Folding patterns of chromosomes III (a, b) and XII (c, d). The heat maps (a, c) and Circos diagrams (b, d) were generated using the intra-chromosomal interactions identified from the HindIII libraries at an FDR threshold of 1%. In the heat maps (a, c), the chromosomal positions of centromeres (dashed pink lines), telomeres (pink hatches), mappable (green hatches) and un-mappable (black hatches) HindIII fragments are indicated. Circos diagrams (b, d) depict each chromosome as a circle. Each arc connects two HindIII fragments and represents a distinct interaction. The shade of each arc, from very light grey to black, is proportional to the negative log of the p-value of the interaction. The chromosomal positions of centromeres (red hexagon), telomeres (red colored area), tRNA genes (blue outer thatches), mappable (green inner hatches) and un-mappable (black inner hatches) HindIII fragments are indicated. Black outer hatches and numbers mark genomic positions. Note that the two ends of chromosome XII (c, d) exhibit extensive local interactions but very little interaction with each other. Separating the ends of chromosome XII are 100–200 rDNA repeats, of which only two copies are depicted here (from coordinates 450 to 470 kb). Additional heat maps and Circos diagrams for all chromosomes are shown in .