Insulator binding data was processed with Model based Analysis Tiling-arrays (MAT) software (Johnson et al., 2006, Proc Natl Acad Sci USA  103:12457-12462 ). We ran paired MAT analysis with MaxGap of 500, MinProbe of 10, and a Bandwidth of 250. We report here the peaks found by MAT at 1% FDR.
Class I was computed as binding sites at 1% FDR for at least 2 components among CP190, BEAF32 and CTCF, with overlap by less than 250bp between their peak center (mid-peak) location.
Class II is defined by Su(Hw) binding sites only; using 2 independent antibodies for Su(Hw), we computed all peaks for both experiments that overlap by less than 250 bp.