PCR / qPCR Primer & Oligo Design

Design primers for a target DNA region, get their Tm/Ta, and QC them for the secondary-structure problems that make a PCR fail.

When to use this

• Design a forward/reverse primer pair to amplify a region of a sequence.
• Compute the Tm / annealing temperature of a primer.
• QC an existing primer pair (GC clamp, 3'-end, hairpins, self/cross dimers, Tm match).

Step 1 — Design a primer pair

tu run DNA_primer_design '{"operation":"primer_design",
  "sequence":"ATGGCG...AACGTG",        # full template; must be >= target_end + flanking primer room
  "target_start":40, "target_end":125,
  "tm_target":60, "product_size_min":80, "product_size_max":140}'