As a Ph.D. student, I'm working on a very interesting project about the genetic evolution of viral RNA sequences.
In this work, I'm looking for possible editing-sites or nucleotide motifs that are favorable to viral polymerase slippage, leading to viral genome evolution. These particular motifs are mostly short repeated sequences (runs of AAA's, TTTT's,...).
I've heard about the MEME-suite, but I'm not really familiar with its different options and programs. What would be the best program in the MEME-suite for this research topic? Otherwise, is there other software that can perform automatic motifs-screening of RNA sequences?