Table 4.

Accuracy and confidence of global, local and GAP3 alignment at various consoles

PAM	Console length r, %	Core shift c, %	Global alignment		Local alignment		GAP3
			Accur., %	Confid., %	Accur., %	Confid., %	Accur., %	Confid., %
120	0	0	82.47	81.47	71.76	76.71	71.42	86.60
120	20	0	79.30	77.59	71.16	72.64	71.58	84.98
120	20	30	75.64	73.39	71.37	72.99	72.26	85.02
120	20	50	72.23	69.83	70.17	72.18	72.19	84.78
120	20	70	69.47	66.93	70.81	72.94	71.03	84.80
120	50	0	77.95	75.77	70.51	69.77	72.66	84.00
120	50	30	72.04	69.08	71.47	70.91	73.06	84.92
120	50	50	53.53	50.96	69.34	69.36	71.80	83.62
120	50	70	20.18	18.98	70.37	71.03	72.14	84.16
120	100	0	76.70	74.11	69.48	67.78	72.18	83.39
120	100	30	53.69	51.45	69.63	68.09	72.12	83.25
120	100	50	4.15	3.71	68.66	67.23	72.15	83.84
120	100	70	0.08	0.05	68.95	68.47	72.47	83.04

The dependence of Accuracy and Confidence values of tree types of alignment on the evolutional distance between cores (PAM), relation of the total length of consoles to the core length (Console length r, %) and the ratio of the absolute value of the difference between console lengths to their total length (Core shift c, %) are shown.