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2. This question illustrates a way of finding runs of complementary sequence in the same RNA molecule used in Question 1 (i.e., regions that can potentially base-pair) by using a dot matrix approach. This type of matrix is made by mfold for predicting RNA secondary structure. The following matrix shows the sequence of the above RNA molecule both across the top of the matrix and down the side:
  1. Make a copy of the matrix in a text file or on a piece of ruled graph paper. Place an X at each position where the bases across the top are capable of base-pairing with those down the side (i.e., G/C and A/U base pairs).
  2. Look for a diagonal row of X's running from the upper right of the matrix to the lower left.
  3. What is the longest run of X's? Describe any symmetry in the matrix. What is the significance of this run?


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