Technical notes on TFBS models presented in HOCOMOCO-v11 1. All the matrices were produced by ChIPMunk motif discovery tool. It accounts for prior "quality" information for each sequence in the input set. The resulting words in the alignment are weighted and thus the position count matrix (PCM) is weighted PCM and may contain floating point numbers. These numbers are treated as counts in a PCM-to-PWM conversion scheme. In case strictly integer counts are required for downstream analysis, we suggest using HOCOMOCO downloads in TRANSFAC format (see Downloads) where the weighted counts were carefully converted to the nearest integers maintaining consistency of the resulting PCMs. 2. The PCM to PWM conversion scheme used in HOCOMOCO follows that of MACRO-APE, see the respective manual, page 20-21 in http://opera.autosome.org/downloads/MACRO-PERFECTOS-APE_manual.pdf The genome-wide dinucleotide frequencies (for human and mouse respectively) were used to estimate P-values for threshold conversion tables. 3. The plain-text files with matrices always use alphabetical order of nucleotides (ACGT) and dinucleotides (AA,AC,AG...TT). 4. The TFBS alignments (*.words) provide information on particular sequence segments used by ChIPMunk to derive the positional matrices. Models inherited from HOCOMOCO v9 were partially based on sites mined from the proprietary TRANSFAC database. The respective aligned words were masked with 'X's. 5.Genome-wide dinucleotide frequencies were used for human and mouse models to compute score thresholds and estimate P-values. Human background (dinucleotide frequencies AA,AC,AG..TT: <>): 0.09774531292656502,0.05049224075299731,0.07019109895771408,0.07682178619511619, 0.0727342790964817,0.05203614856201394,0.010180820713495882,0.07019109895771408, 0.059669884332282236,0.042565262995142815,0.05203614856201394,0.05049224075299731, 0.06469420084013656,0.059669884332282236,0.0727342790964817,0.09774531292656502 Mouse background: 0.09124954151587066,0.05327746891945427,0.07340655447309075,0.07380976720188166, 0.07444027240460285,0.0522326724288473,0.008258817805366036,0.07340655447309075, 0.06218694059369016,0.04063209300331165,0.0522326724288473,0.05327746891945427, 0.06371242131832879,0.06218694059369016,0.07444027240460285,0.09124954151587066