Table 2. Most common motifs found within 5 kb of the TSS and their strand-specific motif results.

Motifs	Counts (on coding strand)	Binom. p-value	KS Test Distance (p-value)
A/T	6559 (2803/3756)	5.2E−32	0.135 (<1E−300)
AC/GT	5072 (2051/3021)	2.1E−42	0.118 (3.1E−15)
CCG/CGG	2833 (1151/1682)	1.7E−23	0.06 (7.2E−3)
AAAT/ATTT	1419 (610/809)	1.4E−7	0.166 (9.1E−9)
AG/CT	1405 (686/719)	0.39	0.07 (0.042)
AGGG/CCCT	1308 (662/646)	0.68	0.07 (0.06)
AAT/ATT	1245 (577/668)	0.011	0.06 (0.15)
AGC/GCT	990 (373/617)	8.36E−15	0.134 (4.7E−4)
AAAC/GTTT	983 (434/549)	2.7E−4	0.188(6.4E−8)
AAC/GTT	952 (460/492)	0.315	0.182 (2.7E−7)
AATG/CATT	876 (452/424)	0.36	0.09 (0.055)
AAAG/CTTT	751 (325/426)	2.6E−4	0.084 (0.146)
AAAAC/GTTTT	651 (304/347)	0.10	0.137 (4.5E−3)
CCCG/CGGG	687 (274/413)	1.28E−7	0.114 (0.027)
AAGG/CCTT	659 (299/350)	0.050	0.092 (0.128)

The most common motifs and their strand-specific counts are displayed. The binomial test (Binom.) p-value is the chance that these strand-specific frequencies deviate from an expected value of 50%. The Kolmogorov-Smirnov (KS) test values provide a measurement of the difference between the distribution of the two different strand-specific motifs, for each motif pair. The p-values shown are not corrected for multiple tests.