Try to find whether your sequence is similar to any sequence which secondary structure has been experimentally studied. In IRESite the regions with studied secondary structures are usually those around the IRES, but in principle would not have to be.

Enter either your plain DNA query sequence or even one or more FASTA-formatted records (for your convenience spaces and numbers from within the sequence are ignored):
Alignment view options:
Matrix:
 
Last change to the database: 2015-04-16 16:45:23 GMT+1