This repository holds the supplementary data for the motif and motif-syntax/grammar discovery tool in the associated manuscript. reports.tar.gz Contains the motif and motif-syntax/grammar analysis reports as HTML files for all analyzed transcription factors (TFs). See included README for more details. models.tar.gz Contains the fine-tuned models. Each TF, this includes the fine-tuned single-task profile model for each task/experiment, and the fine-tuned multi-task profile model over all experiments. motifs.tar.gz Contains the motifs discovered by TF-MoDISco on each profile model, for both the profile and counts heads. This includes the PFM, the CWM, and eCWM. This also includes the motifs that have been merged across the profile/counts heads (i.e. `cpmerged`). motif_hits.tar.gz For each experiment, motif instances were called using FiNeMo on the best-performing model. Motif instances are either called for the profile head, count head, or merged across both heads. Each subdirectory includes: 1) the collapsed and filtered motif instances; 2) the set of peaks for which they come from; 3) a file matching motif instances to their peaks; 4) the co-occurrence of multiple motifs in peaks; and 5) the distance distribution of motif pairs which significantly co-occur. Unless stated otherwise, collapsing is done over all motif patterns.