Figure 2

Outline of the benchmarking test. The diagram shows the benchmarking test used and an example of a noise-disturbed PFM with 75% noise added. In the pair-wise distance matrix in the middle, correct PFM pairs lay in the diagonal (red), all other are false pairs (grey). The panel on the right shows how true and false positives and negatives were assigned using a varying threshold. In the left panel, i is a row, j is a column in the matrix, AT% and GC% are the background AT/GC-content (34%/16%), and noise is the proportion of noise added.