Update how primer3.py masks bases for variants

[tfenne]

We should review how we use the variants from VariantLookup to mask bases in the design sequence. I think we should probably change masking to do something like:

• SNPs should mask just the SNP base
• MNPs (with len(ref) == len(alt)) should mask all the changed bases
• Deletions should mask all deleted sequence (possibly flanking bases too??)
• Insertions should mask the bases either side of the insertion site
• Anything else we probably want to think about masking fairly aggressively