An interactive computer system using a dot matrix approach has been developed and used to determine potentially significant features due to distortions in the B-DNA helix as a result of variations of purine and pyrimidine patterns. Sequences were compared using matrices which were generated using the Calladine-Dickerson rules (C.R. Calladine, 1 Mol. Biol. 161, 343-352, 1982 and R.E. Dickerson,/ Mol. Biol. 766, 419-441, 1983). Having control over various parameters to enhance different aspects of the visual appearance of these matrices was helpful in discovering patterns that were not known a priori. Specifically, it was found that a pattern of alternating doublets of purines and pyrimidines appear to exist in regulatory regions. This event is shown to be beyond probabilistic expectation.