• Run Primer3
  • Exporting sequence
Targets:  :   -   
Flanking region(bp):

 
* Maximum size is 10,000 bp
Avoiding primer design
around target(bp): 		 
Quality: >=  
DP: >=  
Variant sites masking:
Note: The sequence shows preferentially variant type allele regardless of its genotype "heterozygous or homozygous".
Ns in the alignment indicates unmapped site (Depth = 0) as well as site below the threshold of depth and quality user set.
General settings


Product size range:   -   
Primer optimum size:  
Primer max size:  
Primer min size:  
Primer optimum TM:  
Primer max TM:  
Primer min TM:  
Max TM diffrence:  
Primer lowercase masking:
History

Previous result is not found.

Targets:  :   -   
Flanking region(bp):

 
* Maximum size is 10,000 bp
Avoiding primer design
around target(bp): 		 
Quality: >=  
DP: >=  
Variant sites masking:
Note: The sequence being exported with this option shows preferentially variant type allele regardless of its genotype "heterozygous or homozygous".
Ns in the alignment indicates unmapped site (Depth = 0) as well as site above the threshold of depth and quality user set.

Chromosome:
Position:
  		 -    
* Maximum size is 20,000 bp
Quality: >=  
DP: >=  
Line break (bp):   =  
 * Use 0 for non-breaking.

Note: The fasta file being exported shows preferentially variant type allele regardless of its genotype "heterozygous or homozygous".
Ns in the alignment indicates unmapped site (Depth = 0) as well as site below the threshold of depth and quality user set.
Chromosome:
Position:
  		 -  
    * Maximum size is 200,000 bp
ID:
Quality >=  
DP >=  

  • Accession lists

    • Visible lists Hidden lists

  • Accession title

    • ID or NAME   Subtitle   Width  

  • Recovery lists (original)

    • Keyword  
    * The keyword must has over 4 strings.

     


    Position bp    
    History
    : Quality of Variant
    : Depth of All reads
    : Depth of Alternative allele

    To learn more about how to use TASUKE, visit this page.
  • Display Modes

    • Modes shown below can be changed at menu bar.
    SNP only
    SNP frequency is shown by blue gradient.
    Regions with no mapped reads are highlighted with yellow.
    DEPTH
    Average depth value of the block is shown by gray gradient.
    Depth & SNP
    SNP frequency is shown in an inner box on depth background.
  • Mouse
    		•
    Drag Horizontally on the map.
    Double click to zoom in around the clicked point.
    Click on an accession name for changing the reference.
    Click again to restore the reference to the default setting.
  • Shortcut keys
    		•
     Movements 
    ← Moving to the left side window.
    → Moving to the right side window.
    <space> Moving to the right side window.
    <home> Moving to the head of current chr.
    <end> Moving to the tail of current chr.
    ↑ Zoom in.
    <+> Zoom in.
    <-> Zoom out.
    ↓ Zoom out.
     Display modes 
    p DEPTH only
    s SNP only
    i INDEL only
    a SNP and INDEL
    d Show/Hide indicator on map.
    n Show/Hide DEPTH=0
    e On/Off snpEff
    b On/Off Snpblock
    h This manual page.
    You will lose just all of your settings.
    (Data won't be deleted.)
    * It will be reloaded when restore.

    * It will be reloaded.
    : Number of blocks
    : Block Height
    : Block Width

  • ▓ LEVEL 0
    • INTERGENIC
  • ▓ LEVEL 1
    • UPSTREAM
    • DOWNSTREAM
  • ▓ LEVEL 2
    • UTR_5_PRIME
    • UTR_3_PRIME
    • REGULATION
    • INTRAGENIC
    • GENE
    • INTRON_CONSERVED
    • INTRON
    • INTERGENIC_CONSERVED
  • ▓ LEVEL 3
    • SYNONYMOUS_START
    • NON_SYNONYMOUS_START
    • START_GAINED
    • SYNONYMOUS_CODING
    • SYNONYMOUS_STOP
    • EXON
    • CDS
    • TRANSCRIPT
  • ▓ LEVEL 4
    • NON_SYNONYMOUS_CODING
    • CODON_CHANGE
    • CODON_INSERTION
    • CODON_CHANGE_PLUS_CODON_INSERTION
    • CODON_DELETION
    • CODON_CHANGE_PLUS_CODON_DELETION
    • UTR_5_DELETED
    • UTR_3_DELETED
  • ▓ LEVEL 5
    • SPLICE_SITE_ACCEPTOR
    • SPLICE_SITE_DONOR
    • START_LOST
    • EXON_DELETED
    • FRAME_SHIFT
    • STOP_GAINED
    • STOP_LOST
    • RARE_AMINO_ACID

    • What is snpEff?