Comparison of three repeat masking settings. Left panel - The fit results of the WSSD coverage data sample from 39 single BAC-anchored loci (black dots) obtained using the "div10_low", "nodiv_low" and "nodiv_N" masking settings are displayed. The data are fitted to a model of four Gaussian distributions (G1, G2, G3 and G4) drawn in green, red, yellow and magenta, respectively, with their sum drawn in blue. Mean (red vertical line) and sigma (magenta vertical line) values in the box refer to Gaussian G1. On top, the normalized residuals distribution (Pull = (Ndata-Nfit)/σdata, N and σ being the number of events and the error for each bin) is shown. When the pull distribution is fully between -3 and 3, fluctuations are only statistical. Right panel - WSSD outputs and segmentally duplicated regions according to the three masking methods of VV40024H153A08, 153A22, 153C20, 153C22, 153D03 and 153D07 BAC clones.