Required intervals

A required interval is the span that every returned PCR product must contain. Primer sites are placed outside the interval, and the complete amplicon must satisfy --product-size.

How each input mode defines it

Mode	Required interval
sequence	--target-start through --target-end
fasta	Centered interval of --target-width bases
annotated	Every matching named feature
bed	Each BED row
tss	Requested upstream/downstream span around each TSS

For GenBank and SnapGene input, a feature labeled required_interval is used by default. Multiple such features produce independent design results. Other labels can be selected with repeated --required-feature arguments or with --required-features-file.

Search window versus product size

--search-window controls how far smfprimer supplies sequence to Primer3 on each side of the target. --product-size constrains the complete product. Both must be large enough to fit the required interval and two primers.

If no pair is possible, the target is retained in output with status=no_candidates rather than silently discarded.