DigitalGens

Allele-specific primers for KASP, PACE, ASQ and generic AS-PCR. Biallelic SNPs, InDels and complex haplotypes, with automatic tail selection and Tm balancing. An allele-sizing mode trades the fluorophore for a gel: 5′-tails space the allele products into a ladder, so the genotype is read off band length.

TaqMan, MGB and molecular-beacon probes for quantitative allelic discrimination — allele-specific pairs with matched Tms and minimal cross-reactivity, with a multiplex mode.

Rare somatic mutations down to 0.1% allele frequency. Designs the competitive triplet — allele-specific primer, allele-specific probe and common counter-primer — in both orientations, with multiplexing.

Single-base-extension primers for multiplex SNP and InDel genotyping on capillary electrophoresis. Also supports BAC fingerprinting and CpG-methylation minisequencing.

Ligation-dependent half-probe pairs (LPO + RPO) with stuffer sequences and universal tags, for copy-number, SNP and InDel detection by capillary electrophoresis or, for up to 1000 targets, by sequencing.

Flanking primers for microsatellite genotyping by capillary-electrophoresis fragment sizing, with economical universal-tail fluorescent labelling and automatic multiplex dye/size assignment.

General-purpose design engine covering standard, inverse, multiplex, TaqMan/MGB-probe, bisulphite and RPA assays. The quantitative-fluorescent mode generates STR-flanking primers for dosage and copy-number analysis.

Consensus primers designed from a multiple sequence alignment of two or more sequences: every 3′-end fully conserved across all inputs, with optional IUPAC-degenerate 5′-ends for pan-specific amplification of divergent targets.

Cas9 and Cas12a guides with activity and specificity scoring, an off-target search across the sequences you supply, HDR/ssODN donors carrying a silent PAM-blocking change, the primers that screen the edit, prime-editing pegRNAs with a Tm-matched PBS, and base-editing windows with bystander prediction.

Collateral-cleavage detection assays: Cas12a and Cas13a crRNAs with allele-specific synthetic-mismatch discrimination, RPA pre-amplification primers with a T7 promoter where the enzyme needs a transcript, and the quenched ssDNA/ssRNA reporter for fluorescence or lateral flow.

Toehold-mediated strand-displacement exchange probes for high-specificity SNP/allele discrimination. Tunes the probe to a near-thermoneutral reaction and scores single-base mismatches with measured nearest-neighbour thermodynamics.

Virtual PCR against sequences you supply: where each primer, probe, miRNA or gRNA binds, which pairs give an amplicon and at what size, and which bindings are off-target. Mismatches are allowed, so a primer that anneals imperfectly is still found.