Okay I will try that. I'm sure it's possible for those overlaps to occur but if given multiple options, I have to settle for the most energy stable hairpin, which is why prior to this stage the energy scores were filtered for the most stable ones. So far as I can detect there aren't any overlaps of the variety you describe.

In reply to Re^2: Making use of a hash of an array... by Peter Keystrokes
in thread Making use of a hash of an array... by Peter Keystrokes

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