Table 4. The numbers of sequences of the successfully predicted loop/junction structures for (I) all 8452 RNA loops/junctions in TEST-I (II) the 7459 RNA loops and junctions in TEST-II and (III) the 1119 RNA loops and junctions in TEST-III.

TEST-I
	(A)	(B)	(A)	(B)
Top-1	7364	7369	6992	7102
Top-2	7686	7686	7411	7500
Top-3	7796	7862	7715	7665
Top-4	7956	7969	7798	7844
Top-5	8006	8007	7857	7878
TOTAL-	8452

For each dataset, the numbers in columns “A” are calculated from (“”, “true” potential parameters) and (“”, “extracted” potential parameters), obtained from the RNA09 database, and the numbers in columns “B” are calculated from (“”) and (“”), obtained from the Leontis' database respectively. The “Top-” in the first column means that the “correct” structure is in the top lowest-potential conformations.