Table IIa: Position-dependent, orientation-independent pentamers

Distance from ATG		-598 to -500					-499 to -401					-400 to -302					-301 to -203					-202 to -104					-103 to -5					chi2 score	p-value <
Phase		EG	LG	S	G2	M	EG	LG	S	G2	M	EG	LG	S	G2	M	EG	LG	S	G2	M	EG	LG	S	G2	M	EG	LG	S	G2	M
Early G1	ATATA/TATAT	6.02	6.38	1.77	0.17	0.09	0.19	4.26	5.59	0.17	0.00	0.79	2.10	1.83	0.03	1.27	0.21	0.30	0.01	0.09	0.00	5.05	4.32	2.44	0.03	0.29	8.52	1.34	2.44	0.09	1.56	57.35	0.1
	GGCCA/TGGCC	0.00	4.32	0.30	1.24	0.40	10.53	0.01	1.91	0.02	0.11	3.54	2.12	3.24	4.31	1.24	0.15	1.31	0.30	1.24	1.24	4.85	0.01	1.91	0.40	2.55	4.85	2.74	0.51	0.40	0.40	56.17	0.15
	CCGCG/CGCGG	0.04	1.25	3.12	0.06	0.06	2.06	1.25	0.40	2.94	0.79	2.06	0.97	0.25	0.79	1.13	7.09	0.02	0.25	1.13	2.36	2.06	0.48	4.81	5.59	2.36	2.66	5.66	0.25	2.36	0.06	54.31	0.2
Late G1	ACGCG/CGCGT	0.09	1.35	3.09	2.68	2.68	0.01	0.80	1.10	2.68	4.19	0.01	0.47	0.53	4.19	4.19	0.09	3.02	2.06	0.17	6.02	0.46	163.97	15.34	4.19	4.19	4.92	0.47	0.00	4.19	2.68	239.80	0.001
	CGCGA/TCGCG	2.38	2.13	0.07	3.24	3.24	0.49	1.37	0.42	0.22	1.84	1.26	11.79	0.82	3.24	0.22	0.95	2.01	0.02	0.00	0.83	2.38	79.25	8.07	0.18	1.84	5.67	0.36	0.02	3.24	3.24	140.79	0.001
	GACGC/GCGTC	1.64	2.38	0.53	0.96	5.24	0.21	2.38	2.22	5.24	0.29	0.21	0.96	0.12	0.96	3.43	0.21	7.14	0.00	1.45	3.43	0.61	47.73	3.72	0.96	3.43	4.06	0.51	5.07	3.43	5.24	113.77	0.001
	AACGC/GCGTT	0.19	0.17	4.41	1.30	1.30	0.01	0.17	0.38	3.37	0.20	0.05	0.88	0.35	3.37	1.30	0.58	0.88	3.34	1.30	1.30	0.30	55.51	7.48	2.22	1.30	4.29	1.35	0.79	1.30	0.20	99.61	0.001
	GCGAA/TTCGC	3.38	0.35	1.03	0.01	0.01	2.30	0.00	0.03	0.81	1.54	2.30	0.08	0.22	3.69	0.32	1.87	0.08	1.03	0.64	0.81	0.31	30.92	2.71	6.24	1.54	7.84	1.92	1.83	0.81	1.54	76.17	0.001
	GCGTA/TACGC	0.11	2.97	2.04	0.72	0.00	0.11	0.01	1.16	0.60	0.72	0.11	0.40	1.94	1.57	2.75	0.50	0.40	0.47	0.20	0.14	3.44	23.28	3.04	2.75	2.75	1.44	1.34	0.47	2.75	0.14	58.29	0.1
	CGAAA/TTTCG	4.16	0.18	0.34	2.05	3.93	0.00	0.67	0.14	3.93	5.10	0.00	0.61	0.14	0.37	0.11	0.66	2.23	1.14	0.59	0.00	0.00	13.16	5.22	2.54	2.92	0.23	0.08	2.46	0.00	2.92	55.90	0.15
S	GCCAC/GTGGC	0.61	0.17	2.40	0.59	0.96	0.75	0.02	1.37	2.70	1.45	0.00	0.17	3.72	0.96	0.59	0.00	1.00	21.07	0.96	0.01	4.06	3.41	0.62	0.96	0.01	0.14	2.45	0.53	2.00	2.00	55.69	0.15
M	AACCC/GGGTT	5.51	6.09	4.40	0.00	0.14	0.11	5.05	0.00	0.72	2.51	1.19	1.34	1.16	0.20	1.39	0.67	2.13	0.00	3.95	10.26	0.11	5.05	3.17	0.14	0.00	0.00	3.94	0.52	0.14	0.72	60.58	0.05
G2, Late G1	CAGCC/GGCTG	0.00	5.51	0.15	0.55	0.99	1.56	0.14	5.17	8.52	0.99	4.29	0.22	0.57	0.10	5.29	6.15	0.01	0.58	3.48	0.31	0.00	1.05	2.28	0.31	0.31	4.12	8.97	0.14	4.20	0.31	66.27	0.005
Many	GCCGC/GCGGC	1.52	0.61	4.47	2.41	0.22	0.08	0.61	0.64	4.24	0.22	4.77	0.21	0.13	4.24	1.10	2.91	3.09	0.92	4.24	3.92	0.45	2.05	4.47	0.00	0.94	2.64	4.35	0.27	0.22	0.94	56.86	0.15

Clicking on a pentamer retrieves a list of the genes whose upstream regions contain one or more copies of the pentamer.

A list of the 50 highest scoring pentamers is also available.

The number of upstream regions containing one or more copies of a pentamer was counted over intervals of 99 nt in each of the five sets of cell cycle-regulated genes. The interval, measured in nt from the ATG start codon, is indicated at the top of each table. The chi2 contribution made by each of the 30 populations is shown, along with the total value of chi2. The population(s) which make the greatest contribution to chi2 are indicated in bold.
EG: early G1; LG: late G1; S: S; G2: G2; M: M.
p-values for each chi2 value were calculated from a Monte Carlo simulation.