Isochores describe a region of a chromosome where the CG-content is either higher or lower than the whole genome average (42%). A CG-rich isochore is given a dark color, while a CG-poor isochore is a light color.
Isochores were determined by first calculating the CG-content of 100,000 bp windows across the genome. These windows were either labeled H or L depending on whether the window contained a higher or lower GC-content than average. A two-state HMM was created in which one state represented GC-rich regions, and the other GC-poor. It was trained using the first 12 chromosomes. The trained HMM was used to generate traces over all chromosomes. These traces define the boundaries of the isochores, and their type (GC-rich or AT-rich).