Input-format for structure_consensus.pl:

a)One 'common' structure provided (shown for fasta):

>seq1
AGCGUUUACGCGCUCGU
>seq2
UGCGUUUACGCGCUCGU
...
>HELIX
((((...[[[))))]]]

b)Structure provided for every sequence (shown for fasta):

Input example fasta:
>seq1
AGCGUUUACGCGCUCGU
>HELIX_seq1
((((...[[[))))]]]
>seq2
UGCGUUUACGCGCUCGU
...
>HELIX_seq2
.(((...[[[))).]]]
>Helixnr
1-------1'--