Abstract: This invention relates generally to novel means and methods for nucleic acid analysis and detection. More particularly, the present invention relates to a set of oligonucleotide probes, wherein two or more probes, in combination, can specifically detect a target polynucleotide and wherein different combinations of probes provide specificity for detecting and distinguishing different target polynucleotides. The invention also relates to methods for designing such combinations of oligonucleotide probes by way of gene sequence analyses that are preferably carried out using a digital computer, and to methods for interpreting the results of tests using such probe combinations.