Secondary Structure format

  
 

Secondary structure file should include the sequence of the RNA and the base pairing information. The first column is the nucleotide number (index), the second column is the typing (A, C, G, U), and the third column is the index of the nucleotide that is base paired with that nucleotide. If the nucleotide is not based paired, this entry would be zero.  

 

1 G 25

2 U 24

3 U 23

4 C 22

5 G 21

6 C 20

7 G 19

8 A 18

9 A 17

10 G 16

11 U 0

12 A 0

13 A 0

14 C 0

15 C 0

16 C 10

17 U 9

18 U 8

19 C 7

20 G 6

21 U 5

22 G 4

23 G 3

24 A 2

25 C 1

26 A 0

27 U 0

28 U 0

29 U 0