oligo_pool_screen

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Screen a whole set of oligos you already have — every pair for cross-dimers, every oligo for its own hairpin and self-dimer, and the set for duplicates and Tm spread — and get back the conflicts ranked rather than a table of every combination. This is the pool-level answer cross_dimer gives one pair at a time: 51 primers is 1,275 pairs, which is 1,275 separate calls done by hand and one call done here. Not to be confused with multiplex_panel_design, which DESIGNS primers from templates; this takes the primers you have already ordered. A pairing that involves an oligo's 3' END is judged at a weaker ΔG than one that only pairs internally, because that end is where extension starts — the same two-bar rule the multiplex panel designer uses. Every number is a nearest-neighbour calculation over the sequences supplied, not a prediction of what the reaction will do.