The processes of spontaneous mutation are known to be influenced by neighboring DNA. Imperfect nearby repeats in the neighboring DNA have been observed to mutate to form perfect repeats. The repeats may be either direct or inverted. Such a mutational process should create perfect direct and inverted repeats in intergenic DNA. A larger than expected number of direct repeats has generally been observed in a wide range of species in both coding and noncoding DNA. Simulations are carried out to determine how this process might influence the repetitive structure of genomic DNA. These simulations show that small repeats created by this kind of a mutational process can explain the excess number of repeats in intergenic DNA. The simulations suggest that this mechanism may be a common cause of mutations, including single-base changes. The influences of the distance between imperfect repeats and of their degree of similarity are investigated.
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