Custom multiplex tiling PCR panel design tool

Design tiling PCR primers for complete coverage of target sequences. Mark target regions with [ and ] brackets.

Use /.../ to exclude specific regions from primer design.

NCBI Accession:

Upload FASTA:

Upload or paste sequence(s) in FASTA format:

Target sequence(s)

Pre-designed Primers

Report (Primer list)

PCR primer panels

Primer Design Options

Length range (nt)

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Tm range (°C)

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3′-end pattern

PCR product size (bp)

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Gap between amplicons

Non-specific priming control

Overlapping primers

C→T bisulfite conversion

Forward primer tail (5′-3′)

Reverse primer tail (5′-3′)

Target marking: [target region] for single or multiple targets
Exclude regions: /excluded/ to skip specific areas
IUB/IUPAC codes: B=CGT, D=AGT, K=GT, M=AC, N=ACGT, R=AG, S=GC, W=AT, Y=CT

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Export: Select all (Ctrl+A), copy (Ctrl+C), paste into Excel (Ctrl+V)

Provide a single reference/target sequence; mark one or multiple targets with [ ... ] blocks.
Set the desired amplicon size range based on your sequencing platform (NGS vs long-read).