Excision assays were designed as described previously (45 (link)). Briefly, a multiplex PCR assay was designed to produce amplicons of distinct sizes if the Pf prophage was integrated (primers Fwd_1 and Rev produce a smaller band) or excised (primers Fwd_2 and Rev produce a larger band) using Phusion Plus PCR Mastermix (Thermo Scientific # F631L). Primers were used at a final concentration of 0.5 µM and are listed in (Table 3).
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