Position specific variation in the rate of evolution in transcription factor binding sites

Table 3 Motifs identified by MEME that do not correspond to the expected consensus sequences for the transcription factors thought to be regulating the cluster.

Cluster	Factor (expected)	Consensus identified by MEME	Motif subs.	Bg. subs.	Corr.	p-val
TRX2 +	Yap1p	AAAAAGAGGAAAAAA	0.80	0.78	-0.21	0.23
CTT1 +	Msn2/4p	GAAAAAAAAAAAAAA	0.51	0.67	0.13	0.67
Transport ++	Pdr1/3p	AAAGAGAGAAAAAAA	0.57	0.69	0.20	0.76
Ergosterol bio-synthesis++	Upc2p/ Ecm22p	ATCTTTTTTTTTTTT	0.81	0.55	0.06	0.58
60 positions in background sequence					0.08	0.73

These motifs do not show the characteristic correlation with rate of substitution or the substantial decrease in substitution rate observed for the computationally identified motifs with the expected consensus. + indicates clusters taken from hierarchical clustering of yeast data from the Stanford Microarray database [42], ++ indicates clusters taken from hierarchical clustering of 300 genetic perturbations [43].

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