kmers split by 2 adjacent SNPs for allele-specific primers

[dustinlong]

I am interested in using SKA to generate allele-specific LNA-modified primers for clinical outbreak investigation. I have successfully run through the tutorial with a test dataset but am trying to solve the following problem: from a primer-design perspective, it may be optimal to identify split kmers which differ by two adjacent nucleotide rather than just one. Is this something that might be possible with SKA or would be within the scope of future releases?

Many thanks,

Dustin