Table 1.

Intra-motif complexity (IMC) measures of different types of motif models

Model	Order	SEP3MI WT (Replicate 1)	SEP3MI WT (Replicate 2)
Proximal	1	1.471	1.665
Proximal	2	1.752	2.010
Distal	1	1.633	1.901
Distal	2	2.004	2.398

The values quantify the amount of statistical dependencies in the data that can be effectively represented by a particular motif representation. Here, proximal and distal dependence models of first and second order are compared. Since a PWM model has an IMC value of 0 by definition, the results allow to conclude that most additional information beyond mononucleotide frequencies is given by correlations among directly neighboring nucleotides (first-order proximal dependencies). Increasing the model flexibility, either by increasing the order or by allowing distal dependencies yields only a small further improvement in comparison