Fig. 4

Predicting the effects of repeat insertion on nucleosome positioning. Chemical map-based HBA scores and predicted nucleosomal occupancies were calculated for the original and modified BAR1 promoter sequences. The sequences were centered at the dyad position of the repressive nucleosome, in which the indicated repeat sequences were inserted. Horizontal lines at the bottom of each plot indicate the α2-operator (purple), the TATA (blue) element, the coding region of BAR1 (orange), and the insert (red). Note: the sequence insertion caused a shift of the left of the three predicted nucleosomes to the right to cover the α2-operator in the occupancy plots. Overconfidence should not be placed in this shift, as it may simply reflect that the dHMM tends to follow the linker length distribution, which generally does not allow longer linkers