PCR Primer Designer — Design Primer Pairs Online
Design ranked PCR primer pairs from a template, with Tm, GC and dimer checks.
🔒 Nothing you paste is logged or stored on our servers
Design PCR primers from a DNA template in seconds. 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.
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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.
Working on a whole construct rather than one primer pair? Open SeqStudio — the full editor, with live feature annotation, plasmid maps, restriction and primer panels, undo/redo, multi-document tabs and GenBank / SnapGene import and export.
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.
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Guides
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