Figure 7.

MCMC move where a boundary between slow and fast regions is shifted by three root nucleotides. This move is especially important in accurately calculating footprinting posterior probabilities at the edges of functional regions. We do not allow insertions to occur at the beginnings or ends of functional regions, as shown in the alignment on the right. For display purposes, nucleotides emitted from slowly evolving regions are represented as capital letters. While we store internal sequences as Felstenstein wildcards, we display the most likely nucleotide at each position here.

Satija et al. BMC Evolutionary Biology 2009 9:217   doi:10.1186/1471-2148-9-217
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