The input control file can be organized by multiple blocks, however. one block input data is recommended. Each block should contain following three lines of data. 1. The first line contains 5 integer parameters: a. The type of energy rules you selected. If type=0, Tinoco energy rules are used, otherwise Turner energy rules are used. b. Start position in the sequence for your searching region. c. End position in the sequence for your searching region. d. Minimum window size. e. Maximum window size. 2. The second line contains 1 character string, ANS (Yes/No) If ANS(1:1)='Y' means you want chang default parameters for step size of window increasing and the number of randomly shuffled sequences you want. If ANS(1:1)='N' means you use default parameters: Window_Step_size = 2 and number_of_randomly_shuffled_sequences = 200 and the 3rd line is not necessary. 3. The third line contains 2 integer parameters: a. Window_Step_size b. number_of_randomly_shuffled_sequences The random permutation is only performed in the extream cases where the empirical coefficients are not suitable to compute the means and standard deviation of the lowest free energies from a large sample of randomly shuffling sequences.