Site of the CDC 684 inversion. This figure contains the entire sequences for the Lambda Ba04 and Lambda Ba02 rep genes. The 5' nucleotides in black represent regions unique to the prophage rep genes and are in the same directionality in the CDC 684 and Ames Ancestor genomes. The blue and orange nucleotides represent the 3' ends that are homologous to both rep genes, and likely represent the site of recombination that resulted in the 3.3 Mbp inversion in CDC 684. Seven SNPs that define the prophage 3' ends are in larger font, and are labeled 1-7 or 7"-1" for Lambda Ba04 or Lambda Ba02, respectively. In CDC 684, the allele states for these prophages have switched chromosomal positions relative to Ames Ancestor.