(a) Comparison between Ahab and Stubb, local background of orders 1 and 2 in different runs. All runs are on D. melanogaster genome only. (b) Effect of tandem repeat masking of input sequences. "MS_MASKED" and "MS_UNMASKED": STUBBMS, with global background model of order 2, on masked and unmasked sequence respectively. "SS_MASKED" and "SS_UNMASKED": STUBBSS, with local background model of order 1, on masked and unmasked sequence respectively.