Added support for a fixed number of mismatches in RegexpPatterns.
Created a method for generating a set of permutations of a specified
segment of a RegexpPattern. Created a data module, MatchSignificanceData
that iterates over all permutations of the MatchData patterns as
produced by the method above and evaluates their statistical
significance by comparing their frequency in the upstream regions of the
input ORFs to the frequency of the same number of regions simulated by
an O3 Markov model based on the genome background distribution using
Fisher's exact test. Created a data module, SubpatternFilter, which
filters out matches that do not contain a set of specified subpatterns.