LAMP primer design · PrimerDigital

Loop-mediated Isothermal Amplification (LAMP) uses 4–6 primers recognising 6–8 distinct regions of target DNA for highly specific amplification. LAMP reactions occur under isothermal conditions without special thermal cyclers.

Key features: Four core primers + two loop primers for accelerated reaction. DNA products are >20 kb formed from numerous repeats of the 200–350 bp target sequence.

Related sequences: paste two or more variants of the target and tick Consensus design — they are aligned first, and one set is designed whose every oligo fits all of them, as the Universal PCR tool does for a primer pair.

Retrieve sequence from NCBI by accession — chromosomes (NC_), mRNA (NM_), RefSeq contigs

NCBI Accession:

Upload local FASTA file — plain FASTA, multi-FASTA, or sequences

Upload FASTA:

Primer Design Options

Length range (nt)

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Tm range (°C) for standard PCR conditions

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Min. linguistic complexity (%)

3′-end pattern (5′-3′)

Max F2-B2 amplicon size (bp)

Max dimer ΔG at 65 °C (kcal/mol)

Specificity

Non-specific priming control

Low complexity priming control

Allow overlapping primer positions

Methylation

C→T bisulphite conversion (methylation analysis)

Reaction Speed

Loop Primer Design

Related sequences

Consensus design — align the input sequences (≥2) first, then design one set whose every oligo fits all of them

Allow degenerate 5′ end (variable columns become IUPAC codes; the 3′ window stays 100% conserved)

Auto-correct sequence orientation (reverse-complement) before alignment

Conserved 3′-window (nt)

Gap open penalty

Gap extend penalty

Need details? Sequence markup, parameters, output columns and the suggested workflow are documented in Help: LAMP tool · Help: Troubleshooting