For example I have the next sequence:
ACGAGGTTACTACTACTAGTACTACGCC
# _________^^^______
As you can see there is a tandem repeat with monomer TAC. But because of mutation one monomer now is TAG and, for example, exact-tandems tool cannot recognise TACTACTACTAGTACTAC
as one repeat. So how can I identify TACTACTACTAGTACTAC
as one repeat, not two separated by TAG sequence?
The common reason to use TRF is that has been used by a lot of other researchers, and is well cited. However, benchmarks show that it lacks sensitivity, without being particularly specific. Thus, I'd recommend using other tools, or at least adding results from other tools.