In-silico PCR — Predict Primer Amplicons Online
Enter a template and two primers to predict the PCR product, its size and position.
Check primer binding and expected amplicons before ordering primers or setting up a PCR. Paste a template and a forward/reverse primer pair; the tool finds where each primer anneals on either strand and reports every predicted amplicon with its position, length, GC content and full product sequence. It tolerates a configurable number of mismatches, flags 3′-end mismatches that would block extension, and handles circular templates such as plasmids.
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Enter a template and at least one primer.
Either primer may bind as the forward (top-strand) or reverse (bottom-strand) primer, so the order they are entered in does not matter and single-primer products are detected. Coordinates are 1-based on the forward strand. “mm” counts mismatches, and a 3′ mismatch marks a primer whose extending end is not perfectly paired.
Got a band of the wrong size? Find where it came from
Where the gel shows a band the simulation above does not predict, enter the size measured. Every pair of priming sites on the template that would produce that size is reported, including mismatched sites and a single primer priming off both strands, which distinguishes mispriming from a wrong template.
Traced against the template and both primers in the PCR form above.
Still needed: a template in the PCR form above, a forward primer above and a reverse primer above.
How to use the In-silico PCR tool
- 1Paste the template DNA (raw or FASTA); tick “circular” for a plasmid.
- 2Enter your two primers (5'→3'); the tool tries both orientations automatically.
- 3Set the allowed mismatches per primer and read off each predicted product's size, position and sequence.
Frequently asked questions
Does primer order matter?
No. Each primer is tested both as a forward (top-strand) and a reverse (bottom-strand) binder, so they can be pasted in either order. Single-primer products, where one primer has two sites in opposite orientation, are detected too.
How are mismatches handled?
You can allow up to three mismatches per primer. Each predicted product reports how many mismatches each primer has, and separately flags when the 3′-terminal base, the one a polymerase extends from, is not perfectly paired.
Can it handle plasmids and circular templates?
Yes. Enable “circular template” and the tool also finds products that span the origin, capping product length at the template length so it never wraps more than once.