Table 2.

Thresholds and effectiveness of scores derived from human–mouse–rat genome alignments for finding CRMs in the reference set for the HBB complex

	Binary discrimination by position		Discrimination of intervalsb
Method	Threshold	Sn, Spa	Threshold	Snint	True discovery rate
MCS	1.55	0.55	3.3	0.44	0.54
PhastCons	0.031	0.50	0.13	0.50	0.54
Regulatory potential	-0.006	0.61	0	0.78	0.63
Regulatory potential, no HBBc	-0.007	0.60	0	0.78	0.59

^aSn indicates sensitivity; Sp, specificity. Optimal Sn and Sp are determined at the crossover point and thus are equal.

^bThe intervals are evaluated by the maximum score within each interval.

^cRP scores computed using a training set that excludes CRMs from the HBB complex.