In order to accurately use positional information, there is a need to know the probability that two genes will be separated by nonhomologous recombination per unit time.

The following is an exerpt from Pedulla et al., 2003 exemplifying an apparent high degree of rearrangement affecting bacteriophage genomes.

Note that the gene indicated on the top of the list as the best match by Blast keeps changing from one gene to another along the genome.