Supplement to Table Ib: Position-independent, orientation-dependent hexamers

Hexamers with a p-value less than or equal to 0.05 (statistically significant) are indicated in green. Hexamers with a p-value between 0.05 and 0.20 (questionable statistical significance) are indicated in orange. Hexamers with a p-value greater than 0.20 (not statistically significant) are indicated in red.

Hexamers	Number of upstream regions containing one or more copy of the hexamer or its reverse complement						Total chi2 score	Contribution of each dataset to chi2 score					p-value
	Early G1	Late G1	S	G2	M	Non cell cycle-regulated		Early G1	Late G1	S	G2	M
ACGCGT	11	66	16	0	1	265	60.44	1.29	33.34	0.26	13.74	11.82	<0.001
AACGCG	9	48	11	2	1	358	37.99	0.61	21.59	0.54	6.77	8.48	<0.005
CGCGTT	6	42	16	1	1	348	33.99	2.17	15.48	0.83	7.75	7.75	<0.005
GACGCG	7	41	7	4	0	206	33.64	0.75	20.08	1.70	2.48	8.63	<0.005
ACGCGA	3	38	10	5	0	256	30.97	4.19	17.29	0.06	1.24	8.19	<0.01
CGCGTC	9	38	9	2	0	194	29.35	0.03	15.45	0.43	4.95	8.48	<0.05
CGCGAA	4	38	12	7	0	347	25.97	3.63	13.00	0.00	0.41	8.92	<0.10
CCCTTT	23	13	10	11	21	1172	25.34	8.06	7.48	1.71	0.01	8.07	<0.15
TCGCGT	5	32	13	1	1	275	24.29	1.48	10.48	0.87	5.73	5.73	<0.20
CCCCGC	10	5	1	0	1	201	23.67	18.56	0.15	1.59	2.49	0.89	<0.20
TACGCG	1	24	13	1	1	209	23.52	4.73	7.15	3.60	4.02	4.02	>0.20
AGGGTT	2	12	7	12	16	575	20.90	4.56	1.54	0.64	3.26	10.90	>0.20
CCGCTA	8	3	1	0	1	362	19.83	16.07	0.53	0.91	1.90	0.43	>0.20
ACGCGG	6	0	2	0	1	166	18.38	13.80	3.15	0.04	1.32	0.08	>0.20
CGTGCG	1	1	9	3	1	205	18.10	0.87	3.44	12.85	0.30	0.65	>0.20
CACCTC	3	5	2	11	5	464	18.05	0.38	1.84	1.82	13.63	0.38	>0.20
GGGTTA	1	7	1	8	9	386	17.96	2.51	0.48	3.22	4.64	7.11	>0.20
TCCGTG	2	1	7	8	2	317	17.29	0.51	5.14	2.54	8.81	0.29	>0.20
CGAAAT	8	36	10	6	2	844	16.78	0.47	9.44	0.33	1.04	5.51	>0.20
CGCGTA	6	27	11	0	3	221	16.62	0.39	6.78	0.41	6.87	2.18	>0.20
GAGTCA	1	2	6	8	2	451	16.21	1.45	3.25	1.48	9.82	0.22	>0.20
GCGTTT	9	35	19	4	3	729	16.19	0.55	4.51	2.22	3.80	5.11	>0.20
CGCGCG	1	5	4	9	1	172	16.06	1.59	0.57	0.00	12.62	1.27	>0.20
ACCCTT	18	11	6	10	7	739	15.71	10.43	2.84	1.63	0.76	0.05	>0.20
GTGCAC	0	1	6	5	6	350	15.69	2.96	4.46	1.83	2.13	4.31	>0.20
TAGTCA	3	11	13	12	2	671	14.79	2.08	0.78	3.26	6.02	2.66	>0.20
ACCAGA	8	15	19	1	9	588	14.57	0.04	0.56	7.98	5.73	0.26	>0.20
TTCTCG	17	17	7	2	6	747	14.47	9.92	0.00	0.64	3.72	0.19	>0.20
ATCGAT	1	15	3	9	11	693	14.26	4.57	0.13	2.73	1.91	4.92	>0.20
GCGTCT	3	20	7	2	0	360	14.22	0.97	6.92	0.11	1.53	4.68	>0.20
ACCCCG	5	3	0	0	0	180	14.21	10.31	0.01	1.55	1.17	1.17	>0.20
GTAAAC	10	21	13	21	19	881	13.95	1.05	2.39	0.64	6.19	3.67	>0.20
GTCCCA	0	4	6	0	6	312	13.89	2.63	0.46	2.74	2.34	5.73	>0.20
ACAATG	7	19	6	18	8	945	13.89	0.68	0.08	2.42	10.69	0.03	>0.20
CGACGC	4	19	7	1	0	226	13.82	0.24	6.13	0.17	2.75	4.53	>0.20
GCGAAA	7	43	18	14	5	727	13.82	3.73	5.18	0.08	0.13	4.69	>0.20
TCGATG	2	13	0	4	9	602	13.81	1.47	1.05	5.41	0.00	5.88	>0.20
TACTAG	4	18	6	4	15	660	13.81	1.80	0.15	1.05	1.20	9.61	>0.20
GCTTGC	10	15	2	1	2	534	13.53	5.20	1.93	2.49	2.61	1.30	>0.20
GATGAC	4	10	4	13	7	694	13.50	0.81	0.82	1.52	9.97	0.38	>0.20
TTACGC	3	20	14	4	1	448	13.45	2.21	1.92	4.27	0.75	4.30	>0.20
CGCCAC	6	2	10	3	2	325	13.38	1.30	4.54	6.95	0.04	0.55	>0.20
TGCCCT	6	13	7	2	14	508	13.32	0.12	0.20	0.15	2.79	10.06	>0.20
TAACGC	9	23	6	1	2	472	13.27	0.75	5.22	0.47	4.16	2.66	>0.20
CTGACT	4	7	12	5	0	460	13.20	0.08	0.80	8.03	0.20	4.09	>0.20
TTGGCG	1	18	12	5	1	550	13.14	4.25	1.97	3.29	0.03	3.59	>0.20
TTAGGA	15	17	7	13	18	669	13.13	1.06	2.29	3.15	0.75	5.89	>0.20
AGCGAC	9	5	3	8	9	355	13.12	2.08	4.00	1.94	1.85	3.26	>0.20
CCGTGC	1	1	8	4	3	237	13.07	1.15	4.12	6.77	0.92	0.11	>0.20
CAGTTA	17	17	5	4	8	732	12.91	8.84	0.04	2.39	1.60	0.04	>0.20
CTTCAG	7	12	4	14	5	744	12.85	0.00	0.49	2.09	10.06	0.21	>0.20
TATAAG	26	31	14	9	8	1168	12.71	9.18	0.00	0.53	1.16	1.84	>0.20
CGCCGC	8	1	4	5	3	228	12.68	5.98	5.48	0.00	1.21	0.00	>0.20
GTTCGT	5	8	13	1	3	514	12.60	0.00	0.59	8.95	2.61	0.44	>0.20
GGGCTG	1	2	7	3	0	263	12.59	0.61	1.43	8.02	0.64	1.90	>0.20
AAACCC	8	8	8	6	14	669	12.59	0.08	3.55	0.03	0.03	8.90	>0.20
GCCGGG	4	2	6	0	0	198	12.59	2.08	1.15	5.85	1.75	1.75	>0.20
GGTACA	4	19	2	2	2	503	12.53	0.12	7.73	2.32	1.18	1.18	>0.20
GCTTCA	4	17	16	13	3	770	12.39	2.55	0.13	3.24	3.56	2.91	>0.20
GCTGGC	10	4	4	4	2	361	12.39	9.28	2.30	0.09	0.07	0.65	>0.20
ATCTGA	3	21	18	4	6	743	12.38	3.61	0.43	6.30	1.71	0.34	>0.20
ATAGAG	4	21	11	18	11	931	12.35	4.19	0.13	0.19	7.60	0.24	>0.20
GCCACG	7	4	9	4	0	263	12.34	2.36	2.30	4.10	0.07	3.51	>0.20
GACAAA	8	21	17	21	16	1160	12.33	2.34	2.23	0.06	6.47	1.23	>0.20
AAGGGT	6	14	9	14	15	729	12.30	1.31	1.95	0.43	3.59	5.01	>0.20
TGACGC	7	27	5	4	3	370	12.30	0.04	7.39	1.70	1.10	2.06	>0.20
CGATGA	2	20	9	15	7	870	12.30	5.18	0.11	0.15	6.78	0.07	>0.20
GCCACC	2	5	11	3	2	404	12.26	0.84	1.15	9.67	0.04	0.55	>0.20
CCCTGG	1	7	10	2	1	252	12.23	1.74	0.02	8.70	0.37	1.40	>0.20
ACTCTC	6	10	10	4	14	563	12.19	0.21	1.89	0.26	0.92	8.90	>0.20
GCGGAA	9	5	12	11	7	548	12.18	0.43	7.02	1.44	3.24	0.05	>0.20
CCCGTA	1	3	1	6	1	271	12.17	0.48	0.34	0.75	10.27	0.32	>0.20
AAGCGT	12	14	2	2	7	560	12.16	5.75	0.09	3.71	2.15	0.47	>0.20
CACTAG	4	15	2	11	3	434	12.15	0.54	0.62	3.35	6.76	0.88	>0.20
ATCACC	3	10	13	5	12	681	12.14	2.35	1.69	2.65	0.26	5.19	>0.20
GGACGC	1	11	0	1	1	207	12.11	0.74	7.60	2.70	0.54	0.54	>0.20
GCCGCG	6	0	6	4	2	155	12.11	3.12	6.30	1.83	0.71	0.15	>0.20
CGGACT	4	0	5	2	0	220	12.09	2.65	3.85	3.89	0.10	1.61	>0.20
TGGGTG	3	10	10	0	1	504	12.04	0.23	0.31	6.20	3.51	1.79	>0.20
TAATCA	20	15	20	9	12	1176	11.95	4.50	5.05	1.92	0.40	0.07	>0.20
CCGGTT	4	6	2	9	2	315	11.88	0.01	0.52	1.34	9.45	0.55	>0.20
GCCAAC	6	18	4	2	0	470	11.84	0.23	5.36	0.56	1.30	4.39	>0.20
GCACGT	6	1	6	5	1	389	11.83	2.64	4.80	1.48	1.78	1.14	>0.20
GGAGTG	9	6	1	3	2	333	11.83	8.90	0.25	2.30	0.00	0.37	>0.20
GTTGCA	9	17	16	1	4	741	11.72	0.21	0.02	5.27	5.02	1.20	>0.20
GCGCGG	2	4	4	7	0	197	11.70	0.23	0.64	0.16	8.20	2.49	>0.20
TCTACG	10	6	5	4	10	415	11.67	3.13	3.19	0.46	0.24	4.66	>0.20
AAACAC	5	30	19	19	8	1050	11.59	5.20	0.10	0.72	4.32	1.25	>0.20
TGTCAG	12	11	4	3	2	507	11.53	8.62	0.00	0.77	0.60	1.53	>0.20
TTAAAG	16	36	17	6	24	1411	11.52	0.00	0.05	0.24	4.96	6.27	>0.20
CTAGGT	8	9	0	4	1	328	11.49	5.30	0.22	4.25	0.19	1.53	>0.20
GCACGG	1	3	7	3	7	255	11.48	1.74	2.57	2.13	0.00	5.03	>0.20
GATGGG	0	10	0	5	2	374	11.48	2.80	2.76	3.28	2.54	0.09	>0.20
TCCCAT	4	12	14	1	8	592	11.46	0.91	0.20	5.55	3.88	0.93	>0.20
CCGATC	0	0	5	2	2	222	11.46	1.48	3.15	6.12	0.36	0.36	>0.20
AGAGCG	7	2	6	8	5	400	11.44	1.24	6.20	0.06	3.73	0.20	>0.20
CGTATT	13	15	18	19	11	826	11.42	0.02	5.05	0.75	5.60	0.00	>0.20
GCGTGA	1	16	8	1	2	300	11.40	2.82	3.93	1.24	2.34	1.07	>0.20
CCACGA	2	12	3	0	0	388	11.38	0.23	6.16	0.02	2.49	2.49	>0.20
TAGGGT	1	9	6	10	3	353	11.32	2.98	0.13	0.03	7.82	0.36	>0.20