motifs -- LSPS against EPD78 vertebrate promoters using occurrence count motifs-seq -- LSPS against EPD78 vertebrate promoters using sequence count motifs-n-liver -- LSPS against EPD78 non-liver vertebrate promoters using occurrence count motifs-n-liver-seq -- LSPS against EPD78 non-liver vertebrate promoters using sequence count Format: motifs.words -- motif pairs by word count, LSPS against EPD78 vertebrate promoters motifs.seqs -- motif pairs by sequence count, LSPS against EPD78 vertebrate promoters motifs-n-liver.words -- motif pairs by word count, LSPS against EPD78 non-liver vertebrate promoters motifs-n-liver.seqs -- motif pairs by sequence count, LSPS against EPD78 non-liver vertebrate promoters Format: LSPS-orthologs -- includes all the orthologs LSPS -- contains selected promoters from each ortholog set consensus -- contains the consensus sequences used to produce conservation counts consensus_max -- contains the consensus sequences used to for motif discovery (Tables 9 and 12) epd_liver2lspd_msa.map_by_gbacc -- contains a mapping from the epd_liver gene set to the LSPS gene set lspd_msa2epd.map_by_gbacc -- contains a mapping from the LSPS gene set to the epd_liver gene set LSPS-counts -- contains occurrence counts for every motif in LSPS (having the structure considered in the paper). Motifs are organized by structure. For example: XXX..XXX.0 contains motifs with 0 degenerate positions and structure of three bases followed by a gap of length 2 and three more bases. XXXX...XXXX.2 contains motifs with 2 degenerate positions and structure of four bases followed by a gap of length three and four more bases. XXX..XXX will include motifs with 0,1,2 degenerate positions and structure of three bases followed by a gap of length 2 and three more bases. LSPS_conserved-counts -- contains occurrence counts for every motif in the consensus set (having the structure considered in the paper). Motifs are organized as above.