Motif Models

The Count Matrix

Counting bases by column is the first motif model.

highlighted = computed this step

Count each base in each column

The count matrix records how often A, C, G, and T appear at each aligned position.

count column=base totals at one position\text{count column}=\text{base totals at one position}
Count matrixRows are bases and columns are motif positions.BasePosition 1Position 2Position 3Position 4A4001C0300G0140T0003

Strong columns stand out immediately

A fills the first position with count 4, G fills the third position with count 4, and the mixed columns carry smaller alternatives.

first A count=4\text{first A count}=4
Count matrixRows are bases and columns are motif positions.BasePosition 1Position 2Position 3Position 4A4001C0300G0140T0003