Fig. 4
a 2nd and higher-order Markov chains contain cycles. But higher-order Markov chains can be viewed as first order Markov chains by compounding variables. We thereby obtain a tree-structured graph. b Simulating 106 sequences of the same length as our motif and estimated the significance and corresponding 95% confidence interval shown in shaded grey. We compare this with SA and IS using (α=0.5) and 104 samples. c We simulated 104 sequences of length 200bp and calculated the maximum motif match score of all offsets, the 95% confidence interval is shown in shaded grey. To calculate the significance of this maximum, we used the calculation from a single match and employed a Poisson approximation