Hi,

I have performed NGS and have identified a list of genomic deletions indicated by genomic position.

Now, I want to find out if deletions are flanked by direct repeats. I.e, for each individual deletion, are direct repeats presents (say in ~10bp from the deletion start/end point), but direct repeats do not have to be similar between different deletions.

Can anyone point me in the direction of a tool to help me with this? I am looking for something that might output either yes/no answer or better yet some sort of "direct repeat score" for each deletion.

Thanks!