How to Identify Conserved 21-mers Across TE Insertions in Drosophila?

Question

[manikin_python9f]

I am working on a family of transposable elements in Drosophila melanogaster. My goal is to identify short (~21 nt) sequences that are conserved across many insertions so I can design shRNAs for RNAi knockdown. What is the established workflow to:

1. Measure divergence of individual insertions from the consensus sequence.
2. Identify short motifs (e.g., 21-mers) that are present across most insertions, if not all, with minimum mismatch.

[GenoMax]

Do you have the locations/sequence of the regions you are interested in?