I'm annotating a bunch of long contigs from a plant genome.
I'd like to identify microsatellites (2–7 bp), minisatellites (tens of bp) and satellites (hundreds of bp) whitin these contigs.
I know that there are a lots of software to identify the DNA satellite.
I'm thinking to try Tandem Repeats Finder (for minisatellites and satellites) and MISA (for microsatellites).
Do you think that these two software can be enough to catch all the DNA satellite? Are there any better software for these kind of sequences? Is there a specific pipeline?
Thank you for any suggestion!
You can also have a look on FullSSR for Microsatellite.
I have used Phobos with good results.