Degenerate primer complexity
Count how many distinct sequences a degenerate oligo represents, from its IUPAC ambiguity codes — the product of the possibilities at each position.
How it works
Formula
complexity = product over positions of (number of bases the code allows). A/C/G/T = 1; R,Y,S,W,K,M = 2; B,D,H,V = 3; N = 4.
Worked example
ACGTRYN: the four plain bases each contribute 1, R and Y contribute 2 each, and N contributes 4 — so 1×1×1×1×2×2×4 = 16 distinct sequences.
When to use it
When designing degenerate primers (e.g. from a protein motif or across related taxa): higher complexity dilutes each individual sequence in the pool, which can reduce sensitivity and specificity.
Sensible defaults
The default ACGTRYN is a small example representing 16 sequences. Paste your own degenerate design to see its fold-degeneracy.
FAQ
- Why does complexity matter?
- Each distinct oligo is only a fraction of the synthesised pool. Very high degeneracy means any one primer is at low concentration, which can weaken priming and raise mispriming.
- Which codes are supported?
- All standard IUPAC nucleotide codes: A,C,G,T and the ambiguity codes R,Y,S,W,K,M,B,D,H,V,N.