Why not Tandem repeat finder? I guess it is one of the oldest and most used tool to identify tandemly repeated sequences (including microsatellites). I use it a lot and don't need anything else.
Input is sequences in fasta format. You can use one sequence or fasta file with multiple sequences; you can run it using genome as input or seperate gene sequences. Output is informative and easy to parse. There are many options to play around. For example, "maximum period size". If it is "1", then you'll get only AAAAAA; if it is "2", then you'll get AAAAA and CGCGCGC.
You can download your own copy or use it online.
Good luck with your hypothesis!
modified 4.7 years ago
4.7 years ago by
PoGibas ♦ 4.7k