Table 2. Distribution of significantly enriched 5 kbp regions.

WCEseq Library	Significantly Dense 5 kbp Regions
	Total	With TSS (Total: 20240)	With TES (Total: 21020)	Intragenic (Total: 182328)	With Satellite (Total: 3203)
ES	29	2 (6.9%)	2 (6.9%)	12 (41.38%)	11*** (37.93%)
NP	4334	1434*** (33.09%)	367*** (8.47%)	3825*** (88.26%)	55** (1.27%)
MEF	1403	1036*** (73.84%)	179*** (12.76%)	1186*** (84.53%)	38** (2.71%)

The significantly dense (FDR adjusted p-value<1e-4) 5 kbp regions (510,351 regions in total) across three WCEseq libraries were overlapped with gene boundaries (Transcription Start Sites and Transcription End Sites) annotation based on UCSC knownGene database for mm8 and tested for association using 1-tailed Fisher's Exact Test. An overlap with Satellite repeats was also done for comparison. The 5 kbp dense regions are significantly associated to genes and genes boundaries. (Notes: * = p<1e-3 ; ** = p<1e-5 ; *** = p<1e-16 ).