Fig. 4

Specific 6-mers enrichment in linkers are unique to HMDs. a An example of prediction of HMDs by SVM_hypo. The DNA methylation ratio, HMDs at the medaka blastula stage, and SVM prediction score (dark purple indicates a score higher than −1, light purple, lower than −1) are shown. b Performance of classification of HMD versus methylated sequences on chromosome 8 by SVM_hypo. ROC curve and the area under the ROC curve (ROCauc) (top), and precision–recall curve (bottom) are shown. c Comparison of SVM-weights between SVM_hypo and SVM_DNaseI for all 6-mers (left), and boxplots shows the difference of SVM_hypo-weights between the top 20 SVM_DNaseI 6-mers and all 6-mers. P value was calculated using non-paired Wilcoxon test. d A schematic of nucleosome positioning and specific DNA motif distribution in presumptive HMDs