Oh, I see! Yes, an intrachain alignment of an artificial sequence does not by itself give any information about co-evolution, especially since you don't know whether your protein is actually folding. To assess co-evolution you need a multiple sequence alignment between protein homologs containing correlated mutations.

> I understand that similar sequences may fold similarly (although as length increases, I highly doubt it, but IDK).

As long as the sequence similarity is kept between those sequences, length is not an issue.

> Co-evolution suggests that aligned sub-sequences are also proximal

What do you mean by "proximal"? Close in space, or similar in structure?