For example i have the next sequnce:
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 separeted by TAG sequnce?
Try the old and still working Tandem Repeat Finder http://tandem.bu.edu/trf/trf.html
Quite a lot of reviews have been published on the topic. Have a look at e.g.
Detecting short tandem repeats from genome data: opening the software black box
Repeat or not repeat?- Statistical validation of tandem repeat prediction in genomic sequences
Among many more tools (>50), there is:
Perhaps useful, we've implemented the Python3 library TRAL to allow among others easy running, parsing and merging of tandem repeat detection tools.
Also, check out MISA
Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33 2583–2585. dx.doi.org/10.1093/bioinformatics/btx198
See also, MEME-suite (http://meme-suite.org/doc/meme-format.html). It's different tools by which you can discover new repeats (MEME), can look for repeat/motif enrichment in particular region of the genome (CentrMo), can scan your repeat/motif in the genome (FIMO) and many more related analysis.