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 considerably different phenotypically, may have identical 28S sequences), and your fragment is extremely short (100bp; normal phylotyping with 28S uses approx. 800bp), the B sequence you recovered may represent a novel and significantly differentiated Symbiodinium Type.

Also possible, is that the first bp of your sequence that is causing the mismatch to the 'B1' sequence you describe in your results has been incorrectly called. Even if this mismatch were to be ignored, discussions at a sub-cladal level are likely beyond the scope of your sequence especially considering its short length and 'matches' to S. antillogorgium (KT149346), S. pulchrorum (AF060892) and S. minutum (LK934670) to the same extent as B1 (KJ500001 or JN558059; result from blast search).

Still, very intriguing to be finding the B! An enjoyable read.