From my understanding, microsatellite repeats should be consistent (e.g. di-, tri-, tetra-); therefore, allele sizes should be consistently separated by 2, 3, or 4 nucleotides. I am working with a new locus that seems to have multiple repeat lengths. For example, there are repeats of 2 nucleotides, followed by repeats of 3, and then back down to 2. Has any one else had this experience with microsatellites? Is it a biological phenomenon, or likely just scoring error?
This is microsatellite instability. Look https://doi.org/10.1038%2Fnpg.els.0000840
It is so called compound SSR.
Your question is interesting Vanessa. While scanning for microsatellites, you may get repeats like (cag)2gc(at)6. This could arise as a result of same mechanism which is responsible for the variation in repeat number. Alex explain it well. This is compound microsatellite.
Yes, this could be either a chance or recombination or slippage leads this kind of variations in SSRs (composite microsatellites).
Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites
(https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-9-612.pdf)
Relative mutation rates at di-, tri-, and tetranucleotide microsatellite loci
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC19636/pdf/pq001041.pdf)
Vanessa Smilansky you may have a complex repeat, i.e., it may contain several repeat blocks of variable unit length as well as variable intervening sequences. They are common and usually avoided as they are difficult to genotype and analyse. There are difficulties with allele nomenclature and measurement variability between laboratories. Ideally, you should try to use simple repeats (units of identical length and sequence).
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