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Design primers for PCR-RFLP for the Illumina Bovine 55k SNP set

This site was designed to be used to design primers for any SNP in the set with the option of selecting SNP cut by a given restriction enzyme.

The expected method of use is to test different parameters until you have a suitable number of SNP. Then there will be the option to design primers for them

A flatfile of the SNP data is available for download

If the number of SNP returned is less than 10000 then you will be able to design primers against each of them

Co-ordinates of region of interest in Bovine Assembly UMD3.1
Chromosome (integer)StartEnd
Eg; 180000000100000000
Positions cut by restriction enzyme(s)
Minimum interval between adjacent SNP
Minimum number of heterozygotes in my set of 6 samples

Values in the form are sticky click to clear them and start again

SNP for public SNP from Ensembl;
Count 0

SNP were selected for: public SNP from Ensembl; Enzyme restriction site: ;

If the Number of loci looks about right then get the sequences for primer design

Health Warning

All SNP are relative to Hereford reference genome. Most SNP were descovered by low coverage Sanger sequencing and have not been validated. All data is provisional and subject to change.