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?

[manikin_python9f]

Since they are transposons, we don’t know the exact location of them. We know their sequence of insertions from repeatmasker in dm6 genome. Also the consensus sequence is available in TE libraries.