG : 89380

    66 : ThrProProProGlyProGluGly  >>>> Target Intron 3 >>>>  AlaPro{ :    76
         !:!|||||||||..! !!.!.|||           10256 bp          ! !|||{
         SerProProProAsnThrHisGly++                         ++AspPro{
 89379 : AGCCCGCCCCCCAACACCCACGGGgt.........................agGATCCA{ : 79091

    77 : Se}  >>>> Target Intron 4 >>>>  {r}{T}  >>>> Target Intron 5 :    77
         ||}           8846 bp           {|}{ }            365 bp    
         Se}++                         ++{r}{G}++                    
 79090 : TC}gt.........................ag{A}{G}gt.................... : 70239

    78 :  >>>>  {hr}ProArgLeuValProGlyAlaCysPheSer{A}  >>>> Target In :    88
                { !}|||..!|||  !|||||| !!   .!!|||{ }           1536 
              ++{ly}ProGluLeuProProGlyProValLeuSer{G}++              
 70238 : .....ag{GA}CCAGAGCTGCCACCTGGCCCTGTGCTCTCT{G}gt.............. : 69841

    89 : tron 6 >>>>  {rg}ValArgProAlaProLeuArgGln  >>>> Target Intro :    97
         bp           {!!}:!!|||  !  !|||||||||:!!           8240 bp 
                    ++{ly}LeuArgValGlnProLeuArgGlu+-                 
 69840 : ...........ag{GT}CTGCGTGTCCAGCCTCTGCGGGAGga................. : 68279

    98 : n 7 >>>>  ProArgLeuValAlaLeuSerGlu{Pr}  >>>> Target Intron 8 :   105
                     !  !  !!.! !!|||..!|||{  }           3775 bp    
                 ++GluAlaThrAlaProLeuGluGlu{Gl}++                    
 68278 : ........agGAGGCCACTGCCCCCTTGGAGGAG{GA}gt.................... : 60013

   106 :  >>>>  {o}AlaLeuAlaLeuLeuGlyLeuGlyProProProAspAspHisAlaAlaAr :   122
                {!}|||!!!|||! !  !!.!|||||| !! !!||||||...   !.!  !||
              ++{u}AlaPheAlaSerAlaAlaLeuGlyThrAlaProAspSerSerValLeuAr
 60012 : .....ag{A}GCGTTTGCCTCTGCAGCTCTCGGCACCGCTCCTGACTCGTCAGTTTTACG : 56191

   123 : g  >>>> Target Intron 9 >>>>  AspAlaArgGluAlaGluAlaAlaLeuPhe :   132
         |           4104 bp           !  :!!  !:!!  !:!!!.!  !:!!|||
         g++                         ++GlySerLeuGlnArgGlnValLeuIlePhe
 56190 : Tgt.........................agGGGTCTTTGCAGCGACAGGTGCTGATTTTC : 52057

   133 : {P}  >>>> Target Intron 10 >>>>  {he}SerGlyAsnAlaLeuLeuProGl :   141
         { }            427 bp            { !}||||||...||||||  !|||||
         {A}++                          ++{sp}SerGlyArgAlaLeuSerProGl
 52056 : {G}gt..........................ag{AC}AGCGGCCGGGCCTTGAGCCCAGG : 51603

   142 : y{A}  >>>> Target Intron 11 >>>>  {la}GluProAlaAlaHisCysTyrC :   150
         |{|}            8826 bp           {||}|||||| !!:!!|||   ||||
         y{A}+-                          +-{la}GluProProSerHisGlnTyrC
 51602 : A{G}gg..........................aa{CA}GAGCCGCCCTCACACCAATACT : 42750

   151 : ysGlyHisGlnPheGlyGlnPheAlaGly{G}  >>>> Target Intron 12 >>>> :   160
         ||! !  !|||   |||! !  !  !|||{:}            5805 bp         
         ysValAlaGlnArgGlyProAlaHisGly{A}++                          
 42749 : GCGTGGCCCAAAGGGGCCCGGCCCATGGC{A}gt.......................... : 42717

   161 :   {ln}LeuGlyAspGly{Al}  >>>> Target Intron 13 >>>>  {a}AlaMe :   167
           {:!}:!! !!   |||{::}            1198 bp           {!}|||..
         ++{rg}ValArgProGly{Se}+-                          ++{r}AlaGl
 42716 : ag{GA}GTAAGGCCAGGA{AG}ga..........................ag{T}GCCCA : 35696

   168 : tTyrLeuGlyGluValCysThrAlaAlaGlyGluArgTrpGluLeuGlnLeuLysGlyAl :   187
         !:!!  !|||! !! ! !   !|||||||||:!!! !  !|||  !:!!:!!   ! !||
         nHisArgGlyAlaGlyGlyGlyAlaAlaGlyGlnProGlnGluAlaGluValAlaValAl
 35695 : GCACAGGGGCGCAGGGGGAGGAGCCGCAGGGCAGCCCCAGGAGGCCGAGGTAGCTGTGGC : 35636

   188 : aGlyProThrPro :   191
         |||| !!||||||
         aGlyThrThrPro
 35635 : TGGGACCACCCCT : 35622

vulgar: SPP00002307_2.0 7 191 . gi|431899529|gb|KB030957.1|:subseq(464225,100000) 96548 35621 - 101 M 34 102 G 1 0 M 10 30 S 0 2 5 0 2 I 0 2299 3 0 2 S 1 1 M 7 21 S 0 2 5 0 2 I 0 46
93 3 0 2 S 1 1 M 12 36 5 0 2 I 0 10252 3 0 2 M 2 6 S 0 2 5 0 2 I 0 8842 3 0 2 S 1 2 5 0 2 I 0 361 3 0 2 S 1 2 M 10 30 S 0 1 5 0 2 I 0 1532 3 0 2 S 1 2 M 8 24 5 0 2 I 0 8236 3 0 2 M 
8 24 S 0 2 5 0 2 I 0 3771 3 0 2 S 1 1 M 17 51 5 0 2 I 0 4100 3 0 2 M 10 30 S 0 1 5 0 2 I 0 423 3 0 2 S 1 2 M 8 24 S 0 1 5 0 2 I 0 8822 3 0 2 S 1 2 M 17 51 S 0 1 5 0 2 I 0 5801 3 0 2
 S 1 2 M 4 12 S 0 2 5 0 2 I 0 1194 3 0 2 S 1 1 M 26 78
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2013-12-01
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	gene	35622	96548	101	-	.	gene_id 1 ; sequence SPP00002307_2.0 ; gene_o
rientation +
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	96415	96548	.	-	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	96415	96548	.	-	.	insertions 0 ; deletions 1
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	96413	96414	.	-	.	intron_id 1 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	94112	96414	.	-	.	intron_id 1
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	94112	94113	.	-	.	intron_id 0 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	94088	94111	.	-	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	94088	94111	.	-	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	94086	94087	.	-	.	intron_id 2 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	89391	94087	.	-	.	intron_id 2
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	89391	89392	.	-	.	intron_id 1 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	89354	89390	.	-	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	89354	89390	.	-	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	89352	89353	.	-	.	intron_id 3 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	79098	89353	.	-	.	intron_id 3
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	79098	79099	.	-	.	intron_id 2 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	79090	79097	.	-	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	79090	79097	.	-	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	79088	79089	.	-	.	intron_id 4 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	70244	79089	.	-	.	intron_id 4
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	70244	70245	.	-	.	intron_id 3 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	70242	70243	.	-	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	70242	70243	.	-	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	70240	70241	.	-	.	intron_id 5 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	69877	70241	.	-	.	intron_id 5
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	69877	69878	.	-	.	intron_id 4 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	69844	69876	.	-	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	69844	69876	.	-	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	69842	69843	.	-	.	intron_id 6 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	68308	69843	.	-	.	intron_id 6
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	68308	68309	.	-	.	intron_id 5 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	68282	68307	.	-	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	68282	68307	.	-	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	68280	68281	.	-	.	intron_id 7 ; splice_site "GA"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	60042	68281	.	-	.	intron_id 7
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	60042	60043	.	-	.	intron_id 6 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	60016	60041	.	-	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	60016	60041	.	-	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	60014	60015	.	-	.	intron_id 8 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	56241	60015	.	-	.	intron_id 8
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	56241	56242	.	-	.	intron_id 7 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	56189	56240	.	-	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	56189	56240	.	-	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	56187	56188	.	-	.	intron_id 9 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	52085	56188	.	-	.	intron_id 9
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	52085	52086	.	-	.	intron_id 8 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	52054	52084	.	-	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	52054	52084	.	-	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	52052	52053	.	-	.	intron_id 10 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	51627	52053	.	-	.	intron_id 10
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	51627	51628	.	-	.	intron_id 9 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	51600	51626	.	-	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	51600	51626	.	-	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	51598	51599	.	-	.	intron_id 11 ; splice_site "GG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	42774	51599	.	-	.	intron_id 11
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	42774	42775	.	-	.	intron_id 10 ; splice_site "AA"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	42720	42773	.	-	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	42720	42773	.	-	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	42718	42719	.	-	.	intron_id 12 ; splice_site "GT"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	36915	42719	.	-	.	intron_id 12
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	36915	36916	.	-	.	intron_id 11 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	36899	36914	.	-	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	36899	36914	.	-	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice5	36897	36898	.	-	.	intron_id 13 ; splice_site "GA"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	intron	35701	36898	.	-	.	intron_id 13
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	splice3	35701	35702	.	-	.	intron_id 12 ; splice_site "AG"
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	cds	35622	35700	.	-	.	
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	exon	35622	35700	.	-	.	insertions 0 ; deletions 0
gi|431899529|gb|KB030957.1|:subseq(464225,100000)	exonerate:protein2genome:local	similarity	35622	96548	101	-	.	alignment_id 1 ; Query SPP00002307_2.
0 ; Align 96549 8 102 ; Align 96447 43 30 ; Align 94111 54 21 ; Align 89390 62 36 ; Align 79098 74 6 ; Align 69875 78 30 ; Align 68306 89 24 ; Align 60042 97 24 ; Align 56240 106 51
 ; Align 52085 123 30 ; Align 51625 134 24 ; Align 42772 143 51 ; Align 36913 161 12 ; Align 35700 166 78
# --- END OF GFF DUMP ---
#
-- completed exonerate analysi