Secondary structure analysis of CBFB, MYH11, HMGA1, LAMA4, MLL, and AFF4 loci. (A) Comparison of potential to form secondary structure for these genes versus a control. The computed lowest free energy of predicted DNA secondary structures from segments of 300 nt in length, overlapping in 150 nt steps, has been fit to a curve for each gene. The Matlab function polyfit finds coefficients of a polynomial P(X) of degree N that fit the raw data best in a least-squares sense. The analysis was performed over the length of the entire gene plus 125 kb flanking on each side. The arrows indicate where a gene begins and ends. The control sequence was generated by randomizing LAMA4 1000 times. The x axis indicates the size of the analyzed sequences, and the y axis displays the free energy of the predicted structure. Raw data plots for each gene are included in Additional file 3. (B) The most stable structure predicted for each gene, as produced by MFOLD. Each structure represents the 300 nt segment with the lowest ΔG value.