A large set of yeast mRNA 3'-processing regulatory sequences was analyzed statistically, revealing a systematic variation that correlates with measured mRNA stability. Transcripts with relatively short half-lives have a high frequency of inclusion of 3'-processing elements that include the core sequence of binding sites for the PUF proteins, which enhance mRNA turnover. These results suggest that regulatory sequence variation, typically modeled as random, could arise instead from the necessity or advantage of specifying multiple functions in a common sequence element.