Interaction matrix for a portion of human chromosome 1 from a recent Hi-C experiment by Dixon et al. . Each axis represents a location on the chromosome with a step of 40kbp. Densely interacting domains identified by the method of Dixon et al. are shown in red. Alternative domains are shown as dotted black lines on the upper triangular portion of the matrix. Visual inspection of the lower triangular portion suggests domains could be completely nested within another and highly overlapping when compared to Dixon et al.’s domains. This motivates the problem of identifying alternative domains across length scales.