Table 1.

Summary statistics for the alignment of T.th. (1j5e) and E.coli (2avy) as produced by the different methods described in Section 3.2

	Alignment method
		Manual		Automated 3D-to-3D				Sequence-based
	Composite	Basepair	Crystallographer	R3D Align	ARTS	SARA	DIAL	NAST	NW
Number of nucleotides aligned	1414	1208	1488	1400	1115	1460	1506	1482	1431
Number of exact base matches	1098	924	1133	1089	867	1075	1017	1129	1215
Nested cWW aligned	431	431	426	428	301	375	297	422	319
Nested non-cWW aligned	88	88	87	88	60	80	64	88	76
Non-nested cWW aligned	11	11	11	11	11	11	10	11	11
Non-nested non-cWW aligned	75	75	73	76	57	70	56	76	64
Stacking interactions aligned	1375	1169	1391	1372	1040	1310	1248	1375	1223
Base–phosphate interactions aligned	77	32	79	76	66	76	58	78	72
Correspondences agreeing with Composite	1414	1208	1401	1362	1056	1278	1113	1356	1172
Correspondences missing, compared to Composite	0	206	13	52	358	136	301	58	242
Correspondences extra, compared to Composite	0	0	87	38	59	182	392	126	259
Mean local neighborhood discrepancy	0.261	0.251	0.366	0.247	0.286	0.426	1.160	0.391	0.831
Median local neighborhood discrepancy	0.197	0.198	0.210	0.193	0.189	0.223	0.286	0.208	0.223
Global discrepancy of all aligned nucleotides	0.081	0.087	0.099	0.092	0.058	0.096	0.208	0.118	0.196