Primer Scan (Beta)

Check primer specificity for cloning and colony PCR against a selected genome or custom DNA reference.

Note: Bundled references include chromosomal DNA only. Gene annotations are available except for NRRL3.
NRRL3 is assembled in separate DNA segments, which are scanned independently.

Genome selection

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Custom genome

Custom genome sequence

Reference topology

Upload custom genome file

Use an assembled DNA reference with one record per chromosome, plasmid or contig. A/C/G/T/N only; N-containing binding sites are skipped.

Uncompressed FASTA, GenBank or text: up to 60 MB and 50 million bases. Custom reference requirements

Primer pair 1

Forward primer (F1)

Reverse primer (R1)

Expected PCR product size in bp (optional)

Product screening

Annealing temperature Consecutive 3' matches

PCR annealing temperature, °C

Specificity scan settings

Minimum binding length, bp

Maximum binding-region mismatches

Allowed 3' window mismatches

3' strict window, bp

Min amplicon size, bp

Max amplicon size, bp

Review margin below Ta, deg C

Na+ equivalent, mM

Primer concentration, nM

Mg2+, mM

Total dNTPs, mM

Require the final 3' base to match to meet the screen.

Include sites outside the 3' limits for review.

Allow non-binding 5' tails.