Table 1.

Conserved blocks detected in benchmark datasets

Gene	Number of blocks
	Two-step	UCSC	UCR
cfos	0	0	0
hoxb2	8	5	0
pax6	13	11	0
scl	1	0	0
Total	22	16	0

Number of blocks two-step: number of conserved blocks identified using the two-step procedure. For more details on the blocks see Tables 2 (hoxb2), 3 (pax6) and 4 (scl). Number of blocks UCSC: the number of blocks detected by the two-step procedure that were recovered in the USCS genome browser (aligned between mammals and Fugu) [51]. Number of blocks UCR: the number of blocks detected by the two-step procedure that correspond to an ultra-conserved region [20].