Suboptimal exons have a variety of potential uses.
First, suboptimal exons sometimes correspond to real exons which were missed for whatever reason by the optimal parse of the sequence. The probability cutoff C used to determine which potential exons qualify as suboptimal exons can be set to any of a range of values between 0.01 and 1.00. The default value on the web page is 1.00, meaning that no suboptimal exons are printed. For most applications, a cutoff value of about 0.10 is recommended. Setting the value much lower than 0.10 will often lead to an explosion in the number of suboptimal exons, most of which will probably not be useful.