Different OTUs but 100% seq identity

I have stumbled across a result I find confusing. I have my Otus classified at the 97% level. I wanted to see if a certain microbe is in my data. I have a Genbank sequence of that microbe and the Silva classification, with is Bacteria;Proteobacteria;Gammaproteobacteria;Methylococcales;Marine Methylotrophic Group 1. To make blasting easier, I used get.lineage on my fasta file (.precluster.pick.pick.fasta) and used the taxonomy file (.wang.pick.taxonomy) to grab sequences that meet the above taxonomy criteria. I then used this new fasta file as a custom blast database and searched it using the sequence from my microbe of interest. I have two sequences from my custom database that come up as 100% identical to my microbe. Strangely (to me at least), these two sequences are from different Otus. But they are 100% identical to the same thing. An explanation as to how this could be would be greatly appreciated.


How similar are the sequences to each other?

And also, what’s the alignment length of the BLAST results? I don’t know how you’re reading the data exactly, but BLAST has a tendency to rank high identity/low coverage results quite highly (as oppose to low identity, high coverage). How example, you might find that both of your sequences have 100% identity over 30% of the target sequence. Even if they were identical over the same span, that leaves a lot of data unaccounted for.