Table 3.

The ratio of local and global alignment quality parameters on 120 PAM test suite sequences and Balibase sequences

Matrix	120 PAM		Balibase
	Global / Local		Global / Local
	Accuracy	Confidence	Accuracy	Confidence
PAM30	4.8938	2.8277	1.9510	1.3901
PAM60	2.9392	2.0120	1.6041	1.2407
PAM120	1.5422	1.1698	1.3035	1.1033
PAM250	1.1481	1.0251	1.1627	1.0720
Blosum45	1.2203	1.0249	1.1555	1.0575
Blosum50	1.2692	1.0513	1.1873	1.0633
Blosum62	1.3759	1.0676	1.2154	1.0724
Gonnet250	1.1275	1.0345	1.1407	1.0718
Gonnet_p	1.0275	1.0253	1.0058	1.0024
Optima	1.5409	1.3453	1.6990	1.5589
VTML250	1.1245	1.0335	1.1443	1.0765
MIQS	1.1545	1.0397	1.1377	1.0658
Pfasum050	1.1908	1.0443	1.1643	1.0685
Pfasum100	1.3631	1.0746	1.2123	1.0908