Design Sanger sequencing primers across a PCR product, insert, or region of interest using overlapping high-quality read regions.
Sanger Primer Designer is a browser-based tool for Sanger sequencing primer design, primer walking, and coverage across a target region.
Use note: Send candidate primers to Primer Binding Checker for binding-position validation and aim each primer at a high-quality read window.
Accepted file types: .txt, .fa, .fasta, .fna, .ffn, .seq, .gb, .gbk, .genbank. Plain-text DNA, FASTA, or GenBank text only.
Circular DNA/plasmids are not handled as circular yet. For regions that cross base 1, paste the relevant region as linear FASTA or raw DNA sequence.
Use 1-based coordinates. For best Sanger primer placement, include at least 100 bp upstream and 100 bp downstream of the amplification region of interest.
Each read zone generates one forward and one reverse sequencing primer. The low-quality edge is also used as the minimum reliable-window overlap, so fuzzy read ends are covered by reliable sequence from the next read.