Table 5.

Search results using query motif comprising closing basepairs and one central basepair of the kink-turn, shown in Fig. 10c. The candidate shown with blue background is a new kink-turn. In addition to bona fide kink-turn motifs, the search obtains tertiary interactions that have the same core basepairs as kink turns. In the last column, L represents a local motif, C represents a composite motif, and T means the motif comprises tertiary interactions

		Query Motif 2 Search
		Discrepancy	Motifs found by FR3D						Type
Query Motif (Kink-turn):		0.0000	A 80	G 97	G 81	C 93	C 100	G 77	L
PDB File:	1S72	0.2166	A 113	G 47	A 148	U 43	G 50	C 111	C
Number of Search Nucleotides:	6	0.5406	A1341	G1316	C1342	G1312	G1319	U1338	L
Motifs Identified:	8 (All)	0.5887	A1215	G1151	G1216	C1147	A1154	C1212	L
Basepairs Constrained:	1	0.6137	A 939	G1031	G 940	C1026	G1034	C 936	L
Guaranteed Cutoff D0:	0.9	0.6735	A2914	G2826	G2667	C2822	G2829	C2911	C
Relaxed Cutoff D1:	0.9	0.6814	A2875	G2882	G1806	C1786	A2885	U2872	T
Exclude Redundant Candidates:	Yes	0.6912	A 955	A1012	C 81 (5S)	G 102 (5S)	C1015	G 952	T
		0.7125	A1590	G1605	C1593	G1601	G1608	U1587	L
		0.7337	A1294	G 911	U1041	C 930	A 914	A1070	T
		0.7340	A2906	G2851	G2834	C2846	G2855	C2903	C
		0.7631	A 520	G 23	A 639	G1363	U 26	U 517	T
		0.7820	A 80 (5S)	G 102 (5S)	G 956	A1012	C 106 (5S)	G 75 (5S)	T
		0.7859	A1318	G1339	U 27	A 516	C1342	A1313	T
		0.8003	A1459	G1484	A 784	U 862	G1489	C1456	T
		0.8126	A1294	G 911	A1040	C 931	A 913	A1070	C
		0.8274	A 666	G 680	G 209	C 230	G 684	C 663	T
		0.8298	A 247	G 264	G 249	C 250	G 267	C 244	L
		0.8582	A 242	G 269	C 377	G 273	G 379	G 431	T
		0.8731	A1626	G1571	G1510	G1496	C1574	G1621	T