In table 6 we can see that for p-values larger than 10-300 the results given by both methods are exactly the same when we consider order 0 Markov models. As smaller p-values are not well managed by C double precision computation (the exact limit depends on the system), we get wrong results unless log computations are used. Such computations have been implemented for FMCI algorithms (they are quite simple) but not for SR ones (where it is quite more complicated) which explain the differences for patterns at and tcgatc.