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Table 5 Computational time (in seconds) to get the statistics of degenerate patterns (the dot means "any letter") occurring 100 times in an order m = 1 Markovian sequence of length n = 9719 which parameters are estimated on the HIV complete genome sequence using either simple recurrences of finite Markov chain imbedding.

From: Effective p-value computations using Finite Markov Chain Imbedding (FMCI): application to local score and to pattern statistics

pattern atgca at.ca at..a a...a
SR 0.60 8.20 2438.43 105 209.12
FMCI 0.51 1.15 3.01 91.80