B. subtilis tetranucleotide MCM, ROF, and ZOM autocorrelation profiles. Di-, tetra- and hexanucleotide ZOM (top), respectively red, green and blue lines, together with tetranucleotide MCM and ROF (below), respectively green and red lines, based autocorrelation profiles of B. subtilis. Autocorrelation scores (vertical axis) are obtained with 5 kbp sliding windows, overlapping every 2.5 kbp, correlated with mean genomic values. The horizontal axis represents chromosomal position, with each point spanning 5 kbp. Average autocorrelation scores drop progressively for di- to hexanucleotide ZOMs, presumably due to lower departure values between observed and expected tetranucleotide frequencies caused by small sliding windows. ZOM and ROF based profiles appear similar, but the former appear more detailed. Although the hexanucleotide ZOM and tetranucleotide MCM measures had similar average autocorrelation scores, the latter can be observed to vary considerably more than the former. All marked dots represent presumed horizontally acquired DNA, and the two largest dips located close to 2.2 mbp and 2.7 mbp are known prophages.