Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals.

However, intriguingly, we also observe a decreasing trend of conservation in non-TE-associated enhancers as TE enrichment in cell/tissues increases (gray bars in Fig. 2I and Supplementary Fig. 16 shrink with decreasing conservation; Supplementary Fig. 15B ; R = −0.84).

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