

C4 Alignment:
------------
         Query: QUERY_emiliana_scaffold32_hibrida
        Target: scaffold_32
         Model: protein2genome:local
     Raw score: 117
   Query range: 1 -> 125
  Target range: 91488 -> 855026

      2 : ProLeuArgLeuAlaValLeuArgLeuGly{L}  >>>> Target Intron 1 >> :     12
          |||||||||:!!!.!  !|||!.!:!!|||{ }           3287 bp       
          ProLeuArgValValArgLeuHisValGly{A}++                       
  91489 : CCGCTGCGAGTCGTGCGGCTGCACGTGGGA{G}gt....................... :  91522

     13 : >>  {eu}ThrGluProAlaTrpThrSerProLeuAsnPheGlyValArgAspGlyAl :     29
              { !}  !...|||||||||  !||||||! !...  !|||  ! !!  !|||:!
            -+{la}ArgArgProAlaTrpHisSerProArgArgSerGlySerGlyCysGlySe
  91523 : ..cg{CT}CGCCGCCCCGCCTGGCACTCCCCACGCCGGAGTGGGAGCGGGTGCGGGTC :  94857

     30 : aPheAla{Cy}  >>>> Target Intron 2 >>>>  {s}AlaGlyCysSerAla :     37
          !! !|||{||}           91833 bp          {|}..!||||||! !  !
          rCysAla{Cy}++                         -+{s}CysGlyCysPheLeu
  94858 : TTGTGCA{TG}gt.........................gg{T}TGTGGCTGTTTTCTT : 186714

     38 : IleLeuPheAspSerSerAlaLysPhe  >>>> Target Intron 3 >>>>  As :     47
            !!!!||| !!!!!.!!:!!! !              59579 bp          ||
          SerPhePheTyrThrGlySerThrGln++                         -+As
 186715 : TCTTTCTTTTACACAGGTTCGACACAGgt.........................cgGA : 246323

     48 : pSerGlyThrGly{Tr}  >>>> Target Intron 4 >>>>  {p}ProSerPhe :     55
          |:!!|||||||||{||}           49152 bp          {|}||||||!:!
          pAlaGlyThrGly{Tr}++                         ++{p}ProSerTyr
 246324 : CGCCGGCACTGGC{TG}gt.........................ag{G}CCCTCGTAC : 295499

     56 : TrpArgThrAlaAla{G}  >>>> Target Intron 5 >>>>  {lu}SerAlaV :     64
             ..!.!!||||||{!}           60936 bp          {!:}:::||||
          ProGluAlaAlaAla{A}+-                         ++{sp}ThrAlaV
 295500 : CCTGAGGCGGCCGCC{G}gc.........................ag{at}actgccg : 356462

     65 : alGly{T}  >>>> Target Intron 6 >>>>  {yr}ArgGluGluTyr{A}   :     71
          |||||{ }           79892 bp          {  }|||..!..! ! {:}  
          alGly{A}++                         ++{la}ArgArgArgGln{S}++
 356463 : tcggc{g}gt.........................ag{CG}CGGAGACGGCAA{A}gt : 436376

     72 : >>>> Target Intron 7 >>>>  {la}GlyGlyGly{T}  >>>> Target I :     75
                  116442 bp          {:!}|||||||||{ }           5235
                                   ++{er}GlyGlyGly{G}-+             
 436377 : .........................ag{GT}GGAGGAGGT{G}ct............. : 552832

     76 : ntron 8 >>>>  {yr}LeuAspGlyGlySerValArg{Se}  >>>> Target I :     83
          7 bp          { !}! !! !||||||  !  !|||{.!}           1989
                      ++{ly}CysGlyGlyGlyValGlnArg{Gl}++             
 552833 : ............ag{GT}TGCGGCGGGGGCGTTCAACGC{GG}gt............. : 605214

     84 : ntron 9 >>>>  {r}AlaThrGluValHisCysGluAlaCysGly{G}  >>>> T :     94
          9 bp          {!}  !|||:!!  !  !! !..!||||||  !{|}        
                      ++{y}LeuThrLysAsnPhePheArgAlaCysPro{G}++      
 605215 : ............ag{G}CTTACAAAGAATTTCTTTAGGGCCTGCCCT{G}gt...... : 625145

     95 : arget Intron 10 >>>>  {ly}HisLeuGlyHis{V}  >>>> Target Int :     99
             29773 bp           {||}   |||||||||{!}           61232 
                              ++{ly}LeuLeuGlyHis{G}++               
 625146 : ....................ag{ga}ctgctcggccac{g}gt............... : 654933

    100 : ron 11 >>>>  {al}PheLysGlyGlu{G}  >>>> Target Intron 12 >> :    104
          bp           { !}!::  !|||..!{|}           42652 bp       
                     ++{ly}TrpProGlyArg{G}++                        
 654934 : ...........ag{GA}TGGCCAGGTAGA{G}gt........................ : 716180

    105 : >>  {ly}PheAsnThrProIleAspGlnArgHisCys{V}  >>>> Target Int :    115
              {||}|||!:!  !|||:!!|||!    !!..  !{|}           96132 
            ++{ly}PheSerPheProValAspProTyrArgThr{V}++               
 716181 : ..ag{GG}TTCAGCTTTCCAGTTGATCCTTATCGGACT{G}gt............... : 758865

    116 : ron 13 >>>>  {al}AsnSerIleSerLeuAsnPheLysProSer :    125
          bp           {||}  !|||  !!!!!!!:::.!.::!||||||
                     ++{al}PheSerArgArgPheSerLeuArgProSer
 758866 : ...........ag{TC}TTCTCTCGCAGATTCTCGCTGCGACCTTCA : 855026

vulgar: QUERY_emiliana_scaffold32_hibrida 1 125 . scaffold_32 91488 855026 + 117 M 10 30 S 0 1 5 0 2 I 0 3283 3 0 2 S 1 2 M 19 57 S 0 2 5 0 2 I 0 91829 3 0 2 S 1 1 M 14 42 5 0 2 I 0 59575 3 0 2 M 5 15 S 0 2 5 0 2 I 0 49148 3 0 2 S 1 1 M 8 24 S 0 1 5 0 2 I 0 60932 3 0 2 S 1 2 M 4 12 S 0 1 5 0 2 I 0 79888 3 0 2 S 1 2 M 4 12 S 0 1 5 0 2 I 0 116438 3 0 2 S 1 2 M 3 9 S 0 1 5 0 2 I 0 52353 3 0 2 S 1 2 M 7 21 S 0 2 5 0 2 I 0 19895 3 0 2 S 1 1 M 10 30 S 0 1 5 0 2 I 0 29769 3 0 2 S 1 2 M 4 12 S 0 1 5 0 2 I 0 61228 3 0 2 S 1 2 M 4 12 S 0 1 5 0 2 I 0 42648 3 0 2 S 1 2 M 10 30 S 0 1 5 0 2 I 0 96128 3 0 2 S 1 2 M 10 30
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:protein2genome:local 2.2.0
##date 2010-03-10
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold_32	exonerate:protein2genome:local	gene	91489	855026	117	+	.	gene_id 2 ; sequence QUERY_emiliana_scaffold32_hibrida ; gene_orientation +
scaffold_32	exonerate:protein2genome:local	cds	91489	91519	.	+	.	
scaffold_32	exonerate:protein2genome:local	exon	91489	91519	.	+	.	insertions 0 ; deletions 0
scaffold_32	exonerate:protein2genome:local	splice5	91520	91521	.	+	.	intron_id 1 ; splice_site "GT"
scaffold_32	exonerate:protein2genome:local	intron	91520	94806	.	+	.	intron_id 1
scaffold_32	exonerate:protein2genome:local	splice3	94805	94806	.	+	.	intron_id 0 ; splice_site "CG"
scaffold_32	exonerate:protein2genome:local	cds	94807	94867	.	+	.	
scaffold_32	exonerate:protein2genome:local	exon	94807	94867	.	+	.	insertions 0 ; deletions 0
scaffold_32	exonerate:protein2genome:local	splice5	94868	94869	.	+	.	intron_id 2 ; splice_site "GT"
scaffold_32	exonerate:protein2genome:local	intron	94868	186700	.	+	.	intron_id 2
scaffold_32	exonerate:protein2genome:local	splice3	186699	186700	.	+	.	intron_id 1 ; splice_site "GG"
scaffold_32	exonerate:protein2genome:local	cds	186701	186743	.	+	.	
scaffold_32	exonerate:protein2genome:local	exon	186701	186743	.	+	.	insertions 0 ; deletions 0
scaffold_32	exonerate:protein2genome:local	splice5	186744	186745	.	+	.	intron_id 3 ; splice_site "GT"
scaffold_32	exonerate:protein2genome:local	intron	186744	246322	.	+	.	intron_id 3
scaffold_32	exonerate:protein2genome:local	splice3	246321	246322	.	+	.	intron_id 2 ; splice_site "CG"
scaffold_32	exonerate:protein2genome:local	cds	246323	246339	.	+	.	
scaffold_32	exonerate:protein2genome:local	exon	246323	246339	.	+	.	insertions 0 ; deletions 0
scaffold_32	exonerate:protein2genome:local	splice5	246340	246341	.	+	.	intron_id 4 ; splice_site "GT"
scaffold_32	exonerate:protein2genome:local	intron	246340	295491	.	+	.	intron_id 4
scaffold_32	exonerate:protein2genome:local	splice3	295490	295491	.	+	.	intron_id 3 ; splice_site "AG"
scaffold_32	exonerate:protein2genome:local	cds	295492	295517	.	+	.	
scaffold_32	exonerate:protein2genome:local	exon	295492	295517	.	+	.	insertions 0 ; deletions 0
scaffold_32	exonerate:protein2genome:local	splice5	295518	295519	.	+	.	intron_id 5 ; splice_site "GC"
scaffold_32	exonerate:protein2genome:local	intron	295518	356453	.	+	.	intron_id 5
scaffold_32	exonerate:protein2genome:local	splice3	356452	356453	.	+	.	intron_id 4 ; splice_site "ag"
scaffold_32	exonerate:protein2genome:local	cds	356454	356468	.	+	.	
scaffold_32	exonerate:protein2genome:local	exon	356454	356468	.	+	.	insertions 0 ; deletions 0
scaffold_32	exonerate:protein2genome:local	splice5	356469	356470	.	+	.	intron_id 6 ; splice_site "gt"
scaffold_32	exonerate:protein2genome:local	intron	356469	436360	.	+	.	intron_id 6
scaffold_32	exonerate:protein2genome:local	splice3	436359	436360	.	+	.	intron_id 5 ; splice_site "AG"
scaffold_32	exonerate:protein2genome:local	cds	436361	436375	.	+	.	
scaffold_32	exonerate:protein2genome:local	exon	436361	436375	.	+	.	insertions 0 ; deletions 0
scaffold_32	exonerate:protein2genome:local	splice5	436376	436377	.	+	.	intron_id 7 ; splice_site "GT"
scaffold_32	exonerate:protein2genome:local	intron	436376	552817	.	+	.	intron_id 7
scaffold_32	exonerate:protein2genome:local	splice3	552816	552817	.	+	.	intron_id 6 ; splice_site "AG"
scaffold_32	exonerate:protein2genome:local	cds	552818	552829	.	+	.	
scaffold_32	exonerate:protein2genome:local	exon	552818	552829	.	+	.	insertions 0 ; deletions 0
scaffold_32	exonerate:protein2genome:local	splice5	552830	552831	.	+	.	intron_id 8 ; splice_site "CT"
scaffold_32	exonerate:protein2genome:local	intron	552830	605186	.	+	.	intron_id 8
scaffold_32	exonerate:protein2genome:local	splice3	605185	605186	.	+	.	intron_id 7 ; splice_site "AG"
scaffold_32	exonerate:protein2genome:local	cds	605187	605211	.	+	.	
scaffold_32	exonerate:protein2genome:local	exon	605187	605211	.	+	.	insertions 0 ; deletions 0
scaffold_32	exonerate:protein2genome:local	splice5	605212	605213	.	+	.	intron_id 9 ; splice_site "GT"
scaffold_32	exonerate:protein2genome:local	intron	605212	625110	.	+	.	intron_id 9
scaffold_32	exonerate:protein2genome:local	splice3	625109	625110	.	+	.	intron_id 8 ; splice_site "AG"
scaffold_32	exonerate:protein2genome:local	cds	625111	625142	.	+	.	
scaffold_32	exonerate:protein2genome:local	exon	625111	625142	.	+	.	insertions 0 ; deletions 0
scaffold_32	exonerate:protein2genome:local	splice5	625143	625144	.	+	.	intron_id 10 ; splice_site "GT"
scaffold_32	exonerate:protein2genome:local	intron	625143	654915	.	+	.	intron_id 10
scaffold_32	exonerate:protein2genome:local	splice3	654914	654915	.	+	.	intron_id 9 ; splice_site "ag"
scaffold_32	exonerate:protein2genome:local	cds	654916	654930	.	+	.	
scaffold_32	exonerate:protein2genome:local	exon	654916	654930	.	+	.	insertions 0 ; deletions 0
scaffold_32	exonerate:protein2genome:local	splice5	654931	654932	.	+	.	intron_id 11 ; splice_site "gt"
scaffold_32	exonerate:protein2genome:local	intron	654931	716162	.	+	.	intron_id 11
scaffold_32	exonerate:protein2genome:local	splice3	716161	716162	.	+	.	intron_id 10 ; splice_site "AG"
scaffold_32	exonerate:protein2genome:local	cds	716163	716177	.	+	.	
scaffold_32	exonerate:protein2genome:local	exon	716163	716177	.	+	.	insertions 0 ; deletions 0
scaffold_32	exonerate:protein2genome:local	splice5	716178	716179	.	+	.	intron_id 12 ; splice_site "GT"
scaffold_32	exonerate:protein2genome:local	intron	716178	758829	.	+	.	intron_id 12
scaffold_32	exonerate:protein2genome:local	splice3	758828	758829	.	+	.	intron_id 11 ; splice_site "AG"
scaffold_32	exonerate:protein2genome:local	cds	758830	758862	.	+	.	
scaffold_32	exonerate:protein2genome:local	exon	758830	758862	.	+	.	insertions 0 ; deletions 0
scaffold_32	exonerate:protein2genome:local	splice5	758863	758864	.	+	.	intron_id 13 ; splice_site "GT"
scaffold_32	exonerate:protein2genome:local	intron	758863	854994	.	+	.	intron_id 13
scaffold_32	exonerate:protein2genome:local	splice3	854993	854994	.	+	.	intron_id 12 ; splice_site "AG"
scaffold_32	exonerate:protein2genome:local	cds	854995	855026	.	+	.	
scaffold_32	exonerate:protein2genome:local	exon	854995	855026	.	+	.	insertions 0 ; deletions 0
scaffold_32	exonerate:protein2genome:local	similarity	91489	855026	117	+	.	alignment_id 2 ; Query QUERY_emiliana_scaffold32_hibrida ; Align 91489 2 30 ; Align 94809 13 57 ; Align 186702 33 42 ; Align 246323 47 15 ; Align 295493 53 24 ; Align 356456 62 12 ; Align 436363 67 12 ; Align 552820 72 9 ; Align 605189 76 21 ; Align 625112 84 30 ; Align 654918 95 12 ; Align 716165 100 12 ; Align 758832 105 30 ; Align 854997 116 30
# --- END OF GFF DUMP ---
#

