Methods for finding patterns in symbol sequences and a computer readable medium having instructions for performing the methods. Symbol patterns common to each 2-tuple of sequences are represented by a position index numerical array (PINA) or a position index binary array (PIBA). A PINA is a set of position indices each denoting the location in a reference sequence where each symbol in the pattern occurs. A PIBA is a set of bits. Each bit corresponding to a symbol in the identified pattern has a first value. Patterns are combined using the PIBA representations of one tuple taken with the PINA representations of the other tuple. Arrays representing patterns in one tuple are interrogated by a PINA representing each pattern in the other tuple and those places having the first value are identified. The symbols in the reference sequence corresponding to the identified places in the PIBA define the pattern.