Table 1. Context-dependent properties of the MC2020 model.

Context§	G+C TS:TV†	A+T TS:TV†	Sub. Rate††	GC:AT Rate††	EQUIL. G+C‡	EQuil. C-G‡‡	EQUIL. T-A‡‡
A_A/c(T_T)	0.84	0.33	0.76	2.50	21.3	- 32.7	- 32.6
A_T	2.23	0.41	0.53	2.03	26.3	3.4	3.8
T_A	0.99	0.32	0.77	2.20	26.4	- 2.8	- 3.5
A_C/C(G_T)	1.95	1.16	0.47	2.30	30.0	- 0.27	- 14.4
A_G/C(C_T)	4.26	1.50	0.63	1.82	34.1	- 38.4	- 23.4
C_A/C(T_G)	1.72	0.71	0.78	2.01	32.1	25.3	- 21.2
G_A/C(T_C)	1.12	0.82	0.49	2.94	25.5	- 24.3	- 33.9
C_C/C(G_G)	3.07	2.80	0.66	1.57	40.8	40.6	16.0
C_G	3.06	1.24	1.01	1.08	46.4	- 6.1	11.0
G_C	1.41	2.89	0.61	1.95	36.6	5.2	15.1

§–C(N_N) refers to the complement of the matrix. In these cases the two complementary contexts were combined as described in the text

†—TS:TV at sites where the outgroup is a G/C or A/T

††–Substitutions/site x 100. GC:AT Rate gives the ratio of the rate of substitution from an ancestral G or C to the rate of substitution from an ancestral A or T

‡–Equilibrium G+C for the stationary vector of the matrix (see text)

‡‡–Equilibrium C-G and T-A skews for the stationary vector of the matrix