Table 2.

Several point values for the affine gap cost continuous-time functions open(t) and extend(t) for time instances associated to well known substitution matrices. The analytic functions are given in Eq. 2 and depicted in Fig. 6. The parameter values are: ${\mu }_A=1.0023,\lambda =0.4296,r_X=0.6276,r_M=0.7500,{\beta }_{\infty }^{\mathrm{\text{LR}}}=0.3000,{\beta }_{\star }^{\mathrm{\text{LR}}}=0.2134$. The divergence parameter t has been normalized to BLOSUM62

	% Substitutions	Divergence	Open	Extend
	per site	time t
PAM10/VT10	10.0	0.074	–15.79	–1.29
VT20	17.9	0.141	–14.21	–1.25
PAM30	27.1	0.229	–13.14	–1.21
VT40	32.0	0.283	–12.73	–1.18
PAM70	49.8	0.520	–11.72	–1.10
VT80	52.2	0.567	–11.60	–1.09
BLOSUM90	55.8	0.633	–11.46	–1.07
VT100	59.4	0.709	–11.33	–1.05
BLOSUM80	60.9	0.741	–11.28	–1.05
VT120	65.2	0.851	–11.14	–1.02
VT140	70.0	0.995	–11.00	–1.00
BLOSUM62	70.1	1.000	–11.00	–1.00
BLOSUM50	72.9	1.099	–10.93	–0.99
VT160	73.8	1.135	–10.90	–0.98
PAM120	74.9	1.180	–10.88	–0.98
BLOSUM45	76.3	1.245	–10.84	–0.97