Table 3.

The comparison between the number of all possible pairs of windows in input and that of pairs of windows in DotcodeR prediction on human chromosome 21 and mouse chromosome 19

# of pairs of windows in original input	# of pairs of windows in cleaned input	# of pairs of windows in prediction	Reduction (%)
3.18×1012	2.30×1012	6.75×1010	97.07

The cleaned input was generated by removing known repeat and aligned regions from the original input. As for the prediction, we counted only the windows with score of at least 20. Reduction is one minus fraction of the number of pairs of windows in prediction to that of pairs of windows in cleaned input