Fig. 3

Evaluating J factors of in silico generated DNA fragments. a Seven different curves with colors corresponding to the respective set of structural parameters are shown. Each curve reflects the analysis of 20,000 random sequences with lengths between 350 and 4000 bp. The y-axis reflects the orders of magnitude difference between computationally derived J factors and the straight DNA model. The x-axis corresponds to the percentage of sequences for a given order of magnitude difference. b Distributions of J factors for 15,000 random sequences calculated using SET7 with lengths between 350 and 1050 bp. The plot is stratified for the different DNA fragment lengths. Red lines reflect median values, while the blue box shows the 25 and 75 % quantiles. c Average J factors for 20,000 simulated sequences and seven sets of structural parameters are plotted as squares in colors corresponding to the respective set of structural parameters. J factors calculated based on the straight DNA model [31] are shown as black circles and ones based on DNA persistent length [55] are depicted as a dotted line. Lastly, red dots are used to display ten experimentally measured J factors for long DNA sequences as reported in [21]