Provide a target sequence once, then switch between assay designers with the tool tabs. Each tool has its own parameters and its own Generate button; results appear in the Report and Assay Sets tabs above the tool tabs.
Specificity
Multiplex
Designs one dimer-compatible assay per sequence so all targets can run together in a single reaction.
Methylation
Probe Format
Specificity
Multiplex
Designs one dimer-compatible castPCR set per locus so all targets can run together in a single reaction.
Methylation
Probe Format
Readout
Specificity
Methylation
Specificity
Methylation
Ligation site
Specificity
A [REF/ALT] marker sets the ligation site; with alleles, a separate LPO is made for each (common RPO).
Different dyes may share a size range freely — colour tells them apart. Set Dye channels to 1 for a single-colour panel: every product is then separated purely by size, kept at least Min size gap apart (10–20 nt is typical for reliable CE resolution); the panel tries each locus's alternative primer pairs to make that fit.
The tail (e.g. M13) enables cheap fluorescent labelling (one dye-labelled universal primer per colour); the reverse PIG-tail (GTTTCTT) promotes full +A adenylation for sharper peaks. Both 5′-tails are templated into the amplicon, so the M13 tail (+18 nt) and PIG-tail (+7 nt) are already included in the reported product and allele sizes. For >1 dye, give each channel its own universal tail.
Specificity
Methylation
Specificity
Methylation
Reaction Speed
Exporting results: click inside the result area → Ctrl+A → Ctrl+C → paste into Excel.