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.