repeat sequence aligner

Question

[rbpdee]

Hi folks,

I am working with an RNA-binding protein and trying to identify the targets of this RNA-binding protein in human cells by iCLIP. I suspect that this protein may bind RNA coming from repeat elements in the human genome. Does anyone know repeat sequence aligner that could handle these elements?

Also, I would like to know if there exists a curated database for repeat elements. Any other suggestion is always welcome!

Thanks!