Generate PCR products from template and primer sequences. Find primer annealing sites and compute product sizes.
Paste one or more FASTA sequences (max 200,000,000 characters).
Name of the forward primer.
Forward primer sequence (5' to 3', min 10 bases, supports IUPAC codes).
Name of the reverse primer.
Reverse primer sequence (5' to 3', min 10 bases, supports IUPAC codes).
Treat sequences as linear or circular molecules.
Paste one or more DNA template sequences in FASTA format. These represent the molecules (plasmids, genomic DNA) from which PCR products will be generated (limit 200 million characters).
Enter forward and reverse primer sequences (5' to 3' orientation, minimum 10 bases). Primers support IUPAC degenerate codes (R, Y, S, W, K, M, B, D, H, V, N).
Choose "Linear" for PCR fragments or "Circular" for plasmids. Circular topology allows products that span the origin of replication.
Results list all predicted products sorted by size (largest first), showing product length in base pairs, template positions, and the full amplicon sequence.
Primers must be at least 10 bases long and are specified in the 5' to 3' direction. Degenerate sites can be represented using IUPAC DNA characters (R, Y, S, W, K, M, B, D, H, V, N).
Linear: Template DNA is treated as a linear molecule. PCR products are only generated when the forward primer binds upstream of the reverse primer.
Circular: Template DNA is treated as circular (plasmid). Allows detection of products that wrap around the circular molecule.
Results are sorted by product size (largest to smallest). Each product shows the size in base pairs, position in the template, and the primers used.