Supplement to Table Ia: Position-independent, orientation-independent 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/ACGCGT	11	66	16	0	1	265	60.44	1.29	33.34	0.26	13.74	11.82	<0.001
AACGCG/CGCGTT	14	72	22	3	2	634	51.62	1.13	26.66	0.00	11.07	12.76	<0.001
CGCGTC/GACGCG	12	63	13	5	0	376	49.64	0.71	28.52	1.37	5.44	13.60	<0.001
ACGCGA/TCGCGT	8	65	22	6	1	514	47.25	4.59	24.08	0.27	5.33	12.98	<0.001
CGCGTA/TACGCG	7	46	21	1	3	412	33.50	2.65	12.83	2.33	9.49	6.19	<0.001
CCCCGC/GCGGGG	14	6	2	1	1	377	31.37	25.60	0.68	1.50	1.79	1.79	<0.005
CGCGAA/TTCGCG	9	58	20	8	4	650	29.53	3.26	15.76	0.04	2.90	7.58	<0.005
CGACGC/GCGTCG	7	33	11	1	0	417	25.76	0.28	12.05	0.09	5.73	7.60	<0.05
GAGTCA/TGACTC	3	5	12	15	5	887	24.53	1.95	5.78	2.36	14.32	0.12	<0.05
CCGTGC/GCACGG	2	4	15	7	10	480	21.31	2.89	6.50	7.99	0.38	3.55	<0.15
AGTCAG/CTGACT	4	15	19	9	0	806	20.29	1.80	0.13	10.83	0.66	6.87	<0.20
ACGCGG/CCGCGT	11	4	6	0	2	340	20.26	13.77	2.04	0.54	3.36	0.55	<0.20
AGACGC/GCGTCT	11	35	11	5	0	712	19.20	0.06	8.16	0.08	1.82	9.07	>0.20
CGTCTC/GAGACG	0	20	12	2	2	648	17.98	5.92	4.35	3.66	2.02	2.02	>0.20
AAACGC/GCGTTT	17	67	31	10	12	1324	17.96	1.36	7.59	0.78	5.02	3.22	>0.20
GCGTTA/TAACGC	14	41	14	3	5	846	17.07	0.14	7.34	0.05	6.06	3.48	>0.20
CGCGCG/CGCGCG	1	5	4	9	1	172	16.06	1.59	0.57	0.00	12.62	1.27	>0.20
AAACCC/GGGTTT	13	22	10	14	24	1205	15.89	0.03	1.71	2.27	0.29	11.60	>0.20
GTGCAC/GTGCAC	0	1	6	5	6	350	15.69	2.96	4.46	1.83	2.13	4.31	>0.20
CCACCA/TGGTGG	11	20	29	12	8	1075	15.68	0.35	2.28	11.87	0.01	1.17	>0.20
CTAGGA/TCCTAG	3	11	6	13	12	678	15.61	2.62	1.43	0.84	6.26	4.47	>0.20
AGGGTA/TACCCT	20	21	10	20	7	1028	15.34	4.01	1.45	1.71	6.48	1.70	>0.20
GCCACC/GGTGGC	6	11	20	6	7	758	14.33	0.60	2.41	11.07	0.23	0.01	>0.20
ATCGAT/ATCGAT	1	15	3	9	11	693	14.26	4.57	0.13	2.73	1.91	4.92	>0.20
GCGTCA/TGACGC	14	38	9	7	4	699	13.87	0.39	6.51	1.73	1.18	4.05	>0.20
CACGGA/TCCGTG	5	6	14	11	6	622	13.79	0.53	5.14	4.27	3.84	0.00	>0.20
CGCACG/CGTGCG	3	4	11	5	1	405	13.69	0.23	2.30	8.73	0.63	1.79	>0.20
CATTCG/CGAATG	9	22	13	6	21	910	13.69	0.61	0.32	0.04	1.85	10.86	>0.20
AAAGGG/CCCTTT	32	34	24	21	31	2113	13.63	3.20	4.95	0.43	0.00	5.05	>0.20
CACCCA/TGGGTG	6	20	19	4	3	973	13.41	0.76	0.18	7.98	1.71	2.79	>0.20
CTAGTA/TACTAG	6	29	16	7	21	1142	13.39	3.77	0.07	0.04	1.79	7.73	>0.20
CGCCAA/TTGGCG	8	35	23	9	4	1052	13.30	1.92	1.96	3.92	0.56	4.94	>0.20
GCGAAA/TTTCGC	14	60	36	23	11	1437	13.18	3.96	1.84	2.40	0.18	4.80	>0.20
CCACCC/GGGTGG	4	9	14	5	1	561	13.09	0.38	0.56	9.12	0.01	3.03	>0.20
AACCCT/AGGGTT	13	21	14	19	22	1104	13.04	0.18	3.30	0.59	2.75	6.21	>0.20
GGGCAA/TTGCCC	11	12	12	3	15	1012	12.90	0.60	2.31	0.30	2.91	6.78	>0.20
ATTTCC/GGAAAT	29	52	17	29	34	2184	12.88	0.24	0.33	6.40	1.27	4.65	>0.20
CGCCGC/GCGGCG	11	4	8	7	3	476	12.74	5.72	4.93	0.41	0.98	0.69	>0.20
CCAGGG/CCCTGG	1	14	14	3	4	489	12.66	4.09	0.16	7.13	0.97	0.30	>0.20
CGTGTC/GACACG	2	11	14	2	5	493	12.56	2.31	0.07	8.41	1.78	0.00	>0.20
AAGGGT/ACCCTT	22	24	15	23	20	1358	12.41	1.40	4.22	1.29	3.99	1.51	>0.20
CGCGGC/GCCGCG	10	3	9	7	4	333	12.38	3.85	6.33	1.08	0.98	0.14	>0.20
CACTAG/CTAGTG	7	28	4	13	5	821	12.27	0.60	3.26	4.47	2.61	1.33	>0.20
CCGCGC/GCGCGG	7	5	5	9	1	348	12.24	1.47	2.09	0.01	6.47	2.20	>0.20
TCCTAA/TTAGGA	21	28	16	16	27	1246	12.22	0.59	2.53	1.14	0.00	7.96	>0.20
GCGTCC/GGACGC	4	22	4	3	2	416	12.21	0.54	7.77	1.13	0.88	1.90	>0.20
GACGCC/GGCGTC	5	18	11	2	0	506	12.10	0.14	2.32	2.35	2.02	5.26	>0.20
GCGTAA/TTACGC	14	39	21	5	6	877	11.92	0.00	2.88	1.28	4.44	3.32	>0.20
GCGGCC/GGCCGC	3	4	9	8	2	416	11.87	0.38	2.86	3.15	4.64	0.85	>0.20
CACTCC/GGAGTG	15	15	5	4	4	728	11.87	8.88	0.00	1.32	0.83	0.83	>0.20
GCCGCA/TGCGGC	5	12	9	13	2	621	11.83	0.45	0.38	0.15	8.19	2.66	>0.20
GGTCTA/TAGACC	5	18	3	11	2	649	11.76	0.31	1.39	2.73	4.92	2.40	>0.20
ATGGCC/GGCCAT	6	25	15	6	1	812	11.58	0.85	2.25	2.21	0.39	5.88	>0.20
CGCGAC/GTCGCG	1	20	14	4	5	283	11.55	5.38	1.38	3.56	0.92	0.32	>0.20
CTGGCC/GGCCAG	9	11	14	1	4	594	11.49	1.04	0.51	5.55	3.88	0.51	>0.20
GTACCA/TGGTAC	10	38	8	10	6	1058	11.29	0.29	6.51	2.51	0.03	1.95	>0.20
CACCGA/TCGGTG	9	9	11	0	4	620	11.23	2.35	0.56	3.35	4.83	0.14	>0.20
AGCGTC/GACGCT	7	22	1	6	4	675	11.05	0.03	4.58	5.86	0.00	0.58	>0.20
GAATCA/TGATTC	8	36	14	14	23	1458	10.96	3.72	0.23	1.03	0.00	5.97	>0.20
ACTCTC/GAGAGT	8	18	12	6	18	1053	10.94	0.47	0.63	0.00	1.04	8.81	>0.20
GCAACC/GGTTGC	10	20	18	5	2	854	10.94	0.10	0.03	5.12	1.15	4.54	>0.20
CAATGA/TCATTG	12	35	24	23	27	2006	10.92	3.14	1.27	0.02	1.59	4.90	>0.20
TAATCA/TGATTA	29	28	30	21	18	2014	10.86	3.30	5.87	1.31	0.36	0.01	>0.20
CACGCG/CGCGTG	7	24	6	3	2	322	10.84	0.00	5.89	0.55	1.61	2.79	>0.20
ACCAGA/TCTGGT	14	32	24	3	12	1181	10.83	0.00	0.17	3.50	7.15	0.01	>0.20
CGCCAC/GTGGCG	8	7	14	7	3	586	10.75	0.39	3.24	5.55	0.30	1.28	>0.20
CCCCAA/TTGGGG	6	17	18	15	6	689	10.69	1.73	1.01	3.03	3.89	1.04	>0.20
GACTTA/TAAGTC	12	14	19	16	8	905	10.60	0.04	4.26	2.41	3.46	0.43	>0.20
GCCAGC/GCTGGC	15	9	12	8	6	660	10.57	5.58	4.12	0.57	0.06	0.23	>0.20
CTGGTA/TACCAG	7	34	24	8	18	1084	10.50	4.24	0.15	2.34	2.12	1.66	>0.20
CCCAAC/GTTGGG	8	12	17	9	3	793	10.43	0.00	1.54	5.99	0.47	2.42	>0.20
TAGGAA/TTCCTA	21	37	16	20	29	1680	10.39	0.03	0.85	2.54	0.23	6.75	>0.20
CGACCC/GGGTCG	6	2	1	1	3	285	10.37	6.97	1.43	0.91	0.43	0.64	>0.20
ACTGGC/GCCAGT	3	9	12	11	6	820	10.35	2.08	1.99	2.10	4.18	0.00	>0.20
ATCTGA/TCAGAT	9	34	28	10	10	1373	10.34	2.38	0.15	6.17	0.82	0.82	>0.20
AGTCAT/ATGACT	8	31	26	21	13	1451	10.16	4.21	0.38	2.47	2.94	0.15	>0.20
AAAGGC/GCCTTT	33	41	19	14	22	1863	10.10	6.54	0.38	1.41	1.25	0.52	>0.20
CTTTAA/TTAAAG	27	65	25	12	30	2395	10.07	0.03	1.58	1.07	5.44	1.96	>0.20
GCCGGA/TCCGGC	12	9	7	4	2	454	10.04	7.34	0.70	0.03	0.19	1.78	>0.20
CTAGAG/CTCTAG	4	12	8	10	13	813	10.02	1.80	1.20	0.13	1.42	5.46	>0.20
GCCCTA/TAGGGC	2	13	3	7	10	563	9.94	2.45	0.05	2.09	0.69	4.66	>0.20
AACCGG/CCGGTT	5	11	6	13	6	589	9.88	0.45	0.78	0.47	8.19	0.00	>0.20
ACGAAC/GTTCGT	9	21	21	6	5	1029	9.82	0.14	0.02	6.79	1.04	1.82	>0.20
CAACAC/GTGTTG	10	26	25	11	6	1289	9.80	0.62	0.06	6.54	0.01	2.56	>0.20
GTAGAC/GTCTAC	2	13	9	11	3	711	9.78	2.89	0.01	0.37	5.33	1.18	>0.20
GCCAAC/GTTGGC	11	26	14	3	3	904	9.76	0.28	1.84	0.81	3.41	3.41	>0.20
ACACGA/TCGTGT	8	28	19	8	3	832	9.72	0.75	1.04	3.06	0.28	4.58	>0.20
GGGTTA/TAACCC	9	14	5	12	13	773	9.69	0.01	1.11	2.68	2.33	3.56	>0.20
ATAAGG/CCTTAT	28	35	21	13	9	1646	9.66	6.40	0.12	0.01	0.40	2.72	>0.20
TAGTCA/TGACTA	14	23	24	19	8	1243	9.63	0.02	1.97	2.88	2.92	1.84	>0.20
AGTAAA/TTTACT	36	76	23	38	31	2768	9.60	0.18	0.30	6.84	2.24	0.05	>0.20
GAATAC/GTATTC	12	39	21	22	27	1624	9.59	3.14	0.26	0.24	1.05	4.90	>0.20
TTCGAA/TTCGAA	6	19	19	14	6	1044	9.53	1.95	0.51	3.56	2.30	1.20	>0.20
ACATAA/TTATGT	12	56	37	25	26	2191	9.53	7.27	0.04	1.56	0.21	0.45	>0.20
CAGTTA/TAACTG	25	37	12	10	12	1384	9.49	5.37	0.35	2.31	1.16	0.30	>0.20
GTCGAA/TTCGAC	5	24	15	2	8	949	9.48	1.70	1.38	2.00	4.40	0.00	>0.20
CAGGTC/GACCTG	3	25	5	6	7	621	9.47	2.76	4.93	1.70	0.08	0.01	>0.20
CGCCAG/CTGGCG	3	8	11	10	5	580	9.45	1.56	1.89	2.07	3.89	0.03	>0.20
CCAACC/GGTTGG	11	22	13	3	2	829	9.44	0.81	0.97	1.00	2.66	3.99	>0.20
AAGCGG/CCGCTT	13	10	14	9	13	917	9.43	1.12	5.49	0.59	0.02	2.22	>0.20