Problem with constraints

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Nicolas Morando
Joined: 05/22/2017

Hello, everyone. I'm having a problem getting the constraints to work, particularly forcing a string of bases to be single stranded. I tried with an imaginary sequence AUGUUAUUAGGGGGGGGGGGGGGGGGGGAUUGAUUGUAUAGUCCCCCCCCCCCCCCCCCCCCAUGAUGAGUGAU
which is purposefully designed to generate a stem-loop. Then I imposed the constrain "P 45 0 10" in order to undo the pairing in positions 45 to 55. However, this region keeps pairing despite my constraint... Am I doing something wrong?

Thank you in advance for your help.