Top panel: A model for site-specific recombination mediated prophage excision. The top line shows a schematic representation of the prophage in the chromosome with the att sites indicated by colored boxes. Excision of the prophage via site-specific recombination between the attL and attR sites results in a phage free chromosome (with attB) and the phage circle (with attP). Small numbered arrows indicate the location of the different primers used to detect prophage excision products and the blue bars (marked a-e) indicate the resulting PCR products. The primers indicated 1–6 correspond to 1-INF, 2-OUTR, 3-OUTF, 4-INR, 5-F and 6-R primers respectively for each prophage. Bottom panel: Agarose gel electrophoretic analysis of PCR products resulting from prophage excision in B. anthracis Sterne strain 34F2. The set marked as controls corresponds to PCR reactions designed to amplify pag gene (pXOl marker), gmk gene (chromosomal marker) and a negative control amp (pBR322) gene. The four sets of 5 reactions each corresponding to the four prophages is indicated on the lanes by a-e. The corresponding locations of the fragments a-e are shown in panel A.