A recombinase site is two inverted repeats around an asymmetric spacer — ATAACTTCGTATA GCATACAT TATACGAAGTTAT for loxP. Two things follow, and between them they are this whole tool. The arms are a reverse complement of each other, so the site folds into a hairpin stable enough to keep a primer from annealing across it. And the spacer gives the site a direction, so two sites recombine only when their spacers match — which is what makes lox2272, loxN and F3 orthogonal — and same-direction sites excise while opposite ones invert.
So the tool finds every site, measures the hairpin each one actually forms (which usually runs a little past the 34 bp core, into the flank), says which pairs the enzyme can use and what it would do, writes out the resulting alleles, and designs the two assay geometries that work on a hairpin: tear-pin, where primer and reporter pull the arms apart from opposite sides, and break-hairpin, where one long primer starts inside an arm and runs out into unique sequence. To genotype the excision product itself, paste the predicted alleles into Insertion & Knock-in Genotyping.
One sequence, 5′→3′, with or without a FASTA header — the construct as it stands before the recombinase acts. Brackets and slashes are ignored, so a sequence marked up for another tool can be pasted straight in.
One flank of a site is often much easier sequence than the other. With this off, only the left-to-right geometry is tried; with it on, both are, and the report shows each.
Export: use Copy / Download above each report, or click inside a result area → Ctrl+A → Ctrl+C.