What run length is a problem?

There is no hard cut-off, but 3′ complementary runs of about 3+ bases (and especially G/C-rich ones) are worth avoiding. Internal complementarity matters less than 3′-anchored runs.

Does this model thermodynamics?

No. It counts complementary base runs as a fast heuristic. For ΔG-based dimer prediction use a nearest-neighbour tool; this is for quick screening.

Primer-dimer checker

Check a primer pair for self- and cross-dimer risk by scanning 3′ ends for complementary runs, and report each primer’s 3′ GC clamp.

How it works

Formula

An antiparallel complementary stretch of length L between two primers means one primer shares an L-base substring with the reverse complement of the other. The 3′ run is the longest such stretch anchored at a primer’s 3′ end — the end a polymerase extends.

Worked example

Forward AAAAGGGG and reverse AAAACCCC: reverse-complement of the reverse primer is GGGGTTTT, which shares GGGG (4 bp) with the forward primer’s 3′ end — a 4 bp 3′ cross-dimer.

When to use it

When designing or troubleshooting a primer pair: long 3′ complementary runs cause primer-dimers that waste reagent and can dominate low-template reactions. A 1–2 base 3′ GC clamp helps priming; 3+ strong 3′ G/C can promote mispriming.

Sensible defaults

The defaults are two deliberately dimer-prone primers so you can see a non-zero 3′ run. Paste your own candidate pair to evaluate it.

FAQ

What run length is a problem?: There is no hard cut-off, but 3′ complementary runs of about 3+ bases (and especially G/C-rich ones) are worth avoiding. Internal complementarity matters less than 3′-anchored runs.
Does this model thermodynamics?: No. It counts complementary base runs as a fast heuristic. For ΔG-based dimer prediction use a nearest-neighbour tool; this is for quick screening.