Revising MUSSA parameters for well-conserved regions. (A) A 15-bp window and four-way comparison among C. elegans, C. briggsae, C. brenneri, and C. remanei identified the thresholds at which MUSSA matches are observed within a region. Regions capable of driving expression are shown in white and those not capable of driving expression are shown in black. With a threshold of 100%, there is a 77% recovery of expressing regions with perfect specificity. (B) Using five-way comparisons and a 15-bp window among the four above species and C. sp. 3 PS1010, the thresholds where conservation was still observed were identified for each element. The predictive power for identifying functional regions is considerably reduced from the four-way comparison.
