Table 1.

Top hits obtained by searching the five motifs against 1S72 using RNAMotifScan

Ranking	Chain	Location	Score	P-value	FR3D	de novo Clustering	Shape Histogram
Kink-turn
1	0	77-82/92-100	70.2	0.009	*	*	*
2	0	1211-1217/1146-1156	62.1	0.014	*		*
3	0	936-941/1025-1034	55.8	0.022	*	*	*
4	0	1338-1343/1311-1319	54.7	0.024	*		*
5	0	1586-1593/1601-1609	45.4	0.062	(*)		*
6	0	244-250/259-267	44.4	0.072	(*)		*
7	0	2903-2906/2845-2855	43.8	0.078	(*)
C-loop
1	0	1436-1440/1424-1430	40.9	0.033	–	*	–
2	0	2760-2764/2716-2722	39.1	0.041	–	*	–
3	0	1939-1945/1892-1898	38.4	0.044	–		–
4	0	1004-1009/957-964	34.4	0.081	–		–
Sarcin–ricin
1	0	211-215/225-228	42.8	0.007	*	*	–
2	0	1368-1372/2053-2056	42.8	0.007	*	*	–
3	0	2690-2694/2701-2704	42.8	0.007	*	*	–
4	9	76-80/102-105	42.0	0.007	*		–
5	0	461-466/475-478	37.5	0.010	*	*	–
6	0	380-383/406-408	34.4	0.013		*	–
7	0	951-955/1012-1016	33.4	0.015			–
8	0	173-177/159-162	29.8	0.022	*	*	–
9	0	2090-2094/2651-2654	26.2	0.037			–
10	0	1775-1779/1765-1768	25.5	0.042			–
11	0	1542-1545/1640-1643	21.0	0.117			–
12	0	585-590/568-572	20.8	0.126	*		–
13	0	355-360/292-296	20.8	0.126	*		–
Reverse kink-turn
1	0	1661-1666/1520-1530	48.6	0.114	–	*	–
2	0	1530-1536/1649-1661	46.8	0.145	–	*	–
E-loop
1	0	706-708/720-722	21.2	0.052	–	*
2	0	1543-1545/1640-1642	20.6	0.061	–	*
3	0	174-177/159-161	18.7	0.098	–		*
4	0	663-666/680-683	18.6	0.100	–
5	0	586-590/568-571	18.0	0.120	–		*
6	0	356-360/292-295	18.0	0.120	–		*
7	0	2691-2694/2701-2703	17.8	0.130	–		*
8	0	1369-1372/2053-2055	17.8	0.130	–		*
9	0	463-466/475-477	17.8	0.130	–		*
10	0	380-383/406-408	17.8	0.130	–		*

Symbol notations: `*' the motif occurrences are identified by the corresponding method; `(*)' motif occurrences rank below some `related motifs'; `-' the motif is not studied by the corresponding method. The bona fide motifs validated by visual inspection are indicated with bold typeface of their location. The underlined motifs are de novo found by RNAMotifScan (even they might be manually characterized before).