Sites of DNA inversion within EC958 prophage genomes as determined by PacBio assembly of alternate alleles.

1Predicted binding site for DNA invertase shown in capital letters; site of strand exchange is indicated by underlined central dinucleotide with ∧ indicating downstream staggered cut; nucleotides in bold are consistent with the previously determined consensus DNA invertase crossover site [42]; square brackets indicate boundaries of larger imperfect inverted repeats that encode the crossover sites.2Coordinates refer to start and end of 26 bp crossover site in EC958 complete genome; 5prime/3prime orientation is relative to the complete prophage tail fibre gene and prophage genome; c = complement.3Phi1 and Phi4 5prime and 3prime 26 bp crossover sites differ by only 2 and 1 mismatches, respectively.