Table 1. An example of the substitution matrices for the branch from the common ancestor of S. cerevisiae and S. mikatae to S. cerevisiae in the yeast phylogenetic tree.

Background substitution matrix S. cerevisiae					Motif substitution matrix S. cerevisiae
Ancestor	A	C	G	T	Ancestor	A	C	G	T
A	0.7743	0.0347	0.1329	0.0581	A	0.8730	0.0182	0.0783	0.0305
C	0.0583	0.6791	0.0334	0.2292	C	0.0307	0.8170	0.0176	0.1347
G	0.2320	0.0347	0.6752	0.0581	G	0.1366	0.0182	0.8146	0.0306
T	0.0583	0.1369	0.0334	0.7714	T	0.0307	0.0805	0.0176	0.8712