Table 1. Summary Features of MSF and MRF Segments Defined at Different Statistical Stringencies by iSeg.

Segmenta	sd Cutoffb	Countsc	Total Array (%)d	Ave. No. of Segments per 10 kb	Segments Neare Genes (%)f	Segments within Genes (%)	Genes Neare Segments (%)	Median Segment Size (bp)	Median Size of Segments Neare Genes (bp)	Median Size of Segmentse within Genes (bp)
MSF	1.0	4267	6.4	2.96	59	45	64	172	172	172
	1.5	3290	4.4	2.28	58	47	58	167	168	168
	2.0	2597	3.2	1.80	57	44	52	161	160	160
	3.0	1753	2.0	1.22	55	42	40	152	151	152
MRF	1.0	6783	9.3	4.71	41	36	72	117	127	151
	1.5	4908	6.3	3.41	43	32	67	115	131	151
	2.0	3582	4.4	2.49	47	41	59	118	130	142
	3.0	2104	2.1	1.46	48	44	41	112	115	116

^aMSF, MNase-sensitive footprint; MRF, MNase-resistant footprint.

^bsd cutoff: a parameter in the iSeg segmentation algorithm related to the statistical stringency of segmentation.

^cCounts: the total number of segments within the 11 Mb of unique genomic space surveyed by the big-block microarray.

^dProportion: the sum of all segments divided by total array size (bp).

^eNear: within 500 bp.

^fGenes: The 1688 genes of the 39,570 canonical gene models (Maize Filtered Gene Set version 5b) represented on the microarray.