castPCR Genotyping Assays Design

castPCR (Competitive Allele-Specific TaqMan PCR) is a real-time PCR method for detecting and quantifying rare somatic mutations against a large excess of wild-type DNA. By combining allele-specific primers with MGB blocker oligonucleotides that suppress wild-type amplification, it routinely resolves mutant alleles down to ~0.1% — sensitivity well below what Sanger sequencing can reach.

Read Instructions
Retrieve flanking sequence from Ensembl by rsID — validates species, fetches forward-strand context with allele bracket
Enter Ensembl species id (lowercase, underscores). Custom species are stored in this browser.
Upload local FASTA file — plain FASTA, multi-FASTA, or sequences with [REF/ALT] brackets
Primer Design Options
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Specificity

Methylation

Probe Format

Need details? Sequence markup, parameters, output columns and the suggested workflow are documented in Help → castPCR. Exporting results: click inside the result area → Ctrl+A → Ctrl+C → paste into Excel.