A1BG response element positive results

Associate Editor(s)-in-Chief: Henry A. Hoff

Def. nucleotide "sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents", [that] "may be found in both promoter and enhancer regions" are called response elements.

Hypotheses

Main article: Hypotheses

1. A1BG has all known response elements in both promoters.
2. A1BG is transcribed by all known response elements.
3. Each known response element participates in the transcription of A1BG.

Response element positive results

Main article: A1BG regulatory elements and regions

Response elements occurring in promoters for A1BG

Name of elements	Consensus sequences	UTR	Core promoter	Core promoter	Proximal promoter	Proximal promoter	Distal promoter	Distal promoter
(Abbreviations)	Nucleotides	Negative direction	Negative direction	Positive direction	Negative direction	Positive direction	Negative direction	Positive direction
(Authors)	(complements not included)	(4685-2846 nts from ZSCAN22)	(2846-2811 nts from ZSCAN22)	(4300-4265 nts from ZNF 497)	(2811-2596 nts from ZSCAN22)	(4265-4050 nts from ZNF 497)	(2596-<200 nts from ZSCAN22)	(4050-<200 nts from ZNF 497)
ABA responsive elements (ABREs)	ACGTG(G/T)C	Negative strand: CTGTGCA at 3429 Positive strand: ACGTGGC at 4239	-	Positive strand: ACGTGGC at 4344	-	-	-	Positive strand: GACACGT at 2960, ACGTGTC at 1823
Activated B-cell Factor-1s (ABFs)	CGTNNNNN(A/G)(C/T)GA(C/T)	-	-	-	-	-	Positive strand: CGTTCTTTATGAT at 352	Positive strand: CGTCACCGGTGAC at 2073, CGTTCGGTGTGAC at 346
A boxes	TACGTA	Negative strand: TACGTA at 4246	-	-	-	-	-	Positive strand: TACGTA at 3071
boxes A	TGACTCT	-	-	-	Positive strand: TGACTCT at 2788	-	-	Positive strand: TCTCAGT at 2613
Abscisic acid-responsive elements (Pho4s), G boxes	CACGTG	-	-	-	-	-	-	Negative strand: CACGTG at 570 Positive strand: CACGTG at 3884, CACGTG at 2961, CACGTG at 1219, CACGTG at 547
H and ACA boxes	AGAGGA	Positive strand: AGGACA at 4468, AGGACA at 3756, AGGACA at 3389	-	-	Positive strand: ACAGGA at 2690	Negative strand: AGGACA at 4252	Negative strand: AGGACA at 1911	Negative strand: ACAGGA at 3572, AGGACA at 3131, AGGACA at 2460 Positive strand: AGGACA at 3622, ACAGGA at 3620, AGGACA at 144
ACGT-containing elements	ACGT	Negative strand: ACGTG at 4339, CACGT at 3429, ACGTG at 3288, CACGT at 2863	-	Negative strand: TGCAC at 4342	Negative strand: ACGTG at 2760	Positive strand: ACGTG at 4237	Negative strand: ACGTG at 2425, CACGT at 2081, ACGTG at 1999, ACGTG at 1718, CACGT at 1535, CACGT at 1470, ACGTG at 1346, ACGTG at 1338 Positive strand: CACGT at 1772, CACGT at 531, CACGT at 342	Negative strand: CACGT at 3254, ACGTG at 570, CACGT at 569 Positive strand: CACGT at 3960, ACGTG at 3884, CACGT at 3883, CACGT at 3464, ACGTG at 3342, ACGTG at 3321, ACGTG at 2961, CACGT at 2960, CACGT at 2800, CACGT at 2681, CACGT at 2334, CACGT at 2326, CACGT at 2063, ACGTG at 1821, CACGT at 1786, ACGTG at 1471, ACGTG at 1371, ACGTG at 1219, CACGT at 1218, CACGT at 783, ACGTG at 547, CACGT at 546
Activating protein 2 (Murata)	(C/G)CCN(3,4)GG(C/G)	-	-	Negative strand: CCCTGGGGC at 4427, CCCTTGGGG at 4302	-	Negative strand: CCCATGGGG at 4224, CCCCATGGG at 4223	Negative strand: CCCTGCGGC at 1154 Positive strand: CCCAAGGGC at 1820	Negative strand: GCCCTGGGC at 3498, GCCAATGGG at 2911, GCCTCTGGC at 2884, CCCTTAGGG at 2766, GCCACCGGC at 1547, GCCACCGGC at 1295, GCCAGCGGC at 332, CCCTCAGGC at 91 Positive strand: CCCGTTGGC at 3912, CCCTGTGGG at 3533, GCCAACGGG at 3493, CCCAGAGGC at 1961, GCCGGTGGG at 1852, GCCCGCGGG at 1770, CCCGGCGGC at 1758, GCCCCCGGC at 1647, CCCGACGGC at 483, CCCTCCGGG at 372
Activating protein 2 (AP2) (Cohen)	GCCTGGCC	Negative strand: CCGGTCCG at 4103, CGGACCGG at 3130	-	-	-	-	Negative strand: CCGGTCCG at 2520, CGGACCGG at 1200, CCGGTCCG at 649	Negative strand: GCCTGGCC at 3681, GCCTGGCC at 2990, GGCCAGGC at 1176
Activating protein 2 (Cohen)	TCCCCCGCCC	-	-	-	-	-	-	Positive strand: TCCCCCGCCC at 4440
Activating protein 2 (Yao)	TCTTCCC	-	-	-	-	Positive strand: CCCTTCT at 4264	Negative strand: TCTTCCC at 1657, GGGAAGA at 620	-
Activating protein 2 (Yao)	CTCCCA	Negative strand: ACCCTC at 4549, ACCCTC at 4497, ACCCTC at 4303, ACCCTC at 4271, GAGGGT at 4259, ACCCTC at 4153, ACCCTC at 3989, ACCCTC at 3752, ACCCTC at 3714, ACCCTC at 3080	-	-	-	-	Negative strand: ACCCTC at 2221, ACCCTC at 2104, ACCCTC at 1962, ACCCTC at 1930, ACCCTC at 1795, ACCCTC at 1018, ACCCTC at 686, ACCCTC at 550, ACCCTC at 413, GAGGGT at 389	Negative strand: CTCCCA at 3333, CTCCCA at 2532, CTCCCA at 2396, CTCCCA at 2383, TGGGAG at 1782, CTCCCA at 466 Positive strand: CTCCCA at 3880, CTCCCA at 2797, CTCCCA at 182
Activating protein 2 (Yao)	GGCCAA	Positive strand: TTGGCC at 4099, TTGGCC at 3948	-	-	-	-	TTGGCC at 4099, TTGGCC at 3948	Negative strand: GGCCAA at 2609, GGCCAA at 1202, GGCCAA at 691, GGCCAA at 555, GGCCAA at 418
Activating transcription factors (Burton)	(A/C/G)TT(A/G/T)C(A/G)TCA	Positive strand: ATTTCATCA at 2888	-	-	-	-	Positive strand: TGACGAAAC at 313	Negative strand: CTTGCGTCA at 2423, TGACGTAAG at 2207, TGATGAAAC at 2147, CTTTCGTCA at 1184
Activating transcription factors (Kilberg)	(A/G/T)TT(A/G/T)CATCA	-	Positive strand: ATTTCATCA at 2888	-	-	-	-	Negative strand: TGATGAAAC at 2147
Adenylate–uridylate rich elements (AUREs) (Bakheet)	(A/T)(A/T)(A/T)TATTTAT(A/T)(A/T)	Negative strand: TTTTATTTATTA at 4076 Positive strand: AAATAAATAATA at 4077	-	-	-	-	-	-
Adr1ps	TTGG(A/G)G	Negative strand: CCCCAA at 3803, TTGGAG at 3786, CTCCAA at 3260, TTGGGG at 3150, AACCTC at 3118, AACCCC at 2923	-	Negative strand: TTGGGG at 4302	Negative strand: TTGGGG at 2623	-	Negative strand: CTCCAA at 2397, TTGGGG at 2286, TTGGGG at 1859, CTCCAA at 1318, TTGGGG at 1216, CTCCAA at 1027, CTCCAA at 861, TTGGGG at 616	Negative strand: TTGGGG at 2285, CTCCAA at 1278, CTCCAA at 942, CTCCAA at 842, CTCCAA at 606, CCCCAA at 176 Positive strand: TTGGGG at 3939, CTCCAA at 1925, TTGGAG at 1618, TTGGAG at 610, CTCCAA at 304
Aft1s	(C/T)(A/G)CACCC(A/G)	Positive strand: TGGGTGTG at 3185	-	-	-	-	Negative strand: TGGGTGTG at 1804 Positive strand: CGGGTGCG at 2196, CGGGTGCG at 379	Negative strand: TGCACCCG at 3324
AGC boxes	AGCCGCC	-	-	-	-	-	Negative strand: CCGCCGA at 1754	-
AhR responsive element (AHRE-II)	CATGN6C(A/T)TG	Positive strand: CATGGTGGCTCATG at 4116	-	-	-	-	-	-
Androgen response elements (Kouhpayeh)	GGTACAnnnTGTTCT	Negative strand: TGTTCT at 3759, TGTTCT at 3635, TGTTCT at 3340, TGTTCT at 3307 Positive strand: AGAACA at 3668	-	-	Negative strand: TGTACC at 2614	Negative strand: AGAACA at 4068	Negative strand: TGTACC at 2152, TGTACC at 1207, ACATGG at 798, AGAACA at 281 Positive strand: AGAACA at 287, TGTTCT at 45	Negative strand: AGAACA at 3094, TGTTCT at 108 Positive strand: GGTACA at 3901, GGTACA at 3336, GGTACA at 2474, TGTACC at 2032, ACAAGA at 108
Androgen response elements (Wilson)	AGAACAGCCTGTTCT	Negative strand: TGTTCT at 3759, TGTTCT at 3635, TGTTCT at 3340, TGTTCT at 3307 Positive strand: AGAACA at 3668	-	-	-	Negative strand: AGAACA at 4068	Negative strand: AGAACA at 281 Positive strand: AGAACA at 287, TGTTCT at 45	Negative strand: AGAACA at 3094, TGTTCT at 108
Angiotensinogen core promoter elements	(A/C)T(C/T)GTG	Negative strand: CACGAG at 4403, CTCGTG at 3914, CTTGTG at 3669 Positive strand: CACGAG at 4472, CACAAG at 3634, CACAAT at 3515, CACGAG at 3232	-	Negative strand: CTCGTG at 4376	-	-	Negative strand: ATCGTG at 2096, ATTGTG at 340, CACGAT at 336 Positive strand: CACAAG at 2244, CACAAT at 1721, CACGAG at 1182, CACGAG at 708, CACGAG at 572, CACGAG at 435	Negative strand: ATTGTG at 2679, CACGAG at 243 Positive strand: CTCGTG at 3739, CACGAG at 3152, CTTGTG at 3095, CACGAG at 2090, CTCGTG at 1627, CTCGTG at 1207, CTCGTG at 955, CTCGTG at 855, CACAAG at 107
Antioxidant-electrophile responsive elements (Lacher)	GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A	Negative strand: TGACTATGC at 3546 Positive strand: TGAGTTGGC at 4098, TTAAAAGGC at 3442	-	-	-	-	Negative strand: TTAATCGGC at 1237 Positive strand: GCAGTGTAA at 2087, TTAGCCAGC at 504, GCATTTTAA at 192	Negative strand: TGACCAGGC at 2877 Positive strand: TGAAAAAGC at 1750
ATA boxes	AATAAA	Negative strand: AAATAA at 4537 Positive strand: AAATAA at 4221, AAATAA at 4075, AATAAA at 4072, AAATAA at 4071, AATAAA at 3335, AAATAA at 3334, AATAAA at 3014, AAATAA at 3013	-	-	-	Positive strand: AAATAA at 4142	Negative strand: AATAAA at 1726	Negative strand: AATAAA at 3427 Positive strand: AAATAA at 2347
AUUUA AREs (ATTTA) (Siegel)	ATTTA	Negative strand: ATTTA at 4073. Positive strand: ATTTA at 4535	-	-	Negative strand: ATTTA at 2636	Negative strand: ATTTA at 4135	Negative strand: ATTTA at 1698	Positive strand: ATTTA at 3428
Auxin response factors (Stigliani)	(C/G/T)(A/C/T)(G/T)G(C/T)(C/T)(G/T)(C/G)(A/C/T)(A/G/T)	Negative strand: CAGGTTTCTG at 4506, TCGGTCTGCA at 4236, AACCAACCGG at 3948, TACAGACCTC at 3837, TAGGTCGGTA at 3685, TTTGTCTGTA at 2881 Positive strand: CTCCAGCCTG at 4348, CCTGTCTCAA at 4374, CTGAGGCAGG at 4282, CATGCCTGTA at 4122, AGGCAGCATC at 3902, AAGAGGCAGC at 3899, CTCAAGCAAC at 3848, CAGGCTTGAG at 3402, TCTGTCTCAA at 3324, CTCCAGCCTG at 3297, GAGGTTGCTG at 3264, TGGAGACCAG at 3123	-	Negative strand: GAGGCCTCCT at 4407	Positive strand: CATGCCTGTA at 2673	Negative strand: GAGGCCTCAG at 4194, CTGAGGCCTC at 4192 Positive strand: CCTGTTTGTG at 4257	Negative strand: TTTGTTTGTT at 2488, GAGGCCTCCG at 2358, ATGAGGCCTC at 2356, CACCGACCTC at 2071, CTGAGACAGA at 2031, TACCGACCTC at 1748, TATGTCTGTA at 1570, CTTGCTTCCG at 1557, TTTGTTTGTT at 1392, CTGAGACAGA at 1087, GAGGTCGGAG at 1064, CTGAGACAGA at 921, TTTGTCTGTA at 171, CTGGTCGGTA at 38 Positive strand: CTGAGGCAGG at 2568, CATGCCTGTA at 2539, AACAGGCCAG at 2518, AACAAACAGG at 2514, AACAAACAAA at 2489, AGCAAACAAA at 2485, CTCCAGCCTG at 2434, GAGGTTGCAG at 2401, CTGAGGCAGG at 2367, CATGCTGGTG at 2328, TTGAGACCAG at 2263, TTGAGACCAA at 2147, TGGAGGCCAG at 2076, TCTGTCTCAA at 2034, CTCCAGCCTG at 2008, CTGAGGCAGG at 1941, CTTGCCTGAA at 1624, TGCCAGCAGA at 1614, AACAAACCTA at 1590, ATGAAACAAA at 1586, TACAGACATC at 1571, CAGGCTGGAG at 1466, AACAAACAAA at 1393, GAGGTTGCAG at 1322, AGGAGGCAGA at 1314, CTGAGGCAGG at 1288, TTGCGACCAG at 1193, TCTGTCTCAA at 1090, GAGGTTGCAG at 1031, CTGAGGCAGG at 997, TCTGTCTCAA at 924, CTCCAGCCTG at 898, CTGAGGCAGG at 831, AGCCAGCCTG at 507, AAGAGGCCGG at 374	Negative strand: CAGGTCTCAG at 3774, CACCAGCAGC at 3723, AGGCAGCAGG at 3694, CTGGCCTCCA at 3685, CATGTTTGCA at 3341, CTGGTCTCCT at 3302, CAGAAGCCAG at 3220, ATGCAGCAGG at 3147, GTTGTCTCTT at 3056, CAGGCCTCAG at 3040, TTCAGGCCTC at 3038, CTTGTCTGAG at 3007, CTGGCTGCCT at 2889, CAGGCCTCTG at 2882, TGCAGACCTC at 2863, GAGGCTGGTG at 2812, GATGTTGCAG at 2720, TTCAAACAGA at 2652, TAGAAACCAC at 2633, CCTGCCTCAG at 2525, CATGTTGCCT at 2479, TTGCAGCCGC at 2355, CAGGCTGGAG at 2322, TCTGTTTCAT at 2265, TAGGTCTGTT at 2261, TCTGTTGGCA at 2187, ATGAAACCGC at 2150, AGGCAACCAC at 2122, CTCAGGCAAC at 2119, AAGCAGCCAA at 2011, CTCCGACAGG at 1966, CACCGGCCAC at 1850, GCTGTCTGCT at 1734, TTGCAACCTC at 1618, CTGCAGCAAG at 1510, ATGCGGCAAG at 1426, ATGCGGCAAG at 1326, CTCCAACCTA at 1282, CTGCGGCAGC at 1037, CTGCGGCAAG at 1006, CTCCAACCTG at 946, CTCCAACCTG at 846, CTGCGGCAAG at 754, GCGGCCTGAA at 726, CAGCGGCCTG at 724, CTCCAACCTC at 610, CTGCAGCATC at 536, CTTGCTGCAG at 532, GCTGCCGGTG at 486, TGCAGACCGG at 442, AGCAAGCCAC at 342, CGGCAGCAAG at 338, CAGCGGCAGC at 335 Positive strand: TGGAAACCAC at 3949, AGGAGACCGG at 2985, CGGAGACCGA at 2885, CGGCGGCCAC at 1761, CTCCGGCAAG at 1489, CTCCGGCAAG at 1389, AGGAAGCCGG at 764, CCGGTCGCCG at 332, CACAGACCTC at 272, AAGAAACATA at 114
Auxin response factors (Ulmasov)	TGTCTC	Negative strand: TGTCTC at 4519, TGTCTC at 3673 Positive strand: CCTGTCTCAA at 4374, TCTGTCTCAA at 3324	-	-	Negative strand: TGTCTC at 2779	-	Negative strand: TGTCTC at 2444, GAGACA at 2029, TGTCTC at 2018, GAGACA at 1452, GAGACA at 1085, TGTCTC at 1074, GAGACA at 919, TGTCTC at 908 Positive strand: TGTCTC at 2166, TCTGTCTCAA at 2034, TCTGTCTCAA at 1090, TCTGTCTCAA at 924	Negative strand: GTTGTCTCTT at 3056, TGTCTC at 2467, TGTCTC at 2173, TGTCTC at 2079, GAGACA at 712 Positive strand: TGTCTC at 3180, TGTCTC at 3134, TGTCTC at 2653, GAGACA at 2308, GAGACA at 98
Auxin response factors (Boer)	TGTCGG	Negative strand: TGTCGG at 3727	-	-	-	-	-	Negative strand: CCGACA at 1964 Positive strand: TGTCGG at 3896, CCGACA at 3640, CCGACA at 3349, TGTCGG at 3101, CCGACA at 264, TGTCGG at 65
Auxin response factors (ARF5)	(C/G/T)N(G/T)GTC(G/T)	Negative strand: TTTGTCT at 4518, GGGGTCT at 4448, GAGGTCG at 4345, TCGGTCT at 4233, CTGGTCG at 4033, CGACACC at 3959, CGTGTCT at 3917, AGACCTC at 3837, CGGGTCG at 3731, CTTGTCG at 3726, CGACACC at 3711, CAGGTCG at 3701, GGTGTCG at 3694, TAGGTCG at 3682, TGTGTCT at 3672, AGACACA at 3558, TTGGTCT at 3486, AGACAGA at 3321, GAGGTCG at 3294, CGGGTCG at 3209, CGACCCA at 3182, CTGGTCG at 3124, CGACCCG at 3043, CGACCCC at 3037, TTTGTCT at 2878 Positive strand: CCTGTCT at 4371, CCTGTCT at 4210, AGACAAG at 4183, AGACCAG at 4032, TATGTCT at 3833, GTGGTCG at 3813, AGACCAC at 3763, TCTGTCT at 3321, AGACCAG at 3123, TATGTCT at 2986	-	Negative strand: GGGGTCT at 4414, GTGGTCT at 4380 Positive strand: AGACCCA at 4418, CGACACC at 4394, GGGGTCT at 4330	Negative strand: GTTGTCT at 2778, GGGGTCG at 2766 Positive strand: AGACCAG at 2600	Positive strand: CGACCCG at 4179	Negative strand: GTTGTCT at 2443, GAGGTCG at 2431, CGACCAC at 2328, CCTGTCG at 2273, CTGGTCG at 2264, CCTGTCT at 2119, CGACCTC at 2071, AGACAGA at 2031, GCTGTCT at 2017, GAGGTCG at 2005, CGACCCG at 1893, CGACCCG at 1758, CGACCTC at 1748, TATGTCT at 1567, TGGGTCT at 1518, CGACCTC at 1466, AGACAAC at 1454, TGGGTCT at 1411, AGACCCG at 1358, CTGGTCG at 1194, CGACCCG at 1113, AGACAGA at 1087, GTTGTCT at 1073, GAGGTCG at 1061, TAGGTCG at 976, AGACAGA at 921, GTTGTCT at 907, GAGGTCG at 895, CGACCTA at 783, CTGGTCG at 737, CTGGTCG at 728, TCGGTCG at 504, CTTGTCT at 289, TTTGTCT at 168, CTGGTCG at 35 Positive strand: AGACCAG at 2263, AGACCAA at 2147, AGACCAC at 2123, TCTGTCT at 2031, CGACAGA at 2017, AGACATC at 1571, CGTGTCT at 1222, CGACCAG at 1193, TCTGTCT at 1087, CGACAAC at 1070, TCTGTCT at 921, AGACCAG at 727, AGACAGG at 561, AGACAGG at 424	Negative strand: AGACAGC at 3895, CAGGTCT at 3771, AGACCTC at 3552, CTGGTCT at 3299, CTGGTCT at 3245, GTTGTCT at 3053, CAGGTCT at 3019, CTTGTCT at 3004, GTGGTCT at 2941, AGACCTC at 2863, CGGGTCT at 2489, TAGGTCT at 2258, TGTGTCT at 2078, CGACAGG at 1966, GGGGTCT at 1958, CCTGTCT at 1862, GCTGTCT at 1731, GGGGTCT at 1711, GAGGTCG at 1687, AGACACA at 714, AGACCGG at 442, TGTGTCT at 268, TCTGTCT at 100 Positive strand: CGACCCG at 3991, TCTGTCG at 3895, GAGGTCT at 3891, GAGGTCT at 3806, GTGGTCG at 3720, CGACACC at 3642, CTGGTCT at 3548, CGACAAG at 3351, CGACCAG at 3244, CGGGTCG at 3239, TCGGTCT at 3221, GGTGTCG at 3194, TTTGTCT at 3179, CCTGTCT at 3133, TGTGTCG at 3100, TGGGTCT at 3091, AGACCAA at 3023, AGACCGG at 2985, AGACACG at 2959, AGACCGA at 2885, TGTGTCT at 2837, CGACCAC at 2812, CGACCTC at 2772, CGACCTA at 2736, TTTGTCT at 2652, CGACCTC at 2322, AGACAAA at 2262, TTGGTCT at 2228, AGACAAC at 2184, AGACCCC at 1866, CGGGTCT at 1742, CGACCGG at 1738, CGACAGA at 1731, GTGGTCT at 1631, AGACCGC at 1478, GTGGTCG at 1463, GCGGTCG at 1457, AGACCGC at 1378, GTGGTCG at 1363, GCGGTCG at 1357, TCGGTCG at 1271, GTGGTCG at 1127, CGTGTCG at 1054, TCGGTCT at 935, TCGGTCT at 835, CGACCAC at 781, TGTGTCG at 718, GGTGTCG at 634, GTGGTCG at 623, TCGGTCG at 617, CGACCCG at 419, CGACCCG at 388, CCGGTCG at 329, CGACCCC at 279, AGACCTC at 272, CGACACA at 266, GGGGTCT at 204, AGACCAC at 104, AGACAGA at 100, GAGGTCT at 15
B-boxes (Johnson)	TGGGCA	Positive strand: TGCCCA at 4251, TGGGCA at 4191, TGGGCA at 4040, TGCCCA at 3883, TGCCCA at 3854, TGGGCA at 3301	-	-	Positive strand: TGGGCA at 2773	Negative strand: TGGGCA at 4180	Positive strand: TGGGCA at 2438, TGCCCA at 1458, TGGGCA at 1359, TGGGCA at 1114, TGGGCA at 902, TGGGCA at 462	Negative strand: TGCCCA at 3377, TGCCCA at 3237, TGGGCA at 2894, TGGGCA at 1945, TGGGCA at 27 Positive strand: TGCCCA at 3750
boxes B (Sanchez)	TGTCTCA	Positive strand: TGTCTCA at 4373, TGTCTCA at 3323	-	-	-	-	Negative strand: TGTCTCA at 2445, TGAGACA at 2029, TGAGACA at 1085, TGTCTCA at 1075, TGAGACA at 919 Positive strand: TGTCTCA at 2033, TGTCTCA at 1089, TGTCTCA at 923	Negative strand: TGTCTCA at 2468, TGTCTCA at 2174 Positive strand: TGAGACA at 2308
B recognition elements (BREu)	(G/C)(G/C)(G/A)CGCC	Positive strand: GGCGTGG at 3047	-	-	-	-	Negative strand: CCACGCC at 2197, CCGCGCC at 1762, CCTGCGG at 1153, CCACGCC at 380 Positive strand: GGCGTGG at 1897, GGCGTGG at 1244	Negative strand: GGCGCCC at 1770, GGGCGCC at 1769, GGACGCC at 1672, GCACGCC at 1302 Positive strand: GGCGTGG at 2566, CCACGCC at 1764, GGCGCCG at 1438, GGCGCCG at 1338, CGACGCC at 1033, GGCGCGC at 682, CCACGCC at 489
CadC binding domains	TTANNNNT	Negative strand: ATAATTAA at 4541, AAGTGTAA at 4533, TTATTAAT at 4227, ATTATTAA at 4226, TTATTATT at 4224, TTTTTATT at 4221, TTATCTTT at 4081, TATTTATT at 4075, TTATTTAT at 4074, TTTTTATT at 4071, TTAGGGTT at 3978, TGGACATT at 3972, TTACCCTT at 3662, TCCCTATT at 3656, TTATGACT at 3542, TAATGATT at 3472, ATCTATAA at 3467, TAACTATT at 3361, TTAACTAT at 3360, ATTTTTAA at 3356, TTATTTGT at 3337, TGTTTATT at 3334, ATTTTTAA at 3174, TTTGTATT at 3169, TTTTGATT at 3030, TACCGATT at 3008, TTACCGAT at 3007, ATGGATAA at 2997, TACGAATT at 2936, TTACGAAT at 2935, TATATATT at 2873, TTATATAT at 2872 Positive strand: TTATTAAT at 4540, TTAAAAAT at 3355, TTAGATAT at 2982	-	-	Negative strand: TTATATGT at 2641	Negative strand: TTATAATT at 4169, TATTGATT at 4163, TTATTGAT at 4162, TGATTATT at 4159, TTAATCAT at 4148, TTATTAAT at 4145, TCTTGATT at 4133, TTATCACT at 4126 Positive strand: TTACTCCT at 4097	Negative strand: TTATCATT at 2501, TTATGTTT at 2306, TTATGTTT at 1879, TAGAAATT at 1735, ATCTCTAA at 1714, TTATCTCT at 1712, ACCCTTAA at 1694, TTACGGTT at 1636, ATATATAA at 1601, TTTGGATT at 1591, TTATGTCT at 1567, TGTGAATT at 1546, TGGACATT at 1133, TTAGTCCT at 985, TGGACATT at 803, TTATGTTT at 770, TTATGTTT at 636, TGTGCATT at 533, TTATGCTT at 493, TGGACATT at 396, TCACGATT at 337, TTGGAATT at 318, TCTACATT at 247, TCCATATT at 181, TGTGGATT at 64, TTAAGATT at 9 Positive strand: TTATCTTT at 1733, TTAAGTGT at 322, TTAAGAAT at 196	Negative strand: TTATGACT at 3029, TTAGGGCT at 2768, TAGGTATT at 2643, TTGGGATT at 2545, TTAAAATT at 2447, AATTTTAA at 2443, TGTTTATT at 2347, TTAAACAT at 2139, ACAGTTAA at 2135, TGGCTATT at 1976, TTTGTATT at 115 Positive strand: TTATACCT at 3163, TTATCTTT at 2629, TTACACTT at 231
Calcineurin-responsive transcription factors	TG(A/C)GCCNC	Positive strand: GTGGCTCA at 4114, GTGGCTCA at 3963, GTGGCTCA at 3054	-	-	-	-	Positive strand: GTGGCTCA at 2531, GTGGCTCA at 2204, GTGGCTCA at 1769, GTGGCTCA at 1124, GTGGCTCA at 660	Negative strand: TGAGCCAC at 2560, TGAGCCAC at 1291 Positive strand: GCGGCTCA at 1166, GCGGCTCA at 1082, GGGGCTCA at 578
cAMP-responsive elements (CREs), Aca1ps, Sko1ps	TGACGTCA	Negative strand: TGACGTCA at 4317	-	-	-	-	-	-
Carbohydrate response elements	ChoRE1 ACCGG, ChoRE2 CCCAT	Negative strand: ACCGG (Carb) at 4099, TCCGCC (CarbE3) at 3999, ACCGG (Carb) at 3948, GTTCTA (CarbE1) at 3275, ACCGG (Carb) at 3130, TCCGCC (CarbE3) at 3090 Positive strand: CCCAT at 4454 (Carb1), CCCAT at 3855 (Carb1), CCCAT at 3152 (Carb1)	-	Negative strand: ACCGG (Carb) at 4345	Negative strand: ACCGG (Carb) at 2607	Negative strand: CCCAT (Carb1) at 4220, GTTCTA (CarbE1) at 4075, Positive strand: GGCGGA (CarbE3) at 4239, ATCTTG (CarbE1) at 4067	Negative strand: TCCGCC (CarbE3) at 2392, TCCGCC (CarbE3) at 2231, TCCGCC (CarbE3) at 1752, GGCGGA (CarbE3) at 1504, ACCGG (Carb) at 1200, GTTCTA (CarbE1) at 876, TCCGCC (CarbE3) at 856, TCCGCC (CarbE3) at 700, ACCGG (Carb) at 645, TCCGCC (CarbE3) at 427, ATCTTG (CarbE1) at 286 Positive strand: GGCGGA (CarbE3) at 2728, GGCGGA (CarbE3) at 2393, CCCAT (Carb1) at 2288, ACCGG (Carb) at 2191, CCCAT (Carb1) at 1861, GGCGGA (CarbE3) at 1810, TCCGCC (CarbE3) at 1503, GGCGGA (CarbE3) at 857, GGCGGA (CarbE3) at 701, GGCGGA (CarbE3) at 428	Negative strand: CCCAT (Carb1) at 3899, CCCAT (Carb1) at 3334, ACCGG (Carb) at 1846, ACCGG (Carb) at 1546, ACCGG (Carb) at 1294, ACCGG (Carb) at 1210, GGCGGA (CarbE3) at 1203, ACCGG (Carb) at 1042, CACGTG (CarbE2) at 570, ACCGG (Carb) at 442, GGCGGA (CarbE3) at 357 Positive strand: CACGTG (CarbE2) at 3884, CCCAT (Carb1) at 3751, ACCGG (Carb) at 3681, TCCGCC (CarbE3) at 3487, ACCGG (Carb) at 2990, ACCGG (Carb) at 2985, CACGTG (CarbE2) at 2961, ACCGG (Carb) at 2571, TCCGCC (CarbE3) at 2485, ACCGG (Carb) at 2069, ACCGG (Carb) at 1738, CACGTG (CarbE2) at 1219, ACCGG (Carb) at 949, GGCGGA (CarbE3) at 905, ACCGG (Carb) at 849, CACGTG (CarbE2) at 547, ACCGG (Carb) at 199
CAACTC regulatory elements (CAREs)	CAACTC	Positive strand: GAGTTG at 4096, GAGTTG at 3115	-	-	Positive strand: GAGTTG at 2704	-	Negative strand: GAGTTG at 1406, CAACTC at 86 Positive strand: GAGTTG at 2592	Negative strand: CAACTC at 3292 Positive strand: GAGTTG at 3290, GAGTTG at 1621
CArG boxes	CCAAAAAT(G/A)G	Positive strand: CATTAAAAGG at 3441	-	-	-	-	Positive strand: CAAAAAAAAG at 1399	-
Cat8ps	CGG(A/C/G/T)(C/G/T)(A/C/G/T)(A/C/G)(A/C)(A/C/T)GGA	-	-	-	-	-	Negative strand: TCCGTGCCACCG at 2528, TCCGTGCCACCG at 657	-
CAT boxes	CATTCCT	Negative strand: TCCTTAC at 4554	-	-	-	-	-	Negative strand: CATTCCT at 2209 Positive strand: CATTCCT at 2458
C-boxes (Song)	GACGTC	Negative strand: GACGTC at 4316	-	Positive strand: GACGTC at 4316	-	-	-	Positive strand: GACGTC at 3280, GACGTC at 3231, GACGTC at 2858, GACGTC at 1506, GACGTC at 1120, GACGTC at 532, GACGTC at 437, GACGTC at 193
C boxes (Voronina)	GGTGATG	Positive strand: GGTGATG at 3798	-	-	-	-	-	-
C boxes (Samarsky)	AGTAGT	Negative strand: AGTAGT at 3521, AGTAGT at 3418, AGTAGT at 2944, AGTAGT at 2888	-	-	-	-	-	Positive strand: ACTACT at 2144, AGTAGT at 3251
hybrid C/G-boxes (Song)	TGACGTGT	-	-	-	-	-	-	Positive strand: ACACGTCA at 3962
CCAAT-boxes-binding transcription factors (Hap4p)	CCAAT	Positive strand: ATTGG at 3529, CCAAT at 2848	-	-	-	-	Negative strand: ATTGG at 614 Positive strand: ATTGG at 1045, ATTGG at 643	Negative strand: CCAAT at 2908, ATTGG at 24 Positive strand: CCAAT at 3024
Cell cycle boxes (variants) (CCBs)	CACGAAA, ACGAAA and C-CGAAA	-	-	-	-	-	Negative strand: TTTCGT at 2479, TTTCGT at 2473, TTTCGT at 186 Positive strand: ACGAAA at 494, ACGAAA at 312	Negative strand: TTTCGGG at 1752 Positive strand: TTTCGTG at 3600, TTTCGT at 2006
CGCG boxes	(A/C/G)CGCG(C/G/T)	-	-	-	-	-	Negative strand: CCGCGC at 1761, GCGCGT at 161 Positive strand: GCGCGG at 1762	Negative strand: CCGCGC at 1650, CCGCGG at 1437, CCGCGG at 1337, ACGCGG at 971, ACGCGG at 871, GCGCGC at 683, CCGCGC at 681, GCGCGT at 543 Positive strand: CCGCGG at 1769, CCGCGT at 1550, ACGCGT at 1523, ACGCGG at 1498, ACGCGG at 1454, ACGCGT at 1414, ACGCGG at 1398, ACGCGG at 1354, ACGCGT at 1314, CCGCGT at 1298, ACGCGG at 1246, CCGCGC at 1214, ACGCGG at 1162, ACGCGG at 1078, CCGCGT at 1046, CCGCGT at 976, CCGCGT at 876, GCGCGT at 684, GCGCGC at 682, CCGCGC at 542, ACGCGG at 452, CCGCGC at 161
Circadian control elements	CAANNNNATC	Negative strand: CTACCCCAAC at 3804	-	-	-	-	-	-
"Class C" DNA binding sites	CACNAG	Negative strand: CACGAG at 4403, CTCGTG at 3914, CACGGG at 3882 Positive strand: CACGAG at 4472, CACGAG at 3232	-	Negative strand: CTCGTG at 4376 Positive strand: CACGGG at 4275, CACGTG at 3884, CACGGG at 3236, CACGAG at 3152, CACGGG at 3012, CACGTG at 2961	-	Negative strand: CACGGG at 4260	Negative strand: CCCGTG at 1115, CCCGTG at 517 Positive strand: CCCGTG at 1219, CACGAG at 1182, CACGAG at 708, CACGAG at 572, CACGAG at 435	Negative strand: CACGGG at 3749, CACGGG at 1642, CACGGG at 1560, CACGGG at 1224, CGCGTG at 1216, CACGCG at 970, CACGCG at 870, CACGTG at 570, CGCGTG at 544, CACGAG at 243 Positive strand: CACGTG at 3884, CTCGTG at 3739, CACGTG at 2961, CACGAG at 2090, CACGCG at 1726, CTCGTG at 1627, CGCGTG at 1551, CACGCG at 1522, CGCGTG at 1299, CACGCG at 1245, CACGTG at 1219, CTCGTG at 1207, CACGCG at 1161, CGCGTG at 1131, CGCGTG at 1047, CGCGTG at 977, CTCGTG at 955, CGCGTG at 877, CTCGTG at 855, CGCGTG at 685, CACGGG at 573, CACGTG at 547
Cold-responsive elements	CCGAC	Negative strand: GTCGG at 4490, GTCGG at 4481, GTCGG at 4346, CCGAC at 4275, CCGAC at 4144, GTCGG at 4034, CCGAC at 3993, GTCGG at 3727, CCGAC at 3718, GTCGG at 3683, GTCGG at 3295, CCGAC at 3223, GTCGG at 3205, GTCGG at 3125, CCGAC at 3084, CCGAC at 3040	-	-	Negative strand: GTCGG at 2767, CCGAC at 2695, GTCGG at 2651	-	Negative strand: CCGAC at 2561, GTCGG at 2432, CCGAC at 2360, GTCGG at 2265, CCGAC at 2225, CCGAC at 2108, CCGAC at 2068, GTCGG at 2006, CCGAC at 1799, CCGAC at 1755, CCGAC at 1745, CCGAC at 1463, CCGAC at 1281, GTCGG at 1195, CCGAC at 1110, GTCGG at 1062, CCGAC at 990, GTCGG at 896, CCGAC at 824, GTCGG at 729, GTCGG at 505, GTCGG at 36	Negative strand: CCGAC at 3800, CCGAC at 1963, GTCGG at 1529, CCGAC at 997, CCGAC at 897, CCGAC at 791 Positive strand: GTCGG at 3998, GTCGG at 3896, CCGAC at 3639, CCGAC at 3587, CCGAC at 3525, CCGAC at 3348, GTCGG at 3101, CCGAC at 2914, GTCGG at 2897, CCGAC at 2886, CCGAC at 2809, CCGAC at 2769, GTCGG at 2527, GTCGG at 2391, GTCGG at 2353, CCGAC at 2319, GTCGG at 2009, CCGAC at 1818, GTCGG at 1604, GTCGG at 1268, CCGAC at 1030, GTCGG at 932, GTCGG at 832, GTCGG at 614, GTCGG at 512, CCGAC at 480, CCGAC at 416, CCGAC at 276, CCGAC at 263, GTCGG at 65
Copper response elements (CuREs) (Quinn)	TTTGC(T/G)C(A/G)	-	-	-	-	-	Positive strand: CGCGCAAA at 163	-
Copper response elements (CuREs) (Park)	TGTGCTCA	-	-	-	-	-	-	Negative strand: TGAGCACA at 3740
Coupling elements (CE1s) (Watanabe)	GCGTGTC	-	-	-	-	-	-	Positive strand: GCGTGTC at 1053
Coupling elements (CE3s) (Ding)	CACGCG	-	-	-	-	-	-	Negative strand: CGCGTG at 1216, CACGCG at 970, CACGCG at 870, CGCGTG at 544 Positive strand: CACGCG at 1726, CGCGTG at 1551, CACGCG at 1522, CGCGTG at 1299, CACGCG at 1245, CACGCG at 1161, CGCGTG at 1131, CGCGTG at 1047, CGCGTG at 977, CGCGTG at 877, CGCGTG at 685
Cytokinin response regulators (ARR1s)	AGATT(C/T)	-	-	-	-	-	Negative strand: AAATCT at 50 Positive strand: AGATTC at 2452	Negative strand: AGATTT at 2869, GAATCT at 2725, GAATCT at 2243 Positive strand: AGATTC at 122
Cytokinin response regulators (ARR10s)	(A/G)GATA(A/C)G	Negative strand: CGTATCC at 3447	-	-	-	-	-	-
Cytokinin response regulators (ARR12s)	(A/G)AGATA	Negative strand: TATCTT at 4080	-	-	-	-	Negative strand: TATCTC at 1711, AAGATA at 1525, TATCTT at 356, TATCTT at 101 Positive strand: AAGATA at 2177, TATCTT at 1732, AAGATA at 1595, AAGATA at 57	Positive strand: TATCTT at 2628
Cytokinin response regulators (Ferreira)	(G/A)GGAT(T/C)	Negative strand: AATCCT at 3457 Positive strand: GATCCC at 4477, AGGATC at 4288, AGGATC at 4157, AGGATC at 4006, AATCCC at 3976, AATCCC at 3067	-	-	Positive strand: AATCCC at 2678	Negative strand: AGGATC at 4080 Positive strand: GATCCT at 4078	Negative strand: AGGATC at 2093, GATCCT at 1308, AATCCT at 239 Positive strand: GGGATC at 2239, AATCCT at 2091, AATCCC at 1917, GATCCC at 1814, AATCCC at 1782, AATCCC at 1264, AATCCC at 1137, AATCCC at 807, AATCCC at 673, AATCCC at 400	Negative strand: GGGATT at 2545, GATCCT at 2515, GATCCT at 2379 Positive strand: AATCCC at 2766, AATCCC at 2669, AGGATT at 2083
Cytokinin response regulators (Rashotte1)	GATCTT	Positive strand: AAGATC at 3276	-	-	Positive strand: AAGATC at 4076, AAGATC at 4064, GATCTT at 4066	-	Positive strand: AAGATC at 877	Negative strand: AAGATC at 964, AAGATC at 864 Positive strand: AAGATC at 2167
Cytokinin response regulators (Rashotte2)	(G/A)GAT(T/C)	Negative strand: GATCT at 3463, AATCC at 3456, AATCT at 3000, AATCT at 2979 Positive strand: GATCC at 4476, AGATC at 4475, GGATC at 4288, GGATC at 4157, GGATC at 4006, AATCC at 3975, AATCC at 3679, AGATC at 3488, AGATC at 3276, GGATC at 3097, AATCC at 3066	-	-	Positive strand: AATCC at 2677	Negative strand: GATCC at 4081, GGATC at 4080 Positive strand: GATCC at 4077, AGATC at 4076, GATCT at 4065, AGATC at 4064	Negative strand: GGATC at 2093, GGATT at 1591, GATCC at 1307, GGATC at 1306, AATCC at 238, GGATT at 64, AATCT at 50, AGATT at 9 Positive strand: GGATC at 2574, AGATT at 2451, AGATC at 2413, GGATC at 2239, AATCC at 2090, AGATC at 1987, AATCC at 1916, GATCC at 1813, GGATC at 1812, AATCC at 1781, AGATT at 1714, GATCT at 1482, AGATT at 1334, AATCC at 1263, GGATC at 1167, AATCC at 1136, AGATT at 1043, GATCC at 973, AGATC at 972, AGATC at 877, AATCC at 806, GGATC at 703, AATCC at 672, AGATC at 589, AGATT at 583, GGATC at 525, GGATC at 430, AATCC at 399, AATCT at 232	Negative strand: AATCC at 3797, AGATT at 2868, AATCT at 2725, GGATT at 2545, GATCC at 2514, GATCC at 2378, AATCT at 2243, AATCT at 2235, AGATC at 2230, GATCC at 965, AGATC at 964, GATCC at 865, AGATC at 864 Positive strand: GATCC at 3522, GATCC at 3484, AATCC at 2765, AATCC at 2668, GATCC at 2639, GATCC at 2482, GGATC at 2481, AATCC at 2366, AGATC at 2167, GGATT at 2083, AATCC at 150, AGATT at 121
Cytoplasmic polyadenylation elements (CPEs)	TTTTTAT	Negative strand: TTTTTAT at 4220, TTTTTAT at 4070 Positive strand: ATAAAAA at 3172	-	-	-	-	Negative strand: TTTTTAT at 2302, TTTTTAT at 1875, TTTTTAT at 766, TTTTTAT at 632, TTTTTAT at 489 Positive strand: TTTTTAT at 218	-
DAF-16 binding elements	(A/G)(C/T)AAA(C/T)A	Negative strand: GTAAATA at 4536, TATTTAT at 4074, TATTTGT at 3337, TGTTTAT at 3333, TATTTGT at 2876	-	-	-	Negative strand: ACAAACA at 4256	Negative strand: TGTTTGT at 2512, TGTTTGT at 2512, TGTTTGT at 1391 Positive strand: ACAAACA at 2487, GCAAACA at 2483, GCAAACA at 1539	Negative strand: TGTTTGC at 3340, TGTTTAT at 2346 Positive strand: TATTTAC at 3429, ACAAATA at 2346
D boxes (Samarsky)	AGTCTG	Negative strand: AGTCTG at 2947	-	-	-	-	Positive strand: CAGACT at 1616, AGTCTG at 1355, CAGACT at 15	Negative strand: AGTCTG at 3923, CAGACT at 2416 Positive strand: CAGACT at 3924, CAGACT at 3006, CAGACT at 2943
D boxes (Voronina)	TCCTG	Negative strand: TCCTG at 4467, TCCTG at 3755, TCCTG at 3639, TCCTG at 3388 Positive strand: TCCTG at 4545, CAGGA at 4437, CAGGA at 4283, CAGGA at 4171, CAGGA at 4139, TCCTG at 3905, CAGGA at 3250, CAGGA at 3218, CAGGA at 3111	-	Negative strand: TCCTG at 4408	Positive strand: CAGGA at 2690	Negative strand: TCCTG at 4185 Positive strand: TCCTG at 4251	Positive strand: CAGGA at 2588, CAGGA at 2368, CAGGA at 2251, CAGGA at 2135, CAGGA at 1942, TCCTG at 1910, TCCTG at 1840, CAGGA at 1824, CAGGA at 1289, CAGGA at 1276, CAGGA at 998, CAGGA at 985, CAGGA at 851, CAGGA at 832, CAGGA at 715, TCCTG at 595, CAGGA at 579, CAGGA at 442	Negative strand: CAGGA at 3869, TCCTG at 3621, CAGGA at 3572, TCCTG at 3295, CAGGA at 3129, CAGGA at 2746, CAGGA at 2621, TCCTG at 2519, TCCTG at 2500, TCCTG at 2210, TCCTG at 1775, TCCTG at 1117, CAGGA at 708, CAGGA at 425, TCCTG at 143 Positive strand: CAGGA at 3864, CAGGA at 3620, TCCTG at 3130, CAGGA at 2999, TCCTG at 2459, TCCTG at 1669, CAGGA at 758, CAGGA at 219
D-boxes (Motojima)	TGAGTGG	Negative strand: CCACTCA at 3827 Positive strand: CCACTCA at 4487	-	-	-	-	-	Negative strand: TGAGTGG at 3449
Dioxin-responsive elements (DREs)	TNGCGTG	Positive strand: CACGCCA at 3282	-	-	-	-	Negative strand: CACGCCA at 2198, CACGCCA at 381 Positive strand: CACGCCA at 2209, CACGCCA at 1993	Positive strand: TGGCGTG at 2565, CACGCGA at 1727, TCGCGTG at 1131
DNA damage response elements (DRE, core) (Sumrada)	CCGCC	Negative strand: CCGCC at 3999, CCGCC at 3090	-	Negative strand: CCGCC at 4291 Positive strand: CCGCC at 4439, CCGCC at 4429	Negative strand: CCGCC at 2727, CCGCC at 2724	Negative strand: CCGCC at 4238	Negative strand: CCGCC at 2392, CCGCC at 2231, CCGCC at 1809, CCGCC at 1752, CCGCC at 1250, CCGCC at 956, CCGCC at 856, CCGCC at 700, CCGCC at 427 Positive strand: CCGCC at 1503	Negative strand: CCGCC at 1757, CCGCC at 904 Positive strand: CCGCC at 3487, CCGCC at 2485, CCGCC at 1901, CCGCC at 1793, CCGCC at 1202, CCGCC at 1025, CCGCC at 406, CCGCC at 356, CCGCC at 353
Downstream B recognition elements	(A/G)T(A/G/T)(G/T)(G/T)(G/T)(G/T)	Negative strand: GTAGGTG at 4458, GTGGGGT at 4446, GTTTTTT at 4378, GTTTTTT at 4218, ATGTTTT at 4216, GTTGTGT at 4196, GTTTTTT at 4068, ATGTTTT at 4066, AACCAAC at 3945, CCACTAC at 3798, GTGTTTT at 3767, ATGGTGG at 3740, CACCAAC at 3605, AACCAAC at 3532, GTAGTTG at 3523, ATTTGGT at 3484, ATTTGGT at 3365, CCAAAAT at 3350, ATTTGTT at 3338, GTTTTTG at 3328, CCCACAC at 3185, GTATTTT at 3171, ATTTTTG at 3165, GTGGGTT at 3136, ATTTTTT 3026, GTAGTTT at 2890, ATATTTG at 2875, GTTGGGT at 2846 Positive strand: AACCCAT at 4454, AAAAAAT at 4219, ATGGTGG at 4110, AAAAAAT at 4069, CCAACAC at 3981, GTTGGTT at 3944, GTGTTGG at 3942, CCCATAC at 3857, ATGTGGT at 3811, ATGGGGT at 3802, ACAAAAT at 3768, GTGGTTG at 3605, ATTGGTT at 3531, CAACTAT at 3526, AAAACAC at 3512, AAACCAC at 3366, CAAAAAC at 3328, GTGGGTG at 3195, GTGTGGT at 3187, GTGGTGG at 3192, GTGGTGG at 3189, GTGTGGT at 3187, AAAACAT at 3167, ACCCCAT at 3152, ACCCAAC at 3137, GTGGTGG at 3050, AAAAAAC at 3027, AAACCAC at 2972, AAAAAAT at 2930, AAAATAT at 2869, ATATTTT at 2853	Negative strand: GTTGGGT at 2846 Positive strand: AAACAAC at 2843	Negative strand: GTGGGGT at 4397, ACCCCAC at 4287 Positive strand: ACCCCAC at 4398, GTGGGGT at 4328, GTGGGGT at 4286	Negative strand: GTGGGGT at 2764, ACACCAC at 2660, ATGTTTT at 2644, ATATGTT at 2642 Positive strand: GTGGTGG at 2661, GTGTGGT at 2659, CAAAAAT at 2646, CCAACAT at 2612	Negative strand: CAAACAC at 4257, ATGGGGG at 4225, ACCCCAT at 4220, ATTGTTG at 4173, GTGGTTT at 4108 Positive strand: GTTTGTG at 4257, CCAAAAT at 4110	Negative strand: GTTTGTT at 2488, GTTTGTT at 2484, GTGTGGT at 2419, CACCCAC at 2332, GTTTTTT at 2309, ATGTTTT at 2307, GTTTTTT at 2184, ATGTTTT at 2182, GTTTTTT at 2038, CCACCAC at 1902, GTTTTTT at 1882, ATGTTTT at 1880, GTTTGTG at 1540, GTTGGGT at 1516, ACCACAC at 1478, AAAAAAC at 1433, GTTGGGT at 1409, GTTTTTT at 1396, GTTTGTT at 1392, GTTTTTG at 1386, GTTTTTT at 1230, ATGTTTT at 1228, CACCCAC at 1163, GTTTTTT at 1094, AACCCAC at 1048, GTTTTTT at 928, GTGTGGT at 883, ACACCAC at 789, GTTTTTT at 773, ATGTTTT at 771, GTTTTTT at 639, ATGTTTT at 637, ATTGGGG at 616, ACCACAC at 609, GTTTTTT at 487, ATGTTTT at 485, GTTTTGG at 259, ATATTTT at 222, CAAAAAT at 217, ATATTTT at 183, GTTTTGT at 166, ATATGTT at 113, ATTTTGT at 68 Positive strand: CCAACAC at 2549, AACAAAC at 2511, AACAAAC at 2486, ACACCAC at 2420, GTGGGTG at 2332, AAAATAC at 2303, ACCCCAT at 2288, AAAAAAT at 2185, CCAACAT at 2150, AAAAAAT at 2061, GTGGTGG at 1903, GTGGTGG at 1900, AAAATAC at 1876, ACCCCAT at 1861, AAAATAT at 1740, AACAAAC at 1587, AAAATAC at 1564, CAAACAC at 1540, GTGGTGT at 1477, CAAAAAC at 1386, GTGGTGG at 1247, AAAAAAT at 1231, CCAACAT at 1205, GTGGGTG at 1163, ATTGGGT at 1047, ACACCAT at 884, GTGGTGT at 793, GTGGTGG at 790, ATGTGGT at 788, AAAATAC at 767, AAAATAC at 633, ATGGTGT at 608, ATATGGT at 606, AAAAAAT at 488, AAAACAT at 361, AAACAAT at 230 ATGTTTT at 215, ATGGGGT at 204, ATATGGG at 78, ATATGTT at 43	Negative strand: GTGGTGT at 3969, GTGTGGT at 3967, ACCCCAC at 3941, ACACCAT at 3826, GTGGTGG at 3816, ATGTTTG at 3339, ACCAAAC at 3176, AACACAC at 3097, GTGTTGG at 2816, AAACCAC at 2633, ACCACAC at 2601, ATTTTTT at 2451, CAACCAC at 2122, AACCCAC at 2016, AACCTAC at 1283, CCACCAC at 703, CACCCAC at 72, GTGGGGG at 56 Positive strand: ACACCAC at 3968, AAACCAC at 3949, GTGTGGT at 3825, ACACCAC at 3644, GTAGGGT at 3631, ATAGGGT at 3386, CCAATAC at 3026, GTGTGGG at 2965, CCACAAC at 2815, ATGGTGG at 2759, CACCTAC at 2714, CCAAAAC at 2688, CCCCTAT at 2659, GTGTGGT at 2603, ATGGTGT at 2600, ATATGGT at 2591, AAAAAAC at 2452, ACCCTAC at 2409, AAAAAAC at 2282, GTTGGTG at 2122, GTGGGGG at 2020, GTTGGGT at 2015, ATGGGGT at 1891, AACCCAC at 1802, GTGGTGG at 704, GTAGGTG at 700, GTAGGTG at 631, ACAAAAT at 148, GTGGGTG at 72, CCCCTAC at 59
Downstream core elements (DCEs)	CTTC...CTGT...AGC	Negative strand: CTGT at 4507, GCT at 4471, CTGT at 4468, ACAG at 4370, CTGT at 4355, AGC at 4289, GCT at 4241, ACAG at 4209, CTGT at 4181, CTTC at 3936, CTTC at 3909, GCT at 3875, ACAG at 3832, GCT at 3814, AGC at 3813, CTGT at 3756, ACAG at 3622, CTTC at 3610, AGC at 3595, AGC at 3501, CTGT at 3433, CTGT at 3412, CTTC at 3407, CTGT at 3389, ACAG at 3320, GCT at 3231, ACAG at 3201, ACAG at 2985, CTGT at 2948, CTGT at 2880 Positive strand: CTTC at 4528, AGC at 4520, ACAG at 4517, AGC at 4489, AGC at 4480, AGC at 4439, AGC at 4411, GCT at 4402, CTGT at 4399, CTGT at 4369, ACAG at 4356, AGC at 4345, AGC at 4321, AGC at 4296, GCT at 4291, GCT at 4274, GCT at 4262, AGC at 4261, GCT at 4255, AGC at 4229, CTGT at 4208, ACAG at 4197, GCT at 4185, AGC at 4184, GCT at 4143, GCT at 4131, AGC at 4130, CTGT at 4121, GCT at 4112, AGC at 4033, AGC at 4014, GCT at 3992, CTGT at 3970, GCT at 3961, CTGT at 3957, GCT at 3955, ACAG at 3916, AGC at 3912, AGC at 3899, GCT at 3862, AGC at 3845, AGC at 3838, CTTC at 3776, GCT at 3774, AGC at 3773, AGC at 3731, AGC at 3726, ACAG at 3725, GCT at 3717, CTGT at 3709, GCT at 3707, GCT at 3702, AGC at 3701, AGC at 3694, ACAG at 3693, AGC at 3682, ACAG at 3671, GCT at 3647, AGC at 3646, GCT at 3580, CTGT at 3556, CTTC at 3553, AGC at 3494, CTGT at 3426, GCT at 3398, AGC at 3370, CTGT at 3319, AGC at 3309, AGC at 3294, AGC at 3269, CTGT at 3265, GCT at 3263, GCT at 3222, GCT at 3210, AGC at 3209, AGC at 3204, CTGT at 3200, GCT at 3178, AGC at 3177, AGC at 3124, GCT at 3106, AGC at 3105, GCT at 3083, AGC at 3070, CTGT at 3061, GCT at 3052, GCT at 3039, GCT at 3033, AGC at 3032, GCT at 3006, GCT at 2933, AGC at 2915, GCT at 2896, ACAG at 2877	Negative strand: CTTC at 2828, CTTC at 2811	Negative strand: CTGT at 4392, GCT at 4390, GCT at 4372, AGC at 4352, GCT at 4321, GCT at 4312, AGC at 4279 Positive strand: AGC at 4374, ACAG at 4366, GCT at 4356, CTGT at 4332, GCT at 4277	Negative strand: CTTC at 2811, CTTC at 2730, AGC at 2709 Positive strand: AGC at 2780, ACAG at 2777, AGC at 2766, GCT at 2742, AGC at 2741, GCT at 2711, GCT at 2694, ACAG at 2688, GCT at 2682, AGC at 2681, CTGT at 2672, AGC at 2650	Negative strand: CTTC at 4241, GCT at 4175, ACAG at 4069, CTTC at 4061, AGC at 4052 Positive strand: CTTC at 4263, CTGT at 4252, CTTC at 4248, CTTC at 4197	Negative strand: CTTC at 2595, CTTC at 2557, AGC at 2453, GCT at 2409, CTGT at 2271, ACAG at 2164, GCT at 2155, CTGT at 2117, ACAG at 2030, CTGT at 2015, GCT at 2013, GCT at 1983, CTTC at 1655, CTGT at 1569, CTTC at 1555, GCT at 1553, AGC at 1446, GCT at 1330, ACAG at 1221, GCT at 1189, GCT at 1181, GCT at 1155, ACAG at 1086, CTGT at 1068, GCT at 1066, AGC at 1065, GCT at 1039, ACAG at 920, GCT at 911, AGC at 838, CTGT at 746, GCT at 721, AGC at 720, GCT at 707, GCT at 571, CTGT at 559, GCT at 492, ACAG at 478, GCT at 448, GCT at 434, CTGT at 422, CTTC at 367, CTTC at 331, GCT at 310, CTTC at 241, CTGT at 170, AGC at 157, CTTC at 132, CTTC at 81 Positive strand: GCT at 2560, CTGT at 2538, GCT at 2529, ACAG at 2513, AGC at 2478, AGC at 2472, ACAG at 2442, AGC at 2431, AGC at 2406, GCT at 2376, GCT at 2359, GCT at 2347, AGC at 2346, CTGT at 2337, GCT at 2324, AGC at 2314, AGC at 2273, ACAG at 2272, AGC at 2264, GCT at 2224, GCT at 2202, CTGT at 2163, GCT at 2130, AGC at 2129, ACAG at 2118, GCT at 2107, AGC at 2094, GCT at 2067, CTGT at 2029, AGC at 2019, ACAG at 2016, AGC at 2005, AGC at 1980, GCT at 1970, AGC at 1969, GCT at 1921, AGC at 1920, CTGT at 1911, GCT at 1906, GCT at 1889, AGC at 1888, GCT at 1843, GCT at 1798, AGC at 1785, CTGT at 1776, GCT at 1767, GCT at 1754, GCT at 1744, AGC at 1678, AGC at 1611, ACAG at 1566, GCT at 1498, AGC at 1497, GCT at 1487, AGC at 1486, GCT at 1462, CTGT at 1452, GCT at 1448, AGC at 1367, AGC at 1327, GCT at 1280, GCT at 1268, AGC at 1267, CTGT at 1258, AGC at 1235, AGC at 1194, AGC at 1140, CTGT at 1131, GCT at 1122, ACAG at 1117, GCT at 1109, CTGT at 1085, ACAG at 1072, AGC at 1061, CTTC at 1053, AGC at 1036, GCT at 1006, GCT at 989, GCT at 977, AGC at 976, CTGT at 967, AGC at 944, CTGT at 919, AGC at 909, ACAG at 906, AGC at 895, GCT at 890, AGC at 870, GCT at 840, GCT at 823, GCT at 811, AGC at 810, CTGT at 801, GCT at 779, AGC at 778, AGC at 737, AGC at 728, AGC at 676, CTGT at 667, GCT at 658, CTTC at 619, GCT at 598, ACAG at 560, AGC at 540, ACAG at 519, AGC at 504, AGC at 500, CTGT at 477, AGC at 455, ACAG at 423, AGC at 403, CTGT at 394, GCT at 385, GCT at 335, ACAG at 296, ACAG at 288, AGC at 185, ACAG at 167, GCT at 147, AGC at 146, GCT at 138, AGC at 137, AGC at 35, ACAG at 12	Negative strand: GCT at 4027, AGC at 4026, AGC at 4023, AGC at 3997, CTTC at 3994, GCT at 3992, GCT at 3987, GCT at 3983, ACAG at 3974, AGC at 3895, ACAG at 3894, ACAG at 3860, AGC at 3808, GCT at 3776, AGC at 3775, AGC at 3763, GCT at 3638, AGC at 3737, GCT at 3724, AGC at 3723, AGC at 3720, AGC at 3701, GCT at 3696, AGC at 3691, AGC at 3668, CTGT at 3640, GCT at 3638, ACAG at 3635, CTGT at 3622, CTGT at 3617, AGC at 3598, GCT at 3586, ACAG at 3570, GCT at 3524, GCT at 3519, AGC at 3518, AGC at 3513, GCT at 3481, CTGT at 3434, GCT at 3420, ACAG at 3412, CTTC at 3394, CTGT at 3390, GCT at 3368, CTGT at 3349, GCT at 3347, CTTC at 3312, GCT at 3307, GCT at 3274, GCT at 3263, AGC at 3262, CTTC at 3247, GCT at 3240, AGC at 3239, GCT at 3227, AGC at 3223, AGC at 3217, AGC at 3211, ACAG at 3210, GCT at 3195, AGC at 3194, ACAG at 3193, ACAG at 3178, AGC at 3155, GCT at 3151, AGC at 3144, AGC at 3137, ACAG at 3132, AGC at 3125, GCT at 3119, AGC at 3100, ACAG at 3099, CTTC at 3057, AGC at 3041, CTTC at 3031, GCT at 2976, GCT at 2971, AGC at 2970, CTGT at 2957, CTTC at 2947, CTGT at 2931, CTGT at 2925, GCT at 2913, AGC at 2896, GCT at 2885, GCT at 2846, AGC at 2845, ACAG at 2844, ACAG at 2836, GCT at 2808, GCT at 2786, AGC at 2785, GCT at 2768, GCT at 2753, GCT at 2750, AGC at 2749, GCT at 2732, AGC at 2731, AGC at 2703, GCT at 2695, ACAG at 2651, CTTC at 2582, AGC at 2557, AGC at 2536, AGC at 2526, GCT at 2504, ACAG at 2461, GCT at 2435, ACAG at 2413, GCT at 2403, AGC at 2402, AGC at 2399, AGC at 2390, GCT at 2368, CTTC at 2361, AGC at 2352, CTGT at 2342, GCT at 2318, CTGT at 2308, CTGT at 2260, CTGT at 2250, AGC at 2198, GCT at 2194, AGC at 2193, CTGT at 2182, GCT at 2161, GCT at 2155, ACAG at 2131, ACAG at 2124, CTTC at 2107, AGC at 2102, GCT at 2093, GCT at 2089, CTTC at 2095, CTGT at 2074, GCT at 2056, GCT at 2053, AGC at 2052, GCT at 2046, GCT at 2043, AGC at 2008, AGC at 2005, CTGT at 1998, GCT at 1973, ACAG at 1965, CTTC at 1914, GCT at 1907, GCT at 1882, CTGT at 1860, ACAG at 1823, GCT at 1817, GCT at 1777, GCT at 1734, CTGT at 1729, GCT at 1727, AGC at 1678, GCT at 1651, AGC at 1634, AGC at 1625, AGC at 1603, AGC at 1595, GCT at 1576, AGC at 1540, GCT at 1533, AGC at 1532, CTTC at 1516, AGC at 1507, AGC at 1463, AGC at 1457, GCT at 1449, AGC at 1448, GCT at 1442, AGC at 1441, CTTC at 1432, CTTC at 1405, AGC at 1363, AGC at 1357, GCT at 1349, AGC at 1348, GCT at 1342, AGC at 1341, CTTC at 1332, CTTC at 1305, AGC at 1288, GCT at 1274, AGC at 1271, AGC at 1267, CTTC at 1264, AGC at 1232, AGC at 1205, GCT at 1190, GCT at 1177, CTTC at 1153, AGC at 1145, AGC at 1127, AGC at 1121, GCT at 1113, AGC at 1112, GCT at 1106, AGC at 1105, GCT at 1093, CTTC at 1069, AGC at 1064, AGC at 1057, AGC at 1054, ACAG at 1053, AGC at 1037, GCT at 1029, CTTC at 1012, CTGT at 991, AGC at 953, GCT at 938, AGC at 937, AGC at 931, CTTC at 928, CTGT at 916, CTGT at 891, AGC at 853, GCT at 838, AGC at 837, AGC at 831, CTTC at 828, CTGT at 816, AGC at 785, GCT at 777, AGC at 769, CTTC at 760, GCT at 737, CTTC at 733, AGC at 728, AGC at 718, ACAG at 717, GCT at 693, AGC at 692, CTTC at 676, GCT at 652, AGC at 644, AGC at 634, ACAG at 633, AGC at 623, AGC at 617, AGC at 613, GCT at 602, AGC at 601, CTTC at 592, AGC at 560, ACAG at 551, AGC at 533, GCT at 528, GCT at 518, AGC at 511, GCT at 479, AGC at 473, CTTC at 456, AGC at 431, AGC at 427, GCT at 415, GCT at 384, AGC at 383, ACAG at 364, AGC at 339, AGC at 335, AGC at 329, GCT at 275, CTGT at 264, GCT at 262, ACAG at 156, CTGT at 144, CTGT at 98, AGC at 64, ACAG at 63, GCT at 10, GCT at 3 Positive strand: AGC at 3985, ACAG at 3951, CTGT at 3973, CTGT at 3893, CTTC at 3871, CTTC at 3851, GCT at 3799, CTTC at 3762, ACAG at 3744, CTTC at 3667, ACAG at 3618, ACAG at 3576, CTGT at 3569, CTGT at 3530, AGC at 3509, ACAG at 3391, AGC at 3283, AGC at 3272, CTTC at 3216, CTGT at 3131, ACAG at 3052, ACAG at 3003, ACAG at 2926, CTGT at 2843, GCT at 2804, CTTC at 2784, CTTC at 2748, ACAG at 2465, CTGT at 2460, CTGT at 2412, GCT at 2357, ACAG at 2309, GCT at 2215, CTTC at 2192, ACAG at 2171, CTGT at 2130, AGC at 2091, ACAG at 2077, ACAG at 1999, GCT at 1962, AGC at 1927, GCT at 1919, AGC at 1915, ACAG at 1861, GCT at 1835, AGC at 1750, ACAG at 1730, AGC at 1713, AGC at 1687, GCT at 1665, CTTC at 1633, GCT at 1623, CTTC at 1594, GCT at 1584, GCT at 1563, AGC at 1528, AGC at 1517, AGC at 1490, GCT at 1479, GCT at 1446, AGC at 1406, AGC at 1390, GCT at 1379, GCT at 1346, AGC at 1306, CTTC at 1231, GCT at 1227, AGC at 1181, GCT at 1164, GCT at 1155, AGC at 1154, AGC at 1108, GCT at 1101, GCT at 1080, CTTC at 1063, GCT at 1059, AGC at 1013, GCT at 996, ACAG at 992, CTTC at 961, GCT at 951, GCT at 896, ACAG at 892, CTTC at 861, GCT at 851, GCT at 790, CTTC at 768, GCT at 766, AGC at 761, CTTC at 727, AGC at 688, CTTC at 643, GCT at 639, AGC at 593, GCT at 576, CTTC at 559, GCT at 555, AGC at 537, AGC at 457, GCT at 429, GCT at 360, GCT at 308, ACAG at 267, GCT at 242, CTTC at 232, CTTC at 209, GCT at 162, ACAG at 99, ACAG at 81, AGC at 77, CTTC at 48
Downstream promoter elements (DPEs) (Juven-Gershon)	(A/G)G(A/T)(C/T)(A/C/G)T	Negative strand: AGGACC at 4546, AGTCCT at 4437, AGATGT at 4213, AGTTCT at 4179, GGTCCT at 4171, AGTCCT at 4139, GGACAT at 4122, AGATGT at 4063, AGTTCT at 4028, GGTTCT at 4020, GGTTGT at 3980, GGACAT at 3971, ACAACC at 3942, GGACCT at 3907, AGGACC at 3906, ACGACC at 3864, AGACCT at 3836, AGAACC at 3793, GGACCT at 3745, GGTCGT at 3732, AGGTCC at 3585, ATGACT at 3542, ATAACC at 3529, ACGTCT at 3431, GGTTCT at 3274, GGTCCT at 3250, AGTCCT at 3218, GGTTGT at 3138, AGTCCT at 3111, GGTCGT at 3071, GGACAT at 3062, AGATGT at 2989, ATATCT at 2903, GGTTAT at 2849 Positive strand: AGACAT at 4508, AGATCC at 4476, AGAACC at 4451, AGTTCT at 4418, AGACGT at 4236, AGATGT at 3621, AGATAT at 3466, AGACAT at 3434, ATGTCT at 3833, AGGACT at 3640, ATGTCT at 2986, AGATAT at 2982, AGACAT at 2949, AGACAT at 2881	Positive strand: ACAACC at 2844	Negative strand: ATGTCC at 4367 Positive strand: AGGACC at 4409, ACGTCT at 4317	Negative strand: GGACAT at 2673, GGTTGT at 2611 Positive strand: ATGACT at 2786	Negative strand: GGTTCT at 4074 Positive strand: AGGACT at 4186, ACGACC at 4177, ATAACT at 4161, AGAACT at 4131, AGATCC at 4077, AGATCT at 4065	Negative strand: AGTCCT at 2588, GGTTGT at 2548, GGACAT at 2539, AGTTAT at 2497, GGACAT at 2338, ACGACC at 2326, GGACCT at 2269, AGTCCT at 2251, GGTCAT at 2212, GGTTGT at 2149, AGTCCT at 2135, GGACAT at 1912, ACAACT at 1853, AGGACC at 1841, GGTCGT at 1786, AGACAT at 1777, AGAACC at 1649, GGTCGT at 1612, ATGTCT at 1567, AGATAT at 1526, AGTCCT at 1276, GGACAT at 1259, AGATGT at 1225, GGTTGT at 1204, GGTCGT at 1141, GGACAT at 1132, AGTCCT at 985, ACATCT at 970, GGACAT at 968, GGTTCT at 875, GGTCCT at 851, GGACAT at 802, AGTCCT at 715, GGTCGT at 677, GGACAT at 668, AGGACC at 596, AGTCCT at 579, GGTTCT at 557, GGTCGT at 541, AGATGT at 482, AGTCCT at 442, GGTTCT at 420, GGTCGT at 404, GGACAT at 395, ACATCT at 284 Positive strand: ATGACC at 2189, ACGTCT at 1774, AGATAT at 1596, ACATCC at 1572, AGACAT at 1570, ATATCC at 1529, AGATCC at 973, GGATGT at 785, AGATGT at 245, AGACAT at 171, GGATAT at 109, GGATAT at 75	Negative strand: AGAACT at 4048, AGTCCT at 3864, ATGACC at 3784, AGGTCT at 3771, ATGTCC at 3577, GGATGT at 3575, AGACCT at 3551, AGTTAT at 3382, ACGTCT at 3256, GGTTGT at 3051, ATGACT at 3029, GGTTAT at 3025, AGGTCT at 3019, AGTCCT at 2999, AGTTCT at 2955, GGTTCT at 2923, AGACCT at 2862, AGAACC at 2776, GGATGT at 2715, GGATAT at 2660, AGGTCT at 2258, AGAACC at 2225, AGTTCT at 1988, AGAACT at 1951, GGACAT at 1870, AGAACC at 1811, AGATCC at 965, AGATCC at 865, AGTCCT at 758, GGTCCT at 219, AGGTCC at 218, GGACCT at 38 Positive strand: AGGTCC at 4032, AGTCGT at 4024, AGGTCT at 3891, AGTCCT at 3869, ACGTCT at 3831, AGGTCT at 3806, GGTCGT at 3721, GGTTGT at 3634, AGGTCC at 3687, ACGTCC at 3466, AGTTAT at 3425, GGACCT at 3363, AGGACC at 3296, AGACGT at 3279, AGACGT at 3268, AGTCGT at 3156, ATGACC at 3117, AGGTCC at 3111, AGACGT at 3061, AGTCGT at 3042, ACGTCT at 2859, AGACGT at 2857, ACAACC at 2816, ACGTCC at 2745, ACGTCT at 2721, ACGTCC at 2683, AGTCCT at 2621, ATATCC at 2550, AGGACC at 2501, ACATCC at 2255, AGGACT at 2211, AGTCGT at 2199, ACAACC at 2185, AGTCGT at 2103, ACGTCT at 1937, ACATCC at 1875, ACGTCC at 1788, ACGACC at 1779, ACGACC at 1736, GGACGT at 1470, GGTCGT at 1458, GGACGT at 1370, GGTCGT at 1358, ATGACT at 1286, GGACGT at 1119, GGTCCT at 708, ACGTCC at 658, GGTCGT at 618, GGACCT at 599, ACGTCT at 438, GGACGT at 436, GGTCCT at 425, AGACCT at 271, AGACGT at 224, ACGTCC at 194, GGACGT at 192, GGTTCT at 178, GGACCT at 41, AGGTCC at 33, AGGTCT at 15, AGGTCC at 8
Downstream promoter elements (DPEs) (Kadonaga)	(A/G)G(A/T)CGTG	Negative strand: GGTCGTG at 3733, CACGTCT at 3431, GGTCGTG at 3072 Positive strand: AGACGTG at 4237	-	-	-	-	Negative strand: GGTCGTG at 1787, GGTCGTG at 1142, GGTCGTG at 678, GGTCGTG at 542, GGTCGTG at 405 Positive strand: CACGTCC at 3466, CACGTCC at 2683, CACGTCC at 1788, CACGTCT at 1774	Positive strand: AGTCGTG at 3043, AGTCGTG at 2200, AGTCGTG at 2104, GGACGTG at 1471, GGTCGTG at 1459, GGACGTG at 1371, GGTCGTG at 1359, GGTCGTG at 619 Negative strand: CACGTCT at 3256
Downstream promoter elements (DPEs) (Matsumoto)	AGTCTC	Negative strand: AGTCTC at 3645 Positive strand: GAGACT at 4053	-	-	-	-	Positive strand: GAGACT at 1933, AGTCTC at 1445, GAGACT at 1081, GAGACT at 915	Negative strand: AGTCTC at 3188 Positive strand: GAGACT at 3123, AGTCTC at 2730, AGTCTC at 2700, AGTCTC at 2610, GAGACT at 255
E2 boxes	(G/A)CAG(A/C/G/T)TG(A/C/G/T)	Negative strand: ACAGATGT at 4213, ACAGATGT at 2989 Positive strand: ACACCTGT at 3970, ACAGATGA at 3920, GCAACTGC at 3851	-	-	-	-	Negative strand: CCACCTGT at 2117, GCAGTTGG at 1514, ACAGATGT at 1225, ACAGATGT at 482 Positive strand: GCAGGTGG at 2571, ACACCTGT at 1131, CCACCTGT at 394	Negative strand: GCAGATGA at 3476, GCAGGTGC at 3150, GCAGCTGG at 2405, TCACCTGT at 2250, ACAGGTGA at 2128, CCAGCTGC at 2055, ACAGGTGT at 1969, GCAGGTGG at 197
EIN3 binding sites	A(C/T)G(A/T)A(C/T)CT	-	-	-	-	-	Negative strand: ATGAACCT at 329 Positive strand: ATGAACCT at 1957	Negative strand: AGGTTCGT at 1928 Positive strand: AGGTACGT at 1935
Endoplasmic reticulum stress response elements	CCAAT-N9-CCACG, CCACG	Negative strand: CCACG at 3954, CCACG at 3880, CCACG at 3196 Positive strand: CGTGG at 3047	-	Negative strand: CGTGG at 4377 Positive strand: CGTGG at 4343	Negative strand: CGTGG at 2761	Positive strand: CGTGG at 4238	Negative strand: CCACG at 2333, CCACG at 2195, CCACG at 2080, CGTGG at 1339, CCACG at 1254, CCACG at 378 Positive strand: CGTGG at 1897, CGTGG at 1244, CGTGG at 741	Negative strand,: CGTGG at 3813, CCACG at 3604, CCACG at 968, CCACG at 868, CCACG at 775, CCACG at 298, CCACG at 241 Positive strand: CGTGG at 3885, CCACG at 3882, CGTGG at 3601, CGTGG at 3322, CCACG at 3150, CGTGG at 3044, CCACG at 2799, CGTGG at 2566, CCACG at 2333, CCACG at 2088, CCACG at 1762, CGTGG at 1628, CGTGG at 1460, CGTGG at 1360, CGTGG at 1208, CGTGG at 1124, CGTGG at 1040, CGTGG at 956, CGTGG at 856, CGTGG at 788, CCACG at 782, CGTGG at 772, CGTGG at 620, CCACG at 487
Endosperm expressions	TGTGTCA	Negative strand: TGTGTCA at 4198	-	-	-	-	-	Positive strand: TGTGTCA at 3413, TGACACA at 2076
Enhancer boxes	CA(A/C/G/T)(A/C/G/T)TG	Negative strand: CAGATG at 4212, CATTTG at 3482, CAGATG at 2988 Positive strand: CACTTG at 4011, CACCTG at 3969, CAGGTG at 3953, CAGATG at 3919, CAACTG at 3850, CAGATG at 3627, CAGATG at 3620, CACTTG at 3241, CACTTG at 3102, CACTTG at 2920	-	-	CACATG at 2667	Positive strand: CAAGTG at 4202	Negative strand: CACCTG at 2116, CAGTTG at 1513, CAGATG at 1224, CAAGTG at 1179, CACATG at 797, CAGATG at 481, CACATG at 324 Positive strand: CACTTG at 2579, CAGGTG at 2570, CACTTG at 2126, CAGGTG at 2079, CAAATG at 1579, CACCTG at 1172, CACCTG at 1130, CACCTG at 393, CATTTG at 364, CATATG at 41	Negative strand: CACTTG at 4015, CATGTG at 3958, CACATG at 3956, CATGTG at 3902, CAGCTG at 3777, CACATG at 3742, CACATG at 3707, CAGATG at 3475, CATCTG at 3404, CAGCTG at 3241, CAGGTG at 3149, CACCTG at 3046, CACCTG at 2568, CAAGTG at 2510, CACCTG at 2432, CAGCTG at 2404, CAGGTG at 2374, CACCTG at 2249, CAGGTG at 2127, CAGCTG at 2054, CACATG at 2031, CAGGTG at 1968, CACCTG at 958, CACCTG at 858, CACGTG at 570, CAGGTG at 196 Positive strand: CACTTG at 3936, CACGTG at 3884, CAGGTG at 3086, CACGTG at 2961, CAGGTG at 2028, CAGGTG at 1843, CACGTG at 1219, CATGTG at 567, CACGTG at 547, CACCTG at 186
Ethylene responsive elements	ATTTCAAA	-	-	-	-	-	Positive strand: ATTTCAAA at 1383	Negative strand: ATTTCAAA at 2648
Forkhead boxes	(A/G)(C/T)AAA(C/T)A	Negative strand: GTAAATA at 4536, TATTTAT at 4074, TATTTGG at 3364, TATTTGT at 3337, TGTTTAT at 3333, TATTTGA at 3016, TATTTGT at 2876	-	-	-	Negative strand: ACAAACA at 4256	Negative strand: TGTTTGT at 2512, TGTTTGT at 2487, TGTTTGG at 1588, TGTTTGT at 1391 Positive strand: GCAAACA at 2483, GCAAACA at 1539	Negative strand: TGTTTGC at 3340, TGTTTAT at 2346 Positive strand: TATTTAC at 3429
GAAC elements	GAACT	Negative strand: GAACT at 4294, AGTTC at 4178, AGTTC at 4027, GAACT at 4012, AGTTC at 3844, GAACT at 3571, GAACT at 3401, GAACT at 3242, GAACT at 3103 Positive strand: AGTTC at 4417, AGTTC at 4175, AGTTC at 4024, GAACT at 3460	-	-	Negative strand: GAACT at 2714	Negative strand: AGTTC at 4200 Positive strand: GAACT at 4131	Negative strand: GAACT at 2580, GAACT at 2379, GAACT at 2127, GAACT at 1300, GAACT at 1009, GAACT at 843 Positive strand: GAACT at 1685, AGTTC at 1177, AGTTC at 719, AGTTC at 253	Negative strand: GAACT at 4048, AGTTC at 2954, AGTTC at 1987, GAACT at 1951 Positive strand: GAACT at 4016, AGTTC at 2615, AGTTC at 2508
Gibberellic acid responsive elements (GAREs)	TAACAAA	-	-	-	-	-	Negative strand: TTTGTTA at 230	-
GARE-like 1	TAACA(A/G)A	-	-	-	-	-	Negative strand: TTTGTTA at 230 Positive strand: TAACAGA at 13	-
GATA boxes	GATA	Negative strand: TATC at 4078, TATC at 4046, GATA at 3526, TATC at 3446, TATC at 3421, GATA at 2996, GATA at 2975, TATC at 2902, GATA at 2898 Positive strand: GATA at 3655, GATA at 3544, GATA at 3535, GATA at 3465, GATA at 3360, GATA at 2981	-	-	-	Negative strand: TATC at 4123	Negative strand: TATC at 2498, TATC at 1709, TATC at 1703, GATA at 1525, TATC at 468, TATC at 354, TATC at 250, GATA at 234, GATA at 210, TATC at 99 Positive strand: GATA at 2177, TATC at 1730, GATA at 1702, GATA at 1665, GATA at 1595, TATC at 1528, GATA at 353, GATA at 108, GATA at 98, GATA at 74, GATA at 57	Negative strand: TATC at 3383, GATA at 2737, GATA at 2659, GATA at 1837 Positive strand: TATC at 3700, GATA at 3698, GATA at 3258, TATC at 2626, TATC at 2549, GATA at 2157, GATA at 1975, TATC at 1838
GC boxes (Briggs)	(G/T)(G/A)GGCG(G/T)(G/A)(G/A)(C/T)	Negative strand: ACTCCGCCCA at 3092 Positive strand: TGGGCGTGGT at 3048	-	-	-	-	Positive strand: TGGGCGTGGT at 1898, GCTCCGCCTC at 1505	Negative strand: TGGGCGGGAC at 409 Positive strand: GCCACGCCCC at 491
GC boxes SP1 (Ye) (Zhang) core	GGGCGG	Negative strand: CCGCCC at 4000, CCGCCC at 3091	-	Negative strand: GGGCGG at 4439, GGGCGG at 4429, CCGCCC at 4292 Positive strand: CCGCCC at 4440, CCGCCC at 4430	Positive strand: GGGCGG at 2724, GGGCGG at 1809	Positive strand: GGGCGG at 4238	Negative strand: CCGCCC at 1251 Positive strand: GGGCGG at 1809	Negative strand: GGGCGG at 1901, GGGCGG at 1793, GGGCGG at 406, GGGCGG at 353 Positive strand: CCGCCC at 2486, CCGCCC at 1026, CCGCCC at 407
GCC boxes	GCCGCC	-	-	-	Negative strand: GCCGCC at 2727	-	Positive strand: GGCGGC at 1753	Negative strand: GCCGCC at 1757, GCCGCC at 904 Positive strand: CCGCCG at 1902, CCGCCG at 1794, GCCGCC at 356, CCGCCG at 354
General control nonderepressible 4 protein binding site (GCRE)	TGA(C/G/T)T(A/C/G)(A/T)	Negative strand: ACACTCA at 4094, TGAGTCT at 3644, TGACTAT at 3544 Positive strand: AGACTCA at 4055, TGAGTAT at 3829, AGAATCA at 3237	-	Negative strand: ACACTCA at 4336 Positive strand: TGAGTGA at 4338	Positive strand: TGACTCT at 2788	Negative strand: TGATTAT at 4165, TGATTAT at 4158, TTAATCA at 4147	Negative strand: ATACTCA at 276 Positive strand: AGACTCA at 1404, AGAATCA at 293, TGAGTCT at 278, AGAATCA at 198	Negative strand: TGAGTGA at 3712, TGAGTGT at 3592, TGATTGT at 2678, AGAGTCA at 2613, TCAGTCA at 2100 Positive strand: TTACTCA at 3447, AGACTCA at 3008, AGACTCA at 2952, TGACTAA at 2676
Gibberellin responsive elements	AAACAGA	Positive strand: AAACAGA at 4518, AAACAGA at 2878	-	-	-	-	Positive strand: AAACAGA at 168	Negative strand: AAACAGA at 3179, AAACAGA at 2652, TCTGTTT at 2262
Γ-interferon activated sequences (GAS), see STAT5	TTNCNNNAA	Negative strand: TTTCTGTAA at 4509, TTTAAGCAA at 3503, TTTCCAAAA at 3349 Positive strand: TTCCCTGAA at 3782, TTAAGGAAA at 2957, TTGGGGAAA at 2926, TTTCATCAA at 2889	-	-	-	Negative strand: TTCCGGGAA at 4247 Positive strand: TTGTAGTAA at 4118	Negative strand: TTGAGGTAA at 1378, TTTCGTAAA at 189, TTTTCGTAA at 188, TTAAAGAAA at 25 Positive strand: TTCGGGAAA at 2458, TTGCTTGAA at 2380, TTGCCTGAA at 1624, TTTCAAAAA at 1385, TTACTTGAA at 1301, TTGCTTGAA at 1010	Negative strand: TTGCAGGAA at 2747 Positive strand:TTTCCGAAA at 1095, TTCCATGAA at 128
G-protein-coupled receptors (GCR1s), CT boxes	CTTCC	Negative strand: CTTCC at 3611 Positive strand: GGAAG at 3909, CTTCC at 3777, GGAAG at 3610	-	-	Positive strand: GGAAG at 2730	Negative strand: GGAAG at 4263, GGAAG at 4248, CTTCC at 4242 Positive strand: CTTCC at 4249, GGAAG at 4241, GGAAG at 4061	Negative strand: CTTCC at 2558, CTTCC at 1656, CTTCC at 1556, GGAAG at 619 Positive strand: GGAAG at 2557, GGAAG at 331, GGAAG at 241, GGAAG at 81	Negative strand: GGAAG at 3871, GGAAG at 3762, GGAAG at 3667, GGAAG at 2784, GGAAG at 2748, GGAAG at 1594, CTTCC at 1433, CTTCC at 1333, CTTCC at 1070, CTTCC at 734, CTTCC at 677, GGAAG at 209 Positive strand: CTTCC at 3852, GGAAG at 3312, GGAAG at 2582, GGAAG at 1516, GGAAG at 1432, GGAAG at 1405, GGAAG at 1332, GGAAG at 1305, GGAAG at 1264, GGAAG at 1153, GGAAG at 1069, GGAAG at 1012, GGAAG at 928, GGAAG at 828, GGAAG at 760, GGAAG at 733, GGAAG at 676, GGAAG at 592, GGAAG at 456, CTTCC at 210
GGCs	GGC	Negative strand: GCC at 4324, GGC at 4323, GCC at 3999, GGC at 3874, GCC at 3596, GCC at 3090 Positive strand: GCC at 4521, GCC at 4490, GCC at 4481, GCC at 4440, GCC at 4412, GCC at 4346, GCC at 4322, GCC at 4297, GGC at 4279, GGC at 4273, GGC at 4254, GCC at 4249, GGC at 4239, GCC at 4230, GGC at 4190, GCC at 4167, GGC at 4166, GGC at 4142, GCC at 4118, GGC at 4111, GGC at 4103, GCC at 4099, GGC at 4098, GGC at 4039, GCC at 4034, GCC at 4015, GGC at 3997, GGC at 3991, GGC at 3960, GCC at 3948, GGC at 3947, GCC at 3928, GGC at 3927, GGC at 3896, GCC at 3881, GCC at 3873, GGC at 3872, GCC at 3852, GCC at 3839, GCC at 3727, GGC at 3716, GCC at 3683, GGC at 3629, GGC at 3612, GGC at 3597, GGC at 3586, GCC at 3575, GGC at 3574, GCC at 3567, GGC at 3566, GCC at 3561, GGC at 3475, GGC at 3448, GGC at 3442, GGC at 3397, GGC at 3300, GCC at 3295, GCC at 3281, GCC at 3270, GGC at 3227, GGC at 3221, GCC at 3205, GCC at 3197, GCC at 3130, GGC at 3129, GCC at 3125, GGC at 3088, GGC at 3082, GGC at 3051, GGC at 3043, GGC at 3038, GGC at 3005, GGC at 2907	-	Negative strand: GGC at 4437, GGC at 4427, GCC at 4403, GGC at 4402, GCC at 4304, GGC at 4303, GCC at 4291, GCC at 4280, GCC at 4274 Positive strand: GCC at 4439, GCC at 4429, GCC at 4345, GGC at 4344, GGC at 4289, GGC at 4276	Negative strand: GCC at 2727, GCC at 2724 Positive strand: GGC at 2772, GCC at 2767, GCC at 2753, GGC at 2725, GGC at 2722, GGC at 2693, GCC at 2669, GGC at 2662, GCC at 2651, GCC at 2607, GGC at 2606	Negative strand: GCC at 4238, GCC at 4232, GCC at 4227, GGC at 4226, GCC at 4210, GCC at 4190, GGC at 4189, GGC at 4179 Positive strand: GCC at 4259, GCC at 4244, GGC at 4243, GGC at 4236	Negative strand: GCC at 2727, GCC at 2724, GCC at 2524, GCC at 2454, GGC at 2408, GCC at 2392, GCC at 2354, GGC at 2353, GCC at 2317, GGC at 2316, GCC at 2231, GCC at 2197, GCC at 2191, GGC at 2190, GGC at 1982, GCC at 1809, GCC at 1762, GCC at 1752, GCC at 1680, GGC at 1508, GGC at 1501, GGC at 1329, GCC at 1250, GCC at 1238, GGC at 1237, GGC at 1217, GGC at 1154, GGC at 1038, GCC at 956, GCC at 865, GCC at 856, GCC at 700, GCC at 653, GCC at 513, GGC at 751, GGC at 512, GCC at 427, GCC at 380, GCC at 374, GGC at 373 Positive strand: GGC at 2565, GGC at 2559, GCC at 2535, GGC at 2528, GGC at 2520, GCC at 2516, GGC at 2515, GGC at 2437, GCC at 2432, GCC at 2407, GGC at 2390, GGC at 2386, GGC at 2364, GGC at 2358, GCC at 2334, GGC at 2319, GCC at 2315, GCC at 2265, GGC at 2229, GGC at 2223, GCC at 2208, GGC at 2201, GGC at 2153, GGC at 2106, GCC at 2074, GGC at 2073, GGC at 2066, GGC at 2011, GCC at 2006, GCC at 1992, GCC at 1981, GGC at 1964, GGC at 1949, GGC at 1938, GGC at 1905, GGC at 1893, GGC at 1842, GGC at 1820, GGC at 1807, GGC at 1797, GGC at 1766, GGC at 1758, GGC at 1753, GGC at 1750, GGC at 1743, GCC at 1634, GCC at 1620, GCC at 1608, GGC at 1557, GCC at 1503, GGC at 1461, GCC at 1456, GGC at 1358, GCC at 1328, GGC at 1311, GGC at 1285, GGC at 1279, GCC at 1255, GGC at 1248, GGC at 1240, GCC at 1236, GCC at 1200, GGC at 1199, GCC at 1195, GCC at 1153, GGC at 1121, GGC at 1113, GGC at 1108, GCC at 1062, GCC at 1037, GGC at 1020, GGC at 994, GGC at 988, GCC at 964, GGC at 957, GGC at 954, GGC at 949, GCC at 945, GGC at 901, GCC at 896, GCC at 871, GGC at 854, GGC at 828, GGC at 822, GCC at 729, GGC at 698, GGC at 694, GCC at 689, GGC at 688, GCC at 664, GGC at 657, GGC at 649, GCC at 645, GGC at 644, GGC at 597, GGC at 562, GCC at 553, GGC at 552, GGC at 515, GCC at 511, GGC at 510, GCC at 505, GCC at 501, GGC at 461, GCC at 456, GGC at 451, GGC at 425, GCC at 416, GGC at 415, GGC at 384, GCC at 372, GGC at 371, GGC at 263, GGC at 120, GGC at 89, GCC at 36	Negative strand: GGC at 4003, GCC at 3998, GGC at 3991, GGC at 3982, GGC at 3907, GCC at 3896, GCC at 3809, GCC at 3755, GGC at 3754, GCC at 3702, GGC at 3695, GGC at 3688, GCC at 3681, GGC at 3680, GCC at 3676, GGC at 3675, GGC at 3659, GGC at 3637, GGC at 3585, GGC at 3523, GCC at 3499, GGC at 3498, GCC at 3492, GGC at 3485, GGC at 3480, GGC at 3470, GCC at 3431, GGC at 3406, GCC at 3375, GCC at 3359, GGC at 3346, GCC at 3285, GCC at 3235, GCC at 3224, GCC at 3218, GGC at 3118, GCC at 3101, GCC at 3036, GGC at 3035, GCC at 3011, GCC at 2990, GGC at 2989, GCC at 2985, GGC at 2984, GGC at 2912, GCC at 2905, GCC at 2897, GGC at 2893, GCC at 2888, GGC at 2884, GCC at 2878, GGC at 2877, GCC at 2823, GGC at 2807, GGC at 2767, GGC at 2694, GCC at 2571, GGC at 2570, GCC at 2558, GGC at 2551, GCC at 2527, GCC at 2521, GGC at 2503, GGC at 2483, GCC at 2478, GGC at 2434, GCC at 2391, GGC at 2367, GCC at 2353, GGC at 2317, GGC at 2293, GGC at 2186, GGC at 2160, GGC at 2116, GCC at 2069, GGC at 2068, GCC at 2009, GGC at 1993, GGC at 1972, GGC at 1944, GGC at 1917, GGC at 1906, GGC at 1902, GGC at 1899, GGC at 1881, GCC at 1857, GGC at 1856, GCC at 1848, GGC at 1847, GGC at 1816, GCC at 1795, GGC at 1794, GGC at 1791, GCC at 1769, GGC at 1766, GCC at 1757, GCC at 1754, GGC at 1753, GCC at 1738, GGC at 1737, GGC at 1716, GGC at 1699, GCC at 1672, GCC at 1656, GCC at 1646, GGC at 1645, GGC at 1637, GCC at 1604, GCC at 1596, GGC at 1582, GCC at 1569, GGC at 1568, GGC at 1561, GGC at 1547, GCC at 1541, GCC at 1513, GGC at 1512, GCC at 1498, GCC at 1485, GGC at 1484, GGC at 1477, GCC at 1466, GCC at 1454, GGC at 1438, GCC at 1429, GGC at 1428, GGC at 1423, GCC at 1408, GCC at 1398, GCC at 1385, GGC at 1384, GGC at 1377, GCC at 1366, GCC at 1354, GGC at 1338, GCC at 1329, GGC at 1328, GGC at 1323, GCC at 1308, GCC at 1302, GGC at 1295, GCC at 1289, GCC at 1268, GCC at 1261, GGC at 1260, GGC at 1255, GCC at 1246, GCC at 1233, GGC at 1225, GGC at 1211, GGC at 1200, GGC at 1189, GGC at 1176, GCC at 1172, GGC at 1171, GCC at 1162, GCC at 1149, GGC at 1148, GGC at 1092, GCC at 1078, GCC at 1065, GGC at 1043, GGC at 1034, GGC at 1028, GGC at 1023, GCC at 1009, GGC at 1008, GGC at 1003, GCC at 988, GCC at 981, GGC at 980, GGC at 973, GCC at 949, GGC at 948, GCC at 932, GCC at 925, GGC at 924, GGC at 919, GCC at 908, GCC at 904, GCC at 901, GCC at 888, GCC at 881, GGC at 880, GGC at 873, GCC at 849, GGC at 848, GCC at 832, GCC at 825, GGC at 824, GGC at 819, GCC at 808, GCC at 804, GCC at 764, GGC at 763, GGC at 751, GCC at 740, GCC at 729, GCC at 722, GGC at 721, GCC at 673, GGC at 672, GGC at 667, GCC at 645, GGC at 637, GCC at 614, GCC at 595, GCC at 589, GGC at 588, GGC at 583, GCC at 572, GCC at 561, GGC at 553, GGC at 539, GGC at 517, GCC at 512, GGC at 504, GGC at 499, GCC at 482, GGC at 478, GCC at 474, GCC at 459, GCC at 452, GGC at 444, GCC at 432, GCC at 420, GGC at 419, GGC at 414, GGC at 404, GCC at 389, GGC at 388, GGC at 376, GCC at 371, GGC at 370, GGC at 354, GGC at 351, GCC at 340, GGC at 332, GCC at 326, GGC at 325, GGC at 315, GCC at 283, GGC at 282, GGC at 274, GGC at 261, GCC at 248, GGC at 247, GCC at 238, GCC at 212, GGC at 211, GCC at 199, GGC at 198, GGC at 158, GCC at 131, GCC at 92, GGC at 91, GCC at 65, GGC at 26, GGC at 19, GGC at 9 Positive strand: GCC at 4002, GGC at 4001, GGC at 3912, GGC at 3810, GGC at 3798, GCC at 3748, GCC at 3670, GCC at 3605, GCC at 3557, GGC at 3556, GCC at 3515, GCC at 3487, GGC at 3324, GGC at 3225, GGC at 3200, GGC at 2562, GCC at 2485, GGC at 2354, GGC at 2214, GGC at 2149, GGC at 1961, GCC at 1916, GCC at 1901, GCC at 1846, GGC at 1845, GCC at 1793, GCC at 1764, GCC at 1759, GGC at 1758, GGC at 1755, GCC at 1751, GCC at 1714, GCC at 1706, GCC at 1698, GCC at 1690, GCC at 1680, GGC at 1664, GGC at 1647, GCC at 1641, GCC at 1636, GGC at 1608, GCC at 1590, GCC at 1581, GCC at 1559, GCC at 1546, GGC at 1545, GCC at 1529, GGC at 1486, GGC at 1445, GCC at 1437, GGC at 1434, GCC at 1422, GGC at 1386, GGC at 1345, GCC at 1337, GGC at 1334, GCC at 1322, GCC at 1294, GGC at 1293, GCC at 1254, GCC at 1223, GCC at 1210, GGC at 1209, GCC at 1202, GCC at 1170, GGC at 1163, GCC at 1147, GGC at 1098, GCC at 1086, GGC at 1079, GCC at 1042, GGC at 1041, GCC at 1033, GCC at 1025, GCC at 1002, GGC at 995, GCC at 979, GCC at 971, GGC at 950, GCC at 910, GGC at 909, GGC at 902, GGC at 895, GCC at 879, GCC at 871, GGC at 850, GCC at 810, GGC at 809, GGC at 789, GGC at 765, GCC at 762, GCC at 750, GCC at 743, GGC at 742, GGC at 735, GCC at 720, GGC at 678, GCC at 666, GCC at 636, GCC at 582, GGC at 575, GGC at 562, GCC at 538, GCC at 498, GCC at 489, GCC at 484, GGC at 483, GCC at 476, GGC at 475, GCC at 442, GGC at 441, GCC at 411, GCC at 406, GCC at 399, GGC at 392, GCC at 375, GGC at 374, GCC at 356, GCC at 353, GCC at 331, GCC at 324, GGC at 307, GCC at 299, GGC at 74
Glucocorticoid response elements	AGAACA	Negative strand: TGTTCT at 3759, TGTTCT at 3635, TGTTCT at 3340, TGTTCT at 3307 Positive strand: AGAACA at 3668	-	-	-	Negative strand: AGAACA at 4068	Negative strand: AGAACA at 281 Positive strand: AGAACA at 287, TGTTCT at 45	Negative strand: AGAACA at 3094, TGTTCT at 108
GT boxes (Sato)	GGGG(T/A)GGGG	-	-	-	-	-	-	Negative strand: GGGGAGGGG at 2291
Hac1 KAR2	CAGCGTG	-	-	-	-	-	Positive strand: CAGCGTG at 740	Negative strand: CACGCTG at 778
H box (Mitchell)	ANANNA	Negative strand: AAATAA at 4537, AGAGAA at 4527, TTGTCT at 4518, TTCTGT at 4507, TGCTCT at 4473, TCCTGT at 4468, ACACGA at 4402, TCTTTT at 4395, TTCTTT at 4394, TTTTCT at 4392, TCTTTT at 4390, TTCTTT at 4389, TTTTCT at 4387, TTTTTT at 4385, TCTTTT at 4383, TTCTTT at 4382, TTTTCT at 4380, TTTTTT at 4378, TATTAT at 4223, TTTTAT at 4220, TTTTTT at 4218, TGTTTT at 4216, TCCTGT at 3756, TCCTGT at 3389 Positive strand: ACACGA at 4471, TCCTCT at 4428, TGCTCT at 4404, AGAAAA at 4395, AAAGAA at 4393, AAAAGA at 4392, AGAAAA at 4390, AAAGAA at 4388, AAAAGA at 4387, AAAAAA at 4385, AGAAAA at 4383, AAAGAA at 4381, AAAAGA at 4380, AAAAAA at 4378, ATAATA at 4223, AAATAA at 4221, AAAATA at 4220, AAAAAA at 4218, ACAAAA at 4216, TCCTCT at 3790, AGAGGA at 3675, AGAGGA at 3638, AGAGGA at 3387	-	Negative strand: TGCTGT at 4392, TTCTCT at 4386, TGGTCT at 4380, TCATGT at 4365 Positive strand: AGAGAA at 4387	Positive strand: ACAGGA at 2690	Negative strand: ACATGA at 4154, TAGTTT at 4139, TGATTT at 4134, TTTTAT at 4122, TCATTT at 4119, ACATCA at 4116, TGGTTT at 4108, AAATGA at 4094, AGAACA at 4068 Positive strand: AGAGAA at 4387, TCCTGT at 4252, ATATTA at 4168, TAATAT at 4166, TAGTAT at 4149, AAATAA at 4142, AAATCA at 4137, AAAATA at 4122, TCTTGT at 4068, AGAGGA at 4059	Negative strand: TCCTCT at 2370, TCCTCT at 1944, TCCTCT at 1826, TCCTCT at 1291, TCCTCT at 1000, TCCTCT at 834, TCCTCT at 581 Positive strand: TCCTGT at 1911 *	Negative strand: TCCTGT at 3622, ACAGGA at 3572, TCCTCT at 3304, TCCTCT at 2981, AGAGGA at 2793, AGAGGA at 471, TCCTCT at 221, AGAGGA at 207, TCCTGT at 144 Positive strand: TCCTCT at 3650, AGAGGA at 3302, TCCTGT at 3131, TCCTGT at 2460, AGAGGA at 2081, TCCTCT at 710, AGAGGA at 142, TCCTCT at 46 *
H box (Rozhdestvensky)	ACACCA	Negative strand: ACACCA at 3811, TGGTGT at 3764, ACACCA at 3187	-	-	Negative strand: ACACCA at 2659	-	Negative strand: ACACCA at 788 Positive strand: ACACCA at 2419, TGGTGT at 1477, ACACCA at 883, TGGTGT at 793, TGGTGT at 608	Negative strand: TGGTGT at 3969, TGGTGT at 3950, ACACCA at 3825, TGGTGT at 2813, ACACCA at 2603, TGGTGT at 105 Positive strand: ACACCA at 3967, TGGTGT at 3859, ACACCA at 3643, TGGTGT at 2634, TGGTGT at 2600, TGGTGT at 2123
H boxes (Lindsay)	CCTACC	Negative strand: GGTAGG at 4456	-	-	-	-	Negative strand: GGTAGG at 1838 Positive strand: GGTAGG at 119	Negative strand: GGTAGG at 3753, CCTACC' at 1196 Positive strand: GGTAGG at 3629, GGTAGG at 3108, CCTACC at 1879
H boxes (Loake)	CC(A/T)ACCNNNNNNN(A/C)T	Positive strand: AGAAGTGTTGGTTGG at 3946	-	-	-	-	-	-
Heat shock elements (HSEs) (Eastmond)	nGAAn-(5-bp)-nGAAnnTTCn	-	-	-	-	-	Negative strand: GGAATTCACATGAACCTTCA at 332	-
Heat shock elements (HSEs) (Eastmond)	nGA(A/G)n-(5-bp)-nGAAnnTTCn (GAP)	-	-	-	-	-	Negative strand: GGAATTCACATGAACCTTCA at 332	-
Heat shock elements (HSEs) (Eastmond)	nGAAn-(5-bp)-nGA(A/G)nnTTCn (GAP)	-	-	-	-	-	Negative strand: GGAATTCACATGAACCTTCA at 332	-
Heat shock elements (HSEs) (Eastmond)	nGAAn-(5-bp)-nGAAn-(5-bp)-nGAAn	-	Postive strand: AGAAGAAAAAAGAAAAGAGAAGAAA at 2831	-	-	-	-	-
Hex sequences	TGACGTGGC	-	-	Positive strand: TGACGTGGC at 4344	-	-	-	-
High Mobility Group boxes (HMG boxes)	(A/T)(A/T)CAAAG	Positive strand: ATCAAAG at 2891	-	-	-	-	Negative strand: CTTTGTT at 1585, CTTTGTT at 229	-
HNF6s	(A/G/T)(A/T)(A/G)T(C/T)(A/C/G)AT(A/C/G/T)(A/G/T)	Positive strand: TTATTAATTC at 4542, TTATTAATCG at 4229, TAGTTGATAA at 3527 Positive strand: TCATCAACTA at 3525, AAATTGATAA at 3361	-	-	-	Negative strand: TTATTGATTA at 4164, TTATTAATCA at 4147 Positive strand: ATATTAACAA at 4172	Negative strand: GTGTTAATAA at 1725, TAATGAACTT at 1301, ACATGGACAT at 802	Negative strand: ATGTCCATGG at 3581 Positive strand: CCATTGACTC at 3736, GAGTCCATTG at 3732
Homeoboxes	CAAG	Negative strand: CTTG at 4450, CAAG at 4417, CAAG at 4175, CAAG at 4024, CTTG at 3783, CTTG at 3723, CTTG at 3667, CTTG at 3459, CTTG at 3244 Positive strand: CTTG at 4293, CTTG at 4267 CAAG at 4200, CTTG at 4187, CAAG at 4183, CAAG at 4178, CAAG at 4073, CAAG at 4027, CAAG at 4019, CTTG at 4011, CAAG at 3844, CTTG at 3792, CAAG at 3758, CAAG at 3634, CTTG at 3570, CTTG at 3400, CAAG at 3373, CAAG at 3339, CAAG at 3306, CAAG at 3273, CTTG at 3241, CAAG at 3140, CTTG at 3102, CAAG at 2963, CTTG at 2920	-	Negative strand: CTTG at 4388, CTTG at 4299 Positive strand: CTTG at 4443	Negative strand: CTTG at 2716 Positive strand: CTTG at 2713	Negative strand: CTTG at 4130 Positive strand: CTTG at 4067	Negative strand: CTTG at 2381, CTTG at 1955, CTTG at 1684, CTTG at 1551, CTTG at 1302, CAAG at 1177, CTTG at 1011, CTTG at 845, CAAG at 719, CAAG at 344, CTTG at 286, CAAG at 253, CAAG at 44 Positive strand: CTTG at 2579, CTTG at 2378, CAAG at 2244, CTTG at 2126, CAAG at 2022, CTTG at 1972, CTTG at 1926, CAAG at 1817, CTTG at 1648, CTTG at 1618, CTTG at 1606, CAAG at 1496, CTTG at 1299, CTTG at 1008, CAAG at 874, CTTG at 842, CAAG at 692, CAAG at 556, CAAG at 454, CAAG at 419, CTTG at 327, CTTG at 280, CAAG at 114, CAAG at 70	Negative strand: CTTG at 4015, CTTG at 3373, CTTG at 3001, CTTG at 2741, CAAG at 2692, CAAG at 2615, CAAG at 2593, CAAG at 2508, CTTG at 2418, CAAG at 2398, CAAG at 2189, CAAG at 1947, CTTG at 1798, CTTG at 1578, CAAG at 1525, CAAG at 1510, CAAG at 1426, CAAG at 1326, CAAG at 1258, CAAG at 1006, CAAG at 922, CAAG at 822, CAAG at 754, CAAG at 670, CAAG at 586, CTTG at 654, CTTG at 526, CAAG at 502, CAAG at 338, CAAG at 177, CTTG at 129 Positive strand: CTTG at 4047, CTTG at 3936, CTTG at 3855, CTTG at 3837, CAAG at 3624, CAAG at 3351, CTTG at 3093, CAAG at 2954, CAAG at 2933, CAAG at 2922, CTTG at 2775, CTTG at 2578, CTTG at 2224, CAAG at 1987, CTTG at 1950, CAAG at 1926, CTTG at 1810, CAAG at 1489, CAAG at 1389, CAAG at 508, CTTG at 362, CAAG at 305, CAAG at 107
HY boxes	TG(A/T)GGG	Negative strand: CCCTCA at 4498, CCCTCA at 3889, CCCACA at 3184 Positive strand: TGAGGG at 4558, TGTGGG at 3712, TGAGGG at 3652	-	Negative strand: TGTGGG at 4395	Negative strand: CCCTCA at 2702 Positive strand: TGAGGG at 2699	-	Negative strand: TGTGGG at 749 Positive strand: TGAGGG at 88	Negative strand: TGAGGG at 3879, CCCTCA at 3503, TGAGGG at 3479, CCCTCA at 3207, TGAGGG at 258, CCCTCA at 88 Positive strand: TGTGGG at 3533, CCCTCA at 3185, TGTGGG at 2965, CCCACA at 1803, CCCTCA at 1783, CCCTCA at 662, CCCTCA at 494
Hypoxia-inducible factors	ACGTG	Negative strand: ACGTG at 4339, CACGT at 3429, ACGTG at 3288, CACGT at 2863 Positive strand: ACGTG at 4237	-	Positive strand: ACGTG at 4342	Negative strand: ACGTG at 2760	-	Negative strand: ACGTG at 2425, CACGT at 2081, ACGTG at 1999, ACGTG at 1718, CACGT at 1535, CACGT at 1470, ACGTG at 1346, ACGTG at 1338 Positive strand: CACGT at 1772, CACGT at 531, CACGT at 342	Negative strand: CACGT at 3254, ACGTG at 570, CACGT at 569 Positive strand: CACGT at 3960, ACGTG at 3884, CACGT at 3883, CACGT at 3464, ACGTG at 3342, ACGTG at 3321, ACGTG at 2961, CACGT at 2960, CACGT at 2800, CACGT at 2681, CACGT at 2334, CACGT at 2326, CACGT at 2063, ACGTG at 1821, CACGT at 1786, ACGTG at 1471, ACGTG at 1371, ACGTG at 1219, CACGT at 1218, CACGT at 783, ACGTG at 547, CACGT at 546
Hypoxia response elements (HRE)	CACGC	Positive strand: CACGC at 3280, GCGTG at 3046	-	-	-	-	Negative strand: CACGC at 2196, CACGC at 447, CACGC at 379 Positive strand: CACGC at 2207, CACGC at 1991, GCGTG at 1896, GCGTG at 1243, CACGC at 963, GCGTG at 740, CACGC at 663	Negative strand: GCGTG at 2554, GCGTG at 1719, CACGC at 1553, CACGC at 1301, GCGTG at 1242, GCGTG at 1216, CACGC at 1133, CACGC at 1049, GCGTG at 1019, CACGC at 987, CACGC at 969, CACGC at 887, CACGC at 869, CACGC at 803, CACGC at 797, CACGC at 776, GCGTG at 544 Positive strand: GCGTG at 2565, CACGC at 1763, CACGC at 1725, CACGC at 1589, GCGTG at 1555, GCGTG at 1551, CACGC at 1521, GCGTG at 1299, CACGC at 1253, CACGC at 1244, CACGC at 1169, CACGC at 1160, GCGTG at 1135, GCGTG at 1131, CACGC at 1085, GCGTG at 1051, GCGTG at 1047, CACGC at 1017, GCGTG at 977, GCGTG at 877, GCGTG at 799, GCGTG at 795, GCGTG at 685, CACGC at 665, CACGC at 581, CACGC at 497, CACGC at 488
Initiator elements (Inrs) (Juven-Gershon)	YYRNWYY	Negative strand: TTACTCC at 4557, AGTGTAA at 4533, TCACACT at 4361, TCGGACC at 4349, CCAGTTT at 4309, TCGGACC at 4300, GGTCCGA at 4255, CTGCACC at 4238, TCGGTCT at 4233, AAAATAA at 4221, TCACTCT at 4202, TCGAACC at 4188, AGTTCAA at 4177, CCGGTCC at 4170, AGTACGG at 4118, CCGTACC at 4107, CCGGTCC at 4102, TTACACT at 4092, AAAATAA at 4071, TCACTCT at 4051, TTGTATC at 4046, TCGGACC at 4037, AGACCAG at 4032, AGTTCAA at 4026, AGTGTGG at 3967, CCGGTCC at 3951, CTACTTT at 3922, TCATTCT at 3893, GGTCCGG at 3873, CTGGTCC at 3871, GGTATGG at 3858, CTACACC at 3810, CTGTTCT at 3759, GGTCTAG at 3488, TTGGTCT at 3486, TTGATCT at 3463, CCGTATC at 3446, CCGAACT at 3401, AGTCCGA at 3398, TCGTTCT at 3374, TTGTTCT at 3340, TCGTTTT at 3313, TTGTTCT at 3307, TCGGACC at 3298, AGTGCGG at 3281, TCGGTTC at 3273, CCACACC at 3186, TTGTATT at 3169, CCACTTT at 3146, TTGTTCC at 3141, GGACCGG at 3130, TCGGACC at 3128, CCGCACC at 3047, GATTCGA at 3033, TTGATTC at 3031, CCGATTT at 3009, TTGATTC at 2914, AAAGTAG at 2887 Positive strand: GGAATGA at 4555, TTAATTC at 4542, TCACATT at 4533, AGTCCAA at 4502, CCACTTT at 4461, CCACTCC at 4425, CCAGTTC at 4417, AGTGTGA at 4361, CTGCACT at 4340, CCGGACT at 4327, TCACACC at 3967, GGAGTAA at 3891, GGACCAG at 3870, CCATACC at 3858, GATGTGG at 3810, CTGAACC at 3784, AATGCAG at 3772, GGACTGG at 3749, CTGGACT at 3747, GGAACAG at 3725, CCATTTC at 3688, AATCCAG at 3681, CTGCTCC at 3582, CCAGATC at 3488, AAACCAG at 3485, GAACTAG at 3462, GAAGTGA at 3410, AAATTGA at 3358, AAAACAA at 3330, AGAGCAA at 3311, TTGCACT at 3289, TTGAACC at 3245, GGTGTGG at 3186, AAATTAG at 3176, AGACCAG at 3123, AAACTAA at 3030, AAAATAA at 3013, AGAATGG at 3004	Positive strand: AAAACAA at 2842	Negative strand: GGAACAG at 4445, GGTCTGG at 4416, GGAGTGA at 4350, CTGCACC at 4343 Positive strand: CCAGACC at 4416, CCACTCC at 4401, AGAACGA at 4390, GGTACGA at 4372, AGTACAG at 4366, GGAGTAA at 4309	Negative strand: TCGTACT at 2784, TCGGACC at 2770, AGTACGG at 2753, TTGGACC at 2720, TCACACC at 2658, CCACTTT at 2619, TTGTACC at 2614, TCACACC at 2605 Positive strand: CTGCACC at 2761, TTGAACC at 2717, TTGAATC at 2708, AGTGTGG at 2658, AAATCAG at 2649, AGTGTGG at 2605, AGACCAG at 2600	Negative strand: TTAGTTT at 4139, GATTTAG at 4136, TTGATTT at 4134, TCACTCT at 4128, TCATTTT at 4120, GAAATGA at 4094, AGAACAG at 4069 Positive strand: GGACTGG at 4216, GAAACGG at 4210, AAATCAA at 4138, CTAAATC at 4136, GAACTAA at 4133, AAAATAG at 4123, CTACTCC at 4102, TTACTCC at 4096	Negative strand: CCAGTCC at 2587, AGTACGG at 2535, CCGGTCC at 2519, TCATTCT at 2503, TTGTTTT at 2490, TCGTTTT at 2476, TCACTCT at 2449, TCGGACC at 2435, AGTGTGG at 2418, TTGGACC at 2385, CCACTTT at 2282, TCGTACC at 2277, TCGGACC at 2268, TCAAACT at 2257, CCAGTCC at 2250, AGTGCGG at 2208, CCGCTTT at 2157, TTGTACC at 2152, TCAAACT at 2141, TCACATT at 2087, CCGGTCC at 2077, TTACACC at 2065, TCGTTCT at 2023, TCGGACC at 2009, AGTGCGG at 1992, TTGGACC at 1959, CCGTACT at 1953, CCGCACC at 1897, GGACCGA at 1843, AGTGCAG at 1773, TTATACC at 1742, AAAATAG at 1730, TTAATTT at 1697, AGAACGG at 1608, TTGGATT at 1591, TTACTTT at 1582, CCGTTTT at 1561, TTGCTTC at 1555, GATATAG at 1528, CCACACT at 1479, GGTCCGA at 1462, AGAGCGA at 1448, TTGTTTT at 1394, TCGTTTT at 1371, TTATTCT at 1365, TCAGACC at 1356, TTGGATC at 1306, CCGCACC at 1244, CCACTTT at 1212, TTGTACC at 1207, GGACCGG at 1200, TCGGACC at 1198, AGTGTGG at 1128, TCACTCT at 1079, GAAGTGA at 1056, TTGGACC at 1015, TTAGTCC at 984, CCGTACC at 953, TCGGTCC at 948, TCGCTCT at 913, TCGGACC at 899, AGTGTGG at 882, TCGGTTC at 874, CTACACC at 787, TCGCACC at 741, GGACTGG at 734, TCGGACT at 732, CCAGTCC at 714, CCGGTTC at 692, AGTGCGG at 664, CCGGTCC at 648, TTATACC at 605, GGACCGA at 598, CCAGTCC at 578, CCGGTTC at 556, TCGGACC at 508, TCACTTT at 473, TTGTATC at 468, TCGGACC at 459, CCAGTCC at 441, CCGGTTC at 419, CTGCTTT at 312, TCACTCT at 301, TTATACT at 274, TTGGTCC at 262, CTACATT at 247, GATACAA at 213, CCATATT at 181, CCGTACT at 124, CCGTTTC at 93, CTATACC at 77, TTGTTCC at 71 Positive strand: AAAACAA at 2509, AAAGCAA at 2480, AAAGCAA at 2474, GATTCGG at 2454, AGAGTGA at 2447, CTGCACT at 2426, TCACACC at 2418, TTGAACC at 2382, CTACTCC at 2352, AAACTAG at 2313, AATACAA at 2305, AGACCAG at 2263, AGTTTGA at 2257, GGTGCGG at 2197, AAAATGA at 2187, GATACAA at 2180, AGACCAA at 2147, AGTTTGA at 2141, AGTGTAA at 2087, GGTGCAG at 2082, AATGTGG at 2065, AGAGCAA at 2021, CTGCACT at 2000, AGAATGG at 1948, AGACTGA at 1935, AAATTAG at 1887, AATACAA at 1878, AATATGG at 1742, TTATTTT at 1727, GAATTAA at 1696, AAAGCGG at 1680, GAAATGA at 1663, GAAACAA at 1585, AATACAG at 1566, AGAACGA at 1553, AGTGCAA at 1536, CTATATC at 1528, GGTGTGA at 1479, AGTGCAG at 1471, TCGCTCT at 1450, AAAACAA at 1388, CCATTTC at 1380, AGAGCAA at 1369, AGTCTGG at 1356, CCAGTCT at 1354, TTGCACT at 1347, TTGCACC at 1339, TTGAACC at 1303, AAATTAG at 1234, TCACACC at 1128, AGAGTGA at 1077, TCACTCC at 1058, AGATTGG at 1045, TTGAACC at 1012, GATCCAG at 975, AGAGCGA at 911, TCACACC at 882, TTGAACC at 846, GATGTGG at 787, AAATTAG at 777, AATACAA at 769, AGACCAG at 727, AGTTCGA at 721, AAATTGG at 643, AATACAA at 635, AATATGG at 605, AGATTGA at 585, AAATTAG at 499, AATACGA at 492, AGTGCGA at 448, GGTGCGG at 380, AAACTGA at 307, AGAACAG at 288, AATATGA at 274, AAACCAG at 261, AGTTCAA at 255, GATGTAA at 247, GAAACAA at 229, GGTATAA at 181, AAAACAG at 167, CTGCATT at 152, AAACTGA at 130, GATATGG at 77, AAAACAA at 69, GGACCAG at 34, TTGGACC at 32, CTGAATT at 20, AGACTGA at 17	Negative strand: AGAGTGG at 4040, GGTGTGA at 3971, AGTGTGG at 3966, AGTCTGA at 3924, AGAGTGA at 3876, GAACCAG at 3840, AGAATGA at 3835, TCACACC at 3824, AATCCGA at 3799, GAAGCGG at 3670, CTGTTCC at 3625, AGTGTGA at 3594, GGAATGA at 3567, CCAGACC at 3550, GGACCAG at 3547, TCACACT at 3507, AGTGCAG at 3465, GATGCAG at 3460, GGAATGA at 3441, TTGCATC at 3402, CTGTTCC at 3352, TTGCACT at 3343, CCGCATC at 3328, CTGCACC at 3322, CTGCTCC at 3309, CTGGTCT at 3299, TCGCTCT at 3276, CTGGTCT at 3245, GGACCAA at 3174, GAAATGG at 3168, AATATGG at 3162, CCAGTCC at 3084, GGTCTGG at 3021, CCAGTCC at 2998, CTGCTCC at 2978, GGTCTGA at 2943, GATTTGA at 2871, TCAGATT at 2868, GAAATAG at 2626, AGAATGA at 2841, GGTGCAA at 2801, AAAGTGG at 2711, AGAGCAA at 2705, GGACTGA at 2674, GATATAA at 2662, CCACACT at 2636, CCACACC at 2602, TTATACC at 2590, CCGCACC at 2566, CTAATTT at 2440, CTACACC at 2430, GGTGCAA at 2335, AGTGCAG at 2327, TCACTCT at 2306, CTGTTTC at 2263, TCAATCT at 2235, AGATCAA at 2232, CCAGATC at 2230, GAACCAG at 2227, CTGCATT at 2206, TCATATT at 2178, TCGCTTC at 2095, AGTGCAG at 2064, CCAGTCC at 2026, AAAGCAG at 2007, CTATTTC at 1978, GGTGTGG at 1971, GAACTGG at 1953, CCACTTC at 1914, GGTGTGG at 1805, AGTGCAG at 1787, GGTGCGG at 1764, CCAGACT at 1744, GAAGCGG at 1636, AGTGCGG at 1590, CTGCACT at 1472, AATGCGG at 1422, CTGCACT at 1372, AATGCGG at 1322, AGTGCGG at 1254, AGTGCGG at 1170, AGTGCGG at 1086, GGTGCAG at 784, CCGGACT at 746, AGTGCGG at 666, AGTGCGG at 582, AGTGCGG at 498, GGTGCGG at 489, AGACCGG at 442, GGAGCGA at 429, CCACACT at 345, AATGTGA at 230, CTGTTTT at 147, TTGTATT at 115, AGAGTGG at 53 Positive strand: GAACTGG at 4018, CCACACT at 3971, TCACACC at 3966, TCAGACT at 3924, TCACTCC at 3878, AGTGTGG at 3824, CTGGACC at 3787, CCGGACC at 3758, GGACCGG at 3681, CCGGACC at 3679, CCACTCC at 3647, AGAGTGG at 3612, TCACACT at 3594, GGTCTGG at 3550, CTGGTCT at 3548, GATCCGA at 3524, TCGATCC at 3522, AGTGTGA at 3507, CCGATCC at 3484, CTACTCC at 3478, GGAACGG at 3375, GGTACAA at 3337, AGAGTGA at 3317, GGACCAG at 3298, AGTGCAG at 3255, GAAGTAG at 3250, TCGGTCT at 3221, CTGGTTT at 3175, TTATACC at 3162, GGACCAA at 3049, AGTCCGG at 3036, AGACCAA at 3023, CCAGACC at 3021, GGTCCAG at 3018, GGAACAG at 3003, GGACCGG at 2990, CCGGACC at 2988, AGACCGG at 2985, AGACTGA at 2945, CCAGACT at 2943, GGAGTAA at 2902, AGACCGA at 2885, GGTCCGG at 2878, CTGGTCC at 2876, AAACTGG at 2873, CTAAACT at 2871, AGTCTAA at 2868, TTGCTCC at 2806, TCGATTC at 2789, TCGTTTT at 2707, TCAATCC at 2668, CTATATT at 2662, GGTGTGA at 2636, TCAGTCC at 2620, AGTTCAG at 2617, TCAGTTC at 2615, TCAGTCT at 2609, GGTGTGG at 2602, AATATGG at 2590, CCGGTCC at 2574, GGACCGG at 2571, CCGCACT at 2555, GGTACAA at 2475, AGAGTGG at 2470, GGACCGA at 2435, GATGTGG at 2430, AATCCGA at 2368, GGTCCGA at 2318, AAAGTGA at 2304, AGAGTGG at 2247, GGTCTAG at 2230, TTGGTCT at 2228, CCAGTCT at 2222, GGACTGG at 2213, CCGTTCT at 2190, AGTATAA at 2178, CTACTTT at 2146, TTGTACT at 2141, TCAATTT at 2136, GAAGTAG at 2110, CCACACC at 1971, CCGTTCT at 1948, CCGCTCT at 1921, AGAATGG at 1888, GGTCCGG at 1857, GGACCGA at 1817, CCACACC at 1805, GGTCTGA at 1744, CCGCACT at 1720, GGACTGG at 1662, GATGCGA at 1576, CCGCTCT at 1565, AATTCGG at 1541, TCGTTCC at 1511, CCGCTCT at 1481, CCGTTCC at 1427, GAAGCGG at 1408, CCGCTCT at 1381, CCGTTCC at 1327, GAAGCGG at 1308, CCGTTCC at 1259, CCGCTCT at 1229, AAAGCAG at 1183, GGTCCGA at 1177, CCGGTCC at 1175, TCGCTCT at 1061, CCGTTCC at 1007, GGACCGG at 949, TTGGACC at 947, TCGGTCT at 935, CCGTTCC at 923, GGACCGG at 849, TTGGACC at 847, TCGGTCT at 835, CCGTTCC at 823, GGTGCGA at 777, CCGGACT at 725, CCGTTCC at 671, GATGCGA at 652, CCGCTCT at 641, GAAGCGG at 595, CCGTTCC at 587, CCGCTCT at 557, AGAATGA at 524, TCGGTCC at 515, CCGTTCC at 503, GAAGCGG at 459, GGTGTGA at 345, CCGGACC at 286, TTACACT at 230, GGTCCAG at 217, CCGGTCC at 215, AATCCAG at 152, AGTCCGG at 92, CTGGACC at 40, GGTCCGA at 10
Initiator elements (Inrs) (Kugel)	BBCABW	Negative strand: TCTGGG at 4366, GTCACA at 4359, CCCACT at 4353, TGTGAC at 4336, GTCACT at 4319, TCCAGT at 4307, TCTGCA at 4236, TCTGGG at 4205, GTCACT at 4200, AGTGAA at 4161, TCTGAG at 4054, AGTGAA at 4010, TGTGAA at 3983, TGTGGA at 3968, TTCACA at 3939, CTCATT at 3891, TATGGA at 3859, CTCATA at 3829, TCCACT at 3825, TATGCG at 3547, TATGAC at 3541, GTCATT at 3480, TCTGAC at 3425, TTCACT at 3410, AGTGCG at 3280, AGTGAA at 3240, CCCACA at 3184, TCCACT at 3144, AGTGAA at 3101, AGTGGG at 3057, TATGGA at 2994, TTCACA at 2860 Positive strand: AATGAG at 4556, TTCACA at 4531, CCCACT at 4485, TCCACT at 4459, CCCAGA at 4448, TCCACT at 4423, ACTGCA at 4315, GCCAGT at 4415, TGTGAG at 4362, TGCACT at 4340, ACTGCA at 4338, ACTGCA at 4330, AGTGAG at 4320, TGCAGT at 4317, GCCAGA at 4233, AGTGAG at 4201, TGTGAG at 4093, AGTGAG at 4050, CTCACA at 3965, TGTGGC at 3960, CCCATA at 3856, ACTGCC at 3852, TCTGGA at 3836, AATGCA at 3771, ACTGGG at 3750, TGTGGG at 3712, TCCACA at 3692, GCCATT at 3686, AATGGG at 3660, CTCAGA at 3644, GGCACA at 3632, GTCAGA at 3625, GGCAGT at 3600, GGCAGA at 3589, GGCAGT at 3478, TGTGCC at 3561, GGCATA at 3451, GGCATA at 3445, TGCAGA at 3431, TGTGCA at 3429, AGTGAC at 3411, TGCACT at 3289, GCCATT at 3284, TGTGAG at 3268, AATGGC at 3005, TGTGCA at 2863	-	Negative strand: TCTGGG at 4417, TGTGGG at 4395, AGTGAG at 4351, ACTGCA at 4341, CTCACT at 4338, CCCAGA at 4330, TGCAGA at 4317, CTCATT at 4309, AGTGCC at 4274, GTCAGT at 4271 Positive strand: CCCAGA at 4414, CCCACT at 4399, CTCACT at 4350, AGTGAC at 4339, TGTGAG at 4335, AGTGGG at 4326, TCTGCG at 4320, TCCAGT at 4269	Negative strand: ACTGAG at 2787, GTCACT at 2739, GTCACA at 2656, GTCACA at 2603 Positive strand: ACTGCA at 2759, GCCACT at 2756, AGTGAG at 2740, TGCAGT at 2737, GGCACA at 2665, GCCAGT at 2654, TCCACT at 2632, TGTGGC at 2606	Negative strand: CTCAGA at 4195, AATGAG at 4095, ACTGAA at 4090 Positive strand: TGTGCC at 4259, ACTGGG at 4217, AGTGGG at 4204, AGTGAG at 4127, AGTGAC at 4088, CGCAGA at 4056	Negative strand: TCCAGT at 2585, AGTGAA at 2578, TGTGAA at 2551, CTCACT at 2447, GTCACT at 2404, TCCAGT at 2248, AGTGCG at 2207, ACTGGC at 2190, TATGAC at 2162, GTCACA at 2085, TCTGAG at 2026, AGTGCG at 1991, GTCACT at 1978, TCTGAC at 1934, TGCAGA at 1774, AGTGCA at 1772, TCTGAA at 1617, TGTGAA at 1544, GGCAGT at 1511, AGTGAC at 1492, CTCAGA at 1444, TCTGAG at 1403, GTCAGA at 1354, GTCACT at 1325, AATGAA at 1298, GGCACA at 1220, AGTGGA at 1171, TGTGGA at 1129, TCTGAG at 1082, CTCACT at 1077, AGTGAG at 1057, ACTGAA at 1052, CCCACT at 1049, GTCACT at 1034, TGTGCG at 963, TCTGAG at 916, GCCACT at 868, GGCAGA at 754, TGTGGG at 749, TCCAGT at 712, AGTGCG at 663, TCCAGT at 576, TCCAGT at 568, TGCATT at 533, TGTGCA at 531, TCCAGT at 439, TGTGCA at 342, TTCACA at 322, GTCACT at 299, CTCAGA at 278, CCCAGT at 206, TCCATA at 179, TGTGGA at 62, TCTGAC at 16 Positive strand: AGTGAG at 2448, TGCACT at 2426, ACTGCA at 2424, AGTGAG at 2405, TGCAGT at 2402, GCCAGT at 2211, AATGAC at 2188, TGCAGT at 2083, TGTGGC at 2066, TGCACT at 2000, ACTGCA at 1998, GCCACT at 1995, AGTGAG at 1979, TGCAGT at 1976, GGCAGA at 1967, AATGGC at 1949, ACTGAG at 1936, TATGGC at 1743, TGCACA at 1719, AATGCC at 1634, AATGAA at 1581, AGTGCA at 1535, TCCAGT at 1532, CCCAGA at 1518, ACTGCA at 1494, CTCACT at 1491, TGCAGT at 1472, AGTGCA at 1470, CCCAGA at 1411, TCCATT at 1378, TCTGGG at 1357, TCCAGT at 1352, TGCACT at 1347, AGTGAG at 1326, TGCAGT at 1323, GGCAGA at 1314, CTCACA at 1126, AGTGGC at 1121, GGCACA at 1116, AGTGAG at 1078, TTCACT at 1056, AGTGAG at 1035, TGCAGT at 1032, GGCAGA at 1023, GGCACA at 960, AGTGGA at 523, GGCACA at 518, AGTGAA at 472, AGTGCG at 447, ACTGAC at 308, AGTGAG at 300, TATGAG at 275, GGCACA at 266, GTCACT at 208, TGCATT at 152, ACTGAA at 131, TATGGG at 78, GCCATA at 39, ACTGAA at 18	Negative strand: GTCACT at 2425, TGCAGT at 2328, AGTGCA at 2326, TTCACT at 2304, CTCAGA at 2239, GTCAGA at 2222, TGCATT at 2206, ACTGCA at 2204, CTCATA at 2176, TATGGC at 2160, TTCAGT at 2098, GCCACT at 2072, AGTGGC at 2068, TGCAGT at 2065, AGTGCA at 2063, CTCAGT at 2060, TCCACA at 2029, CCCAGT at 2024, GGCACT at 1996, TCTGGC at 1993, TGTGGC at 1972, ACTGGG at 1954, TGCAGA at 1937, TCCACT at 1912, TCTGGG at 1865, TGCACA at 1822, TGTGGA at 1806, AGTGCA at 1786, CCCAGA at 1742, AGTGCG at 1725, GGCATT at 1702, AGTGCG at 1589, CGCACA at 1556, ACTGCA at 1505, CCCACT at 1502, TCTGCG at 1496, TCTGGC at 1477, TGCACT at 1472, AATGCG at 1421, CGCAGA at 1416, TCTGCG at 1396 TCTGGC at 1377, TGCACT at 1372 CGCAGA at 1316, AATGCG at 1321, ACTGAG at 1287, AGTGCG at 1253, CCCAGT at 1250, TGCACA at 1220, AGTGCG at 1169, AGTGCG at 1160, CGCACA at 1136, AGTGCG at 1085, CGCACA at 1052, TGTGGC at 1023, ACTGCG at 1001, GCCACA at 984, GCCAGA at 935, TGTGGC at 919, ACTGCC at 901, GCCACA at 884, GCCAGA at 835, CGCACA at 800, TGTGGC at 819, ACTGCG at 749, CGCACT at 686, AGTGCG at 665, TCCACA at 632, AGTGCG at 581, TGCACA at 548, AGTGCG at 497, CCCAGA at 468, TGCAGA at 438, CGCAGA at 396, ACTGGG at 348, GCCACA at 343, TCTGGA at 271, TCTGAG at 256, ACTGCC at 238, TGTGAA at 231, TCTGCA at 224, CCCAGA at 204, GTCACA at 155, AGTGGG at 54 GGCATT at 22, TCCAGA at 15 Positive strand: ACTGGA at 4019, GTCACA at 3964, TCCACT at 3934, TTCAGA at 3922, CTCACT at 3876, GTCACT at 3843, CCCAGT at 3820, ACTGGA at 3785, TCCAGA at 3771, AGTGCC at 3748, TCCATT at 3731, CTCACT at 3712, AGTGGG at 3613, GCCAGA at 3608, CTCACA at 3592, TCTGGA at 3551, TGTGGG at 3533, TGTGAG at 3508, AGTGAC at 3318, TGCAGA at 3256, AGTGCA at 3254, CTCAGA at 3187, ACTGAA at 3030, TCCAGA at 3019, TGTGGG at 2965, ACTGAA at 2946, AGTGAC at 2930, TCTGGA at 2862, TATGAA at 2740, TCCATA at 2642, TTCAGT at 2618, CTCAGT at 2613, GTCAGT at 2607, CGCACT at 2555, TTCACT at 2511, CCCAGA at 2489, GTCACA at 2464, TGTGGA at 2431, CGCAGT at 2423, TCTGAA at 2417, TCCACT at 2375, AGTGAC at 2341, AGTGGG at 2313, AGTGAG at 2305, TCCAGA at 2258, AGTGGA at 2248, TCCAGT at 2220, ACTGGC at 2214, TCCACT at 2128, GTCAGT at 2100, TCCACA at 1969, CCCAGA at 1958, AATGGG at 1889, CCCACA at 1803, TCTGAA at 1745, CGCACT at 1720, CCCAGA at 1711, TGTGCC at 1698, ACTGGG at 1663, TGTGCC at 1559, TGTGCC at 1223, TGTGAC at 1139, CGCACA at 1020, TGTGCG at 987, TGTGCG at 887, TGTGCG at 803, TGTGCA at 569, AATGAA at 525, TCTGGC at 441, TCTGCC at 399, TGTGAC at 346, TCTGAC at 236, TCCAGT at 153
Initiator-like elements	TTCTCT	Negative strand: AGAGAA at 4527, TTCTCT at 3380	-	Negative strand: TTCTCT at 4386 Positive strand: AGAGAA at 4387, AGAGAA at 3406	Negative strand: TTCTCT at 2826, TTCTCT at 2809 Positive strand: AGAGAA at 2827	-	Positive strand: AGAGAA at 2810, TTCTCT at 622	Negative strand: TTCTCT at 1990, TTCTCT at 139, TTCTCT at 119 Positive strand: AGAGAA at 3056
Inositol/choline-responsive elements (ICREs) (Schwank)	TYTTCACATGY contains the core sequence CANNTG	-	-	-	-	-	Positive strand: ACATTTGAAGA at 368	Negative strand: GCACCTGAAGA at 962, GCACCTGAAGA at 862
Inositol/choline-responsive elements (ICRE) (Case, Lopes)	CATGTGAAAT includes the canonical basic helix-loop-helix (bHLH) binding site CANNTG (Lopes et al. 1991)	-	-	-	Positive strand: AGCTGAAAT at 2747	-	-	-
Interferon regulatory factor (IRF3)	GCTTTCC	-	-	-	-	-	Positive strand: GGAAAGC at 1678	Negative strand: GCTTTCC at 1097
IFN-stimulated response elements (ISREs) (Lu)	GAAANNGAAA	-	-	-	-	-	Negative strand: TTTCGTTTTC at 2477	Negative strand: GAAATAGAAA at 2629
IRS consensus (Fujii)	AANNGAAA	Negative strand: TTTCTTTT at 4395, TTTCTTTT at 4390, TTTCTTTT at 4383, TTTCTTTT at 4086 Positive strand: AAAAGAAA at 4394, AAAAGAAA at 4389, AAAAGAAA at 4382, AATAGAAA at 4081	Negative strand: TTTCTTTT at 2839, TTTCTCTT at 2827, TTTCTTTT at 2822 Positive strand: AAAAGAAA at 2838, AAAAGAAA at 2821	Negative strand: TTTCTCTT at 4387	Negative strand: TTTCTCTT at 2810, TTTCTTTT at 2805 Positive strand: AAAAGAAA at 2800	-	Negative strand: TTTCGTTT at 2481, TTTCGTTT at 2475, TTTCTTTT at 2056, AATAGAAA at 1733, TTTCCTTT at 1642 Positive strand: AAAAGAAA at 2055, AAGGGAAA at 1660, AAAGGAAA at 1642, AAAAGAAA at 1630, AAATGAAA at 1582, AAAAGAAA at 226, TTTCTTTT at 26	Negative strand: AAAGGAAA at 2831, AATAGAAA at 2629, TTTCTTTT at 2279 Positive strand: TTTCCTTT at 2831, AAAAGAAA at 2278, AACGGAAA at 134
Tryptophan residues (Lu)	GAAA	Negative strand: TTTC at 4504, GAAA at 4461, TTTC at 4391, TTTC at 4386, TTTC at 4379, TTTC at 4082, GAAA at 3984, TTTC at 3923, TTTC at 3664, TTTC at 3440, TTTC at 3377, TTTC at 3344, GAAA at 3075, GAAA at 3018, TTTC at 2891, TTTC at 2857 Positive strand: GAAA at 4394, GAAA at 4389, GAAA at 4382, GAAA at 4085, GAAA at 4081, GAAA at 3922, TTTC at 3688, GAAA at 3663, GAAA at 3591, GAAA at 3507, GAAA at 3376, GAAA at 3342, GAAA at 3146, GAAA at 2967, GAAA at 2957, GAAA at 2926, TTTC at 2884	Negative strand: TTTC at 2835, TTTC at 2823, TTTC at 2818 Positive strand: GAAA at 2838, GAAA at 2831, GAAA at 2821, GAAA at 2814, TTTC at 1603, TTTC at 1380, TTTC at 22	Negative strand: TTTC at 4383 Positive strand: GAAA at 4382	Negative strand: TTTC at 2806, TTTC at 2801, TTTC at 2797 Positive strand: GAAA at 2804, GAAA at 2800, GAAA at 2746, GAAA at 2619	Negative strand: GAAA at 4091 Positive strand: GAAA at 4207	Negative strand: GAAA at 2552, TTTC at 2477, TTTC at 2471, GAAA at 2216, TTTC at 2174, GAAA at 2099, TTTC at 2052, GAAA at 1790, GAAA at 1733, GAAA at 1687, TTTC at 1677, TTTC at 1638, TTTC at 1627, TTTC at 1548, GAAA at 1418, TTTC at 1399, GAAA at 1145, TTTC at 1106, TTTC at 943, GAAA at 681, GAAA at 545, GAAA at 408, GAAA at 347, TTTC at 223, TTTC at 184, TTTC at 136, TTTC at 104, TTTC at 93, TTTC at 54, GAAA at 47, GAAA at 25 Positive strand: GAAA at 2505, GAAA at 2458, GAAA at 2282, GAAA at 2157, GAAA at 2055, GAAA at 1855, GAAA at 1676, GAAA at 1660, GAAA at 1642, GAAA at 1630, GAAA at 1625, GAAA at 1582, GAAA at 1212, GAAA at 494, GAAA at 473, GAAA at 357, GAAA at 312, GAAA at 303, GAAA at 226, GAAA at 135, GAAA at 126, GAAA at 102, GAAA at 52	Negative strand: AAAG at 3928, GAAA at 3926, AAAG at 3919, GAAA at 3918, GAAA at 3794, AAAG at 3597, GAAA at 3596, GAAA at 3165, AAAG at 3064, AAAG at 2918, GAAA at 2917, GAAA at 2831, AAAG at 2827, AAAG at 2708, TTTC at 2645, GAAA at 2629, GAAA at 2623, AAAG at 2535, TTTC at 2301, TTTC at 2275, TTTC at 2263, TTTC at 2164, GAAA at 2146, AAAG at 2004, TTTC at 1978, TTTC at 1749, TTTC at 1600, TTTC at 1180, TTTC at 1096, AAAG at 1090, GAAA at 1089, GAAA at 290, TTTC at 136 Positive strand: GAAA at 3945, TTTC at 3928, TTTC at 3919, TTTC at 3597, GAAA at 3397, TTTC at 3064, TTTC at 2918, TTTC at 2827, TTTC at 2708, GAAA at 2585, TTTC at 2535, GAAA at 2278, GAAA at 2273, GAAA at 2163, TTTC at 2004, GAAA at 1981, GAAA at 1830, GAAA at 1746, GAAA at 1599, GAAA at 1179, GAAA at 1095, TTTC at 1090, GAAA at 134, GAAA at 110
Jasmonic acid-responsive elements (JAREs)	TGACG	Negative strand: TGACG at 4337, TGACG at 4329, CGTCA at 4317, TGACG at 4314, TGACG at 3851, CGTCA at 3600, CGTCA at 3478	-	Positive strand: TGACG at 4340	Negative strand: TGACG at 2758, CGTCA at 2737	-	Negative strand: TGACG at 2423, CGTCA at 2402, CGTCA at 2083, TGACG at 1997, CGTCA at 1976, TGACG at 1493, CGTCA at 1472, CGTCA at 1323, CGTCA at 1032 Positive strand: CGTCA at 1511, TGACG at 309	Negative strand: CGTCA at 2423, TGACG at 1834, CGTCA at 1184. Positive strand: CGTCA at 3962, CGTCA at 3461, TGACG at 3319, CGTCA at 3281, CGTCA at 3232, TGACG at 2822, CGTCA at 2328, TGACG at 2203, CGTCA at 2065, TGACG at 2042, TGACG at 1504, TGACG at 1000, TGACG at 900, TGACG at 748, TGACG at 237
Krüppel-like factors	GGGNN(G/T)(G/T)(G/T)	Negative strand: GGGTCGGG at 4482, GGGTAGGT at 4457, GGGTCTTG at 4450, GGGTTGTG at 3981, GGGTATGG at 3858, CACTACCC at 3800, GGGACTTG at 3783, GGGTCGTG at 3733, ACCAACCC at 3607, CACCACCC at 3193, GGGTTGTT at 3139, GGGTCGTG at 3072, CCCGACCC at 3042 Positive strand: AACTGCCC at 3853, AACAGCCC at 3728, GGGCCTTG at 3570, GGGTGTGG at 3186, GGGCGTGG at 3047, GGGGCTGG at 3041	Positive strand: AACAACCC at 2845	Negative strand: GGGGCGGG at 4440, GGGAGGGG at 4435, GGGGCGGG at 4430, GGGTCTGG at 4416, CACCGCCC at 4292 Positive strand: CCAGACCC at 4417, GGGTCTGT at 4332	Positive strand: GGGAGTTG at 2704, AAACCCCC at 2624	Negative strand: CCCTGCCC at 4233 Positive strand: GGGACTGG at 4216, AACGACCC at 4178	Negative strand: GGGTTGTG at 2549, CACCACCC at 1904, GGGTCGTG at 1787, GGGCAGTT at 1512, CACCGCCC at 1251, GGGTCGTG at 1142, GGGTCGTG at 678, CCCGGCCC at 514, GGGTCGTG at 405, CAACTCCC at 88 Positive strand: GGGCGTGG at 1897, GGGCGTGG at 1244, GGGCCGGG at 514, GGGAAGTT at 83	Negative strand: GGGAGGGG at 3981, ACCTCCCC at 3555, GGGTGGGG at 3542, CCCGTCCC at 3204, GGGCAGGG at 2297, GGGAGGGG at 2291, GGGGAGGG at 2290, GGGACTTT at 2273, CACCCCCC at 2021, CCACCCCC at 2020, CCCACCCC at 2019, ACCCACCC at 2018, ACAGTCCC at 1827, GGGTGTGG at 1805, CCCTTCCC at 1071, GGGACTGT at 916, GGGACTGT at 816, GGGGAGTG at 495, GGGCGTTG at 448, GGGCTGGG at 418, GGGGCTGG at 417, GGGACGGG at 412, GGGCCTGG at 286, GGGCTGTG at 265, GGGGCTGT at 264, GGGCATTG at 23 Positive strand: GGGCCGTG at 4005, ACACTCCC at 3906, CACCACCC at 3817, GGGAGTGT at 3505, CACGTCCC at 3467, GGGAGTGT at 3209, GGGTCTTG at 3093, CACAACCC at 2817, AAACCCCC at 2286, AAAACCCC at 2285, AAAAACCC at 2284, ACAGACCC at 1865, CACGTCCC at 1789, CCACGCCC at 1765, AAAAGCCC at 1752, AACGCCCC at 1708, GGGACTGG at 1662, ACCGCCCC at 1027, CACCGCCC at 1026, AACGTCCC at 659, CACGCCCC at 491, CCACGCCC at 490, ACCCGCCC at 407, GGGTGGGT at 71
Leu3 transcription factors	(C/G)C(G/T)NNNN(A/C)G(C/G)	Negative strand: GCGAACTCGG at 4297, CCGAGTACGG at 4118, CCGACTCCGC at 3998, CCGTCGTAGG at 3903, CCTGGTCCGG at 3873, CCGACTCCGC at 3089 Positive strand: CCTCAGGAGC at 4439, GCTACTCAGG at 4138, GCTGAGGCGG at 3999, GCTACTCAGG at 3217, GCTGAGGCGG at 3090	-	Negative strand: CCTGGGGCGG at 4429 Positive strand: CCTCCCCCGC at 4438, CCTCACTCGC at 4353	Negative strand: CCGTGTACGG at 2669 Positive strand: GCTACACAGG at 2689	-	Negative strand: CCGAGTACGG at 2535, CCGACTCCGC at 2230, CCGAGTGCGG at 2208, CCGCCCACGG at 1255, GCTCAAACGC at 1188, CCGTGTGCGG at 964, GCGAGGTCGG at 896, CCTCCAACGC at 864, CCGAGTGCGG at 664 Positive strand: GCTACTCCGG at 2354, CCTGGACAGC at 2273, GCTGAGGCGG at 2231, CCGGGTGCGG at 2197, GCGACAGAGC at 2019, GCTACTCAGG at 1275, GCTAATCAGG at 984, GCGCTCCAGC at 895, GCTACTAAGG at 818, CCTGACCAGC at 737, CCTGGGCCGG at 513, CCGGGTGCGG at 380	Negative strand: CCTCAGCAGC at 4026, CCTGGGAAGC at 3763, CCTGGGCAGC at 2896, CCTGGCCAGG at 2574, CCTCCCAAGC at 2399, CCTGTGTAGG at 2255, CCGAGGACGC at 1671, GCGAGTGCGG at 1590, GCTCTTAAGC at 1540, CCGCGGCAGC at 1441, CCTTCCGCGG at 1437, CCGCGGCAGC at 1341, CCTTCCGCGG at 1337, CCTACTGAGC at 1288, CCGAGTGCGG at 1170, CCGCGAGAGC at 1105, CCGAGTGCGG at 1086, CCGACTGCGG at 1002, GCGCACTCGC at 689, CCTTCCGCGC at 681, CCGAGTGCGG at 582, CCGCAGACGG at 399, CCGAGGGAGG at 314, GCTCCAGAGG at 17 Positive strand: CCGTGAGAGG at 4010, CCGAAGTCGG at 3998, CCGATATCGG at 3702, CCGCCAACGG at 3492, CCTTACGAGG at 3370, CCGCACTCGG at 2558, CCGTCCGAGG at 1909, CCGCGGGAGG at 1773, GCGGCCACGC at 1763, CCTCCAGCGC at 1689, GCTCCTGCGG at 1672, CCGCTCACGC at 1589, GCGGAAGCGG at 1308, CCGCGTGCGG at 1302, GCTCACGCGG at 1162, GCTCTCGAGC at 1108, GCGTGTGCGG at 804, GCGCGTGAGC at 688, CCGGAAGCGG at 595, CCTCGCTCGG at 432, CCTTTTGAGG at 295, CCGGTCCAGG at 218
-35 sequence	TTGACA	Negative strand: TTGACA at 4399	-	-	-	-	Negative strand: TTGACA at 477	-
M-boxes	TCACATGA	-	-	-	-	-	Negative strand: TCACATGA at 325	-
Met31ps	AAACTGTG	Positive strand: AAACTGTG at 4400	-	-	-	-	-	-
Metal responsive elements (MRE)	TGC(A/G)C(A/C/G/T)C	Positive strand: TGCACTC at 4341, TGCACTC at 3290, GTGTGCA at 2863	-	-	Positive strand: TGCACCC at 2762	-	Negative strand: GAGTGCA at 1772, GTGTGCA at 531 Positive strand: TGCACTC at 2427, TGCACTC at 2001, GAGTGCA at 1470, TGCACTC at 1348, TGCGCTC at 891	Negative strand: GGGTGCA at 3883, TGCACCC at 3323, TGCACAC at 2963, GGGTGCA at 2800, GAGTGCA at 2326, GAGTGCA at 1786, TGCGCCC at 1657, GTGCGCA at 1523, TGCGCCC at 1499, TGCACTC at 1473, TGCGCCC at 1399, TGCACTC at 1373, TGCGCCC at 1247, TGCACAC at 1221, GCGTGCA at 1218, GGGCGCA at 976, GGGCGCA at 876, GCGCGCA at 684, TGCACAC at 549, GCGTGCA at 546, TGCGCCC at 453 Positive strand: TGCGCCC at 972, TGCGCCC at 872
Middle sporulation element (MSE) (Branco)	ACACAAA	Negative strand: TTTGTGT at 3513	-	-	-	-	Negative strand: TTTGTGT at 1541	Positive strand: TTTGTGT at 2835
Midsporulation element (MSE) (Ozsarac)	C(A/G)CAAA(A/T)	Negative strand: TTTTGTG at 3512 Positive strand: CACAAAA at 3767	-	-	-	-	Positive strand: CGCAAAA at 164	-
Multicopy inhibitor of the GAL1 promoter (MIG1)	(C/G)(C/T)GGGG	Negative strand: GTGGGG at 4445, GTGGGG at 3058 Positive strand: CCCCAG at 4447, CTGGGG at 3037	-	Positive strand: CCCCGC at 4428, CCCCAG at 4413, CCCCAC at 4398, GTGGGG at 4327, CCCCGG at 4304, GTGGGG at 4285 Negative strand: CTGGGG at 4426, CTGGGG at 4411, GTGGGG at 4396, CCCCAG at 4329, CCCCAC at 4287	Negative strand: GTGGGG at 2763 Positive strand: CCCCAG at 2765	Positive strand: CTGGGG at 4218	Negative strand: GTGGGG at 750, CCCCAG at 205	Positive strand: GTGGGG at 3614, GTGGGG at 2019, CCCCAG at 1957, CCCCGC at 1792, CCCCAG at 1710, CCGGGG at 391, CCGGGG at 373, CCCCGG at 248, CCGGGG at 201 Negative strand: GTGGGG at 4042, CCCCGG at 4002, CCCCAC at 3941, CCCCGG at 3557, GTGGGG at 3542, GTGGGG at 3451, CCCCAG at 3015, CTGGGG at 1955, CCCCAG at 1892, CTGGGG at 1866, GCGGGG at 1708, GCGGGG at 1027, GCGGGG at 491, CCCCGC at 393, CCCCGG at 375, CTGGGG at 349, CTGGGG at 279, CCCCAG at 203, GTGGGG at 55
Musashi binding elements (MBEs)	(G/A)U1–3AGU	Negative strand: ACTAC at 3807, ACTAC at 3798, GTAGT at 3616, ACTAT at 3544, ACTAT at 3535, GTAGT at 3521, GTAGT at 3418, GTAGT at 3415, GTAGT at 3394, ACTAT at 3360, GTAGT at 2944, GTAGT at 2941, GTAGT at 2888 Positive strand: GTAGT at 4124, ATAGT at 4047, ACTAC at 3736, ACTAT at 3526, ACTAT at 2975	-	Positive strand: GTAGT at 4362	Positive strand: ACTAAAT at 2636	Negative strand: ATTTAGT at 4137 Positive strand: ACTAAT at 4164, ACTAAT at 4157, ATTAGT at 4147, ACTAAAT at 4135, ATAGT at 4124, GTAGT at 4116, GTAGT at 4085	Negative strand: ACTAT at 1702, ACTAT at 1665, ATTAGT at 982, ACTAT at 353, ACTAC at 142 Positive strand: GTAGT at 2541, ATAGT at 2499, GTAGT at 2340, ATAGT at 1704, ATAGT at 469, ATAGT at 251, ACTAT at 210, ATTAGT at 155	Negative strand: ACTAC at 2427, ATAGT at 1839 Positive strand: ACTAC at 3845, GTAGT at 3251, ACTAAC at 2677, GTTAGT at 2338, ACTAC at 2143
Myeloblastosis recognition element (MRE)	A(A/C)C(A/T)A(A/C)C	Negative strand: GGTAGGT at 4457, ACCAACC at 3946, ACCAACC at 3606, GGTTGTT at 3139	Positive strand: AACAACC at 2844	-	-	-	Negative strand: GTTTGTT at 2488, GTTTGTT at 2484, GTTTGTT at 1392 Positive strand: AACAAAC at 2511, AACAAAC at 2486, AACAAAC at 1587, AACAAAC at 1390	Positive strand: GGTAGGT at 3109 Negative strand: ACCAAAC at 3176
Myocyte enhancer factors (MEFs)	(C/T)TA(A/T)(A/T)(A/T)(A/T)TA(A/G)	Negative strand: TTATTATTAA at 4226	-	-	-	Positive strand: CTAATATTAA at 4169	Negative strand: CTATATATAA at 1601	Negative strand: CTAATTTTAA at 2443
Nanos/Pumilio response element (PREs)	TGTAAAT	Negative strand: TGTAAAT at 4535	-	-	-	-	-	-
N-boxes (Lee)	CCGGAA	Negative strand: TTCCGG at 4167, CCGGAA at 3569	-	-	-	Negative strand: TTCCGG at 4244	-	Positive strand: CCGGAA at 1797, CCGGAA at 1515, TTCCGG at 1513, CCGGAA at 1431, TTCCGG at 1429, CCGGAA at 1331, TTCCGG at 1329, CCGGAA at 1263, TTCCGG at 1261, CCGGAA at 1011, TTCCGG at 1009, CCGGAA at 927, TTCCGG at 925, CCGGAA at 827, TTCCGG at 825, CCGGAA at 675, TTCCGG at 673, CCGGAA at 591, TTCCGG at 589, TTCCGG at 212
N-boxes (Bai)	CACGAG	Negative strand: CACGAG at 4403, CTCGTG at 3914 Positive strand: CACGAG at 4472, CACGAG at 3232	-	Negative strand: CTCGTG at 4376	-	-	Positive strand: CACGAG at 1182, CACGAG at 708, CACGAG at 572, CACGAG at 435	Negative strand: CACGAG at 243 Positive strand: CTCGTG at 3739, CACGAG at 3152, CACGAG at 2090, CTCGTG at 1627, CTCGTG at 1207, CTCGTG at 955, CTCGTG at 855
N-boxes (Gao)	CACGGC or CACGAC, CACG(A/G)C	Negative strand: CACGAC at 3956, GTCGTG at 3733, GTCGTG at 3072	-	-	-	-	Negative strand: GTCGTG at 1787, GTCGTG at 1142, GCCGTG at 959, GTCGTG at 678, GTCGTG at 542, GTCGTG at 405	Negative strand: GCCGTG at 3812, CACGGC at 1699, CACGGC at 980, CACGGC at 880, GTCGTG at 79 Positive strand: GCCGTG at 4005, GTCGTG at 3043, GTCGTG at 2200, GTCGTG at 2104, GCCGTG at 1639, GTCGTG at 1459, GTCGTG at 1359, GTCGTG at 1123, GTCGTG at 1039, GTCGTG at 787, GTCGTG at 619
N-boxes (Leal)	CACNAG	Negative strand: CACGAG at 4403, CTAGTG at 4159, CTAGTG at 4008, CTCGTG at 3914, CACCAG at 3812, CTGGTG at 3763, CTTGTG at 3669, CTAGTG at 3490, CTAGTG at 3278, CTAGTG at 3099 Positive strand: CACGAG at 4472, CACAAG at 3634, CACTAG at 3493, CACTAG at 3369, CACGAG at 3232	-	Negative strand: CTCGTG at 4376 Positive strand: CACCAG at 4379	-	Negative strand: CTGGTG at 2812	Negative strand: CTAGTG at 2576, CTAGTG at 2415, CTAGTG at 2241, CTGGTG at 2123, CTAGTG at 1989, CACTAG at 1481, CTAGTG at 1169, CTAGTG at 879, CTAGTG at 705, CTAGTG at 527, CTAGTG at 432 Positive strand: CTGGTG at 2328, CACAAG at 2244, CACGAG at 1182, CACGAG at 708, CACGAG at 572, CACGAG at 435	Negative strand: CACCAG at 3719, CACCAG at 2995, CACTAG at 2638, CACCAG at 2604, CTAGTG at 2169, CACCAG at 1630, CACCAG at 1462, CACCAG at 1362, CTGGTG at 1142, CACCAG at 1126, CTGGTG at 781, CACCAG at 706, CACCAG at 622, CACGAG at 243, CTGGTG at 104 Positive strand: CTCGTG at 3739, GACCAC at 3716, CACGAG at 3152, GAACAC at 3095, CACCAG at 2940, CACTAG at 2513, CACTAG at 2377, CACGAG at 2090, GAGCAC at 1627, GAGCAC at 1207, GAGCAC at 955, GAGCAC at 855, CACAAG at 107
Non-DiTyrosine 80 transcription factor DNA binding domain (Ndt80)	(A/G/T)NC(A/G)CAAA(A/T)	Negative strand: TTTTGTGTT at 3514 Positive strand: ACCACAAAA at 3767	-	-	-	-	-	-
Nuclear factor of activated T cells (NFATs)	GGAAAA	Negative strand: TTTTCC at 3441, TTTTCC at 3345 Positive strand: GGAAAA at 2968, GGAAAA at 2927	-	-	-	-	Negative strand: TTTTCC at 1107, TTTTCC at 105 Positive strand: GGAAAA at 2459	Negative strand: GGAAAA at 291 Positive strand: GGAAAA at 135
Nutrient-sensing response element 1	GTTTCATCA	-	-	-	-	-	-	Negative strand: ACTACTTTG at 2147
Oaf1 transcription factor	CGGN3TNAN9-12CCG	-	-	-	-	-	Negative strand: CGGTCATGAAACCCTCCGACTCCG at 2229	Positive strand: CGGACGTGAGACCGCTCTCCG at 1484, CGGACGTGAGACCGCTCTCCG at 1384
ORESARA1 (ORE1) (Matallana)	(A/C/G)(A/C)GT(A/G)N5,6(C/T)AC(A/G)	Negative strand: GCGTAGAAGACACA at 3558, AAGTAGTTTCTACG at 2895	-	-	-	-	Positive strand: ACATCCTCAAATGAA at 1581, CAGTGGATCACACG at 530, GCACATAATATGAG at 275	Negative strand: CCGTGGTGGGTCACA at 3822, GCACCGGCGCGTGCA at 1218, GCATCGGCGCGTGCA at 546 Positive strand: GCGTAGAGGGTACA at 3336
ORESARA1 (ORE1) (Olsen)	T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T)	Negative strand: TGACGTGAG at 4341, TAACGTGAG at 3290 Positive strand: ATCACGCCA at 3282	-	-	-	-	Negative strand: TGACGTGAG at 2427, TGACGTGAG at 2001, TAACGTGTT at 1720, CTCACGTCA at 1472, TAACGTGAG at 1348 Positive strand: CTCACGCCA at 2209, ATCACGCCA at 1993, CACACGTAA at 533	Positive strand: TACACGTCA at 3962, TTACGTAAG at 3073, CTTACGTAA at 3072, CTCACGTCA at 2328, TGACGTAAG at 2207, TGGCGTACG at 2154
p53 response elements	(A/G)(A/G)(A/G)C(A/T)(A/T)G(C/T)(C/T)(C/T)	Positive strand: AGACAAGCTT at 4186	-	-	-	-	Positive strand: AGACTTGCCT at 1621, AGGCAAGCCT at 457	-
p53 response elements (Long1)	CAGGCCC	-	-	-	-	-	-	Negative strand: GGGCCTG at 285, CAGGCCC at 93 Positive strand: GGGCCTG at 745
p53 response elements (Long2)	GGGCGTG	Positive strand: GGGCGTG at 3046	-	-	-	-	Positive strand: GGGCGTG at 1896, GGGCGTG at 1243	Negative strand: GGGCGTG at 1719 Positive strand: CACGCCC at 1765, CACGCCC at 1591, CACGCCC at 490
P-box (Mena)	(A/T)AAAG	Negative strand: CTTTT at 4395, CTTTT at 4390, CTTTT at 4383, TAAAG at 3688, TAAAG at 2884 Positive strand: AAAAG at 4391, AAAAG at 4386, AAAAG at 4379, AAAAG at 3440, AAAAG at 3344, CTTTT at 3019, TAAAG at 2857	-	-	Positive strand: AAAAG at 2835, AAAAG at 2823, AAAAG at 2818, AAAAG at 2806, AAAAG at 2797	Positive strand: CTTTA at 4092	Negative strand: TAAAG at 1603, TAAAG at 1380, TAAAG at 22 Positive strand: AAAAG at 2477, AAAAG at 2471, TAAAG at 2174, AAAAG at 2052, CTTTA at 1734, AAAAG at 1627, TAAAG at 1548, CTTTT at 1419, AAAAG at 1399, AAAAG at 1106, AAAAG at 943, CTTTA at 348, AAAAG at 223, AAAAG at 184, AAAAG at 104, CTTTA at 48, AAAAG at 54, CTTTT at 26	Negative strand: AAAAG at 2708, CTTTA at 2586, CTTTT at 2279, CTTTT at 2274, AAAAG at 2004, CTTTT at 1747, CTTTT at 135 Positive strand: CTTTT at 3927, CTTTA at 3795, CTTTA at 3166, TAAAG at 2645, CTTTA at 2624, AAAAG at 2275, TAAAG at 1978, AAAAG at 1749, CTTTT at 291, AAAAG at 136
P-box (Motojima)	TGAGTTCA	-	-	-	-	-	Positive strand: TGAGTTCA at 1178	-
P-box (Yu)	GTAA(T/C)	Negative strand: ATTAC at 3658, GTAAT at 3436, GTAAC at 3285, GTAAT at 2951 Positive strand: GTAAT at 3973, ATTAC at 3469, GTAAT at 3064	-	Positive strand: GTAAC at 4310	Positive strand: GTAAT at 2675	-	Negative strand: GTAAC at 1343, GTAAC at 886, GTAAT at 173, GTAAT at 153 Positive strand: GTAAT at 2088, GTAAT at 1914, GTAAT at 1779, GTAAT at 1707, ATTAC at 1296, GTAAT at 1261, GTAAT at 1134, GTAAT at 804, GTAAT at 670, GTAAC at 613, GTAAT at 534, GTAAT at 397, GTAAT at 248	Negative strand, positive direction: GTAAC at 3732 Positive strand, positive direction: GTTAC at 2909, GTAAC at 2903, GTAAC at 1703, GTTAC at 227, GTAAC at 23
Peroxisome proliferator-activated receptor alpha	CGACCCC	Negative strand: CGACCCC at 3037	-	-	Positive strand: CCCCAGC at 2766	-	-	Positive strand: CGACCCC at 279
Pho4ps	CAC(A/G)T(T/G)	Negative strand: TTACAC at 4091, AACGTG at 3288, CACGTT at 2864 Positive strand: CACATT at 4533	-	-	Positive strand: CACATG at 2667	-	Negative strand: CACATT at 2087, TTACAC at 2064, AACGTG at 1718, CACGTT at 1536, AACGTG at 1346, AACGTG at 1338, CACATG at 797, CACATT at 612, CACATG at 324 Positive strand: CACGTT at 343	Negative strand: CATGTG at 3958, CACATG at 3956, CATGTG at 3902, CACATG at 3742, CACATG at 3707, CACATG at 2031, CACGTG at 570, AATGTG at 229 Positive strand: CACGTG at 3884, CACGTG at 2961, CACGTT at 2801, CACGTT at 2335, CACGTG at 1219, CACGTG at 547
Pollen1 elements	AGAAA	Negative strand: TTTCT at 4505, TTTCT at 4392, TTTCT at 4387, TTTCT at 4380, TTTCT at 4083, TTTCT at 3924, TTTCT at 3665, TTTCT at 3378, TTTCT at 2892 Positive strand: AGAAA at 4394, AGAAA at 4389, AGAAA at 4382, AGAAA at 4085, AGAAA at 4081, AGAAA at 3591, AGAAA at 3376, AGAAA at 3342	Negative strand: TTTCT at 2836, TTTCT at 2824, TTTCT at 2819 Positive strand: AGAAA at 2838, AGAAA at 2831, AGAAA at 2821, AGAAA at 2814	Negative strand: TTTCT at 4384 Positive strand: AGAAA at 4382	Negative strand: TTTCT at 2807, TTTCT at 2802, TTTCT at 2798 Positive strand: AGAAA at 2804, AGAAA at 2800	-	Negative strand: TTTCT at 2175, TTTCT at 2053, AGAAA at 1733, TTTCT at 1628, TTTCT at 1549, AGAAA at 1418, TTTCT at 1400, AGAAA at 347, TTTCT at 224, TTTCT at 55, AGAAA at 47, AGAAA at 25 Positive strand: AGAAA at 2505, AGAAA at 2055, AGAAA at 1630, TTTCT at 1604, AGAAA at 357, AGAAA at 303, AGAAA at 226, AGAAA at 135, AGAAA at 102, AGAAA at 52, TTTCT at 23	Negative strand: AGAAA at 3918, AGAAA at 2629, TTTCT at 2276, TTTCT at 2165, TTTCT at 1979, TTTCT at 137 Positive strand: TTTCT at 3929, AGAAA at 3397, TTTCT at 3065, AGAAA at 2585, AGAAA at 2278, AGAAA at 1981, AGAAA at 110
Polycomb response elements (PRE)	GCCAT	Positive strand: GCCAT at 3685, ATGGC at 3629, GCCAT at 3283, ATGGC at 3005, ATGGC at 2907	-	-	-	-	Positive strand: ATGGC at 2153, ATGGC at 1949, ATGGC at 1743, ATGGC at 954, GCCAT at 38	Positive strand: TACCG at 2160
Pribnow boxes	TATAAT	Negative strand: TATAAT at 3468, TATAAT at 3454	-	-	-	-	Negative strand: ATTATA at 603, ATTATA at 272	Negative strand: TATAAT at 729, ATTATA at 727
Prolamin boxes	TG(A/T)AAAG	Negative strand: TGTAAAG at 2884	-	-	-	-	Positive strand: TGAAAAG at 1627	Negative strand: TGAAAAG at 3928 Positive strand: TGAAAAG at 2275
Pyrimidine boxes	CCTTTT	Negative strand: CCTTTT at 2968, CCTTTT at 2927 Positive strand: AAAAGG at 3441, AAAAGG at 3345	-	-	-	-	Negative strand: CCTTTT at 2459 Positive strand: AAAAGG at 1107, AAAAGG at 105	Negative strand: CCTTTT at 135 Positive strand: CCTTTT at 291
Q elements See Retinoic acid response element	AGGTCA	Positive strand: AGGTCA at 4307	-	Negative strand: AGGTCA at 4269	-	-	Negative strand: AGGTCA at 1532, AGGTCA at 1352 Positive strand: AGGTCA at 2585, AGGTCA at 2248, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439	Negative strand: TGACCT at 4019, TGACCT at 3785, AGGTCA at 2220, AGGTCA at 153
Quinone reductase response element (QRDRE) (Yao)	TCCCCT of TCCCCTTGCGTG	-	-	-	-	-	-	Negative strand: TCCCCT at 1073 Positive strand: TCCCCT at 3665, TCCCCT at 2657, TCCCCT at 321
Rap1 reduced consensus	(A/G)(A/C)ACCC(A/G)N(A/G)C(A/C)(C/T)(A/C)	-	-	-	-	-	-	Positive strand: GAACCCACACCTC at 1807
Reb1 bound and exact occurrences	TTACCC(G/T)	Negative strand: TTACCCT at 3661	-	-	-	-	-	Positive strand: TTACCCT at 3170, TTACCCG at 2912
Retinoic acid response element	AG(A/G)TCA	Negative strand: TGATCT at 3463	-	-	-	-	Positive strand: AGATCA at 2414, AGATCA at 1988, TGATCT at 1482, AGATCA at 878, AGATCA at 590	Positive strand: AGATCA at 2168
Glucose transporter gene repressor (Rgt1)	CGG(A/G)(A/T)N(A/T)(A/T)	Negative strand: ATTTTCCG at 3442	-	-	Positive strand: CGGAAGTT at 2732	-	Negative strand: TTTTCCG at 1108, AACTCCCG at 89 Positive strand: CGGGAAAA at 2459	Negative strand: ATGAGGGC at 3480, TTATAGGC at 2551 Positive strand: CGGGTCAA at 3380
classic RORE motif (RORE)	A(A/T)NTAGGTCA	-	-	-	-	-	Negative strand: ATATAGGTCA at 1532	-
variant RORE motif	C(T/A)(G/A)GGNCA	Negative strand: CTGGGACA at 4369, CTGGGACA at 4208	-	-	-	-	Positive strand: CAAGGTCA at 2248, CAAGGGCA at 1821	Negative strand: CTGGGACA at 3530, TGCCCCAG at 3015, TGGCCCAG at 1741
R response elements (RRE)	CATCTG	Negative strand: CAGATG at 4212, CAGATG at 2988 Positive strand: CAGATG at 3919, CAGATG at 3627, CAGATG at 3620	-	-	-	-	Negative strand: CAGATG at 1224, CAGATG at 481	Negative strand: CAGATG at 3475, CATCTG at 3404
Serum response elements (SRE) see CArG boxes	ACAGGATGT	-	-	-	-	-	-	Negative strand: ACAGGATGT at 3575
Servenius sequences	GGACCCT	Negative strand: GGACCCT at 4548, GGACCCT at 4496, GGACCCT at 4302	-	-	-	-	Negative strand: GGACCCT at 1961, GGACCCT at 1017	Negative strand: GGACCCT at 189 Positive strand: GGACCCT at 3760, GGACCCT at 288
Sp1-box 1 (Motojima)	GGGGCT	Negative strand: AGCCCC at 3037 Positive strand: GGGGCT at 3039	-	Positive strand: AGCCCC at 4426, AGCCCC at 4411	-	Negative strand: AGCCCC at 4218	-	Negative strand: GGGGCT at 3983, GGGGCT at 1029, GGGGCT at 415, GGGGCT at 262 Positive strand: AGCCCC at 1955, AGCCCC at 1866, GGGGCT at 576, AGCCCC at 349, AGCCCC at 279
Sp1-box 2 (Motojima)	CTGCCC	Positive strand: CTGCCC at 3853	-	-	-	Negative strand: CTGCCC at 4233	Negative strand: GGGCAG at 1510, GGGCAG at 753 Positive strand: GGGCAG at 1822	Negative strand: GGGCAG at 3472, GGGCAG at 2895, GGGCAG at 2295, CTGCCC at 741 Positive strand: GGGCAG at 3202, CTGCCC at 412
Sp-1 (Sato)	CCGCCCC	-	-	Negative strand: GGGGCGG at 4439, GGGGCGG at 4429	-	Positive strand: GGGGCGG at 4238	-	Negative strand: GGGGCGG at 1793, GGGGCGG at 353 Positive strand: CCGCCCC at 1027
Sp1 (Yao)	GCGGC	-	-	-	Negative strand: GCCGC at 2726 Positive strand: GCGGC at 2725	-	Negative strand: GCGGC at 1154 Positive strand: GCGGC at 1753, GCGGC at 957	Negative strand: GCCGC at 3226, GCCGC at 2355, GCGGC at 1902, GCGGC at 1794, GCCGC at 1756, GCCGC at 1648, GCGGC at 1637, GCGGC at 1582, GCGGC at 1438, GCGGC at 1423, GCGGC at 1338, GCGGC at 1323, GCGGC at 1255, GCGGC at 1171, GCGGC at 1148, GCGGC at 1034, GCGGC at 1003, GCCGC at 903, GCGGC at 751, GCGGC at 721, GCGGC at 667, GCGGC at 637, GCGGC at 583, GCGGC at 499, GCGGC at 354, GCGGC at 332 Positive strand: GCCGC at 1918, GCGGC at 1758, GCCGC at 1583, GCCGC at 1548, GCCGC at 1296, GCCGC at 1212, GCGGC at 1163, GCGGC at 1079, GCCGC at 1044, GCCGC at 638, GCCGC at 540, GCCGC at 355
SP1 (Zhang)	(G/T)GGGCGG(G/A)(G/A)(C/T)	-	-	-	-	-	-	Negative strand: TGGGCGGGAC at 409
STAT5	TTCNNNGAA	Positive strand: TTCCCTGAA at 3782, TTCGTTGAA at 3506	-	-	-	Negative strand: TTCCGGGAA at 4247	-	Positive strand: TTCCATGAA at 128
Sterile 12 (Ste12p)	TGAAAC	Negative strand: TGAAAC at 4462, TGAAAC at 3985, TGAAAC at 3076 Positive strand: TGAAAC at 3147	-	-	Positive strand: TGAAAC at 2620	-	Negative strand: TGAAAC at 2553, TGAAAC at 2217, TGAAAC at 2100, TGAAAC at 1791, TGAAAC at 1688, TGAAAC at 1146, TGAAAC at 682, TGAAAC at 546, TGAAAC at 409 Positive strand: TGAAAC at 2283, TGAAAC at 1856, TGAAAC at 1583, TGAAAC at 1213, TGAAAC at 474, TGAAAC at 127	Negative strand: GTTTCA at 2302, GTTTCA at 2264, TGAAAC at 2147
Stress-response elements (STREs)	CCCCT	Negative strand: CCCCT at 2924 Positive strand: CCCCT at 3059	-	Negative strand: AGGGG at 4435	-	-	Positive strand: CCCCT at 617	Negative strand: AGGGG at 3981, AGGGG at 3664, AGGGG at 3654, CCCCT at 3615, AGGGG at 3468, AGGGG at 2656, AGGGG at 2291, AGGGG at 1790, CCCCT at 1073, AGGGG at 320, AGGGG at 259, AGGGG at 246, CCCCT at 86 Positive strand: CCCCT at 4043, CCCCT at 3665, CCCCT at 3656, AGGGG at 3555, CCCCT at 3543, CCCCT at 3452, AGGGG at 3199, AGGGG at 3078, CCCCT at 2657, CCCCT at 2287, CCCCT at 1867, AGGGG at 1072, CCCCT at 492, CCCCT at 321, AGGGG at 174, AGGGG at 84, CCCCT at 57
Sucrose boxes	NNAATCA	Negative strand: TGATTCC at 3474, TGATTTT at 3163, TGATTCG at 3032, TGATTCG at 2915 Positive strand: AGAATCA at 3237	-	-	Negative strand: TGATTGT at 2678, TGATTTA at 2636 Positive strand: GAAATCA at 2749, AAAATCA at 2648	Negative strand: TGATTAT at 4165, TGATTAT at 4158, TTAATCA at 4147, TGATTTA at 4135 Positive strand: TAAATCA at 4137	Negative strand: TGATTTT at 2299, TGATTTC at 2174, TGATTTT at 1872, TGATTCC at 818, TGATTTT at 763, TGATTTT at 629, GTAATCA at 155 Positive strand: CTAATCA at 982, AGAATCA at 293, AGAATCA at 198	Negative strand: GCAATCA at 2338
TACTAAC boxes	TACTAA(C/T)	-	-	-	-	Positive strand: TACTAAT at 4157, ATTAGTA at 4148	-	-
TAGteams	CAGGTAG	-	-	-	-	-	-	Negative strand: CAGGTAG at 4035, CTACCTG at 1198
Tapetum boxes	TCGTGT	Negative strand: ACACGA at 4402, TCGTGT at 3915 Positive strand: ACACGA at 4471	-	-	-	-	-	Negative strand: TCGTGT at 80 Positive strand: TCGTGT at 3740
TATA boxes	TATA(A/T)A(A/T)(A/G)	Negative strand: TTTATATA at 2871 Positive strand: TATATAAA at 2874	-	-	-	-	Negative strand: TATATAAA at 1602, TATATATA at 1600 Positive strand: TATAAAAG at 223, TTTTTATA at 219, TATAAAAG at 184	-
TAT boxes (Yang)	TATAAAA	Negative strand: TTTTATA at 2869, TATAAAA at 2853	-	-	-	-	Negative strand: TTTTATA at 1740 Positive strand: TATAAAA at 222, TTTTATA at 219, TATAAAA at 183	-
TAT boxes (Fan)	TATCCAT	Negative strand: ATGGATA at 2996	-	-	-	-	-	-
T boxes (Conlon)	TCACACCT	Positive strand: TCACACCT at 3968	-	-	-	-	Positive strand: TCACACCT at 1129	-
T boxes (Zhang)	AACGTT	-	-	-	-	-	-	Positive strand: AACGTT at 2691, AACGTT at 1614
TEA consensus sequences	CATTC(C/T)	Negative strand: CATTCT at 3893 Positive strand: GGAATG at 4554, AGAATG at 3003	-	-	-	-	Negative strand: CATTCT at 2503 Positive strand: AGAATG at 1947	Negative strand: AGAATG at 3834, GGAATG at 3566, GGAATG at 3440, GGAATG at 3366, CATTCT at 3074, AGAATG at 3068, AGAATG at 2840, CATTCC at 2208, AGAATG at 1419, AGAATG at 1319 Positive strand: CATTCC at 2457, AGAATG at 1887, AGAATG at 523
Tec1	GAATGT	-	-	-	-	-	-	Positive strand: ACATTC at 2456
Telomeric repeat DNA-binding factors (TRFS)	TTAGGG	Negative strand: TTAGGG at 3976, TTAGGG at 3067	-	-	Negative strand: TTAGGG at 2678	-	Negative strand: TTAGGG at 1917, TTAGGG at 1782, TTAGGG at 1264, TTAGGG at 1137, TTAGGG at 807, TTAGGG at 673, TTAGGG at 400	Negative strand: TTAGGG at 2766, TTAGGG at 2669 Positive strand: CCCTAA at 2545
Thyroid hormone response elements (TREs)(THRs)	AGGTCA	Positive strand: AGGTCA at 4307	-	Negative strand: AGGTCA at 4269	-	-	Negative strand: AGGTCA at 1532, AGGTCA at 1352 Positive strand: TGACCTT at 4019, TGACCTT at 3785, AGGTCA at 2248, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439	Negative strand: AGGTCA at 2220, AGGTCA at 153
Transcription factor 3 (TCF3)	GTCTGGT	-	-	-	-	-	Negative strand: GTCTGGT at 2122	Negative strand: ACCAGAC at 3549, GTCTGGT at 3022, GTCTGGT at 103 Positive strand: ACCAGAC at 2942
Unfolded protein response element (URE) (UPRE-1)	CANCNTG	Positive strand: CAGCCTG at 4348, CATGGTG at 4109, CAGCCTG at 4036, CATCCTG at 3905, CACCCTG at 3743, CAGCCTG at 3297, CAAGGTG at 3143, CAGCCTG at 3127	-	Negative strand: CATCATG at 4364	Negative strand: CACCGTG at 2664 Positive strand: CAGCCTG at 2769, CATGGTG at 2616, CAACATG at 2613	Negative strand: CATCCTG at 4185	Negative strand: CATCATG at 2342, CATCTTG at 286 Positive strand: CACGGTG at 2526, CAGCCTG at 2434, CATGCTG at 2325, CATGGTG at 2279, CAGCATG at 2276, CAGCCTG at 2267, CAACATG at 2151, CAGCCTG at 2008, CATGTTG at 1852, CATCCTG at 1840, CAGGCTG at 1463, CATGGTG at 1209, CAACATG at 1206, CAGCCTG at 1197, CAGCCTG at 898, CAGCGTG at 740, CAGCCTG at 731, CACGGTG at 655, CATCCTG at 595, CAGCCTG at 507	Negative strand: CACCATG at 3827, CAGGCTG at 3639, CAGGATG at 3574, CAGGGTG at 3539, CACCCTG at 2967, CATGTTG at 2476, CACCATG at 2473, CAGGCTG at 2319, CATGATG at 2143, CAACCTG at 946, CAACCTG at 846, CACGCTG at 778 Positive strand: CACGTTG at 2802, CATGGTG at 2599
Unfolded protein response elements (UPRE)	TGACGTG(G/A)	Negative strand: TGACGTGA at 4340	-	Positive strand: TGACGTGG at 4343	Negative strand: TGACGTGG at 2761	-	Negative strand: TGACGTGA at 2426, CCACGTCA at 2083, TGACGTGA at 2000, TCACGTCA at 1472	Positive strand: TGACGTGG at 3322, TCACGTCA at 2328, TCACGTCA at 2065
Upstream stimulating factors (USFs)	GCC(A/T)NN(C/G/T)(A/G)	Negative strand: CGGTCCAC at 3953 Positive strand: CAGATGGC at 3629	-	-	-	-	Negative strand: CGGTCCAC at 2079	Negative strand: GCCACATG at 3707 Positive strand: GTAGACCG at 3406, GTGGACCG at 2570, CAGGTGGC at 1845, GTCCACCG at 198
UUA rich elements (Siegel)	TTATTTA(A/T)(A/T)	Negative strand: TTATTTATT at 4075	-	-	-	-	-	-
V boxes	(A/G)TT(A/T)(C/T)	Negative strand: ATAAT at 4538, AAAAT at 4512, GTTTC at 4504, GTTTT at 4376, GTTTT at 4310, GAAAC at 4462, ATTAT at 4223, GTTTT at 4216, ATTAT at 4077, GTTTT at 4066, GAAAC at 3985, GTTTT at 3767, ATTAC at 3658, ATTAT at 3538, ATAAC at 3528, ATAAT at 3468, ATAAT at 3454, ATTTT at 3439, GTAAT at 3436, ATTTT at 3353, AAAAT at 3350, GTTTT at 3326, GTTTT at 3313, GTAAC at 3285, ATTTT at 3171, ATTTT at 3163, GAAAC at 3076, ATTTT at 3024, AAAAT at 3021, ATTTT at 3010, ATAAT at 2998, ATAAT at 2977, GTAAT at 2951, GTTTC at 2891, GTTTT at 2866, ATTTC at 2857, AAAAT at 2854, GTTAT at 2849 Positive strand: ATTTT at 4511, AAAAC at 4396, AAAAC at 4311, ATAAT at 4225, ATAAT at 4222, AAAAT at 4219, AAAAT at 4088, ATAAT at 4076, AAAAT at 4069, GTAAT at 3973, AAAAT at 3768, ATTTC at 3688, ATAAT at 3657, GAAAC at 3592, ATAAT at 3537, AAAAC at 3510, ATTAC at 3469, AAAAT at 3355, GTTTT at 3349, AAAAC at 3328, AAAAT at 3314, AAAAT at 3173, AAAAC at 3165, GAAAC at 3147, GTAAT at 3064, AAAAC at 3027, AAAAT at 3011, AAAAC at 2969, GAAAC at 2958, AAAAT at 2930, ATTTC at 2884, AAAAT at 2867, ATTTT at 2853	Positive strand: AAAAC at 2840	-	Negative strand: GTTTT at 2795, GTTTT at 2644 Positive strand: GAAAT at 2747, GTAAT at 2675, AAAAT at 2646, GAAAC at 2620	Negative strand: ATAAT at 4168, ATTAT at 4165, ATTAT at 4158, ATTTT at 4120, GTTTT at 4109, GAAAT at 4092 Positive strand: TAATA at 4165, TAATA at 4158, TAAAA at 4120, CAAAA at 4109	Negative strand: GAAAC at 2553, GTTAT at 2497, GTTTT at 2490, GTTTT at 2476, GTTTT at 2307, ATTTT at 2299, GAAAC at 2217, GTTTT at 2182, ATTTC at 2174, GAAAC at 2100, GTTTT at 2036, GTTTT at 1880, ATTTT at 1872, GAAAC at 1791, ATTTT at 1737, GAAAT at 1734, AAAAT at 1728, ATTAT at 1708, GAAAC at 1688, GTTTC at 1638, GTTTT at 1561, ATTTC at 1548, AAAAC at 1433, GTTTT at 1394, GTTTT at 1384, GTTTT at 1371, GTTAT at 1362, GTAAC at 1343, GTTTT at 1228, GAAAC at 1146, GTTTT at 1092, GTTTT at 926, GTAAC at 886, GTTTT at 771, ATTTT at 763, GAAAC at 682, GTTTT at 637, ATTTT at 629, ATTAT at 602, GAAAC at 546, GTTTT at 485, GAAAC at 409, GAAAT at 348, ATTAT at 271, GTTTT at 257, ATTAT at 249, ATAAT at 236, ATTTT at 222, AAAAT at 217, AAAAT at 191, ATTTT at 183, GTAAT at 173, GTTTT at 164, GTAAT at 153, GTTTC at 93, ATTTT at 66, GAAAT at 48, AAAAC at 28 Positive strand: AAAAC at 2507, AAAAC at 2491, AAAAC at 2310, AAAAT at 2301, GAAAC at 2283, AAAAT at 2185, GAAAT at 2158, GTAAT at 2088, AAAAT at 2061, GTAAT at 1914, AAAAT at 1884, AAAAT at 1874, GAAAC at 1856, GTAAT at 1779, AAAAT at 1738, ATTTT at 1727, ATTAT at 1724, GTAAT at 1707, GAAAT at 1661, GAAAC at 1643, GAAAT at 1631, ATTTC at 1603, GAAAC at 1583, AAAAT at 1562, AAAAC at 1386, ATTTC at 1380, AAAAC at 1372, ATTAC at 1296, GTAAT at 1261, AAAAT at 1231, GAAAC at 1213, GTAAT at 1134, GTAAT at 804, AAAAT at 774, AAAAT at 765, GTAAT at 670, AAAAT at 640, AAAAT at 631, GTAAC at 613, GTAAT at 534, AAAAT at 496, AAAAT at 488, GAAAC at 474, GTAAT at 397, AAAAC at 359, GAAAC at 313, GAAAC at 304, ATAAT at 270, AAAAC at 258, GTAAT at 248, GAAAC at 227, GTTTT at 215, ATTTT at 190, AAAAC at 165, GAAAC at 127, AAAAC at 67, ATTTC at 22	Negative strand: GAAAT at 3795, GTAAC at 3732, GTTAT at 3382, GAAAT at 3166, GTTAT at 3025, GAAAC at 2832, GTTTT at 2687, ATTTC at 2645, GAAAC at 2630, GAAAT at 2624, ATTAT at 2547, AAAAC at 2495, ATTTT at 2449, AAAAT at 2446, ATTTT at 2441, GTTTC at 2301, GTTTC at 2263, GAAAC at 2147, ATTTC at 1978, AAAAC at 292, GTTTT at 147 Positive strand: GTTAT at 3425, CAATA at 3382, GTTAT at 3159, GTTTC at 3064, CAATA at 3025, GTTAC at 2909, GTTTC at 2827, GTTTT at 2707, CAAAA at 2687, TAAAG at 2645, TAATA at 2547, GTTTC at 2535, GTTTT at 2494, TAAAA at 2449, ATTTT at 2445, TAAAA at 2441, CAAAG at 2301, CAAAG at 2263, GTTTT at 2003, TAAAG at 1978, GTTAC at 227, CAAAA at 147
Vitamin D response elements (VDRE)	(A/G)G(G/T)TCA	Negative strand: TGAACC at 4268, TGAACT at 4012, TGACCC at 3750, TGAACT at 3242, TGAACT at 3103, TGAACC at 2921 Positive strand: AGGTCA at 4307, AGTTCA at 4176, AGTTCA at 4025, TGAACC at 3784, TGAACC at 3245	-	Negative strand: AGGTCA at 4269	Positive strand: TGAACC at 2717	Negative strand: TGACCC at 4217, AGTTCA at 4201	Negative strand: TGAACT at 2580, TGAACT at 2127, TGAACC at 1927, AGGTCA at 1532, AGGTCA at 1352, TGAACT at 1300, TGAACC at 328 Positive strand: AGGTCA at 2585, TGAACC at 2382, AGGTCA at 2248, TGAACC at 1956, TGAACC at 1303, AGTTCA at 1178, TGAACC at 1012, TGAACC at 846, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439, AGTTCA at 254, GGGTCA at 206	Negative strand: TGACCT at 4019, TGAACC at 3937, TGAACC at 3838, GGGTCA at 3820, TGACCA at 3785, AGGTCA at 2220, TGACCC at 1663, AGGTCA at 153 Positive strand: TGAACT at 4016, GGGTCA at 3379, GGGTCA at 3082, AGTTCA at 2616, GGTTCA at 2594, AGTTCA at 2509, GGGTCA at 2024, TGACCC at 1954, GGGTCA at 1250, TGACCC at 348
W boxes	(C/T)TGAC(C/T)	Negative strand: GGTCAA at 4416, GGTCAA at 4308, CTGACC at 3749	-	Negative strand: GGTCAG at 4270	-	Positive strand: CTGACC at 4216	Negative strand: CTGACT at 1935, GGTCAG at 1353, CTGACC at 734, TTGACT at 307, TTGACT at 130, CTGACT at 17 Positive strand: GGTCAG at 2586, GGTCAG at 2249, GGTCAG at 713, GGTCAG at 577, GGTCAG at 440	Negative strand: TTGACC at 4018, CTGACT at 2945, TTGACC at 2873, AGTCAG at 2619, AGTCAA at 2614, AGTCAG at 2608, GGTCAG at 2221, AGTCAG at 2101, CTGACC at 1662, CTGACC at 2213 Positive strand: TTGACT at 3735, GGTCAA at 3380, GGTCAG at 3083, GGTCAG at 2997, CTGACT at 2674, GGTCAG at 2606, AGTCAG at 2099, GGTCAG at 2025, TTGACC at 1953
X core promoter elements	(A/G/T)(C/G)G(C/T)GG(A/G)A(C/G)(A/C)	Negative strand: TGGTGGGACC at 3744	-	-	-	-	Positive strand: GCTCCCACCT at 392	Positive strand: GGTCCCACCC at 3541, GGGTGGAAGC at 1406, TCTCCCACCT at 185
Xenobiotic response elements (XREs)	GCGTG	Positive strand: CACGC at 3280, GCGTG at 3046	-	-	-	-	Negative strand: CACGC at 2196, CACGC at 447, CACGC at 379 Positive strand: CACGC at 2207, CACGC at 1991, GCGTG at 1896, GCGTG at 1243, CACGC at 963, GCGTG at 740, CACGC at 663	Negative strand: GCGTG at 2554, GCGTG at 1719, CACGC at 1553, CACGC at 1301, GCGTG at 1242, GCGTG at 1216, CACGC at 1133, CACGC at 1049, GCGTG at 1019, CACGC at 987, CACGC at 969, CACGC at 887, CACGC at 869, CACGC at 803, CACGC at 797, CACGC at 776, GCGTG at 544 Positive strand: GCGTG at 2565, CACGC at 1763, CACGC at 1725, CACGC at 1589, GCGTG at 1555, GCGTG at 1551, CACGC at 1521, GCGTG at 1299, CACGC at 1253, CACGC at 1244, CACGC at 1169, CACGC at 1160, GCGTG at 1135, GCGTG at 1131, CACGC at 1085, GCGTG at 1051, GCGTG at 1047, CACGC at 1017, GCGTG at 977, GCGTG at 877, GCGTG at 799, GCGTG at 795, GCGTG at 685, CACGC at 665, CACGC at 581, CACGC at 497, CACGC at 488
Yap recognition sequences	TTACTAA	Positive strand: TTACTAA at 3472	-	-	-	-	-	-
YY1 binding sites	CCATCTT	-	-	-	-	-	Negative strand: CCATCTT at 1654	-
Z boxes	A(C/T)A(C/G)GT(A/G)T	Positive strand: ACACCTGT at 3970, ATACCTAT at 2996	-	-	-	-	Positive strand: ACACCTGT at 1131	Negative strand: ACAGGTGT at 1969 Positive strand: ACACGTGT at 2962

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

See also

• A1BG gene transcription core promoters
• A1BG gene transcriptions
• A1BG regulatory elements and regions
• A1BG response element gene transcriptions
• A1BG response element negative results
• A1BG response element positive results
• Complex locus A1BG and ZNF497

External links

• GenomeNet KEGG database
• Home - Gene - NCBI
• NCBI All Databases Search
• NCBI Site Search

{{Phosphate biochemistry}}