Figure 3

Contingency table construction for the motif CCAGACT. Contingency table construction for the motif CCAGACT. The forward reference (5' to 3') is displayed at the top; below, its complement is shown (3' to 5'). F-reads are indicated as red arrows, R-reads as blue arrows. F-intervals are marked in the forward reference, R-intervals are marked in the reverse complementary reference. Two F-positions (last position in an F-interval) and one R-position (first position in an R-interval) are indicated by vertical boxes. The corresponding individual contingency tables and the resulting joint contingency for the motif CCAGACT are shown below the alignments. Note that F-positions and R-positions both contribute to the motif's contingency table, as described in the Algorithm section.