The parser now gracefully skips over positions with N or other ambiguous bases (e.g., R , Y , S , W ) in the template sequence without crashing, instead of treating them as hard mismatches. This is particularly useful for designing primers from draft genomes or metagenomic scaffolds.
These primers show high specificity and minimal 3'-end stability – ideal for SYBR Green qPCR. primer3 0.4.0