Table 1.

List of Tracks available on the Repeat Browser

Track	Description
Mapping Alignments	Alignments of each individual repeat instance in hg38 back to the Repeat Browser consensus.
Mapping Coverage	A coverage plot for the mapping alignments from the above track.
Annotations (ORFs and UTRs)	Gene annotations of the repeat element as annotated in Dfam or detected by searching the RepeatMasker peptide library.
Self Alignments	Alignment of all other Repeat Browser Consensuses against the currently viewed consensus.
GENCODEv32	Alignments of GENCODEv32 annotated coding sequences, UTRs of protein-coding genes, and ncRNAs to the RepeatBrowser.
Tandem Repeats	Detected tandem sequence repeats within the consensus full-length repeat elements.
ENCODE Tracks	DNAse hypersensitive sites, histone marks (UW collection) and TF ChIP-seq (TFBS collection) from ENCODE lifted to the Repeat Browser.
KZNF Tracks (Imbeault/Trono 2017 & Schmittges/Hughes 2016)	Lifting of reprocessed data from large KZNF ChIP-seq screens.
TF Differentiation Data (Tsankov 2014)	Lifting of large scale ChIP-seq dataset of TFs involved in differentiation of iPSCs to multiple cell types.
Stem Cell Naive State Data (Theunissen 2016)	Lifting of H3K9me3 and Kap1 ChIP-SEQ from primed and naïve human pluripotent stem cells.