PCR Primer Designer — Design Primer Pairs Online
Design ranked PCR primer pairs from a template, with Tm, GC and dimer checks.
🔒 Local processing — pasted sequences are not uploaded
Design PCR primers from a DNA template without leaving the browser. Paste a sequence (optionally marking a region the product must span), set your length, Tm, GC and amplicon-size preferences, and get ranked forward/reverse primer pairs scored on nearest-neighbor Tm, GC content, 3′ clamp, hairpins and cross-dimers. Copy the primers or export the whole set as CSV — a fast, no-signup alternative to dated primer pickers.
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Candidate primers are scored on length, nearest-neighbour Tm, GC content, 3′ GC clamp and self-structure, then paired by amplicon size, Tm match and cross-dimer. Tm uses SantaLucia (1998) thermodynamics under the conditions set above. Verify specificity against your template/genome before ordering.
How to use the Primer Designer tool
- 1Paste a DNA template (raw or FASTA), and optionally mark a target region.
- 2Adjust the length, Tm, GC and amplicon-size constraints if needed, or keep the defaults.
- 3Click Design primers, then copy the best pair or export all candidates as CSV.
Frequently asked questions
- How are primers scored and ranked?
- Each candidate is scored on how close its length, nearest-neighbor Tm and GC content are to your targets, plus a 3′ GC-clamp check and self-dimer/hairpin screening. Pairs are then ranked by combined penalty, the Tm match between the two primers, and cross-dimer ΔG.
- Does it check primer specificity against my genome?
- No — it designs primers from the template you paste. To confirm a pair amplifies only your intended target, check them with the In-silico PCR tool against your full template or use a specificity search before ordering.
- What melting-temperature model does it use?
- SantaLucia (1998) nearest-neighbor thermodynamics under the reaction conditions you set (oligo, Na⁺, Mg²⁺, dNTP), the same engine as the Oligo Analyzer.