Figure 1
From: Measuring similarities between transcription factor binding sites
CREB versus ATF matrices: The distance D is computed for each possible alignment between the two matrices. For each aligned column, we calculated the χ2 scores. D is then the number of χ2 values which exceed the threshold 
= 7.81 For shift= 0, the two matrices are not properly aligned, D = 7. For shift= 3, the two matrices are properly aligned, D = 0.