In-silico PCR — Predict Primer Amplicons Online
Enter a template and two primers to predict the PCR product, its size and position.
🔒 Local processing — pasted sequences are not uploaded
Check primer binding and expected amplicons before ordering primers or setting up 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 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 order does not matter and single-primer products are detected. Coordinates are 1-based on the forward strand; “mm” counts mismatches and a 3′ mismatch flags a primer whose extending end is not perfectly paired.
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 you can paste them 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.