Scaling behavior of rate correlations. To determine the importance of regional effects on the correlations, we normalized the substitution rate of each repeat with respect to the average substitution rate in its local neighborhood, varying the bin size and hence the scope of the neighborhood. We then recalculated the correlations as a function of bin size. While the correlations are stable for bin sizes larger than 500 kb, they decrease in all three comparisons as the bin size becomes smaller. These results indicate that much of the correlations are due to regional effects on the scale of ~10–500 kb.