Clustal Omega - convert from distance into # of substitutions
It uses a gonet matrix to compare each of these two sequences. Since you you could have insertions and extensions as well as substitutions, it becomes a 3 parameter problem. 1*open + 6*penalty + substitution_penalty = X. X can be solved by a linear combination of substitution_penalties, extensions, and insertions. So I think this will be really really hard

with that being said. Clustal outputs the multiple sequence alignment. Why don't you just look at sequence 1 and sequence 2 and see what the insertions and substitutions are!