. Author manuscript; available in PMC: 2010 Mar 14.

Published in final edited form as: J Math Biol. 2007 Aug 11;56(1-2):215–252. doi: 10.1007/s00285-007-0110-x

Table 6.

Search results for query motif shown in Fig. 11a, from a GNRA hairpin loop in H.m. 23S rRNA, using a sequential continuity constraint, a basepair constraint, and two base stacking constraints. In the Type column, RH represents a related hairpin

		Discrepancy	Motifs found by FR3D					Type
Query Motif (GNRA):		0.0000	C 804	G 805	A 807	A 808	G 809
PDB File:	1S72	0.1408	C2695	G2696	G2698	A2699	G2700
Number of Search Nucleotides:	5	0.1568	C2248	G2249	G2251	A2252	G2253
Motifs Identified:	21 (All)	0.1687	C 89	G 90	G 92	A 93	G 94	in 5S
Basepairs Constrained:	1	0.2077	C1862	G1863	A1865	A1866	G1867
Stacking Constraints:	2	0.2405	G2876	G2877	A2879	A2880	C2881
Guaranteed Cutoff D₀:	0.8	0.2562	G 690	G 691	A 693	A 694	C 695
Relaxed Cutoff D₁:	0.8	0.2598	G1628	G1629	A1631	A1632	C1633
Sequential Constraint:	Yes	0.2799	G1054	G1055	A1057	A1058	C1060
Exclude Redundant Candidates:	Yes	0.3027	C 252	U 253	A 255	C 256	G 257
		0.3152	C 217	C 218	G 221	A 222	G 223
		0.3288	C1793	G1794	A1796	A1797	G1799
		0.3528	C2411	G2412	A2414	A2415	G2416
		0.3801	C2629	G2630	G2632	A2633	G2634
		0.3905	C 576	G 577	G 579	A 580	G 581
		0.4120	U 468	G 469	G 471	A 472	A 473
		0.4943	U1326	G1327	A1329	A1330	A1331
		0.5350	U 493	C 494	G 496	A 498	G 499
		0.6009	G1468	C1469	A1471	C1472	C1474
		0.6314	C1275	U1276	A1278	A1280	C1281
		0.7151	C1594	G1595	A1598	U1599	G1600	RH
		0.7350	U 733	U 734	A 736	A 737	G 738