Input-format for 2analysis.pl:

One 'common' structure provided

as fasta:

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

as mase:

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