A large number of HJs are present within TEs. More importantly, every HJ form is highly associated with a specific TE family, providing novel data for HJ and TE co-evolution.

By creating a comprehensive genomic map of TE-associated HJs, we found HJ hotspots and correlated HJ GC content with the different HJ forms. We also discuss the importance of differential HJ distribution in the frequency of recombination across human chromosomes.

The phylogenies of TEs that contain HJs propose interplay between both active and inactive TEs with HJs.

HJs genomic coordinates are highly correlated with those of gene TSS (transcription start site). This may result in the shuffling of gene information through recombination events.