Abstract: The present invention relates to methods for the design and/or production of a probe or primer that is capable of hybridizing to a plurality of sites in a sample comprising nucleic acid. Furthermore, the present invention provides methods for detecting and amplifying nucleic acid using such a probe or primer, for example, for identification of a strain, species or genera. Probe or primer sequences are determined by reference to codon usage bias of a target nucleic acid. In addition, the present invention provides methods for determining codon distribution and/or base pair distance between codons in a nucleic acid.