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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