The Jukes-Cantor correction is used to calculate nucleotide distances and synonymous and nonsynonymous substitution distances. If the proportion of sites that are different (nucleotides, synonymous, or nonsynonymous) is greater than or equal to 75%, the Jukes-Cantor correction cannot be applied. If you see this error message, then this has happened for one or more pairs in your data. If you wish to know which pair(s), use the Distances|Pairwise option. All such pairs will be shown in the Distance Matrix Dialog with a red n/c.