Blasting your clade B PDAM2-Moo sequence, there is no match at 100% query coverage and 100% identity. At best you always have a 1bp mis-match. Is this an error in the sequence uploaded? If not, then I think some thought should be given to what this mis-match effectively represents.

Given that the 28S marker is a relatively low-resolution marker (i.e. multiple ITS2-defined subclades, that can be...