Table 2. This table shows the total number of mouse gene sequences containing at least one denatured (D) or Z-DNA (Z) region near their TSS at T = 305 K and  = −0.07.

Algorithm	1000 bp 5′		250 bp 5′		1000 bp 3′		250 bp 3′
BDZtrans	D	Z	D	Z	D	Z	D	Z
	462	2789	34	1180	256	1954	21	618
SIDD	708		51		364		42
SIBZ	3443		1527		2457		844

These are sites in a given sequence where the probability of transition is at least 0.8. The regions in which these alternate structures regions are counted extend either 250 or 1000 bp downstream (3′) or upstream (5′) of the TSS. The results from the BDZtrans, SIDD, and SIBZ algorithms are compared.