A second computer program was designed that analyzed the datasets from the mixed analysis for the frequency of occurrence of the stored fingerprints. Each dataset derived from a pool of 96 colonies (6 complex fragment mixtures in 2 corresponding lanes on two corresponding gels) was queried for the concurrent occurrence of the peaks / fragments of each fingerprint, respectively (see Fig. 4). As an example, for a certain cDNA fingerprint the the peak from SCA for restriction enzyme DdeI was determined at 326,5 bp. In one lane in a MA there are multiple peaks stemming from DdeI digestion (50.3, 67.4, 98.5,.....326.7....500.1...). The computer program checked if the peak for Dde I was contained in the complex peak mixture derived from the Dde I digest, considering a certain bandwidth. In the example above, 326.7 bp in the MA would be considered as a hit. The computer program did the same for the other 5 restriction enzymes. When all peaks are simultaneously present in one dataset from a pool of colonies the counter for this fingerprint/gene goes up by one. It is possible to adjust the program to query the data with only a subset of the 6 restriction enzymes of the fingerprints.