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Ancestral repeats: Substitution parameters for context-dependent model frequencies and a second-order Markov chain at the root. Substitution parameter estimates (mean and 95% credibility intervals) for each of the twelve entries of the general time-reversible model in each of the sixteen neighbouring base combination using context-dependent model frequencies and a second-order Markov chain to specify the ancestral root distribution. Note that the log-scale is used for the y-axis.
