Fig. 1.

The probability functions of each dinucleotide to construct the probability matrix in our model are simple sinusoids with a variable periodicity, except for the dinucleotides starting with a cytosine (CA, CC, CG and CT), which are assumed not to affect nucleosome position. In these graphs the periodicity is 10.0 bp. The dinucleotides TA, TT, AA, and GC were given an equal probability amplitude B. GC has half a helical turn offset compared to the first three dinucleotides. The probability functions of the other dinucleotides are such that the sum of probability functions starting with the same nucleotide is unity.