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11.4. Alternative structures

The command line option "/prevent=i,j,k" prevents the region STARTING at i and ENDING at j pairing for k bases. Other options include "/force=i,j,k" to give a different set of intial conditions. These will influence all the possible folding conformations.

See $ GENHELP MFOLD folding_constraints for a more complete discussion.

Optional exercise

Examine the cucumber mosaic virus-associated satellite RNA sequence. The sequence is in the EMBL database as entry name CUSATRN5, or as accession number J02061. Note the variety of different structures with very similar theoretical stabilities.

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