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Table 2.

Binding site conservation for five known transcription factors

Name	Consensus	S. cer. sites^a	S. par. sites^a	S. mik. sites^a	Conserved sites^b	Percent conserved^c	P(cons)^d	False discovery rate
ABF1	RTCRYNNNNNACG	671	670	666	470	70.0	0.017	0.024
GAL4	CGGNNNNNNNNNNNCCG	144	152	134	21	14.6	0.022	0.153
MCM1	CCNNNWWRGG	963	1019	911	194	20.1	0.023	0.112
NDT80	YGNCACAAAW	141	133	141	59	41.8	0.006	0.015
UME6	TSGGCGGCTAW	82	86	86	63	76.8	0.002	0.003

a The number of matches to the PWM in each genome.

b The number of conserved matches to the PWM.

c The percentage of matches to the PWM that are conserved.

d The probability of motif conservation.