Multiplex PCR panel design
multiplex_panel_designRead-onlyIdempotent
Choose one primer pair per target so the whole panel works in one tube: no cross-dimer between any two of the primers, every amplicon resolvable from every other on the gel you will run, and one annealing temperature that serves all of them. Searches combinations rather than picking each target's best pair in isolation, which is what makes panels fail — and when no compatible panel exists it names the target pairs that cannot be multiplexed at all, so you know which one to redesign.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| targets | Yes | 2-8 targets to amplify in one reaction. | |
| ampliconMax | No | Panel-wide default product size ceiling. | |
| ampliconMin | No | Panel-wide default product size floor, for targets that set none. | |
| maxTmSpread | No | Widest Tm difference tolerated across every primer in the panel, in °C — one annealing temperature has to serve all of them. | |
| agarosePercent | No | Gel the panel will be read on. Omit and the percentage whose resolving window contains the amplicons is chosen and reported — a panel of small products judged on a 1% gel reads as all-comigrating, which is about the gel rather than the primers. | |
| dimerThresholdDG | No | ΔG (kcal/mol) at or below which a cross-dimer involving a primer's 3' END is a conflict. That end is where extension starts, so it matters at a weaker ΔG than an internal pairing. | |
| candidatesPerTarget | No | Candidate pairs considered per target (max 6). More finds a panel where fewer cannot, at the cost of a larger search. | |
| internalDimerThresholdDG | No | The looser bar for a cross-dimer that pairs internally and only sequesters primer. |