Parameter estimates under our HMM for the four human in vivo data sets.

Medians and 80% credible intervals (CIs) of the posterior distribution of the parameters under our HMM are reported. The lower and upper limit of the 80% CI represent the 10- and 90-percentile, respectively. For hemi-preference ratios, one-sided 80% CIs are reported; that is, the lower limit is the 20-percentile of the distribution. Measurement error probability refers specifically to the inappropriate bisulfite conversion probability per CpG per strand (see Materials and Methods for detail). Except for mean association lengths and hemi-preference ratios, estimates reported here were obtained under a uniform (0,1) prior. Entries with an are sensitive to the choice of the prior distribution; in other words, the data are less informative about these parameters.