A method of determining whether two patterns having a plurality of homologous regions match, comprising: generating a set of decisions associated with values (k,n) for determining whether the patterns match, where k, is a number of non similar homologous regions from a sample of size, n, of the homologous regions; constraining the decisions so that a probability of providing a false negative decision that there is no match when in fact there is a match is less than or equal to a predetermined upper bound; configuring the association of decisions and pairs (k,n) to minimize running time of a computer programmed to use the set of decisions to determine whether there is a match; and using a computer programmed with the set of decisions to determine if the patterns match.