The frequency of two-base tracts in eukaryotic genomes

The frequency of two-base tracts is surveyed in a wide range of eukaryotic genomes using the special program TRACTS. All three two-base families are surveyed: R.Y (A,G.C,T), K.M (A,C.G,T), and S;W (A.T and G.C). Data for the human β-globin complex, for the tobacco chloroplast, and for 247 nt mammalian promoter regions are presented. All two-base tracts longer than three or four bases are overrepresented to an extent surpassing by far their occurrence in a randomized DNA population in the majority of the genomic regions analyzed; 20–30 long tracts are quite frequent, against the statistical odds. R.Y tracts are found at the largest excess, K.M tract to a slightly lesser extent, while S.W tracts are found at a moderate yet significant excess. The majority of the tracts manifest only a limited extent of tandem repeat structures. The idea that the two base tracts serve as unwinding elements is considered. Preseented at the NATO Advanced Research Workshop onGenome Organization and Evolution, Spetsai, Greece, 16–22 September 1992