Abstract: A method for matching character strings to a reference character string is disclosed. One or more processors receive a plurality of character strings. The one or more processors match each of the plurality of character strings to a main reference character string and registers a match to positions on the main reference character string that satisfy a pre-set match criteria. The one or more processors match each of the plurality of character strings to an alternate reference character string and registers a match to positions on the alternate reference character string that satisfy the pre-set match criteria. The alternate reference character string is derived from the main character string. The one or more processors identifies a match for each of the plurality of character strings that match to either a position on the main reference character string or the alternate reference character string.