SNP/InDel Genotyping — TaqMan/MGB/Molecular beacon Probe Design

Automated design of allele-discriminating probe–primer sets for SNP and InDel genotyping by quantitative PCR (qPCR) using dual-labelled probes.

Supports TaqMan (hydrolysis), MGB (minor groove binder) and Molecular beacon (hairpin-shaped) dual-labelled probes formats. Sequences can be fetched directly from Ensembl by rsID or loaded from a local FASTA file. All primers and probes are screened for Tm, hairpins, primer–dimer interactions, repeat masking, and linguistic complexity. Enable Multiplex PCR to design a dimer-compatible assay set per target, so multiple SNPs/InDels can be genotyped together in a single reaction.

Retrieve flanking sequence from Ensembl by rsID — validates species, fetches forward-strand context with allele bracket

Species:

rsIDs:

Enter Ensembl species id (lowercase, underscores). Custom species are stored in this browser.

Flank size (±bp):

Retrieve flanking sequence from NCBI by rsID — validates species, fetches forward-strand context with allele bracket

Human rsIDs:

Flank size (±bp):

Upload local FASTA file — plain FASTA, multi-FASTA, or sequences with [REF/ALT] brackets

Upload FASTA:

Primer Design Options

Length range (nt)

–

Tm range (°C) for standard PCR conditions

–

PCR product size (bp)

–

3′-end pattern (5′-3′)

Forward tail (5′-3′)

Reverse tail (5′-3′)

Specificity

Non-specific priming control

Low complexity priming control

Allow overlapping primer positions

Multiplex

Multiplex PCR

Designs one dimer-compatible assay per sequence so all targets can run together in a single reaction.

Methylation

C→T bisulfite conversion (methylation analysis)

Probe Format

TaqMan probe (18–28 nt)

MGB probe (12–28 nt)

Molecular beacon probe (18–35 nt)

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