Contains parameters for computing transition probabilities
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length-one numeric vector
The maximum probability that the current state is the same as the preceding state. See details
Diagonal elements of the transition probability matrix are
computed as e^-2*d/taup, where d is the distance between markers
i and i-1 and
taup is typically in the range of 1xe10. This
probability is constrained to be no larger than
probabilities on the off-diagonal elements are the same and are
subject to the constraint that the rows of the transition
probability matrix sum to 1.
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