CENH3 nucleosome core lengths and AA/TT contents. (A) Number of reads per read length (bp). Genome-matching reads with unambiguous termini favour a length of around 155 bp. 'total genome' includes everything that aligned to the maize genome, version 1. The three centromere elements are shown separately. See also Additional File 1, part B. (B) The frequency of AA or TT dimers at each position along the read lengths. The reads were aligned at their starts and the number of AA or TT dimers counted at each position for each aggregated set. We arbitrarily cut off the analysis at position 200 in order to avoid statistical noise from the low number of reads with lengths greater than 200 bases. In the total genomic reads, the change in AA/TT content visible near position 155 suggests a subtle distinction in nucleotide content between the nucleosome core DNA and linker DNA. The CentC, CRM1, and CRM2 reads were identified by blastall alignments. See also Additional File 1, part C.