Secondary structure significance

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Joined: 06/08/2012

We are examining sequences that border chromosomal deletion breakpoints and trying to find reasons for apparent instability of such reasons. I happened upon Mfold while looking for an algorithm to predict secondary structures. With some of the breakpoint sequences, I get what I think are fairly elaborate structures, but upon putting in a random sequence (e.g. a similar length sequence from a gene or a cloning vector- not the MCS), there are some surprisingly complex structures there also. The question therefore is one of significance. Is there a 'cut-off' for a sequence of X nucleotides, having a CG composition of Y%? Many thanks for your time.