When comparing multiple sequences, one may find that alignment reveals no region with sufficient consensus to accommodate a unique single oligonucleotide for use as a primer or probe. In some cases, only one or two nucleotides are mismatched. When designing primers for those regions, one may choose to introduce a degenerate site, or "wobble", to compensate for the variability in the target sequence. Letter codes are used to represent the combination of two or more different nucleotide phosphoramidites blended at equimolar ratios prior to coupling at that position in the sequence. The final product is a blend of two or more different sequences made simultaneously during one synthesis.

2 nucleotide wobble
R = A+G
W = A+T
M = A+C
Y = C+T
S = C+G
K = G+T

3 nucleotide wobble
B = C+T+G
D = A+G+T
H = A+C+T
V = A+C+G

Universal wobble
N = A+C+T+G