Finding non-regulatory regions genome wide for TF-binding ananlysis

Question

[mc2548]

I have ATAC-seq reads genome wide and my next step is to look for enriched motifs or TF-binding motifs in these regions. As control I was planning on using non-open regions in the genome.

Is there any way to extract the non-coding regions in the genome which does not have ATAC peaks but is of same length as input sequences?