Start-to-start distance analysis of nucleosome spacing on CRM1 and CRM2. (A) A schematic description of the start-to-start distance analysis. Three 155-bp nucleosomes (represented by purple circles) starting 190 bp apart give rise to 155-bp reads with alignments of both orientations--forward in blue, reverse in red. Distances between the start of the first forward alignment and start of the first reverse alignment correspond to the length of one nucleosome core. Distances between start of the first forward alignment and subsequent reverse alignments increase by 190 bp, corresponding to an additional nucleosome core and linker region. (B) A short range start-to-start distance analysis for CRM1 and CRM2 nucleosomes. The number of starts separated by each possible distance was quantified in terms of a coincidence index value. We arbitrarily cut off this plot at 650 bp to emphasize the presence of a peak at ~155 bases (as well as two subsequent peaks separated by ~190 bp). Vertical lines are spaced every 20 bp. (C) A long range start-to-start distance analysis for CRM2 CENH3 nucleosomes. Distances between start positions from alignments of opposite orientations were calculated and the number of starts separated by each possible distance between -7577 and +7577 bp quantified in terms of a coincidence index value. The length of the CRM2 reference sequence is 7577 bp, precluding any longer distances. For a random sampling of alignment pairs, the probability is lowest in order for them to be separated by the longest possible distance (the element's length), as there is only one possible combination for either the positive or negative extreme. In contrast, the number of combinations that allow for a distance of zero is almost as large as the length of the element. Hence, the triangular shape of the plot, with a peak centred near zero and tapering off in both directions. Vertical lines are spaced every 190 bp.