The statistical analysis of direct repeats in nucleic acid sequences

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Abstract
Sequence symmetries in DNA and RNA are being discovered at an increasing rate. Conjectures and hypotheses are being proposed for their possible structural and functional role in the nucleic acid. In this paper a probability model is studied which evaluates the probabilities of various repeats occurring by chance alone. Expressions are derived for the mean and variance of the statistics employed. The central limit theorem for dependent trials is used to obtain the asymptotic distributions. An indication is given of how to use the model to search for various gene amplification events in the evolutionary history of the sequences.