What makes a pair diagnostic?

A pair that amplifies on one template and not on the others, or amplifies at a length that separates on a gel. The tool marks those pairs rather than leaving you to compare the product table by eye.

Does it check primers against templates they were not designed for?

Yes, that is the point of the screen: every primer is checked against every template in the set, and its off-target binding is counted and reported.

Where do the templates come from?

From the project. Open sequences, the current selection, or pasted bases, so a panel is screened against the real records rather than retyped identifiers.

Amplify · experimental

Multiplex PCR

A multiplex fails on the pairs nobody checked. Build the pool and the template set, then screen every compatible pair against every template and read what would actually amplify, including the products you did not intend.

Open Multiplex PCR Open the Primer test sample

Real sequences (GenBank plasmid, FASTA, and a protein family) for the Primer Designer

What it does

01A primer pool and a template set built from open sequences, selections or pasted bases
02Every compatible pair screened against every template, with the predicted product for each
03Per-primer off-target binding counts, so a primer that binds where it should not is visible
04The diagnostic pairs that distinguish one template from another on a gel
05A virtual gel of the predicted products, band by band

What it runs on

Screening runs on the `@ports/multiplex` port of pydna `primer_screen`, validated against pydna. The panel runs on @ports/fusion, @ports/gel, @ports/multiplex, @ports/pcr, @ports/primer.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Questions

What makes a pair diagnostic?: A pair that amplifies on one template and not on the others, or amplifies at a length that separates on a gel. The tool marks those pairs rather than leaving you to compare the product table by eye.
Does it check primers against templates they were not designed for?: Yes, that is the point of the screen: every primer is checked against every template in the set, and its off-target binding is counted and reported.
Where do the templates come from?: From the project. Open sequences, the current selection, or pasted bases, so a panel is screened against the real records rather than retyped identifiers.

Also searched as

multiplex PCR design · primer pool screening · diagnostic PCR primer design · multiplex primer compatibility · off-target primer binding check · pcr panel design tool · primer pool design tool · amplicon panel design · tiling amplicon design · check a primer pool for dimers