H box gene transcriptions

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Editor-In-Chief: Henry A. Hoff

File:A green bean.jpg
Green beans grow from Phaseolus vulgaris. Credit: wanko from Japan.{{free media}}

The "H-box [is] from the bean chalcone synthase gene Chs15 [23,24]."[1]

The "Phaseolus vulgaris chalcone synthase (PvCHS15)" gene has three H boxes between the G box and the TATA box, where each binds to MYB, KAP 2, and KAP 1 downstream from the G box, respectively.[1]

"Functional studies with the H-box indicated that it cannot function to a high level alone. Gain of function experiments, however, show that it is active in combination with a G-Box element [...] in transgenic tobacco plants in establishing the characteristic tissue-specific pattern of expression and mutations in either the H-box or G-Box reduced the response to tobacco mosaic virus (TMV) infection [24,30]."[1]

"A bZIP protein from soybean binds to the G-Box in the bean Chs15 promoter [36•]. This protein, G/HBF-1, can also bind to the adjacent H-box."[1]

"Although the mRNA and protein levels of G/HBF-1 do not increase during the induction of its putative target genes, the protein itself is rapidly phosphorylated and in vitro phosphorylation enhances binding to one (H-box III) out of the three H-boxes present in the Chs15 promoter."[1]

H box in animals

"A testis/brain RNA-binding protein, TB-RBP, binds to the Y- and H-boxes in the Prm2 3′ UTR and represses translation of a reporter mRNA in rabbit reticulocyte lysates [9]. The Y- and H-boxes are found in many transcripts expressed in the testis and brain, including Prm1, Prm2, Tnp1, and Tau [10]."[2]

H box (Mitchell) consensus sequences

"The box H/ACA snoRNAs were most recently recognized as a small RNA family by virtue of an ACA trinucleotide located 3 nt upstream of the mature snoRNA 3' end (41). In addition to this ACA box, they have the consensus H box sequence (5'-ANANNA-3') but have no other primary sequence identity. Despite this lack of primary sequence conservation, the H and ACA boxes are embedded in an evolutionarily conserved hairpin-hinge-hairpin-tail core secondary structure with the H box in the single-stranded hinge region and the ACA box in the single-stranded tail (5, 16)."[3]

The "3' end of mature hTR (45) has an ACA trinucleotide 3 nt upstream of its 3' end. In addition, the 3' region of hTR contains a single H box consensus sequence (5'-AGAGGA-3')."[3]

"Comparison with the murine telomerase RNA (mTR) (7) suggests that the snoRNA-like features of hTR are evolutionarily conserved. The mTR 3' end (nt 169 to 397 as numbered in reference 25) has ~76% sequence identity with the corresponding region of hTR (nt 211 to 451) and includes consensus H (5'-ACAGGA-3') and ACA box sequences."[3]

H boxes (Mitchell) samplings

For the Basic programs testing consensus sequence 3'-ANANNA-5' (starting with SuccessablesHbox3.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. Negative strand, negative direction: 64, AAATAA at 4537, AGAGAA at 4527, ACACGA at 4402, ACATCA at 4124, ACATTA at 3973, ACACCA at 3811, AGACGA at 3707, AGAAGA at 3554, ACACCA at 3187, AGATGA at 3159, ACATTA at 3064, AAAGTA at 2886, ATAAAA at 2853, ACATTA at 2675, ACACCA at 2659, ACATCA at 2541, ACATCA at 2340, AGATGA at 2295, AGATGA at 2170, ACATTA at 2088, ACATTA at 1914, AGATGA at 1868, ACATTA at 1779, ATAGAA at 1732, AAAATA at 1729, ATAAAA at 1727, AAAGAA at 1605, ATATAA at 1601, ACACTA at 1480, AGACAA at 1453, AAAAAA at 1432, AAAAAA at 1431, AAAAAA at 1430, AAAAAA at 1429, AAAAAA at 1428, AAAAAA at 1427, AAAAAA at 1426, AAAAAA at 1425, AAAAAA at 1424, AAAAAA at 1423, AAAAAA at 1422, AAAAAA at 1421, AGAAAA at 1419, ACATTA at 1261, ACATTA at 1134, ACATTA at 804, ACACCA at 788, AGATGA at 759, ACATTA at 670, AGATGA at 625, ATACCA at 606, ACATTA at 397, ATACTA at 352, ACATGA at 325, AGAACA at 281, ACATTA at 248, AGATAA at 235, AAAATA at 218, ACAAAA at 215, ATACAA at 213, ACAAGA at 45, ATACAA at 43, AGAAAA at 26, AAAGAA at 24.
  2. Negative strand, positive direction: 32, ACATGA at 4154, ACATCA at 4116, AAATGA at 4094, AGAACA at 4068, AAAAGA at 3929, ACACCA at 3825, ACATGA at 3708, AAAGCA at 3599, ACAGGA at 3572, AGATGA at 3476, ACAGTA at 3414, ACAGCA at 3212, AGAGCA at 3138, AGAACA at 3094, AAAGAA at 3066, ACAGAA at 2838, AAAGGA at 2829, AGAGGA at 2793, AGAGCA at 2704, ATATAA at 2662, ACACTA at 2637, AAACCA at 2632, ATAGAA at 2628, ACACCA at 2603, ATACCA at 2591, AGATCA at 2231, ACATGA at 2141, AAAGCA at 2006, ACAGCA at 1055, AGAGGA at 471, AGAGGA at 207, AGAAGA at 49.
  3. Positive strand, negative direction: 263, ACACGA at 4471, 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, AGACAA at 4182, AGAAAA at 4086, AAAGAA at 4084, ATAGAA at 4080, ATAATA at 4077, AAATAA at 4075, AAATAA at 4071, AAAATA at 4070, AAAAAA at 4068, ACAAAA at 4066, AGACCA at 4031, AGATGA at 3920, AGAGCA at 3913, ACAAAA at 3767, AGACCA at 3762, ACAAGA at 3759, AGAGGA at 3675, AGAACA at 3668, AAAGAA at 3666, AGAGGA at 3638, ACAAGA at 3635, ATAATA at 3538, ACACAA at 3514, AAAACA at 3511, AGATCA at 3489, AAACCA at 3484, ATATTA at 3468, ATATTA at 3454, ACATTA at 3436, ACATCA at 3415, AGAGAA at 3406, ACATCA at 3394, AGAGGA at 3387, AAACCA at 3365, AGAAAA at 3343, ACAAGA at 3340, AAACAA at 3338, AAATAA at 3334, AAACAA at 3330, AAAACA at 3329, AGAGCA at 3310, ACAAGA at 3307, AGATCA at 3277, AAATTA at 3175, ATAAAA at 3171, ACATAA at 3169, AAAACA at 3166, AGACCA at 3122, AAACTA at 3029, AAAAAA at 3026, AAATAA at 3013, AAAATA at 3012, AAACCA at 2971, ACATTA at 2951, ACATCA at 2941, AAAAAA at 2929, ATATAA at 2873, AAAATA at 2868, AAACAA at 2842, AAAACA at 2841, AGAAAA at 2839, AAAGAA at 2837, AAAAGA at 2836, AAAAAA at 2834, AGAAAA at 2832, AGAAGA at 2829, AGAGAA at 2827, AAAAGA at 2824, AGAAAA at 2822, AAAGAA at 2820, AAAAGA at 2819, AAAAAA at 2817, AGAAAA at 2815, AGAAGA at 2812, AGAGAA at 2810, AAAAGA at 2807, AGAAAA at 2805, AAAGAA at 2803, AAAGAA at 2799, AAAAGA at 2798, AGAGCA at 2781, AAATCA at 2749, ACAGGA at 2690, AAATCA at 2648, ACAAAA at 2644, ATACAA at 2642, AGACCA at 2599, AAACAA at 2509, AAAACA at 2508, AGAAAA at 2506, ATAGTA at 2500, ACAAAA at 2490, AAACAA at 2488, AAACAA at 2484, AAAGCA at 2479, AAAGCA at 2473, AAAAAA at 2470, AAAAAA at 2469, AAAAAA at 2468, AAAAAA at 2467, AAAAAA at 2466, AAAAAA at 2465, AAAAAA at 2464, AAAAAA at 2463, AAAAAA at 2462, AAAAAA at 2461, ACACCA at 2419, AGATCA at 2414, AAACTA at 2312, AAAAAA at 2309, ACAAAA at 2307, ATACAA at 2305, AAAATA at 2302, ACAGCA at 2274, AGACCA at 2262, AAATGA at 2187, AAAAAA at 2184, ACAAAA at 2182, ATACAA at 2180, AGACCA at 2146, AGACCA at 2122, AAAAAA at 2060, AAAAAA at 2059, AAAAAA at 2058, AGAAAA at 2056, AAAGAA at 2054, AAAAGA at 2053, AAAAAA at 2051, AAAAAA at 2050, AAAAAA at 2049, AAAAAA at 2048, AAAAAA at 2047, AAAAAA at 2046, AAAAAA at 2045, AAAAAA at 2044, AAAAAA at 2043, AAAAAA at 2042, AAAAAA at 2041, AAAAAA at 2040, AAAAAA at 2039, AAAAAA at 2038, AGAGCA at 2020, AGATCA at 1988, AAATTA at 1886, AAAAAA at 1883, AAAAAA at 1882, ACAAAA at 1880, ATACAA at 1878, AAAATA at 1875, AGACCA at 1835, AAAATA at 1739, ATAGTA at 1705, AAATGA at 1700, ATACCA at 1668, AAATGA at 1663, AAAGGA at 1640, AAAGAA at 1629, AAAAGA at 1628, AAACAA at 1585, AAATGA at 1580, AAAATA at 1563, AAAGAA at 1550, AAAAGA at 1400, AAAAAA at 1398, AAAAAA at 1397, AAAAAA at 1396, ACAAAA at 1394, AAACAA at 1392, AAACAA at 1388, AAAACA at 1387, AGAGCA at 1368, ATAAGA at 1365, AAATTA at 1233, AAAAAA at 1230, ACAAAA at 1228, AAAAAA at 1105, AAAAAA at 1104, AAAAAA at 1103, AAAAAA at 1102, AAAAAA at 1101, AAAAAA at 1100, AAAAAA at 1099, AAAAAA at 1098, AAAAAA at 1097, AAAAAA at 1096, AAAAAA at 1095, AAAAAA at 1094, ACAACA at 1071, AAAAAA at 942, AAAAAA at 941, AAAAAA at 940, AAAAAA at 939, AAAAAA at 938, AAAAAA at 937, AAAAAA at 936, AAAAAA at 935, AAAAAA at 934, AAAAAA at 933, AAAAAA at 932, AAAAAA at 931, AAAAAA at 930, AAAAAA at 929, AAAAAA at 928, ACACCA at 883, AGATCA at 878, AAATTA at 776, AAAAAA at 773, ACAAAA at 771, ATACAA at 769, AAAATA at 766, AGACCA at 726, AAAAAA at 639, ACAAAA at 637, ATACAA at 635, AAAATA at 632, AGATCA at 590, AAATTA at 498, ATACGA at 492, AAAATA at 489, AAAAAA at 487, ACAAAA at 485, AAAACA at 360, AGAAAA at 358, ATAGAA at 356, ACAGAA at 290, AGAACA at 287, ATATGA at 274, ATAATA at 271, ACATAA at 269, AAACCA at 260, AAACAA at 229, AAAGAA at 225, AAAAGA at 224, ATAAAA at 222, AAAGCA at 186, ATAAAA at 183, ACATTA at 173, AAAACA at 166, ATACAA at 113, AAAGGA at 106, AGAAAA at 103, ATAGAA at 101, AAACAA at 69, AAAACA at 68, AAAAGA at 55, AGAAAA at 53.
  4. Positive strand, positive direction: 42, AGAGAA at 4387, ATATTA at 4168, AAATAA at 4142, AAATCA at 4137, AAAATA at 4122, AGAGGA at 4059, ACACCA at 3967, AAACCA at 3948, ACACCA at 3643, ACAGGA at 3620, AGAAGA at 3395, ACAGAA at 3393, AGACGA at 3307, AGAGGA at 3302, AGAAGA at 3058, AGAGAA at 3056, AGACCA at 3022, AGACGA at 2976, AAAACA at 2453, AAAAAA at 2451, AAATAA at 2347, AAAAAA at 2281, AGAAAA at 2279, AAAGAA at 2277, AAAAGA at 2276, AAAGTA at 2265, AGACAA at 2261, AGACAA at 2183, ATAAGA at 2180, AGAGTA at 2175, AGATCA at 2168, AGAGGA at 2081, AAAGAA at 1980, AGACGA at 1734, AAAGCA at 1182, ACAAAA at 147, AGAGGA at 142, AAAAGA at 137, ATAAGA at 117, ACATAA at 115, ACAAGA at 108, AGACCA at 103.
  5. Inverse complement, negative strand, negative direction: 270, TTGTCT at 4518, TTCTGT at 4507, TGCTCT at 4473, TCCTGT at 4468, 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, TTGTGT at 4196, TTCTGT at 4181, TCTTTT at 4086, TTCTTT at 4085, TTATCT at 4079, TATTAT at 4077, TTATTT at 4072, TTTTAT at 4070, TTTTTT at 4068, TGTTTT at 4066, TTGTAT at 4045, TACTTT at 3922, TCGTGT at 3915, TGTTTT at 3767, TGGTGT at 3764, TGTTCT at 3759, TCCTGT at 3756, TTGTGT at 3670, TCTTGT at 3668, TGTTCT at 3635, TAGTCT at 3618, TATTAT at 3538, TTGTGT at 3513, TTTTGT at 3511, TCGTTT at 3497, TGGTCT at 3486, TCATTT at 3481, TGATCT at 3463, TAATTT at 3438, TAGTAT at 3420, TCCTGT at 3389, TTCTCT at 3380, TTCTTT at 3376, TCTTTT at 3343, TTCTTT at 3342, TGTTCT at 3340, TTATTT at 3335, TTGTTT at 3331, TTTTGT at 3329, TCGTTT at 3312, TGTTCT at 3307, TGCTCT at 3233, TATTTT at 3171, TTGTAT at 3168, TTTTGT at 3166, TGATTT at 3162, TTTTTT at 3026, TTATTT at 3014, TTTTAT at 3012, TAATCT at 3000, TAATCT at 2979, TCCTTT at 2967, TCCTTT at 2957, TAGTCT at 2946, TTTTTT at 2929, TAGTTT at 2890, TTGTCT at 2878, TTATAT at 2870, TTTTAT at 2868, TTTTGT at 2841, TCTTTT at 2839, TTCTTT at 2838, TTTTCT at 2836, TTTTTT at 2834, TCTTTT at 2832, TTCTTT at 2831, TCTTCT at 2829, TTCTCT at 2826, TTTTCT at 2824, TCTTTT at 2822, TTCTTT at 2821, TTTTCT at 2819, TTTTTT at 2817, TCTTTT at 2815, TTCTTT at 2814, TCTTCT at 2812, TTCTCT at 2809, TTTTCT at 2807, TCTTTT at 2805, TTCTTT at 2804, TTCTTT at 2800, TTTTCT at 2798, TTGTCT at 2778, TGTTTT at 2644, TTATAT at 2639, TGATTT at 2635, TTGTTT at 2510, TTTTGT at 2508, TCTTTT at 2506, TTCTTT at 2505, TGTTTT at 2490, TTGTTT at 2489, TTGTTT at 2485, TCGTTT at 2481, TCGTTT at 2475, TTTTTT at 2470, TTTTTT at 2469, TTTTTT at 2468, TTTTTT at 2467, TTTTTT at 2466, TTTTTT at 2465, TTTTTT at 2464, TTTTTT at 2463, TTTTTT at 2462, TTTTTT at 2461, TTGTCT at 2443, TAGTGT at 2416, TCCTCT at 2370, TTTTTT at 2309, TGTTTT at 2307, TTATGT at 2304, TTTTAT at 2302, TGATTT at 2298, TAGTGT at 2242, TTTTTT at 2184, TGTTTT at 2182, TTCTAT at 2177, TGATTT at 2173, TTTTTT at 2060, TTTTTT at 2059, TTTTTT at 2058, TCTTTT at 2056, TTCTTT at 2055, TTTTCT at 2053, TTTTTT at 2051, TTTTTT at 2050, TTTTTT at 2049, TTTTTT at 2048, TTTTTT at 2047, TTTTTT at 2046, TTTTTT at 2045, TTTTTT at 2044, TTTTTT at 2043, TTTTTT at 2042, TTTTTT at 2041, TTTTTT at 2040, TTTTTT at 2039, TTTTTT at 2038, TCCTCT at 1944, TTTTTT at 1883, TTTTTT at 1882, TGTTTT at 1880, TTATGT at 1877, TTTTAT at 1875, TGATTT at 1871, TCCTCT at 1826, TTTTAT at 1739, TTATCT at 1710, TACTAT at 1702, TAATTT at 1697, TGGTCT at 1670, TACTAT at 1665, TCCTTT at 1642, TTCTTT at 1630, TTTTCT at 1628, TCGTCT at 1614, TTCTAT at 1595, TTGTTT at 1586, TACTTT at 1582, TTATGT at 1565, TTTTAT at 1563, TTGTGT at 1541, TTTTCT at 1400, TTTTTT at 1398, TTTTTT at 1397, TTTTTT at 1396, TGTTTT at 1394, TTGTTT at 1393, TTGTTT at 1389, TTTTGT at 1387, TCGTTT at 1370, TATTCT at 1365, TCCTCT at 1291, TTTTTT at 1230, TGTTTT at 1228, TTTTTT at 1105, TTTTTT at 1104, TTTTTT at 1103, TTTTTT at 1102, TTTTTT at 1101, TTTTTT at 1100, TTTTTT at 1099, TTTTTT at 1098, TTTTTT at 1097, TTTTTT at 1096, TTTTTT at 1095, TTTTTT at 1094, TTGTCT at 1073, TGTTGT at 1071, TCCTCT at 1000, TTTTTT at 942, TTTTTT at 941, TTTTTT at 940, TTTTTT at 939, TTTTTT at 938, TTTTTT at 937, TTTTTT at 936, TTTTTT at 935, TTTTTT at 934, TTTTTT at 933, TTTTTT at 932, TTTTTT at 931, TTTTTT at 930, TTTTTT at 929, TTTTTT at 928, TTGTCT at 907, TAGTGT at 880, TCCTCT at 834, TTTTTT at 773, TGTTTT at 771, TTATGT at 768, TTTTAT at 766, TGATTT at 762, TTTTTT at 639, TGTTTT at 637, TTATGT at 634, TTTTAT at 632, TGATTT at 628, TCCTCT at 581, TTCTGT at 559, TAGTGT at 528, TGCTTT at 494, TTTTAT at 489, TTTTTT at 487, TGTTTT at 485, TTGTAT at 467, TTCTGT at 422, TTTTGT at 360, TCTTTT at 358, TACTAT at 353, TGCTTT at 312, TAGTGT at 295, TTGTCT at 289, TCTTGT at 287, TATTAT at 271, TTCTTT at 226, TTTTCT at 224, TATTTT at 222, TATTTT at 183, TTGTCT at 168, TTTTGT at 166, TTCTTT at 135, TACTTT at 126, TCCTAT at 108, TCTTTT at 103, TCCTAT at 74, TTTTGT at 68, TTCTAT at 57, TTTTCT at 55, TCTTTT at 53, TTGTCT at 13.
  6. Inverse complement, negative strand, positive direction: 55, TGCTGT at 4392, TTCTCT at 4386, TGGTCT at 4380, TCATGT at 4365, TAGTTT at 4139, TGATTT at 4134, TTTTAT at 4122, TCATTT at 4119, TGGTTT at 4108, TGGTGT at 3969, TGGTGT at 3950, TCCTGT at 3622, TTCTTT at 3397, TCTTCT at 3395, TCCTCT at 3304, TGGTCT at 3299, TGGTCT at 3245, TCTTCT at 3058, TTGTCT at 3053, TTGTCT at 3004, TCCTCT at 2981, TTCTGT at 2957, TGGTCT at 2941, TTCTGT at 2925, TGGTGT at 2813, TTCTTT at 2585, TTTTGT at 2453, TTTTTT at 2451, TAATTT at 2440, TTTTTT at 2281, TCTTTT at 2279, TTCTTT at 2278, TTTTCT at 2276, TTCTGT at 2182, TATTCT at 2180, TCATAT at 2177, TAGTGT at 2170, TGCTAT at 2157, TCATCT at 2111, TTCTCT at 1990, TTCTTT at 1981, TCGTCT at 1493, TCGTCT at 1393, TCCTCT at 221, TGTTTT at 147, TCCTGT at 144, TTCTCT at 139, TTTTCT at 137, TTCTCT at 119, TATTCT at 117, TTGTAT at 114, TTCTTT at 110, TGTTCT at 108, TGGTGT at 105, TCGTGT at 80.
  7. Inverse complement, positive strand, negative direction: 50, TCCTCT at 4428, TGCTCT at 4404, TCATCT at 4058, TGCTGT at 3957, TGATGT at 3808, TCCTCT at 3790, TGCTGT at 3709, TTCTGT at 3556, TCTTCT at 3554, TTCTGT at 3319, TGCTGT at 3265, TGCTAT at 2898, TATTTT at 2853, TACTTT at 2216, TACTGT at 2163, TCCTGT at 1911, TTATCT at 1731, TTTTAT at 1729, TATTTT at 1727, TTATTT at 1726, TTCTAT at 1525, TGATCT at 1482, TGGTGT at 1477, TTTTTT at 1432, TTTTTT at 1431, TTTTTT at 1430, TTTTTT at 1429, TTTTTT at 1428, TTTTTT at 1427, TTTTTT at 1426, TTTTTT at 1425, TTTTTT at 1424, TTTTTT at 1423, TTTTTT at 1422, TTTTTT at 1421, TCTTTT at 1419, TTCTTT at 1418, TGGTGT at 793, TTCTCT at 622, TGGTGT at 608, TAATAT at 603, TTCTTT at 347, TCTTGT at 281, TAATAT at 272, TTTTAT at 218, TGTTTT at 215, TTCTTT at 47, TGTTCT at 45, TCTTTT at 26, TTCTTT at 25.
  8. Inverse complement, positive strand, positive direction: 40, TCCTGT at 4252, TAATAT at 4166, TAGTAT at 4149, TCTTGT at 4068, TTTTCT at 3929, TGGTGT at 3859, TCGTGT at 3740, TCCTCT at 3650, TACTGT at 3569, TGGTCT at 3548, TTATTT at 3427, TCATCT at 3416, TCGTCT at 3214, TTGTCT at 3179, TGGTTT at 3175, TCCTGT at 3131, TTGTGT at 3096, TCTTGT at 3094, TACTGT at 2843, TTGTGT at 2835, TCCTTT at 2831, TCGTTT at 2706, TTGTCT at 2652, TGGTGT at 2634, TTATCT at 2627, TCCTTT at 2623, TGGTGT at 2600, TAATAT at 2548, TCCTGT at 2460, TGATGT at 2428, TACTGT at 2412, TGGTCT at 2228, TACTTT at 2146, TGGTGT at 2123, TGCTAT at 1837, TGGTCT at 1631, TCCTCT at 710, TACTGT at 62, TCTTCT at 49, TCCTCT at 46.

H boxes (Mitchell) UTRs

Negative strand

  1. Negative strand, negative direction: AAATAA at 4537, AGAGAA at 4527, TTGTCT at 4518, TTCTGT at 4507, TGCTCT at 4473, TCCTGT at 4468, TCCTCT at 4428, TGCTCT at 4404, ACACGA at 4402, TTCTTT at 4394, TTCTTT at 4389, TTCTTT at 4382, TTGTGT at 4196, TTCTGT at 4181, ACATCA at 4124, TTCTTT at 4085, TTATCT at 4079, TTATTT at 4072, TCATCT at 4058, TTGTAT at 4045, ACATTA at 3973, TGCTGT at 3957, TACTTT at 3922, TCGTGT at 3915, ACACCA at 3811, TGATGT at 3808, TCCTCT at 3790, TGGTGT at 3764, TCCTGT at 3756, TGCTGT at 3709, AGACGA at 3707, TTGTGT at 3670, TAGTCT at 3618, TTCTGT at 3556, AGAAGA at 3554, TTGTGT at 3513, TCGTTT at 3497, TGGTCT at 3486, TCATTT at 3481, TGATCT at 3463, TAATTT at 3438, TAGTAT at 3420, TCCTGT at 3389, TTCTCT at 3380, TTCTTT at 3376, TTCTTT at 3342, TTATTT at 3335, TTGTTT at 3331, TTCTGT at 3319, TCGTTT at 3312, TGCTGT at 3265, TGCTCT at 3233, ACACCA at 3187, TTGTAT at 3168, TGATTT at 3162, AGATGA at 3159, ACATTA at 3064, TTATTT at 3014, TAATCT at 3000, TAATCT at 2979, TCCTTT at 2967, TCCTTT at 2957, TAGTCT at 2946, TGCTAT at 2898, TAGTTT at 2890, AAAGTA at 2886, TTGTCT at 2878, TTATAT at 2870, ATAAAA at 2853.

Positive strand

  1. Positive strand, negative direction: ACACGA at 4471, 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, AGACAA at 4182, AGAAAA at 4086, AAAGAA at 4084, ATAGAA at 4080, ATAATA at 4077, AAATAA at 4075, AAATAA at 4071, AAAATA at 4070, AAAAAA at 4068, ACAAAA at 4066, AGACCA at 4031, AGATGA at 3920, AGAGCA at 3913, ACAAAA at 3767, AGACCA at 3762, ACAAGA at 3759, AGAGGA at 3675, AGAACA at 3668, AAAGAA at 3666, AGAGGA at 3638, ACAAGA at 3635, ATAATA at 3538, ACACAA at 3514, AAAACA at 3511, AGATCA at 3489, AAACCA at 3484, ATATTA at 3468, ATATTA at 3454, ACATTA at 3436, ACATCA at 3415, AGAGAA at 3406, ACATCA at 3394, AGAGGA at 3387, AAACCA at 3365, AGAAAA at 3343, ACAAGA at 3340, AAACAA at 3338, AAATAA at 3334, AAACAA at 3330, AAAACA at 3329, AGAGCA at 3310, ACAAGA at 3307, AGATCA at 3277, AAATTA at 3175, ATAAAA at 3171, ACATAA at 3169, AAAACA at 3166, AGACCA at 3122, AAACTA at 3029, AAAAAA at 3026, AAATAA at 3013, AAAATA at 3012, AAACCA at 2971, ACATTA at 2951, ACATCA at 2941, AAAAAA at 2929, ATATAA at 2873, AAAATA at 2868.

H boxes (Mitchell) negative direction core promoters

  1. Negative strand, negative direction: TTCTTT at 2838, TTCTTT at 2831, TTCTCT at 2826, TTCTTT at 2821, TTCTTT at 2814.
  2. Positive strand, negative direction: AAACAA at 2842, AAAACA at 2841, AGAAAA at 2839, AAAGAA at 2837, AAAAGA at 2836, AAAAAA at 2834, AGAAAA at 2832, AGAAGA at 2829, AGAGAA at 2827, AAAAGA at 2824, AGAAAA at 2822, AAAGAA at 2820, AAAAGA at 2819, AAAAAA at 2817, AGAAAA at 2815, AGAAGA at 2812.

H boxes (Mitchell) positive direction core promoters

  1. Negative strand, positive direction: TGCTGT at 4392, TTCTCT at 4386, TGGTCT at 4380, TCATGT at 4365.
  2. Positive strand, positive direction: AGAGAA at 4387.

H boxes (Mitchell) negative direction proximal promoters

  1. Negative strand, negative direction: TTCTCT at 2809, TTCTTT at 2804, TTCTTT at 2800, TTGTCT at 2778, ACATTA at 2675, ACACCA at 2659, TTATAT at 2639, TGATTT at 2635.
  2. Positive strand, negative direction: AGAGAA at 2810, AAAAGA at 2807, AGAAAA at 2805, AAAGAA at 2803, AAAGAA at 2799, AAAAGA at 2798, AGAGCA at 2781, AAATCA at 2749, ACAGGA at 2690, AAATCA at 2648, ACAAAA at 2644, ATACAA at 2642, AGACCA at 2599.

H boxes (Mitchell) positive direction proximal promoters

  1. Negative strand, positive direction: ACATGA at 4154, TAGTTT at 4139, TGATTT at 4134, TCATTT at 4119, ACATCA at 4116, TGGTTT at 4108, AAATGA at 4094, AGAACA at 4068.
  2. Positive strand, positive direction: 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.

H boxes (Mitchell) negative direction distal promoters

Negative strand

  1. Negative strand, negative direction: ACATCA at 2541, TTGTTT at 2510, TTCTTT at 2505, TTGTTT at 2489, TTGTTT at 2485, TCGTTT at 2481, TCGTTT at 2475, TTGTCT at 2443, TAGTGT at 2416, TCCTCT at 2370, ACATCA at 2340, TTATGT at 2304, TGATTT at 2298, AGATGA at 2295, TAGTGT at 2242, TTCTAT at 2177, TGATTT at 2173, AGATGA at 2170, ACATTA at 2088, TTCTTT at 2055, TCCTCT at 1944, ACATTA at 1914, TTATGT at 1877, TGATTT at 1871, AGATGA at 1868, TCCTCT at 1826, ACATTA at 1779, ATAGAA at 1732, TTATCT at 1710, TACTAT at 1702, TAATTT at 1697, TGGTCT at 1670, TACTAT at 1665, TCCTTT at 1642, TTCTTT at 1630, TCGTCT at 1614, AAAGAA at 1605, ATATAA at 1601, TTCTAT at 1595, TTGTTT at 1586, TACTTT at 1582, TTATGT at 1565, TTGTGT at 1541, ACACTA at 1480, AGACAA at 1453, AAAAAA at 1432, AAAAAA at 1431, AAAAAA at 1430, AAAAAA at 1429, AAAAAA at 1428, AAAAAA at 1427, AAAAAA at 1426, AAAAAA at 1425, AAAAAA at 1424, AAAAAA at 1423, AAAAAA at 1422, AAAAAA at 1421, AGAAAA at 1419, TTGTTT at 1393, TTGTTT at 1389, TCGTTT at 1370, TCCTCT at 1291, ACATTA at 1261, ACATTA at 1134, TTGTCT at 1073, TCCTCT at 1000, TTGTCT at 907, TAGTGT at 880, TCCTCT at 834, ACATTA at 804, ACACCA at 788, TTATGT at 768, TGATTT at 762, AGATGA at 759, ACATTA at 670, TTATGT at 634, TGATTT at 628, AGATGA at 625, ATACCA at 606, TCCTCT at 581, TTCTGT at 559, TAGTGT at 528, TGCTTT at 494, TTGTAT at 467, TTCTGT at 422, ACATTA at 397, TACTAT at 353, ATACTA at 352, ACATGA at 325, TGCTTT at 312, TAGTGT at 295, TTGTCT at 289, AGAACA at 281, ACATTA at 248, AGATAA at 235, TTCTTT at 226, AAAATA at 218, ACAAAA at 215, ATACAA at 213, TTGTCT at 168, TTCTTT at 135, TACTTT at 126, TCCTAT at 108, TCCTAT at 74, TTCTAT at 57, ACAAGA at 45, ATACAA at 43, AGAAAA at 26, AAAGAA at 24, TTGTCT at 13.

Positive strand

  1. Positive strand, negative direction: AAACAA at 2509, AAAACA at 2508, AGAAAA at 2506, ATAGTA at 2500, ACAAAA at 2490, AAACAA at 2488, AAACAA at 2484, AAAGCA at 2479, AAAGCA at 2473, AAAAAA at 2470, AAAAAA at 2469, AAAAAA at 2468, AAAAAA at 2467, AAAAAA at 2466, AAAAAA at 2465, AAAAAA at 2464, AAAAAA at 2463, AAAAAA at 2462, AAAAAA at 2461, ACACCA at 2419, AGATCA at 2414, AAACTA at 2312, AAAAAA at 2309, ACAAAA at 2307, ATACAA at 2305, AAAATA at 2302, ACAGCA at 2274, AGACCA at 2262, TACTTT at 2216, AAATGA at 2187, AAAAAA at 2184, ACAAAA at 2182, ATACAA at 2180, TACTGT at 2163, AGACCA at 2146, AGACCA at 2122, AAAAAA at 2060, AAAAAA at 2059, AAAAAA at 2058, AGAAAA at 2056, AAAGAA at 2054, AAAAGA at 2053, AAAAAA at 2051, AAAAAA at 2050, AAAAAA at 2049, AAAAAA at 2048, AAAAAA at 2047, AAAAAA at 2046, AAAAAA at 2045, AAAAAA at 2044, AAAAAA at 2043, AAAAAA at 2042, AAAAAA at 2041, AAAAAA at 2040, AAAAAA at 2039, AAAAAA at 2038, AGAGCA at 2020, AGATCA at 1988, TCCTGT at 1911, AAATTA at 1886, AAAAAA at 1883, AAAAAA at 1882, ACAAAA at 1880, ATACAA at 1878, AAAATA at 1875, AGACCA at 1835, AAAATA at 1739, TTATCT at 1731, TTTTAT at 1729, TATTTT at 1727, TTATTT at 1726, ATAGTA at 1705, AAATGA at 1700, ATACCA at 1668, AAATGA at 1663, AAAGGA at 1640, AAAGAA at 1629, AAAAGA at 1628, AAACAA at 1585, AAATGA at 1580, AAAATA at 1563, AAAGAA at 1550, TTCTAT at 1525, TGATCT at 1482, TGGTGT at 1477, TTCTTT at 1418, AAAAGA at 1400, AAAAAA at 1398, AAAAAA at 1397, AAAAAA at 1396, ACAAAA at 1394, AAACAA at 1392, AAACAA at 1388, AAAACA at 1387, AGAGCA at 1368, ATAAGA at 1365, AAATTA at 1233, AAAAAA at 1230, ACAAAA at 1228, AAAAAA at 1105, AAAAAA at 1104, AAAAAA at 1103, AAAAAA at 1102, AAAAAA at 1101, AAAAAA at 1100, AAAAAA at 1099, AAAAAA at 1098, AAAAAA at 1097, AAAAAA at 1096, AAAAAA at 1095, AAAAAA at 1094, ACAACA at 1071, AAAAAA at 942, AAAAAA at 941, AAAAAA at 940, AAAAAA at 939, AAAAAA at 938, AAAAAA at 937, AAAAAA at 936, AAAAAA at 935, AAAAAA at 934, AAAAAA at 933, AAAAAA at 932, AAAAAA at 931, AAAAAA at 930, AAAAAA at 929, AAAAAA at 928, ACACCA at 883, AGATCA at 878, TGGTGT at 793, AAATTA at 776, AAAAAA at 773, ACAAAA at 771, ATACAA at 769, AAAATA at 766, AGACCA at 726, AAAAAA at 639, ACAAAA at 637, ATACAA at 635, AAAATA at 632, TTCTCT at 622, TGGTGT at 608, TAATAT at 603, AGATCA at 590, AAATTA at 498, ATACGA at 492, AAAATA at 489, AAAAAA at 487, ACAAAA at 485, AAAACA at 360, AGAAAA at 358, ATAGAA at 356, TTCTTT at 347, ACAGAA at 290, AGAACA at 287, ATATGA at 274, TAATAT at 272, ATAATA at 271, ACATAA at 269, AAACCA at 260, AAACAA at 229, AAAGAA at 225, AAAAGA at 224, ATAAAA at 222, AAAGCA at 186, ATAAAA at 183, ACATTA at 173, AAAACA at 166, ATACAA at 113, AAAGGA at 106, AGAAAA at 103, ATAGAA at 101, AAACAA at 69, AAAACA at 68, AAAAGA at 55, AGAAAA at 53, TTCTTT at 47, TTCTTT at 25.

H boxes (Mitchell) positive direction distals

Negative strand

  1. Negative strand, positive direction: TGGTGT at 3969, TGGTGT at 3950, AAAAGA at 3929, ACACCA at 3825, ACATGA at 3708, TCCTGT at 3622, AAAGCA at 3599, ACAGGA at 3572, AGATGA at 3476, ACAGTA at 3414, TTCTTT at 3397, TCCTCT at 3304, TGGTCT at 3299, TGGTCT at 3245, ACAGCA at 3212, AGAGCA at 3138, AGAACA at 3094, AAAGAA at 3066, TTGTCT at 3053, TTGTCT at 3004, TCCTCT at 2981, TTCTGT at 2957, TGGTCT at 2941, TTCTGT at 2925, ACAGAA at 2838, AAAGGA at 2829, TGGTGT at 2813, AGAGGA at 2793, AGAGCA at 2704, ATATAA at 2662, ACACTA at 2637, AAACCA at 2632, ATAGAA at 2628, ACACCA at 2603, ATACCA at 2591, TTCTTT at 2585, TAATTT at 2440, TTCTTT at 2278, AGATCA at 2231, TTCTGT at 2182, TAGTGT at 2170, TGCTAT at 2157, ACATGA at 2141, TCATCT at 2111, AAAGCA at 2006, TTCTCT at 1990, TTCTTT at 1981, TCGTCT at 1493, TCGTCT at 1393, ACAGCA at 1055, AGAGGA at 471, TCCTCT at 221, AGAGGA at 207, TCCTGT at 144, TTCTCT at 139, TTCTCT at 119, TTGTAT at 114, TTCTTT at 110, TGGTGT at 105, TCGTGT at 80, AGAAGA at 49.

Positive strand

  1. Positive strand, positive direction: ACACCA at 3967, AAACCA at 3948, TGGTGT at 3859, TCGTGT at 3740, TCCTCT at 3650, ACACCA at 3643, ACAGGA at 3620, TACTGT at 3569, TGGTCT at 3548, TTATTT at 3427, TCATCT at 3416, AGAAGA at 3395, ACAGAA at 3393, AGACGA at 3307, AGAGGA at 3302, TCGTCT at 3214, TTGTCT at 3179, TGGTTT at 3175, TCCTGT at 3131, TTGTGT at 3096, AGAAGA at 3058, AGAGAA at 3056, AGACCA at 3022, AGACGA at 2976, TACTGT at 2843, TTGTGT at 2835, TCCTTT at 2831, TCGTTT at 2706, TTGTCT at 2652, TGGTGT at 2634, TTATCT at 2627, TCCTTT at 2623, TGGTGT at 2600, TAATAT at 2548, TCCTGT at 2460, AAAACA at 2453, AAAAAA at 2451, TGATGT at 2428, TACTGT at 2412, AAATAA at 2347, AAAAAA at 2281, AGAAAA at 2279, AAAGAA at 2277, AAAAGA at 2276, AAAGTA at 2265, AGACAA at 2261, TGGTCT at 2228, AGACAA at 2183, ATAAGA at 2180, AGAGTA at 2175, AGATCA at 2168, TACTTT at 2146, TGGTGT at 2123, AGAGGA at 2081, AAAGAA at 1980, TGCTAT at 1837, AGACGA at 1734, TGGTCT at 1631, AAAGCA at 1182, TCCTCT at 710, ACAAAA at 147, AGAGGA at 142, AAAAGA at 137, ATAAGA at 117, ACATAA at 115, ACAAGA at 108, AGACCA at 103, TACTGT at 62, TCCTCT at 46.

H boxes (Mitchell) random dataset samplings

  1. HboxMr0: 71, ACAAAA at 4524, AGATTA at 4463, ACATAA at 4450, AGATGA at 4445, ATAAGA at 4442, ACATCA at 4437, AAAACA at 4432, AGACAA at 4235, AAAGTA at 3758, ACAACA at 3729, AGAAAA at 3657, ACAGAA at 3655, ATATAA at 3602, AAAGCA at 3597, ACAATA at 3577, AAAGTA at 3484, AAAGTA at 3340, ACAAAA at 3171, AGAATA at 3150, ATAGGA at 2939, AGACGA at 2908, ATATTA at 2852, AAATCA at 2809, ATAGGA at 2799, AAACGA at 2779, ATAAAA at 2737, AAAATA at 2697, AGAATA at 2677, ACACTA at 2555, AGAGGA at 2529, ATATTA at 2374, ACAAAA at 2333, AGACAA at 2331, ATAATA at 2263, AAATAA at 2261, AAAATA at 2260, AGACAA at 2183, ACACCA at 2165, AAAACA at 2086, ATACTA at 1964, AGAATA at 1961, AGAGAA at 1959, AGAGTA at 1872, AGATCA at 1853, AAATAA at 1790, AAACAA at 1576, AAAGGA at 1530, AAACGA at 1502, ATAAAA at 1499, AAATAA at 1497, ATAATA at 1492, ACAAGA at 1436, AAACCA at 1324, AAACCA at 1244, AGACGA at 1237, AGATGA at 1126, AAACCA at 1088, AAACTA at 833, AGAAAA at 634, AAAGAA at 632, AAAAGA at 593, ACAGCA at 579, AAATTA at 546, ATAGAA at 542, AAACAA at 502, AAACCA at 284, ATAAAA at 199, AAATAA at 197, AAAATA at 196, ATAATA at 146, AAATAA at 144.
  2. HboxMr1: 91, ATAGCA at 4504, AAACGA at 4456, ATAAAA at 4431, AGAAAA at 4354, ACAGAA at 4352, AGAGCA at 4258, AGAACA at 4240, ACAGAA at 4238, AAAAAA at 4011, AAAAAA at 4010, ATAGCA at 3887, AAAATA at 3884, AAACGA at 3875, AAAAGA at 3824, ATACGA at 3751, AGAGCA at 3746, AAAGGA at 3724, AGAATA at 3696, AAAACA at 3602, ATACAA at 3571, AAACCA at 3536, AAAAAA at 3488, ACAAAA at 3486, ACATAA at 3473, AAAGGA at 3449, AAATGA at 3442, ATATTA at 3417, AAAATA at 3364, ACAAGA at 3314, ACAGGA at 3275, AAAACA at 3272, AGAAAA at 3269, AGAGAA at 3267, ACACTA at 3259, ACAGCA at 3241, ACAAAA at 3175, AAATCA at 3170, ACATTA at 3144, AGAATA at 3081, AAAAAA at 3064, AAAAAA at 3063, AAAAAA at 3062, AAAAAA at 3061, AGATCA at 2996, ACATTA at 2911, AAAAAA at 2855, AGAAAA at 2798, AGACAA at 2749, ACAATA at 2699, ACATCA at 2620, AGAACA at 2607, AAAGGA at 2591, ACACTA at 2472, AAAGGA at 2459, ACAGCA at 2441, ACAAGA at 2420, ATAGTA at 2370, AAACCA at 2246, ACATGA at 1967, AAACGA at 1958, ACAAGA at 1947, ATACAA at 1945, ATACGA at 1826, ACAATA at 1823, AAACAA at 1821, AAAACA at 1820, AGATCA at 1780, AAAAGA at 1777, AAAACA at 1709, AGAGTA at 1552, AAAAAA at 1441, AAACGA at 1405, ACATCA at 1344, AAAACA at 1053, AGAAGA at 889, AAAGCA at 884, AAACCA at 784, ATAGGA at 754, ACAGCA at 745, AAACGA at 616, ACACTA at 372, ATATTA at 367, AGATTA at 362, ATATGA at 341, ATACAA at 300, AAAATA at 167, ATAAAA at 165, AGATAA at 163, AGAAGA at 160, ATATTA at 141, ACAGCA at 36.
  3. HboxMr2: 82, ATAACA at 4473, ACAACA at 4327, AAACAA at 4325, AAAACA at 4324, ACAAAA at 4322, AAAGCA at 4317, AAATCA at 4311, ACAAGA at 4199, AGACAA at 4197, ATAAGA at 4194, AAACTA at 4161, AAAGTA at 4156, ACATTA at 4069, ATAGTA at 4029, ATAATA at 3946, AGATAA at 3944, ATATAA at 3855, AAATGA at 3800, AAATTA at 3788, ACATTA at 3723, ATAGTA at 3689, ACAGCA at 3622, AGATTA at 3613, ATATTA at 3519, ACATAA at 3252, AAACCA at 3210, AAACCA at 3172, AAACAA at 3168, AAAGCA at 3151, ATAGGA at 3132, AGAGGA at 3038, AAAGAA at 2939, AAAGCA at 2915, AGACGA at 2904, ACAACA at 2832, AAAATA at 2666, ATATCA at 2481, AAACCA at 2443, AAATCA at 2384, AAAAGA at 2341, AGAAAA at 2339, AGAGCA at 2208, AAACAA at 2191, AAAACA at 2190, ACAAGA at 2029, AAACTA at 1852, AGAAAA at 1849, AAAGAA at 1847, AAAAGA at 1846, AGAAAA at 1844, ATAGAA at 1842, ATAATA at 1839, ACATAA at 1837, ACAGTA at 1832, AGATGA at 1827, ACAGCA at 1800, ATACCA at 1784, ACATTA at 1779, ATATGA at 1758, AAACCA at 1631, AAATTA at 1553, ATAGCA at 1432, ATATTA at 1327, AGACTA at 1115, ACAGTA at 1090, ACAGCA at 1042, ATAATA at 990, ACAGAA at 944, AAAACA at 941, AAAAAA at 939, AAAAAA at 938, AAAAAA at 937, AGAACA at 908, ACACAA at 510, AGAAAA at 472, AAATGA at 371, AGAAAA at 368, AGATTA at 337, AAACTA at 312, ATAAAA at 309, AAAGGA at 253, ACACAA at 60.
  4. HboxMr3: 62, ATAAAA at 4445, ATAAGA at 4418, AAATTA at 4345, AGAAAA at 4341, AGAGGA at 4292, AAACCA at 4240, AAACTA at 4228, AAAATA at 4175, ACAGCA at 4086, AAATAA at 3942, ATATTA at 3889, ATAGCA at 3806, ATAATA at 3799, AGACCA at 3738, AAAGGA at 3714, ACAAGA at 3644, AAAGCA at 3616, AAAGGA at 3597, AGACAA at 3486, AGAAGA at 3432, AGAGAA at 3430, AGACCA at 3388, AGACCA at 3307, AAACAA at 3265, AAAACA at 3264, AAAAAA at 3262, ATAGCA at 2963, AAACAA at 2923, AAAACA at 2922, AAAAAA at 2920, AGAAAA at 2918, AGATAA at 2774, ATAACA at 2747, ACAATA at 2744, AGACAA at 2742, ACATTA at 2732, ACACAA at 2702, AGAAGA at 2682, AGAGAA at 2680, AGAAGA at 2675, AAAGAA at 2082, AAAAGA at 2081, ATAAAA at 2079, AAACTA at 1853, AAATCA at 1837, AGAAAA at 1834, AAACTA at 1800, AAATTA at 1646, ACAGGA at 1344, ATAAGA at 1099, AGACCA at 1075, ATACCA at 828, AGACCA at 724, ATAAGA at 658, AGAAAA at 569, ACACTA at 564, ATAACA at 561, AAAAAA at 551, AAAAAA at 550, AAAAAA at 549, AAATGA at 539, ACATTA at 322.
  5. HboxMr4: 58, AAAATA at 4472, ACAAGA at 4397, AAATTA at 4373, ACAGCA at 4360, AAAGCA at 4326, AAATCA at 4186, ATATTA at 4163, AAACCA at 3907, AAAAAA at 3879, ACAGTA at 3479, AAACCA at 3447, AAAAAA at 3444, AAACTA at 3417, ACATTA at 3370, ACACTA at 3039, ATAAGA at 2995, AAAGAA at 2951, AGACGA at 2881, AAAGCA at 2876, AAAGGA at 2698, ACACCA at 2656, AAAAAA at 2514, AGAAAA at 2512, AAAAAA at 2339, AGAAAA at 2337, ACAAGA at 2306, ATATTA at 2297, ATACGA at 2230, AAAGTA at 2182, AGAAAA at 2179, AAACGA at 2137, AAAAGA at 1998, ACAAAA at 1971, ACACAA at 1969, AGAGCA at 1805, AAAATA at 1778, ACAAAA at 1776, ACACAA at 1774, AGAATA at 1694, ACAAGA at 1691, ATATGA at 1686, AAAGTA at 1643, AGAAAA at 1612, ATAGCA at 1592, AGACCA at 1574, ACAATA at 1569, AAAACA at 1251, AAAAAA at 1249, ATAGAA at 1098, AGATTA at 946, AAACTA at 602, AAACGA at 535, AAACAA at 531, AAATTA at 479, ATATTA at 164, AGAATA at 151, ATATCA at 116, AAACCA at 56.
  6. HboxMr5: 58, AAAGAA at 4338, AAAAGA at 4337, AAAAGA at 4323, AGAATA at 4306, AAATGA at 4286, AAAGAA at 4213, AAACGA at 4208, AAAATA at 4167, AGAGCA at 3978, ATAAGA at 3973, ACAATA at 3970, AAATGA at 3965, AAATTA at 3930, AAATTA at 3783, ACATAA at 3671, AAACTA at 3514, AAAGCA at 3478, ACAGAA at 3392, AAAGGA at 3363, AAAGGA at 3350, ACATAA at 3346, ATACCA at 3112, AAAATA at 3109, ATAGTA at 3049, ACATAA at 3043, ACATCA at 2924, AAAAAA at 2773, AAATGA at 2768, AAAGAA at 2764, ATACGA at 2279, AGAAAA at 2259, ATATGA at 1780, AGATCA at 1747, ACATCA at 1686, AAATGA at 1566, ACAGCA at 1520, AGACCA at 1458, AGAAGA at 1331, AGAGAA at 1329, ACAGCA at 1285, AAATTA at 1272, AAACTA at 1211, AGAACA at 1196, ACAACA at 1169, AAACAA at 1167, AGATAA at 1143, AAATTA at 1065, AAAAGA at 1035, ATACCA at 939, AGACCA at 765, AGATTA at 691, ATATAA at 671, AGAAGA at 556, ATAGAA at 540, AGAGCA at 380, AAACAA at 262, AAATCA at 135, AAAGAA at 30.
  7. HboxMr6: 71, ACAAAA at 4522, ATACAA at 4520, ATACAA at 4491, ACAGAA at 4402, ACAATA at 4397, ACAACA at 4394, AAAACA at 4327, AGATCA at 4311, AGAGGA at 4154, ATAACA at 4136, AGAGGA at 4031, ATAGAA at 3949, AAATTA at 3865, ACAACA at 3773, AAATGA at 3699, ATAAAA at 3696, AAATTA at 3683, ATAGAA at 3504, AAACCA at 3303, ATACGA at 3219, ACAGTA at 3209, AAATGA at 3190, AAAGCA at 2864, AAAAAA at 2861, ATAACA at 2725, ACATAA at 2723, ACATGA at 2602, ACAGGA at 2593, ACAAGA at 2588, ATACAA at 2586, ACAGAA at 2567, AGAGCA at 2506, ACAGTA at 2380, ATACTA at 2374, AGAGCA at 2326, ACATAA at 2315, ATATAA at 2239, ATAACA at 2206, AAAGTA at 2183, ATAACA at 2169, ACAATA at 2051, AGATAA at 2000, ATACAA at 1915, AGATAA at 1815, AAATTA at 1783, ACAAAA at 1779, ACAACA at 1608, AAAGGA at 1501, AAAGCA at 1444, AAAAAA at 1441, AAAAGA at 1239, AGACTA at 1204, ACAGAA at 1102, AAAGGA at 973, ACAAAA at 970, AGAGTA at 799, ACATCA at 794, ATAGGA at 778, AAACTA at 773, AAAAAA at 770, AAAAAA at 769, AAAAAA at 768, AAATGA at 749, AGAGTA at 711, AGAACA at 646, ATATCA at 627, AGAGGA at 372, ATATGA at 246, ATACAA at 180, AGAAAA at 69, ACAACA at 41.
  8. HboxMr7: 76, AAAGGA at 4550, AAAGAA at 4400, AAAGAA at 4396, AAAAGA at 4395, ATAAAA at 4393, AAACCA at 4204, AGATTA at 4147, ACACTA at 4116, AGATAA at 4076, AAATGA at 3964, ATACTA at 3923, AAAATA at 3920, ACAAAA at 3789, AAACAA at 3787, ATACAA at 3783, AGACCA at 3760, AAATAA at 3632, AGACAA at 3416, ACAGAA at 3408, AGATTA at 3375, AAAACA at 3158, ATAATA at 3107, ATATAA at 3056, AAACGA at 2983, AAATTA at 2957, ACAGTA at 2899, AAAGCA at 2892, ACAGGA at 2793, AAAGTA at 2771, ACAGAA at 2683, AAAATA at 2513, AAAATA at 2503, AGATTA at 2403, ACAGAA at 2280, AGAATA at 2238, AAAGGA at 2219, ATAGGA at 2068, AAAATA at 2065, ACACTA at 2037, AAATGA at 1953, AAATGA at 1835, ATAGCA at 1819, AGAAGA at 1796, ACATTA at 1650, AAAAGA at 1538, AGAATA at 1444, ATATAA at 1413, AGACCA at 1268, ACACCA at 1207, AAATGA at 1186, ACAGAA at 1128, AAATGA at 1114, AAATGA at 1037, AGAATA at 994, AGAAGA at 991, AAACTA at 886, AAAGAA at 819, AGATAA at 792, ATAACA at 741, ACAAGA at 705, ATAGGA at 529, ACAGAA at 515, ATACCA at 477, ACAAAA at 429, AAACAA at 427, AGAATA at 417, ATAGCA at 376, AAAGCA at 362, ACAAAA at 359, ATATTA at 308, AGATGA at 302, AAACTA at 282, ATATTA at 207, AAATAA at 144, AAAATA at 143, AGAAAA at 141.
  9. HboxMr8: 79, AAATAA at 4554, ACACTA at 4498, AGAACA at 4495, ATAGAA at 4493, ACACGA at 4339, AGACCA at 4293, ATAGGA at 4225, ACAAAA at 4211, ATAGCA at 4198, AAAAAA at 4111, AGAAAA at 4109, AAACGA at 4100, ACAAAA at 4097, ATATAA at 3982, ATATTA at 3912, AAAGAA at 3874, ATACGA at 3700, AAAGTA at 3685, AGATAA at 3578, ATATTA at 3557, ATATTA at 3506, AGAGGA at 3479, AAAAAA at 3103, AAAGTA at 3098, AAAGAA at 3079, AAATCA at 2981, ACACCA at 2711, AAAAAA at 2699, AAACAA at 2656, AAAACA at 2409, AGACCA at 2229, ATATGA at 2190, ACATTA at 2185, AGAATA at 2169, AAAGAA at 2167, AAAAGA at 2166, ACAAAA at 2132, AAACAA at 2130, AGAGAA at 2116, AAAAGA at 2113, AAACAA at 2103, AAAACA at 2102, AAATTA at 2083, AAATTA at 1959, ACACCA at 1949, ATAACA at 1842, ATACCA at 1798, AAAGAA at 1686, AAAAGA at 1685, ACATTA at 1506, AGATCA at 1501, AAAAAA at 1476, AGAGAA at 1293, AAACGA at 1037, AAAAAA at 1034, ATAAAA at 1032, ACAATA at 990, AAATGA at 964, ATAAAA at 926, AAAGAA at 883, ATATTA at 878, AGATCA at 865, ATACTA at 850, ATAATA at 783, AAACTA at 724, ATAAAA at 707, AAACCA at 558, ACACCA at 493, AAACAA at 479, ACATAA at 434, AAAAAA at 388, ATAGGA at 335, AGATGA at 326, AAAGAA at 312, AAAAGA at 311, AGAAAA at 282, ACAACA at 232, ACACTA at 200, AAATCA at 141.
  10. HboxMr9: 75, AGATGA at 4486, ATAACA at 4431, AAAGGA at 4318, AGAGGA at 4185, ATAATA at 4170, AGATAA at 4168, AGAGTA at 4151, ACATAA at 4141, AAATTA at 4055, AAAAGA at 3856, AGAAAA at 3853, AAACGA at 3847, AAACTA at 3794, ACAAAA at 3784, ATATCA at 3775, AGAGAA at 3489, ATAGCA at 3469, AAACAA at 3459, ACAACA at 3454, ACACAA at 3452, AAACTA at 3309, ACACCA at 3187, AAAACA at 3184, AAACGA at 3153, ATATAA at 3149, ACATAA at 3083, ATACCA at 3078, ACAATA at 3075, AAACTA at 3069, ACATGA at 2920, AAAATA at 2911, AGAATA at 2846, ATAAAA at 2622, AAAGAA at 2460, AGACGA at 2426, AAACTA at 2390, ACAAAA at 2387, AAACAA at 2385, AGAGTA at 2380, AAACAA at 2091, AAAACA at 2090, AAATGA at 2078, ATAGAA at 1929, AAACGA at 1867, ACAAAA at 1750, AAACAA at 1748, AGAGCA at 1512, ACAAAA at 1408, AAAGGA at 1383, AAATAA at 1379, AAAAAA at 1304, AAAAAA at 1303, AAAAAA at 1302, AAAAAA at 1301, ACAAAA at 1299, ACATAA at 1227, ATAACA at 1224, AAATTA at 1167, ACATTA at 1157, ACACAA at 1097, ACAACA at 948, ATAGGA at 943, AAAAAA at 678, ATAGCA at 673, AAAGGA at 589, AGAAAA at 586, AAAATA at 407, AAAAAA at 405, AAAAAA at 404, AGAAAA at 402, ACACGA at 381, AGACGA at 286, AAACCA at 182, ACAACA at 72, ACAGTA at 14.
  11. HboxMr0ci: 105, TGCTGT at 4533, TGTTTT at 4376, TCCTCT at 4371, TTATTT at 4228, TATTAT at 4226, TTCTAT at 4223, TATTTT at 4202, TTATTT at 4201, TTGTTT at 4179, TGCTTT at 4175, TCTTGT at 4105, TTATCT at 4102, TGCTAT at 4014, TTTTAT at 4005, TCATAT at 3962, TCTTTT at 3942, TTCTGT at 3930, TAATTT at 3694, TTCTGT at 3668, TTATCT at 3618, TCGTAT at 3562, TGTTAT at 3471, TTATGT at 3375, TCTTCT at 3266, TCATCT at 3263, TGTTTT at 3182, TTGTTT at 3181, TGGTTT at 3177, TCATGT at 3098, TGTTTT at 3080, TAGTTT at 3030, TGATTT at 3023, TCGTCT at 2985, TTTTTT at 2955, TACTTT at 2952, TTGTAT at 2935, TCATAT at 2850, TCTTCT at 2830, TGATTT at 2825, TCATCT at 2812, TTTTCT at 2569, TCTTCT at 2542, TTATAT at 2372, TAGTTT at 2343, TCCTGT at 2253, TTGTAT at 2244, TGTTAT at 2177, TCATAT at 2150, TATTTT at 2145, TTATAT at 2142, TTATGT at 2113, TACTTT at 2109, TCCTAT at 2060, TTATGT at 2054, TCTTAT at 2052, TGGTGT at 2025, TGCTCT at 1998, TGTTCT at 1979, TTCTCT at 1974, TTTTCT at 1972, TGTTTT at 1970, TACTAT at 1965, TGGTGT at 1939, TACTCT at 1906, TGGTTT at 1901, TTATGT at 1824, TTTTAT at 1822, TGATTT at 1819, TCGTTT at 1755, TTTTCT at 1673, TGTTTT at 1671, TTGTTT at 1670, TTATTT at 1642, TGGTTT at 1638, TATTTT at 1569, TCCTGT at 1551, TCGTAT at 1543, TGATTT at 1459, TTTTTT at 1454, TTTTTT at 1453, TACTCT at 1427, TTTTCT at 1195, TCCTCT at 1134, TACTTT at 1020, TCCTGT at 1009, TTGTAT at 987, TGCTTT at 983, TACTCT at 853, TTTTTT at 656, TCTTTT at 654, TTCTTT at 653, TGTTTT at 605, TAATGT at 602, TAGTTT at 563, TTTTAT at 496, TATTTT at 494, TAATTT at 474, TCTTAT at 338, TTTTAT at 226, TTTTTT at 224, TTTTTT at 223, TTGTAT at 155, TGTTGT at 153, TAATGT at 150, TGTTGT at 17.
  12. HboxMr1ci: 78, TTTTAT at 4495, TGATCT at 4399, TAGTTT at 4270, TTTTTT at 4229, TTTTTT at 4228, TGCTTT at 4225, TGGTAT at 4209, TGATAT at 4163, TGCTCT at 4064, TGATTT at 4034, TTGTGT at 3975, TGGTCT at 3958, TCTTGT at 3864, TATTCT at 3702, TCCTTT at 3645, TTATTT at 3610, TTTTAT at 3608, TAGTGT at 3511, TTTTTT at 3455, TCGTAT at 3413, TTATCT at 3378, TGTTAT at 3376, TGGTTT at 3342, TGATGT at 3286, TTATCT at 3099, TTATTT at 3095, TCTTAT at 3093, TTTTAT at 3046, TTTTTT at 3032, TCCTTT at 3012, TGATGT at 2949, TCTTTT at 2673, TGATCT at 2627, TAATGT at 2527, TGGTAT at 2507, TCTTTT at 2288, TACTTT at 2179, TGATAT at 2174, TTGTTT at 2162, TATTTT at 2141, TAGTGT at 2024, TCATAT at 1994, TCCTGT at 1802, TGGTGT at 1743, TTTTTT at 1665, TCGTTT at 1655, TAGTGT at 1580, TTCTCT at 1566, TTATGT at 1544, TTTTTT at 1484, TGGTTT at 1392, TCGTGT at 1378, TTCTTT at 1278, TTTTCT at 1276, TTATAT at 1266, TATTAT at 1264, TAATTT at 1243, TGTTCT at 1218, TGATAT at 1107, TAATGT at 1047, TAGTGT at 969, TGGTTT at 922, TAGTCT at 904, TTTTCT at 831, TAATTT at 827, TATTTT at 767, TTCTAT at 764, TCCTTT at 711, TCCTTT at 653, TTATGT at 533, TACTAT at 376, TTATAT at 365, TTATAT at 339, TGGTCT at 286, TTTTGT at 281, TATTAT at 251, TGCTCT at 133, TTGTCT at 7.
  13. HboxMr2ci: 70, TTTTGT at 4486, TCGTAT at 4245, TGTTAT at 4216, TGATTT at 4143, TGTTTT at 4113, TTATTT at 4072, TAGTAT at 4030, TCCTCT at 3967, TGATCT at 3762, TCCTCT at 3628, TTATTT at 3616, TTATCT at 3576, TTCTTT at 3572, TGATAT at 3535, TGGTTT at 3492, TCGTCT at 3386, TCCTCT at 3234, TCATCT at 3225, TGCTTT at 3188, TAATTT at 3115, TTGTCT at 3099, TGGTCT at 2962, TCCTGT at 2879, TCTTAT at 2852, TTTTTT at 2825, TTCTCT at 2740, TTGTCT at 2535, TGTTGT at 2533, TTTTGT at 2530, TTCTTT at 2466, TGGTTT at 2462, TACTAT at 2411, TCGTAT at 2355, TTGTTT at 2348, TCATCT at 2169, TGCTCT at 2164, TCGTGT at 1998, TCCTCT at 1977, TAGTCT at 1899, TTTTTT at 1681, TAGTTT at 1653, TTATGT at 1584, TTCTGT at 1513, TGGTAT at 1387, TATTTT at 1374, TGGTCT at 1338, TTGTAT at 1272, TCTTGT at 1270, TGATTT at 1245, TCCTGT at 1204, TGATCT at 1193, TCATCT at 1061, TGGTTT at 1056, TGGTTT at 1026, TTATGT at 862, TTTTAT at 860, TAATCT at 828, TAGTCT at 783, TCGTTT at 738, TCCTGT at 725, TCGTTT at 717, TGATGT at 701, TCTTCT at 696, TCGTTT at 445, TATTTT at 262, TGTTTT at 245, TAATGT at 242, TCCTTT at 223, TCATCT at 202, TATTTT at 34.
  14. HboxMr3ci: 85, TGATCT at 4373, TAATTT at 4349, TACTGT at 4335, TGCTTT at 4322, TGTTTT at 4101, TTGTTT at 4100, TCTTGT at 4098, TAATTT at 4093, TTTTTT at 4072, TGCTTT at 4069, TAATTT at 4050, TGGTCT at 4012, TTGTTT at 4004, TATTGT at 4002, TTGTAT at 3999, TATTAT at 3890, TAGTGT at 3852, TAATAT at 3800, TTTTGT at 3760, TCTTTT at 3693, TTCTTT at 3692, TCCTCT at 3543, TGGTTT at 3531, TGGTGT at 3294, TTTTTT at 3167, TGATAT at 3121, TTTTTT at 3067, TCCTCT at 3030, TAGTTT at 3021, TCGTTT at 3016, TAGTTT at 2955, TCTTTT at 2811, TTGTCT at 2808, TTGTTT at 2783, TAATTT at 2615, TATTCT at 2606, TGCTTT at 2469, TCATTT at 2326, TCCTAT at 2283, TTGTTT at 2266, TACTTT at 2223, TAGTGT at 2204, TCGTGT at 2199, TGCTTT at 2025, TGATTT at 2018, TTTTTT at 1914, TTTTTT at 1913, TCTTAT at 1872, TCCTTT at 1847, TCCTAT at 1637, TAGTGT at 1572, TTATGT at 1562, TCATTT at 1558, TTCTTT at 1541, TAGTCT at 1266, TGCTCT at 1152, TCATGT at 1133, TGATCT at 1126, TGGTTT at 1110, TGATTT at 1087, TTGTTT at 1029, TTTTGT at 1027, TCTTTT at 1025, TTCTTT at 1024, TCTTCT at 1022, TCTTCT at 988, TCATTT at 924, TAATTT at 919, TTATCT at 771, TCCTTT at 733, TGTTGT at 639, TCGTCT at 614, TCATGT at 577, TTGTTT at 531, TGCTCT at 467, TTGTTT at 449, TAATTT at 408, TCCTGT at 350, TTCTGT at 334, TCTTCT at 332, TGCTTT at 316, TGCTTT at 287, TATTTT at 170, TCTTTT at 148, TGGTCT at 26.
  15. HboxMr4ci: 89, TTATGT at 4540, TTTTAT at 4538, TTTTAT at 4526, TACTTT at 4523, TCCTAT at 4488, TCTTCT at 4478, TCTTAT at 4463, TGGTTT at 4423, TCTTAT at 4301, TTATAT at 4253, TAATAT at 4161, TAATGT at 4053, TGCTGT at 4039, TACTGT at 3992, TCTTCT at 3987, TAATCT at 3984, TCTTTT at 3926, TTATGT at 3866, TACTCT at 3852, TTGTCT at 3797, TTATAT at 3720, TAATTT at 3672, TTATGT at 3538, TTTTAT at 3536, TGTTTT at 3533, TTGTTT at 3532, TTTTGT at 3517, TATTTT at 3515, TTATTT at 3514, TCTTAT at 3512, TATTTT at 3354, TGGTGT at 3325, TGGTTT at 3205, TTATTT at 3017, TAGTAT at 3007, TGGTGT at 2759, TGGTTT at 2591, TAGTGT at 2485, TTGTTT at 2437, TAGTTT at 2398, TTATAT at 2295, TTTTGT at 2257, TATTTT at 2255, TTATTT at 2254, TTGTCT at 2163, TACTTT at 2127, TACTTT at 2018, TCCTTT at 2012, TGATGT at 1822, TTGTAT at 1794, TTTTGT at 1792, TCTTTT at 1790, TTCTTT at 1789, TCTTGT at 1766, TCCTTT at 1731, TCTTCT at 1701, TAATCT at 1698, TCATAT at 1684, TTATCT at 1679, TCATTT at 1675, TTCTAT at 1588, TCATCT at 1533, TCTTTT at 1423, TTTTAT at 1407, TTGTCT at 1353, TATTGT at 1351, TTTTAT at 1348, TAATGT at 1315, TGCTGT at 1310, TTATAT at 1262, TCGTTT at 1186, TGCTCT at 1066, TGGTAT at 973, TTTTTT at 846, TTTTTT at 845, TTTTTT at 844, TCCTTT at 827, TCCTGT at 801, TAGTCT at 609, TCCTTT at 593, TCTTTT at 472, TTCTTT at 471, TTCTTT at 365, TTTTCT at 363, TCGTTT at 360, TTATCT at 167, TATTAT at 165, TGATAT at 114, TTTTCT at 44.
  16. HboxMr5ci: 71, TGGTTT at 4536, TATTCT at 4505, TGATAT at 4502, TGATTT at 4195, TAATCT at 4184, TAGTTT at 4108, TCATTT at 4054, TAGTCT at 4009, TGATGT at 3711, TTTTTT at 3706, TATTTT at 3704, TTCTTT at 3694, TTATTT at 3655, TTATTT at 3628, TTTTCT at 3439, TTTTTT at 3357, TTTTTT at 3356, TGGTTT at 3269, TTCTTT at 3222, TCTTCT at 3195, TAGTAT at 3050, TTTTTT at 2954, TCTTGT at 2853, TTGTGT at 2837, TATTGT at 2835, TGATGT at 2782, TGGTGT at 2732, TTTTAT at 2708, TTCTTT at 2559, TCGTTT at 2543, TTCTTT at 2527, TGTTCT at 2442, TTATAT at 2179, TTGTCT at 2173, TGTTTT at 2074, TAATCT at 2062, TTCTTT at 1980, TTTTCT at 1978, TACTCT at 1622, TGATTT at 1447, TTTTTT at 1416, TAGTTT at 1413, TAATCT at 1317, TCTTTT at 1265, TAGTCT at 1262, TGTTTT at 1149, TAATGT at 1146, TAATTT at 1109, TCGTTT at 1093, TCGTCT at 1019, TGGTCT at 1014, TTATGT at 975, TGTTCT at 958, TCGTTT at 947, TGGTTT at 932, TATTTT at 860, TTATTT at 859, TTATTT at 855, TGTTTT at 831, TGCTGT at 724, TTGTGT at 323, TTTTGT at 321, TAGTTT at 318, TATTTT at 273, TTATTT at 272, TTTTAT at 270, TACTGT at 169, TGCTGT at 164, TTCTAT at 148, TATTTT at 111, TGGTAT at 90.
  17. HboxMr6ci: 78, TGGTTT at 4530, TCGTCT at 4510, TTCTGT at 4483, TGGTTT at 4479, TAATAT at 4427, TCTTGT at 4412, TTGTGT at 4365, TCTTCT at 4321, TTATTT at 4265, TTCTCT at 4004, TCTTCT at 4002, TCCTTT at 3956, TGCTTT at 3923, TTATTT at 3857, TCATTT at 3760, TGCTGT at 3566, TTCTTT at 3474, TATTCT at 3472, TGCTTT at 3352, TCCTTT at 3294, TCCTTT at 3281, TCCTCT at 3269, TTCTAT at 3180, TCCTCT at 3124, TGATCT at 3048, TCGTTT at 3013, TGGTGT at 2946, TCCTAT at 2854, TTATCT at 2808, TTTTGT at 2652, TCGTAT at 2513, TTCTCT at 2444, TATTGT at 2420, TTTTAT at 2417, TCTTTT at 2394, TAGTTT at 2344, TAATGT at 2102, TAGTTT at 2077, TAATAT at 2036, TAATGT at 2003, TACTTT at 1993, TCTTCT at 1988, TTGTCT at 1985, TGTTAT at 1749, TTGTGT at 1746, TCTTGT at 1744, TACTCT at 1728, TTTTGT at 1702, TAATTT at 1654, TAGTTT at 1631, TTCTTT at 1530, TTCTCT at 1517, TCTTTT at 1372, TCTTCT at 1356, TCATGT at 1341, TAGTTT at 1317, TACTGT at 1312, TTATGT at 1289, TGCTTT at 1259, TTATTT at 1143, TCGTCT at 1085, TGCTGT at 997, TTGTAT at 913, TGATCT at 880, TAGTTT at 875, TATTGT at 860, TTATAT at 832, TCTTAT at 830, TGTTCT at 827, TGCTGT at 824, TAATTT at 815, TAGTCT at 803, TTATGT at 472, TGGTAT at 434, TAATTT at 402, TTCTGT at 262, TTATTT at 186, TGGTGT at 99.
  18. HboxMr7ci: 65, TATTCT at 4534, TGTTAT at 4522, TTATGT at 4519, TCCTCT at 4505, TAATGT at 4445, TGCTCT at 4367, TGGTCT at 4356, TCGTGT at 4302, TTCTGT at 4272, TTTTCT at 4270, TGGTTT at 4267, TTATAT at 4253, TCGTAT at 4192, TCCTGT at 4129, TACTTT at 4120, TACTTT at 3927, TAATTT at 3913, TGGTTT at 3727, TATTGT at 3600, TCCTAT at 3585, TCCTTT at 3579, TGGTAT at 3474, TTTTTT at 3459, TTTTTT at 3458, TTTTTT at 3457, TTTTTT at 3456, TTTTTT at 3455, TAATTT at 3452, TCCTTT at 3275, TCCTAT at 3224, TCCTTT at 3173, TGGTCT at 3122, TGCTTT at 2837, TGTTTT at 2821, TATTTT at 2517, TTGTTT at 2449, TAATTT at 2253, TAATTT at 2242, TCCTCT at 2126, TAGTTT at 2118, TCATTT at 1893, TTCTTT at 1888, TGTTCT at 1886, TTATTT at 1808, TCCTCT at 1627, TAGTGT at 1531, TCGTGT at 1401, TCTTCT at 1359, TTATGT at 1326, TCATCT at 1158, TCGTTT at 1088, TGATCT at 1003, TGCTGT at 876, TAGTTT at 766, TTCTAT at 737, TAGTCT at 719, TTCTGT at 714, TTTTCT at 712, TGGTTT at 608, TTTTGT at 492, TTTTTT at 349, TATTAT at 309, TAATGT at 246, TCATAT at 205, TGATTT at 110.
  19. HboxMr8ci: 60, TAGTTT at 4397, TCCTAT at 4352, TACTAT at 4307, TACTCT at 3947, TGGTTT at 3923, TATTGT at 3510, TATTAT at 3507, TCCTGT at 3449, TAGTTT at 3396, TGCTTT at 3380, TCATTT at 3334, TGGTTT at 3120, TTCTAT at 3068, TATTGT at 2967, TAGTAT at 2964, TAATCT at 2927, TTTTTT at 2543, TGATTT at 2540, TTGTTT at 2382, TTATTT at 2331, TCTTAT at 2329, TCCTAT at 2324, TTTTAT at 2293, TTTTTT at 2291, TGATCT at 2193, TTATAT at 2188, TCGTAT at 2140, TTGTCT at 2035, TAGTTT at 1924, TCGTCT at 1876, TAGTTT at 1850, TCGTTT at 1832, TACTCT at 1772, TCTTCT at 1397, TTATCT at 1366, TACTTT at 1350, TTATCT at 1337, TTCTGT at 1283, TTGTTT at 1230, TCCTAT at 1198, TTATGT at 1171, TGTTAT at 1169, TGCTTT at 1164, TAGTTT at 981, TTTTGT at 955, TCATAT at 876, TATTTT at 740, TTATTT at 739, TAATTT at 728, TTCTTT at 651, TTGTAT at 568, TGGTGT at 535, TCTTGT at 402, TTCTAT at 264, TGTTCT at 217, TATTTT at 166, TTTTAT at 77, TCGTCT at 63, TTGTTT at 44, TATTCT at 34.
  20. HboxMr9ci: 79, TTGTAT at 4336, TTTTGT at 4334, TCTTTT at 4332, TATTTT at 4271, TATTCT at 4179, TTATAT at 3989, TCATGT at 3778, TCGTTT at 3594, TTGTTT at 3413, TCTTGT at 3411, TTTTTT at 3387, TTGTAT at 3317, TAATGT at 3296, TACTTT at 3255, TTGTTT at 3168, TGATTT at 3115, TCTTCT at 3106, TCGTTT at 3027, TATTCT at 2970, TCGTTT at 2898, TGCTAT at 2815, TTCTCT at 2753, TGGTTT at 2706, TCCTAT at 2618, TCTTAT at 2580, TTTTGT at 2513, TTCTAT at 2347, TTTTCT at 2345, TCATTT at 2341, TCTTTT at 2313, TTCTTT at 2312, TACTGT at 2253, TTGTTT at 2248, TGGTGT at 2203, TTATAT at 2123, TTATCT at 1991, TCGTAT at 1983, TCATGT at 1974, TTCTTT at 1942, TTGTAT at 1925, TCCTTT at 1907, TGATTT at 1741, TTGTTT at 1734, TCCTTT at 1542, TCTTCT at 1537, TGTTCT at 1534, TCATGT at 1531, TTTTCT at 1353, TGTTTT at 1124, TGTTTT at 1078, TTGTAT at 1073, TTCTCT at 1052, TTATTT at 967, TGGTCT at 926, TTTTTT at 902, TGGTGT at 850, TTTTTT at 836, TATTTT at 834, TTATTT at 808, TGTTTT at 717, TTCTGT at 714, TCGTTT at 705, TTGTAT at 620, TACTGT at 551, TGGTAT at 474, TTTTGT at 469, TATTTT at 467, TTATTT at 466, TGCTAT at 440, TTCTAT at 353, TTTTCT at 351, TCGTTT at 347, TTTTAT at 161, TATTTT at 159, TGCTAT at 156, TTGTTT at 96, TGGTTT at 92, TTGTCT at 24, TAGTGT at 18.

HboxMr arbitrary UTRs

  1. HboxMr0: ACAAAA at 4524, AGATTA at 4463, ACATAA at 4450, AGATGA at 4445, ATAAGA at 4442, ACATCA at 4437, AAAACA at 4432, AGACAA at 4235, AAAGTA at 3758, ACAACA at 3729, AGAAAA at 3657, ACAGAA at 3655, ATATAA at 3602, AAAGCA at 3597, ACAATA at 3577, AAAGTA at 3484, AAAGTA at 3340, ACAAAA at 3171, AGAATA at 3150, ATAGGA at 2939, AGACGA at 2908, ATATTA at 2852.
  2. HboxMr2: ATAACA at 4473, ACAACA at 4327, AAACAA at 4325, AAAACA at 4324, ACAAAA at 4322, AAAGCA at 4317, AAATCA at 4311, ACAAGA at 4199, AGACAA at 4197, ATAAGA at 4194, AAACTA at 4161, AAAGTA at 4156, ACATTA at 4069, ATAGTA at 4029, ATAATA at 3946, AGATAA at 3944, ATATAA at 3855, AAATGA at 3800, AAATTA at 3788, ACATTA at 3723, ATAGTA at 3689, ACAGCA at 3622, AGATTA at 3613, ATATTA at 3519, ACATAA at 3252, AAACCA at 3210, AAACCA at 3172, AAACAA at 3168, AAAGCA at 3151, ATAGGA at 3132, AGAGGA at 3038, AAAGAA at 2939, AAAGCA at 2915, AGACGA at 2904.
  3. HboxMr4: AAAATA at 4472, ACAAGA at 4397, AAATTA at 4373, ACAGCA at 4360, AAAGCA at 4326, AAATCA at 4186, ATATTA at 4163, AAACCA at 3907, AAAAAA at 3879, ACAGTA at 3479, AAACCA at 3447, AAAAAA at 3444, AAACTA at 3417, ACATTA at 3370, ACACTA at 3039, ATAAGA at 2995, AAAGAA at 2951, AGACGA at 2881, AAAGCA at 2876.
  4. HboxMr6: ACAAAA at 4522, ATACAA at 4520, ATACAA at 4491, ACAGAA at 4402, ACAATA at 4397, ACAACA at 4394, AAAACA at 4327, AGATCA at 4311, AGAGGA at 4154, ATAACA at 4136, AGAGGA at 4031, ATAGAA at 3949, AAATTA at 3865, ACAACA at 3773, AAATGA at 3699, ATAAAA at 3696, AAATTA at 3683, ATAGAA at 3504, AAACCA at 3303, ATACGA at 3219, ACAGTA at 3209, AAATGA at 3190, AAAGCA at 2864, AAAAAA at 2861.
  5. HboxMr8: AAATAA at 4554, ACACTA at 4498, AGAACA at 4495, ATAGAA at 4493, ACACGA at 4339, AGACCA at 4293, ATAGGA at 4225, ACAAAA at 4211, ATAGCA at 4198, AAAAAA at 4111, AGAAAA at 4109, AAACGA at 4100, ACAAAA at 4097, ATATAA at 3982, ATATTA at 3912, AAAGAA at 3874, ATACGA at 3700, AAAGTA at 3685, AGATAA at 3578, ATATTA at 3557, ATATTA at 3506, AGAGGA at 3479, AAAAAA at 3103, AAAGTA at 3098, AAAGAA at 3079, AAATCA at 2981.
  6. HboxMr0ci: TGCTGT at 4533, TGTTTT at 4376, TCCTCT at 4371, TTATTT at 4228, TATTAT at 4226, TTCTAT at 4223, TATTTT at 4202, TTATTT at 4201, TTGTTT at 4179, TGCTTT at 4175, TCTTGT at 4105, TTATCT at 4102, TGCTAT at 4014, TTTTAT at 4005, TCATAT at 3962, TCTTTT at 3942, TTCTGT at 3930, TAATTT at 3694, TTCTGT at 3668, TTATCT at 3618, TCGTAT at 3562, TGTTAT at 3471, TTATGT at 3375, TCTTCT at 3266, TCATCT at 3263, TGTTTT at 3182, TTGTTT at 3181, TGGTTT at 3177, TCATGT at 3098, TGTTTT at 3080, TAGTTT at 3030, TGATTT at 3023, TCGTCT at 2985, TTTTTT at 2955, TACTTT at 2952, TTGTAT at 2935, TCATAT at 2850.
  7. HboxMr2ci: TTTTGT at 4486, TCGTAT at 4245, TGTTAT at 4216, TGATTT at 4143, TGTTTT at 4113, TTATTT at 4072, TAGTAT at 4030, TCCTCT at 3967, TGATCT at 3762, TCCTCT at 3628, TTATTT at 3616, TTATCT at 3576, TTCTTT at 3572, TGATAT at 3535, TGGTTT at 3492, TCGTCT at 3386, TCCTCT at 3234, TCATCT at 3225, TGCTTT at 3188, TAATTT at 3115, TTGTCT at 3099, TGGTCT at 2962, TCCTGT at 2879, TCTTAT at 2852.
  8. HboxMr4ci: TTATGT at 4540, TTTTAT at 4538, TTTTAT at 4526, TACTTT at 4523, TCCTAT at 4488, TCTTCT at 4478, TCTTAT at 4463, TGGTTT at 4423, TCTTAT at 4301, TTATAT at 4253, TAATAT at 4161, TAATGT at 4053, TGCTGT at 4039, TACTGT at 3992, TCTTCT at 3987, TAATCT at 3984, TCTTTT at 3926, TTATGT at 3866, TACTCT at 3852, TTGTCT at 3797, TTATAT at 3720, TAATTT at 3672, TTATGT at 3538, TTTTAT at 3536, TGTTTT at 3533, TTGTTT at 3532, TTTTGT at 3517, TATTTT at 3515, TTATTT at 3514, TCTTAT at 3512, TATTTT at 3354, TGGTGT at 3325, TGGTTT at 3205, TTATTT at 3017, TAGTAT at 3007.
  9. HboxMr6ci: TGGTTT at 4530, TCGTCT at 4510, TTCTGT at 4483, TGGTTT at 4479, TAATAT at 4427, TCTTGT at 4412, TTGTGT at 4365, TCTTCT at 4321, TTATTT at 4265, TTCTCT at 4004, TCTTCT at 4002, TCCTTT at 3956, TGCTTT at 3923, TTATTT at 3857, TCATTT at 3760, TGCTGT at 3566, TTCTTT at 3474, TATTCT at 3472, TGCTTT at 3352, TCCTTT at 3294, TCCTTT at 3281, TCCTCT at 3269, TTCTAT at 3180, TCCTCT at 3124, TGATCT at 3048, TCGTTT at 3013, TGGTGT at 2946, TCCTAT at 2854.
  10. HboxMr8ci: TAGTTT at 4397, TCCTAT at 4352, TACTAT at 4307, TACTCT at 3947, TGGTTT at 3923, TATTGT at 3510, TATTAT at 3507, TCCTGT at 3449, TAGTTT at 3396, TGCTTT at 3380, TCATTT at 3334, TGGTTT at 3120, TTCTAT at 3068, TATTGT at 2967, TAGTAT at 2964, TAATCT at 2927.

HboxMr alternate UTRs

  1. HboxMr1: ATAGCA at 4504, AAACGA at 4456, ATAAAA at 4431, AGAAAA at 4354, ACAGAA at 4352.
  2. HboxMr3: ATAAAA at 4445, ATAAGA at 4418, AAATTA at 4345, AGAAAA at 4341, AGAGGA at 4292.
  3. HboxMr5: AAAGAA at 4338, AAAAGA at 4337, AAAAGA at 4323, AGAATA at 4306, AAATGA at 4286.
  4. HboxMr7: AAAGGA at 4550, AAAGAA at 4400, AAAGAA at 4396, AAAAGA at 4395, ATAAAA at 4393.
  5. HboxMr9: AGATGA at 4486, ATAACA at 4431, AAAGGA at 4318.
  6. HboxMr1ci: TTTTAT at 4495, TGATCT at 4399, TAGTTT at 4270.
  7. HboxMr3ci: TGATCT at 4373, TAATTT at 4349, TACTGT at 4335, TGCTTT at 4322.
  8. HboxMr5ci: TGGTTT at 4536, TATTCT at 4505, TGATAT at 4502.
  9. HboxMr7ci: TATTCT at 4534, TGTTAT at 4522, TTATGT at 4519, TCCTCT at 4505, TAATGT at 4445, TGCTCT at 4367, TGGTCT at 4356, TCGTGT at 4302, TTCTGT at 4272, TTTTCT at 4270, TGGTTT at 4267.
  10. Hboxr9ci: TTGTAT at 4336, TTTTGT at 4334, TCTTTT at 4332, TATTTT at 4271.
  1. HboxMr1: AGAGCA at 4258, AGAACA at 4240, ACAGAA at 4238.
  2. HboxMr3: AAACCA at 4240, AAACTA at 4228, AAAATA at 4175, ACAGCA at 4086.
  3. HboxMr5: AAAGAA at 4213.
  4. HboxMr7: AAACCA at 4204, AGATTA at 4147, ACACTA at 4116, AGATAA at 4076.
  5. HboxMr9: AGAGGA at 4185, ATAATA at 4170, AGATAA at 4168, AGAGTA at 4151, ACATAA at 4141, AAATTA at 4055.
  6. HboxMr1ci: TTTTTT at 4229, TTTTTT at 4228, TGCTTT at 4225, TGGTAT at 4209, TGATAT at 4163, TGCTCT at 4064.
  7. HboxMr3ci: TGTTTT at 4101, TTGTTT at 4100, TCTTGT at 4098, TAATTT at 4093, TTTTTT at 4072, TGCTTT at 4069, TAATTT at 4050.
  8. HboxMr5ci: TGATTT at 4195, TAATCT at 4184, TAGTTT at 4108, TCATTT at 4054.
  9. HboxMr7ci: TTATAT at 4253, TCGTAT at 4192, TCCTGT at 4129, TACTTT at 4120.
  10. HboxMr9ci: TATTCT at 4179.
  1. HboxMr1: AAAAAA at 4011, AAAAAA at 4010, ATAGCA at 3887, AAAATA at 3884, AAACGA at 3875, AAAAGA at 3824, ATACGA at 3751, AGAGCA at 3746, AAAGGA at 3724, AGAATA at 3696, AAAACA at 3602, ATACAA at 3571, AAACCA at 3536, AAAAAA at 3488, ACAAAA at 3486, ACATAA at 3473, AAAGGA at 3449, AAATGA at 3442, ATATTA at 3417, AAAATA at 3364, ACAAGA at 3314, ACAGGA at 3275, AAAACA at 3272, AGAAAA at 3269, AGAGAA at 3267, ACACTA at 3259, ACAGCA at 3241, ACAAAA at 3175, AAATCA at 3170, ACATTA at 3144, AGAATA at 3081, AAAAAA at 3064, AAAAAA at 3063, AAAAAA at 3062, AAAAAA at 3061, AGATCA at 2996, ACATTA at 2911, AAAAAA at 2855.
  2. HboxMr3: AAATAA at 3942, ATATTA at 3889, ATAGCA at 3806, ATAATA at 3799, AGACCA at 3738, AAAGGA at 3714, ACAAGA at 3644, AAAGCA at 3616, AAAGGA at 3597, AGACAA at 3486, AGAAGA at 3432, AGAGAA at 3430, AGACCA at 3388, AGACCA at 3307, AAACAA at 3265, AAAACA at 3264, AAAAAA at 3262, ATAGCA at 2963, AAACAA at 2923, AAAACA at 2922, AAAAAA at 2920, AGAAAA at 2918.
  3. HboxMr5: 58, AAAGAA at 4338, AAAAGA at 4337, AAAAGA at 4323, AGAATA at 4306, AAATGA at 4286, AAAGAA at 4213, AAACGA at 4208, AAAATA at 4167, AGAGCA at 3978, ATAAGA at 3973, ACAATA at 3970, AAATGA at 3965, AAATTA at 3930, AAATTA at 3783, ACATAA at 3671, AAACTA at 3514, AAAGCA at 3478, ACAGAA at 3392, AAAGGA at 3363, AAAGGA at 3350, ACATAA at 3346, ATACCA at 3112, AAAATA at 3109, ATAGTA at 3049, ACATAA at 3043, ACATCA at 2924.
  4. HboxMr7: AAATGA at 3964, ATACTA at 3923, AAAATA at 3920, ACAAAA at 3789, AAACAA at 3787, ATACAA at 3783, AGACCA at 3760, AAATAA at 3632, AGACAA at 3416, ACAGAA at 3408, AGATTA at 3375, AAAACA at 3158, ATAATA at 3107, ATATAA at 3056, AAACGA at 2983, AAATTA at 2957, ACAGTA at 2899, AAAGCA at 2892.
  5. HboxMr9: AAAAGA at 3856, AGAAAA at 3853, AAACGA at 3847, AAACTA at 3794, ACAAAA at 3784, ATATCA at 3775, AGAGAA at 3489, ATAGCA at 3469, AAACAA at 3459, ACAACA at 3454, ACACAA at 3452, AAACTA at 3309, ACACCA at 3187, AAAACA at 3184, AAACGA at 3153, ATATAA at 3149, ACATAA at 3083, ATACCA at 3078, ACAATA at 3075, AAACTA at 3069, ACATGA at 2920, AAAATA at 2911, AGAATA at 2846.
  6. HboxMr1ci: TGATTT at 4034, TTGTGT at 3975, TGGTCT at 3958, TCTTGT at 3864, TATTCT at 3702, TCCTTT at 3645, TTATTT at 3610, TTTTAT at 3608, TAGTGT at 3511, TTTTTT at 3455, TCGTAT at 3413, TTATCT at 3378, TGTTAT at 3376, TGGTTT at 3342, TGATGT at 3286, TTATCT at 3099, TTATTT at 3095, TCTTAT at 3093, TTTTAT at 3046, TTTTTT at 3032, TCCTTT at 3012, TGATGT at 2949.
  7. HboxMr3ci: TAATTT at 4050, TGGTCT at 4012, TTGTTT at 4004, TATTGT at 4002, TTGTAT at 3999, TATTAT at 3890, TAGTGT at 3852, TAATAT at 3800, TTTTGT at 3760, TCTTTT at 3693, TTCTTT at 3692, TCCTCT at 3543, TGGTTT at 3531, TGGTGT at 3294, TTTTTT at 3167, TGATAT at 3121, TTTTTT at 3067, TCCTCT at 3030, TAGTTT at 3021, TCGTTT at 3016, TAGTTT at 2955.
  8. HboxMr5ci: TAGTCT at 4009, TGATGT at 3711, TTTTTT at 3706, TATTTT at 3704, TTCTTT at 3694, TTATTT at 3655, TTATTT at 3628, TTTTCT at 3439, TTTTTT at 3357, TTTTTT at 3356, TGGTTT at 3269, TTCTTT at 3222, TCTTCT at 3195, TAGTAT at 3050, TTTTTT at 2954, TCTTGT at 2853.
  9. HboxMr7ci: TACTTT at 3927, TAATTT at 3913, TGGTTT at 3727, TATTGT at 3600, TCCTAT at 3585, TCCTTT at 3579, TGGTAT at 3474, TTTTTT at 3459, TTTTTT at 3458, TTTTTT at 3457, TTTTTT at 3456, TTTTTT at 3455, TAATTT at 3452, TCCTTT at 3275, TCCTAT at 3224, TCCTTT at 3173, TGGTCT at 3122.
  10. Hboxr9ci: TTATAT at 3989, TCATGT at 3778, TCGTTT at 3594, TTGTTT at 3413, TCTTGT at 3411, TTTTTT at 3387, TTGTAT at 3317, TAATGT at 3296, TACTTT at 3255, TTGTTT at 3168, TGATTT at 3115, TCTTCT at 3106, TCGTTT at 3027, TATTCT at 2970, TCGTTT at 2898.

HboxMr arbitrary negative direction core promoters

  1. HboxMr2: ACAACA at 2832.
  2. HboxMr0ci: TCTTCT at 2830, TGATTT at 2825, TCATCT at 2812.
  3. HboxMr2ci: TTTTTT at 2825.

HboxMr alternate negative direction core promoters

  1. HboxMr9: AGAATA at 2846.
  2. HboxMr3ci: TCTTTT at 2811.
  3. HboxMr5ci: TTGTGT at 2837, TATTGT at 2835.
  4. HboxMr7ci: TGCTTT at 2837, TGTTTT at 2821.
  5. HboxMr9ci: TGCTAT at 2815.

HboxMr arbitrary positive direction core promoters

  1. HboxMr1: ATAAAA at 4431, AGAAAA at 4354, ACAGAA at 4352.
  2. HboxMr3: ATAAAA at 4445, ATAAGA at 4418, AAATTA at 4345, AGAAAA at 4341, AGAGGA at 4292.
  3. HboxMr5: AAAGAA at 4338, AAAAGA at 4337, AAAAGA at 4323, AGAATA at 4306, AAATGA at 4286.
  4. HboxMr7: AAAGAA at 4400, AAAGAA at 4396, AAAAGA at 4395, ATAAAA at 4393.
  5. HboxMr9: ATAACA at 4431, AAAGGA at 4318.
  6. HboxMr1ci: TGATCT at 4399, TAGTTT at 4270.
  7. HboxMr3ci: TGATCT at 4373, TAATTT at 4349, TACTGT at 4335, TGCTTT at 4322.
  8. HboxMr7ci: TAATGT at 4445, TGCTCT at 4367, TGGTCT at 4356, TCGTGT at 4302, TTCTGT at 4272, TTTTCT at 4270, TGGTTT at 4267.
  9. Hboxr9ci: TTGTAT at 4336, TTTTGT at 4334, TCTTTT at 4332, TATTTT at 4271.

HboxMr alternate Core positives

  1. HboxMr0: AGATGA at 4445, ATAAGA at 4442, ACATCA at 4437, AAAACA at 4432.
  2. HboxMr2: ACAACA at 4327, AAACAA at 4325, AAAACA at 4324, ACAAAA at 4322, AAAGCA at 4317, AAATCA at 4311.
  3. HboxMr4: ACAAGA at 4397, AAATTA at 4373, ACAGCA at 4360, AAAGCA at 4326.
  4. HboxMr6: ACAGAA at 4402, ACAATA at 4397, ACAACA at 4394, AAAACA at 4327, AGATCA at 4311.
  5. HboxMr8: ACACGA at 4339, AGACCA at 4293.
  6. HboxMr0ci: TGTTTT at 4376, TCCTCT at 4371.
  7. HboxMr4ci: TGGTTT at 4423, TCTTAT at 4301.
  8. HboxMr6ci: TAATAT at 4427, TCTTGT at 4412, TTGTGT at 4365, TCTTCT at 4321, TTATTT at 4265.
  9. HboxMr8ci: TAGTTT at 4397, TCCTAT at 4352, TACTAT at 4307.

HboxMr arbitrary negative direction proximal promoters

  1. HboxMr0: AAATCA at 2809, ATAGGA at 2799, AAACGA at 2779, ATAAAA at 2737, AAAATA at 2697, AGAATA at 2677.
  2. HboxMr2: AAAATA at 2666.
  3. HboxMr4: AAAGGA at 2698, ACACCA at 2656.
  4. HboxMr6: ATAACA at 2725, ACATAA at 2723, ACATGA at 2602.
  5. HboxMr8: ACACCA at 2711, AAAAAA at 2699, AAACAA at 2656.
  6. HboxMr2ci: TTCTCT at 2740.
  7. HboxMr4ci: TGGTGT at 2759.
  8. HboxMr6ci: TTATCT at 2808, TTTTGT at 2652.

HboxMr alternate Proximal negatives

  1. HboxMr1: AGAAAA at 2798, AGACAA at 2749, ACAATA at 2699, ACATCA at 2620, AGAACA at 2607.
  2. HboxMr3: AGATAA at 2774, ATAACA at 2747, ACAATA at 2744, AGACAA at 2742, ACATTA at 2732, ACACAA at 2702, AGAAGA at 2682, AGAGAA at 2680, AGAAGA at 2675.
  3. HboxMr5: AAAAAA at 2773, AAATGA at 2768, AAAGAA at 2764.
  4. HboxMr7: ACAGGA at 2793, AAAGTA at 2771, ACAGAA at 2683.
  5. HboxMr9: ATAAAA at 2622.
  6. HboxMr1ci: TCTTTT at 2673, TGATCT at 2627.
  7. HboxMr3ci: TCTTTT at 2811, TTGTCT at 2808, TTGTTT at 2783, TAATTT at 2615, TATTCT at 2606.
  8. HboxMr5ci: TGATGT at 2782, TGGTGT at 2732, TTTTAT at 2708.
  9. HboxMr9ci: TTCTCT at 2753, TGGTTT at 2706, TCCTAT at 2618.

HboxMr arbitrary positive direction proximal promoters

  1. HboxMr1: AGAGCA at 4258, AGAACA at 4240, ACAGAA at 4238.
  2. HboxMr3: AAACCA at 4240, AAACTA at 4228, AAAATA at 4175, ACAGCA at 4086.
  3. HboxMr5: AAAGAA at 4213.
  4. HboxMr7: AAACCA at 4204, AGATTA at 4147, ACACTA at 4116, AGATAA at 4076.
  5. HboxMr9: AGAGGA at 4185, ATAATA at 4170, AGATAA at 4168, AGAGTA at 4151, ACATAA at 4141, AAATTA at 4055.
  6. HboxMr1ci: TTTTTT at 4229, TTTTTT at 4228, TGCTTT at 4225, TGGTAT at 4209, TGATAT at 4163, TGCTCT at 4064.
  7. HboxMr3ci: TGTTTT at 4101, TTGTTT at 4100, TCTTGT at 4098, TAATTT at 4093, TTTTTT at 4072, TGCTTT at 4069, TAATTT at 4050.
  8. HboxMr5ci: TGATTT at 4195, TAATCT at 4184, TAGTTT at 4108, TCATTT at 4054.
  9. HboxMr7ci: TTATAT at 4253, TCGTAT at 4192, TCCTGT at 4129, TACTTT at 4120.
  10. HboxMr9ci: TATTCT at 4179.

HboxMr alternate Proximal positives

  1. HboxMr0: AGACAA at 4235.
  2. HboxMr2: ACAAGA at 4199, AGACAA at 4197, ATAAGA at 4194, AAACTA at 4161, AAAGTA at 4156, ACATTA at 4069.
  3. HboxMr4: AAATCA at 4186, ATATTA at 4163.
  4. HboxMr6: AGAGGA at 4154, ATAACA at 4136.
  5. HboxMr8: ATAGGA at 4225, ACAAAA at 4211, ATAGCA at 4198, AAAAAA at 4111, AGAAAA at 4109, AAACGA at 4100, ACAAAA at 4097.
  6. HboxMr0ci: TTATTT at 4228, TATTAT at 4226, TTCTAT at 4223, TATTTT at 4202, TTATTT at 4201, TTGTTT at 4179, TGCTTT at 4175, TCTTGT at 4105, TTATCT at 4102.
  7. HboxMr2ci: TCGTAT at 4245, TGTTAT at 4216, TGATTT at 4143, TGTTTT at 4113, TTATTT at 4072.
  8. HboxMr4ci: TTATAT at 4253, TAATAT at 4161, TAATGT at 4053.
  9. HboxMr6ci: TTATTT at 4265.

HboxMr arbitrary negative direction distal promoters

  1. HboxMr0: ACACTA at 2555, AGAGGA at 2529, ATATTA at 2374, ACAAAA at 2333, AGACAA at 2331, ATAATA at 2263, AAATAA at 2261, AAAATA at 2260, AGACAA at 2183, ACACCA at 2165, AAAACA at 2086, ATACTA at 1964, AGAATA at 1961, AGAGAA at 1959, AGAGTA at 1872, AGATCA at 1853, AAATAA at 1790, AAACAA at 1576, AAAGGA at 1530, AAACGA at 1502, ATAAAA at 1499, AAATAA at 1497, ATAATA at 1492, ACAAGA at 1436, AAACCA at 1324, AAACCA at 1244, AGACGA at 1237, AGATGA at 1126, AAACCA at 1088, AAACTA at 833, AGAAAA at 634, AAAGAA at 632, AAAAGA at 593, ACAGCA at 579, AAATTA at 546, ATAGAA at 542, AAACAA at 502, AAACCA at 284, ATAAAA at 199, AAATAA at 197, AAAATA at 196, ATAATA at 146, AAATAA at 144.
  2. HboxMr2: AAAATA at 2666, ATATCA at 2481, AAACCA at 2443, AAATCA at 2384, AAAAGA at 2341, AGAAAA at 2339, AGAGCA at 2208, AAACAA at 2191, AAAACA at 2190, ACAAGA at 2029, AAACTA at 1852, AGAAAA at 1849, AAAGAA at 1847, AAAAGA at 1846, AGAAAA at 1844, ATAGAA at 1842, ATAATA at 1839, ACATAA at 1837, ACAGTA at 1832, AGATGA at 1827, ACAGCA at 1800, ATACCA at 1784, ACATTA at 1779, ATATGA at 1758, AAACCA at 1631, AAATTA at 1553, ATAGCA at 1432, ATATTA at 1327, AGACTA at 1115, ACAGTA at 1090, ACAGCA at 1042, ATAATA at 990, ACAGAA at 944, AAAACA at 941, AAAAAA at 939, AAAAAA at 938, AAAAAA at 937, AGAACA at 908, ACACAA at 510, AGAAAA at 472, AAATGA at 371, AGAAAA at 368, AGATTA at 337, AAACTA at 312, ATAAAA at 309, AAAGGA at 253, ACACAA at 60.
  3. HboxMr4: AAAAAA at 2514, AGAAAA at 2512, AAAAAA at 2339, AGAAAA at 2337, ACAAGA at 2306, ATATTA at 2297, ATACGA at 2230, AAAGTA at 2182, AGAAAA at 2179, AAACGA at 2137, AAAAGA at 1998, ACAAAA at 1971, ACACAA at 1969, AGAGCA at 1805, AAAATA at 1778, ACAAAA at 1776, ACACAA at 1774, AGAATA at 1694, ACAAGA at 1691, ATATGA at 1686, AAAGTA at 1643, AGAAAA at 1612, ATAGCA at 1592, AGACCA at 1574, ACAATA at 1569, AAAACA at 1251, AAAAAA at 1249, ATAGAA at 1098, AGATTA at 946, AAACTA at 602, AAACGA at 535, AAACAA at 531, AAATTA at 479, ATATTA at 164, AGAATA at 151, ATATCA at 116, AAACCA at 56.
  4. HboxMr6: ACAGGA at 2593, ACAAGA at 2588, ATACAA at 2586, ACAGAA at 2567, AGAGCA at 2506, ACAGTA at 2380, ATACTA at 2374, AGAGCA at 2326, ACATAA at 2315, ATATAA at 2239, ATAACA at 2206, AAAGTA at 2183, ATAACA at 2169, ACAATA at 2051, AGATAA at 2000, ATACAA at 1915, AGATAA at 1815, AAATTA at 1783, ACAAAA at 1779, ACAACA at 1608, AAAGGA at 1501, AAAGCA at 1444, AAAAAA at 1441, AAAAGA at 1239, AGACTA at 1204, ACAGAA at 1102, AAAGGA at 973, ACAAAA at 970, AGAGTA at 799, ACATCA at 794, ATAGGA at 778, AAACTA at 773, AAAAAA at 770, AAAAAA at 769, AAAAAA at 768, AAATGA at 749, AGAGTA at 711, AGAACA at 646, ATATCA at 627, AGAGGA at 372, ATATGA at 246, ATACAA at 180, AGAAAA at 69, ACAACA at 41.
  5. HboxMr8: ACACCA at 2711, AAAAAA at 2699, AAACAA at 2656, AAAACA at 2409, AGACCA at 2229, ATATGA at 2190, ACATTA at 2185, AGAATA at 2169, AAAGAA at 2167, AAAAGA at 2166, ACAAAA at 2132, AAACAA at 2130, AGAGAA at 2116, AAAAGA at 2113, AAACAA at 2103, AAAACA at 2102, AAATTA at 2083, AAATTA at 1959, ACACCA at 1949, ATAACA at 1842, ATACCA at 1798, AAAGAA at 1686, AAAAGA at 1685, ACATTA at 1506, AGATCA at 1501, AAAAAA at 1476, AGAGAA at 1293, AAACGA at 1037, AAAAAA at 1034, ATAAAA at 1032, ACAATA at 990, AAATGA at 964, ATAAAA at 926, AAAGAA at 883, ATATTA at 878, AGATCA at 865, ATACTA at 850, ATAATA at 783, AAACTA at 724, ATAAAA at 707, AAACCA at 558, ACACCA at 493, AAACAA at 479, ACATAA at 434, AAAAAA at 388, ATAGGA at 335, AGATGA at 326, AAAGAA at 312, AAAAGA at 311, AGAAAA at 282, ACAACA at 232, ACACTA at 200, AAATCA at 141.
  6. HboxMr0ci: TTTTCT at 2569, TCTTCT at 2542, TTATAT at 2372, TAGTTT at 2343, TCCTGT at 2253, TTGTAT at 2244, TGTTAT at 2177, TCATAT at 2150, TATTTT at 2145, TTATAT at 2142, TTATGT at 2113, TACTTT at 2109, TCCTAT at 2060, TTATGT at 2054, TCTTAT at 2052, TGGTGT at 2025, TGCTCT at 1998, TGTTCT at 1979, TTCTCT at 1974, TTTTCT at 1972, TGTTTT at 1970, TACTAT at 1965, TGGTGT at 1939, TACTCT at 1906, TGGTTT at 1901, TTATGT at 1824, TTTTAT at 1822, TGATTT at 1819, TCGTTT at 1755, TTTTCT at 1673, TGTTTT at 1671, TTGTTT at 1670, TTATTT at 1642, TGGTTT at 1638, TATTTT at 1569, TCCTGT at 1551, TCGTAT at 1543, TGATTT at 1459, TTTTTT at 1454, TTTTTT at 1453, TACTCT at 1427, TTTTCT at 1195, TCCTCT at 1134, TACTTT at 1020, TCCTGT at 1009, TTGTAT at 987, TGCTTT at 983, TACTCT at 853, TTTTTT at 656, TCTTTT at 654, TTCTTT at 653, TGTTTT at 605, TAATGT at 602, TAGTTT at 563, TTTTAT at 496, TATTTT at 494, TAATTT at 474, TCTTAT at 338, TTTTAT at 226, TTTTTT at 224, TTTTTT at 223, TTGTAT at 155, TGTTGT at 153, TAATGT at 150, TGTTGT at 17.
  7. HboxMr2ci: TTGTCT at 2535, TGTTGT at 2533, TTTTGT at 2530, TTCTTT at 2466, TGGTTT at 2462, TACTAT at 2411, TCGTAT at 2355, TTGTTT at 2348, TCATCT at 2169, TGCTCT at 2164, TCGTGT at 1998, TCCTCT at 1977, TAGTCT at 1899, TTTTTT at 1681, TAGTTT at 1653, TTATGT at 1584, TTCTGT at 1513, TGGTAT at 1387, TATTTT at 1374, TGGTCT at 1338, TTGTAT at 1272, TCTTGT at 1270, TGATTT at 1245, TCCTGT at 1204, TGATCT at 1193, TCATCT at 1061, TGGTTT at 1056, TGGTTT at 1026, TTATGT at 862, TTTTAT at 860, TAATCT at 828, TAGTCT at 783, TCGTTT at 738, TCCTGT at 725, TCGTTT at 717, TGATGT at 701, TCTTCT at 696, TCGTTT at 445, TATTTT at 262, TGTTTT at 245, TAATGT at 242, TCCTTT at 223, TCATCT at 202, TATTTT at 34.
  8. HboxMr4ci: TGGTTT at 2591, TAGTGT at 2485, TTGTTT at 2437, TAGTTT at 2398, TTATAT at 2295, TTTTGT at 2257, TATTTT at 2255, TTATTT at 2254, TTGTCT at 2163, TACTTT at 2127, TACTTT at 2018, TCCTTT at 2012, TGATGT at 1822, TTGTAT at 1794, TTTTGT at 1792, TCTTTT at 1790, TTCTTT at 1789, TCTTGT at 1766, TCCTTT at 1731, TCTTCT at 1701, TAATCT at 1698, TCATAT at 1684, TTATCT at 1679, TCATTT at 1675, TTCTAT at 1588, TCATCT at 1533, TCTTTT at 1423, TTTTAT at 1407, TTGTCT at 1353, TATTGT at 1351, TTTTAT at 1348, TAATGT at 1315, TGCTGT at 1310, TTATAT at 1262, TCGTTT at 1186, TGCTCT at 1066, TGGTAT at 973, TTTTTT at 846, TTTTTT at 845, TTTTTT at 844, TCCTTT at 827, TCCTGT at 801, TAGTCT at 609, TCCTTT at 593, TCTTTT at 472, TTCTTT at 471, TTCTTT at 365, TTTTCT at 363, TCGTTT at 360, TTATCT at 167, TATTAT at 165, TGATAT at 114, TTTTCT at 44.
  9. HboxMr6ci: TCGTAT at 2513, TTCTCT at 2444, TATTGT at 2420, TTTTAT at 2417, TCTTTT at 2394, TAGTTT at 2344, TAATGT at 2102, TAGTTT at 2077, TAATAT at 2036, TAATGT at 2003, TACTTT at 1993, TCTTCT at 1988, TTGTCT at 1985, TGTTAT at 1749, TTGTGT at 1746, TCTTGT at 1744, TACTCT at 1728, TTTTGT at 1702, TAATTT at 1654, TAGTTT at 1631, TTCTTT at 1530, TTCTCT at 1517, TCTTTT at 1372, TCTTCT at 1356, TCATGT at 1341, TAGTTT at 1317, TACTGT at 1312, TTATGT at 1289, TGCTTT at 1259, TTATTT at 1143, TCGTCT at 1085, TGCTGT at 997, TTGTAT at 913, TGATCT at 880, TAGTTT at 875, TATTGT at 860, TTATAT at 832, TCTTAT at 830, TGTTCT at 827, TGCTGT at 824, TAATTT at 815, TAGTCT at 803, TTATGT at 472, TGGTAT at 434, TAATTT at 402, TTCTGT at 262, TTATTT at 186, TGGTGT at 99.
  10. HboxMr8ci: TTTTTT at 2543, TGATTT at 2540, TTGTTT at 2382, TTATTT at 2331, TCTTAT at 2329, TCCTAT at 2324, TTTTAT at 2293, TTTTTT at 2291, TGATCT at 2193, TTATAT at 2188, TCGTAT at 2140, TTGTCT at 2035, TAGTTT at 1924, TCGTCT at 1876, TAGTTT at 1850, TCGTTT at 1832, TACTCT at 1772, TCTTCT at 1397, TTATCT at 1366, TACTTT at 1350, TTATCT at 1337, TTCTGT at 1283, TTGTTT at 1230, TCCTAT at 1198, TTATGT at 1171, TGTTAT at 1169, TGCTTT at 1164, TAGTTT at 981, TTTTGT at 955, TCATAT at 876, TATTTT at 740, TTATTT at 739, TAATTT at 728, TTCTTT at 651, TTGTAT at 568, TGGTGT at 535, TCTTGT at 402, TTCTAT at 264, TGTTCT at 217, TATTTT at 166, TTTTAT at 77, TCGTCT at 63, TTGTTT at 44, TATTCT at 34.

HboxM Alternate Distal negatives

  1. HboxMr1: AAAGGA at 2591, ACACTA at 2472, AAAGGA at 2459, ACAGCA at 2441, ACAAGA at 2420, ATAGTA at 2370, AAACCA at 2246, ACATGA at 1967, AAACGA at 1958, ACAAGA at 1947, ATACAA at 1945, ATACGA at 1826, ACAATA at 1823, AAACAA at 1821, AAAACA at 1820, AGATCA at 1780, AAAAGA at 1777, AAAACA at 1709, AGAGTA at 1552, AAAAAA at 1441, AAACGA at 1405, ACATCA at 1344, AAAACA at 1053, AGAAGA at 889, AAAGCA at 884, AAACCA at 784, ATAGGA at 754, ACAGCA at 745, AAACGA at 616, ACACTA at 372, ATATTA at 367, AGATTA at 362, ATATGA at 341, ATACAA at 300, AAAATA at 167, ATAAAA at 165, AGATAA at 163, AGAAGA at 160, ATATTA at 141, ACAGCA at 36.
  2. HboxMr3: AAAGAA at 2082, AAAAGA at 2081, ATAAAA at 2079, AAACTA at 1853, AAATCA at 1837, AGAAAA at 1834, AAACTA at 1800, AAATTA at 1646, ACAGGA at 1344, ATAAGA at 1099, AGACCA at 1075, ATACCA at 828, AGACCA at 724, ATAAGA at 658, AGAAAA at 569, ACACTA at 564, ATAACA at 561, AAAAAA at 551, AAAAAA at 550, AAAAAA at 549, AAATGA at 539, ACATTA at 322.
  3. HboxMr5: ATACGA at 2279, AGAAAA at 2259, ATATGA at 1780, AGATCA at 1747, ACATCA at 1686, AAATGA at 1566, ACAGCA at 1520, AGACCA at 1458, AGAAGA at 1331, AGAGAA at 1329, ACAGCA at 1285, AAATTA at 1272, AAACTA at 1211, AGAACA at 1196, ACAACA at 1169, AAACAA at 1167, AGATAA at 1143, AAATTA at 1065, AAAAGA at 1035, ATACCA at 939, AGACCA at 765, AGATTA at 691, ATATAA at 671, AGAAGA at 556, ATAGAA at 540, AGAGCA at 380, AAACAA at 262, AAATCA at 135, AAAGAA at 30.
  4. HboxMr7: AAAATA at 2513, AAAATA at 2503, AGATTA at 2403, ACAGAA at 2280, AGAATA at 2238, AAAGGA at 2219, ATAGGA at 2068, AAAATA at 2065, ACACTA at 2037, AAATGA at 1953, AAATGA at 1835, ATAGCA at 1819, AGAAGA at 1796, ACATTA at 1650, AAAAGA at 1538, AGAATA at 1444, ATATAA at 1413, AGACCA at 1268, ACACCA at 1207, AAATGA at 1186, ACAGAA at 1128, AAATGA at 1114, AAATGA at 1037, AGAATA at 994, AGAAGA at 991, AAACTA at 886, AAAGAA at 819, AGATAA at 792, ATAACA at 741, ACAAGA at 705, ATAGGA at 529, ACAGAA at 515, ATACCA at 477, ACAAAA at 429, AAACAA at 427, AGAATA at 417, ATAGCA at 376, AAAGCA at 362, ACAAAA at 359, ATATTA at 308, AGATGA at 302, AAACTA at 282, ATATTA at 207, AAATAA at 144, AAAATA at 143, AGAAAA at 141.
  5. HboxMr9: AAAGAA at 2460, AGACGA at 2426, AAACTA at 2390, ACAAAA at 2387, AAACAA at 2385, AGAGTA at 2380, AAACAA at 2091, AAAACA at 2090, AAATGA at 2078, ATAGAA at 1929, AAACGA at 1867, ACAAAA at 1750, AAACAA at 1748, AGAGCA at 1512, ACAAAA at 1408, AAAGGA at 1383, AAATAA at 1379, AAAAAA at 1304, AAAAAA at 1303, AAAAAA at 1302, AAAAAA at 1301, ACAAAA at 1299, ACATAA at 1227, ATAACA at 1224, AAATTA at 1167, ACATTA at 1157, ACACAA at 1097, ACAACA at 948, ATAGGA at 943, AAAAAA at 678, ATAGCA at 673, AAAGGA at 589, AGAAAA at 586, AAAATA at 407, AAAAAA at 405, AAAAAA at 404, AGAAAA at 402, ACACGA at 381, AGACGA at 286, AAACCA at 182, ACAACA at 72, ACAGTA at 14.
  6. HboxMr1ci: TAATGT at 2527, TGGTAT at 2507, TCTTTT at 2288, TACTTT at 2179, TGATAT at 2174, TTGTTT at 2162, TATTTT at 2141, TAGTGT at 2024, TCATAT at 1994, TCCTGT at 1802, TGGTGT at 1743, TTTTTT at 1665, TCGTTT at 1655, TAGTGT at 1580, TTCTCT at 1566, TTATGT at 1544, TTTTTT at 1484, TGGTTT at 1392, TCGTGT at 1378, TTCTTT at 1278, TTTTCT at 1276, TTATAT at 1266, TATTAT at 1264, TAATTT at 1243, TGTTCT at 1218, TGATAT at 1107, TAATGT at 1047, TAGTGT at 969, TGGTTT at 922, TAGTCT at 904, TTTTCT at 831, TAATTT at 827, TATTTT at 767, TTCTAT at 764, TCCTTT at 711, TCCTTT at 653, TTATGT at 533, TACTAT at 376, TTATAT at 365, TTATAT at 339, TGGTCT at 286, TTTTGT at 281, TATTAT at 251, TGCTCT at 133, TTGTCT at 7.
  7. HboxMr3ci: TGCTTT at 2469, TCATTT at 2326, TCCTAT at 2283, TTGTTT at 2266, TACTTT at 2223, TAGTGT at 2204, TCGTGT at 2199, TGCTTT at 2025, TGATTT at 2018, TTTTTT at 1914, TTTTTT at 1913, TCTTAT at 1872, TCCTTT at 1847, TCCTAT at 1637, TAGTGT at 1572, TTATGT at 1562, TCATTT at 1558, TTCTTT at 1541, TAGTCT at 1266, TGCTCT at 1152, TCATGT at 1133, TGATCT at 1126, TGGTTT at 1110, TGATTT at 1087, TTGTTT at 1029, TTTTGT at 1027, TCTTTT at 1025, TTCTTT at 1024, TCTTCT at 1022, TCTTCT at 988, TCATTT at 924, TAATTT at 919, TTATCT at 771, TCCTTT at 733, TGTTGT at 639, TCGTCT at 614, TCATGT at 577, TTGTTT at 531, TGCTCT at 467, TTGTTT at 449, TAATTT at 408, TCCTGT at 350, TTCTGT at 334, TCTTCT at 332, TGCTTT at 316, TGCTTT at 287, TATTTT at 170, TCTTTT at 148, TGGTCT at 26.
  8. HboxMr5ci: TTCTTT at 2559, TCGTTT at 2543, TTCTTT at 2527, TGTTCT at 2442, TTATAT at 2179, TTGTCT at 2173, TGTTTT at 2074, TAATCT at 2062, TTCTTT at 1980, TTTTCT at 1978, TACTCT at 1622, TGATTT at 1447, TTTTTT at 1416, TAGTTT at 1413, TAATCT at 1317, TCTTTT at 1265, TAGTCT at 1262, TGTTTT at 1149, TAATGT at 1146, TAATTT at 1109, TCGTTT at 1093, TCGTCT at 1019, TGGTCT at 1014, TTATGT at 975, TGTTCT at 958, TCGTTT at 947, TGGTTT at 932, TATTTT at 860, TTATTT at 859, TTATTT at 855, TGTTTT at 831, TGCTGT at 724, TTGTGT at 323, TTTTGT at 321, TAGTTT at 318, TATTTT at 273, TTATTT at 272, TTTTAT at 270, TACTGT at 169, TGCTGT at 164, TTCTAT at 148, TATTTT at 111, TGGTAT at 90.
  9. HboxMr7ci: TATTTT at 2517, TTGTTT at 2449, TAATTT at 2253, TAATTT at 2242, TCCTCT at 2126, TAGTTT at 2118, TCATTT at 1893, TTCTTT at 1888, TGTTCT at 1886, TTATTT at 1808, TCCTCT at 1627, TAGTGT at 1531, TCGTGT at 1401, TCTTCT at 1359, TTATGT at 1326, TCATCT at 1158, TCGTTT at 1088, TGATCT at 1003, TGCTGT at 876, TAGTTT at 766, TTCTAT at 737, TAGTCT at 719, TTCTGT at 714, TTTTCT at 712, TGGTTT at 608, TTTTGT at 492, TTTTTT at 349, TATTAT at 309, TAATGT at 246, TCATAT at 205, TGATTT at 110.
  10. HboxMr9ci: TCTTAT at 2580, TTTTGT at 2513, TTCTAT at 2347, TTTTCT at 2345, TCATTT at 2341, TCTTTT at 2313, TTCTTT at 2312, TACTGT at 2253, TTGTTT at 2248, TGGTGT at 2203, TTATAT at 2123, TTATCT at 1991, TCGTAT at 1983, TCATGT at 1974, TTCTTT at 1942, TTGTAT at 1925, TCCTTT at 1907, TGATTT at 1741, TTGTTT at 1734, TCCTTT at 1542, TCTTCT at 1537, TGTTCT at 1534, TCATGT at 1531, TTTTCT at 1353, TGTTTT at 1124, TGTTTT at 1078, TTGTAT at 1073, TTCTCT at 1052, TTATTT at 967, TGGTCT at 926, TTTTTT at 902, TGGTGT at 850, TTTTTT at 836, TATTTT at 834, TTATTT at 808, TGTTTT at 717, TTCTGT at 714, TCGTTT at 705, TTGTAT at 620, TACTGT at 551, TGGTAT at 474, TTTTGT at 469, TATTTT at 467, TTATTT at 466, TGCTAT at 440, TTCTAT at 353, TTTTCT at 351, TCGTTT at 347, TTTTAT at 161, TATTTT at 159, TGCTAT at 156, TTGTTT at 96, TGGTTT at 92, TTGTCT at 24, TAGTGT at 18.

HboxM Arbitrary positive direction distal promoters

  1. HboxMr1: AAAAAA at 4011, AAAAAA at 4010, ATAGCA at 3887, AAAATA at 3884, AAACGA at 3875, AAAAGA at 3824, ATACGA at 3751, AGAGCA at 3746, AAAGGA at 3724, AGAATA at 3696, AAAACA at 3602, ATACAA at 3571, AAACCA at 3536, AAAAAA at 3488, ACAAAA at 3486, ACATAA at 3473, AAAGGA at 3449, AAATGA at 3442, ATATTA at 3417, AAAATA at 3364, ACAAGA at 3314, ACAGGA at 3275, AAAACA at 3272, AGAAAA at 3269, AGAGAA at 3267, ACACTA at 3259, ACAGCA at 3241, ACAAAA at 3175, AAATCA at 3170, ACATTA at 3144, AGAATA at 3081, AAAAAA at 3064, AAAAAA at 3063, AAAAAA at 3062, AAAAAA at 3061, AGATCA at 2996, ACATTA at 2911, AAAAAA at 2855, AGAAAA at 2798, AGACAA at 2749, ACAATA at 2699, ACATCA at 2620, AGAACA at 2607, AAAGGA at 2591, ACACTA at 2472, AAAGGA at 2459, ACAGCA at 2441, ACAAGA at 2420, ATAGTA at 2370, AAACCA at 2246, ACATGA at 1967, AAACGA at 1958, ACAAGA at 1947, ATACAA at 1945, ATACGA at 1826, ACAATA at 1823, AAACAA at 1821, AAAACA at 1820, AGATCA at 1780, AAAAGA at 1777, AAAACA at 1709, AGAGTA at 1552, AAAAAA at 1441, AAACGA at 1405, ACATCA at 1344, AAAACA at 1053, AGAAGA at 889, AAAGCA at 884, AAACCA at 784, ATAGGA at 754, ACAGCA at 745, AAACGA at 616, ACACTA at 372, ATATTA at 367, AGATTA at 362, ATATGA at 341, ATACAA at 300, AAAATA at 167, ATAAAA at 165, AGATAA at 163, AGAAGA at 160, ATATTA at 141, ACAGCA at 36.
  2. HboxMr3: AAATAA at 3942, ATATTA at 3889, ATAGCA at 3806, ATAATA at 3799, AGACCA at 3738, AAAGGA at 3714, ACAAGA at 3644, AAAGCA at 3616, AAAGGA at 3597, AGACAA at 3486, AGAAGA at 3432, AGAGAA at 3430, AGACCA at 3388, AGACCA at 3307, AAACAA at 3265, AAAACA at 3264, AAAAAA at 3262, ATAGCA at 2963, AAACAA at 2923, AAAACA at 2922, AAAAAA at 2920, AGAAAA at 2918, AGATAA at 2774, ATAACA at 2747, ACAATA at 2744, AGACAA at 2742, ACATTA at 2732, ACACAA at 2702, AGAAGA at 2682, AGAGAA at 2680, AGAAGA at 2675, AAAGAA at 2082, AAAAGA at 2081, ATAAAA at 2079, AAACTA at 1853, AAATCA at 1837, AGAAAA at 1834, AAACTA at 1800, AAATTA at 1646, ACAGGA at 1344, ATAAGA at 1099, AGACCA at 1075, ATACCA at 828, AGACCA at 724, ATAAGA at 658, AGAAAA at 569, ACACTA at 564, ATAACA at 561, AAAAAA at 551, AAAAAA at 550, AAAAAA at 549, AAATGA at 539, ACATTA at 322.
  3. HboxMr5: 58, AAAGAA at 4338, AAAAGA at 4337, AAAAGA at 4323, AGAATA at 4306, AAATGA at 4286, AAAGAA at 4213, AAACGA at 4208, AAAATA at 4167, AGAGCA at 3978, ATAAGA at 3973, ACAATA at 3970, AAATGA at 3965, AAATTA at 3930, AAATTA at 3783, ACATAA at 3671, AAACTA at 3514, AAAGCA at 3478, ACAGAA at 3392, AAAGGA at 3363, AAAGGA at 3350, ACATAA at 3346, ATACCA at 3112, AAAATA at 3109, ATAGTA at 3049, ACATAA at 3043, ACATCA at 2924, AAAAAA at 2773, AAATGA at 2768, AAAGAA at 2764, ATACGA at 2279, AGAAAA at 2259, ATATGA at 1780, AGATCA at 1747, ACATCA at 1686, AAATGA at 1566, ACAGCA at 1520, AGACCA at 1458, AGAAGA at 1331, AGAGAA at 1329, ACAGCA at 1285, AAATTA at 1272, AAACTA at 1211, AGAACA at 1196, ACAACA at 1169, AAACAA at 1167, AGATAA at 1143, AAATTA at 1065, AAAAGA at 1035, ATACCA at 939, AGACCA at 765, AGATTA at 691, ATATAA at 671, AGAAGA at 556, ATAGAA at 540, AGAGCA at 380, AAACAA at 262, AAATCA at 135, AAAGAA at 30.
  4. HboxMr7: AAATGA at 3964, ATACTA at 3923, AAAATA at 3920, ACAAAA at 3789, AAACAA at 3787, ATACAA at 3783, AGACCA at 3760, AAATAA at 3632, AGACAA at 3416, ACAGAA at 3408, AGATTA at 3375, AAAACA at 3158, ATAATA at 3107, ATATAA at 3056, AAACGA at 2983, AAATTA at 2957, ACAGTA at 2899, AAAGCA at 2892, ACAGGA at 2793, AAAGTA at 2771, ACAGAA at 2683, AAAATA at 2513, AAAATA at 2503, AGATTA at 2403, ACAGAA at 2280, AGAATA at 2238, AAAGGA at 2219, ATAGGA at 2068, AAAATA at 2065, ACACTA at 2037, AAATGA at 1953, AAATGA at 1835, ATAGCA at 1819, AGAAGA at 1796, ACATTA at 1650, AAAAGA at 1538, AGAATA at 1444, ATATAA at 1413, AGACCA at 1268, ACACCA at 1207, AAATGA at 1186, ACAGAA at 1128, AAATGA at 1114, AAATGA at 1037, AGAATA at 994, AGAAGA at 991, AAACTA at 886, AAAGAA at 819, AGATAA at 792, ATAACA at 741, ACAAGA at 705, ATAGGA at 529, ACAGAA at 515, ATACCA at 477, ACAAAA at 429, AAACAA at 427, AGAATA at 417, ATAGCA at 376, AAAGCA at 362, ACAAAA at 359, ATATTA at 308, AGATGA at 302, AAACTA at 282, ATATTA at 207, AAATAA at 144, AAAATA at 143, AGAAAA at 141.
  5. HboxMr9: AAAAGA at 3856, AGAAAA at 3853, AAACGA at 3847, AAACTA at 3794, ACAAAA at 3784, ATATCA at 3775, AGAGAA at 3489, ATAGCA at 3469, AAACAA at 3459, ACAACA at 3454, ACACAA at 3452, AAACTA at 3309, ACACCA at 3187, AAAACA at 3184, AAACGA at 3153, ATATAA at 3149, ACATAA at 3083, ATACCA at 3078, ACAATA at 3075, AAACTA at 3069, ACATGA at 2920, AAAATA at 2911, AGAATA at 2846, ATAAAA at 2622, AAAGAA at 2460, AGACGA at 2426, AAACTA at 2390, ACAAAA at 2387, AAACAA at 2385, AGAGTA at 2380, AAACAA at 2091, AAAACA at 2090, AAATGA at 2078, ATAGAA at 1929, AAACGA at 1867, ACAAAA at 1750, AAACAA at 1748, AGAGCA at 1512, ACAAAA at 1408, AAAGGA at 1383, AAATAA at 1379, AAAAAA at 1304, AAAAAA at 1303, AAAAAA at 1302, AAAAAA at 1301, ACAAAA at 1299, ACATAA at 1227, ATAACA at 1224, AAATTA at 1167, ACATTA at 1157, ACACAA at 1097, ACAACA at 948, ATAGGA at 943, AAAAAA at 678, ATAGCA at 673, AAAGGA at 589, AGAAAA at 586, AAAATA at 407, AAAAAA at 405, AAAAAA at 404, AGAAAA at 402, ACACGA at 381, AGACGA at 286, AAACCA at 182, ACAACA at 72, ACAGTA at 14.
  6. HboxMr1ci: TGATTT at 4034, TTGTGT at 3975, TGGTCT at 3958, TCTTGT at 3864, TATTCT at 3702, TCCTTT at 3645, TTATTT at 3610, TTTTAT at 3608, TAGTGT at 3511, TTTTTT at 3455, TCGTAT at 3413, TTATCT at 3378, TGTTAT at 3376, TGGTTT at 3342, TGATGT at 3286, TTATCT at 3099, TTATTT at 3095, TCTTAT at 3093, TTTTAT at 3046, TTTTTT at 3032, TCCTTT at 3012, TGATGT at 2949, TCTTTT at 2673, TGATCT at 2627, TAATGT at 2527, TGGTAT at 2507, TCTTTT at 2288, TACTTT at 2179, TGATAT at 2174, TTGTTT at 2162, TATTTT at 2141, TAGTGT at 2024, TCATAT at 1994, TCCTGT at 1802, TGGTGT at 1743, TTTTTT at 1665, TCGTTT at 1655, TAGTGT at 1580, TTCTCT at 1566, TTATGT at 1544, TTTTTT at 1484, TGGTTT at 1392, TCGTGT at 1378, TTCTTT at 1278, TTTTCT at 1276, TTATAT at 1266, TATTAT at 1264, TAATTT at 1243, TGTTCT at 1218, TGATAT at 1107, TAATGT at 1047, TAGTGT at 969, TGGTTT at 922, TAGTCT at 904, TTTTCT at 831, TAATTT at 827, TATTTT at 767, TTCTAT at 764, TCCTTT at 711, TCCTTT at 653, TTATGT at 533, TACTAT at 376, TTATAT at 365, TTATAT at 339, TGGTCT at 286, TTTTGT at 281, TATTAT at 251, TGCTCT at 133, TTGTCT at 7.
  7. HboxMr3ci: TAATTT at 4050, TGGTCT at 4012, TTGTTT at 4004, TATTGT at 4002, TTGTAT at 3999, TATTAT at 3890, TAGTGT at 3852, TAATAT at 3800, TTTTGT at 3760, TCTTTT at 3693, TTCTTT at 3692, TCCTCT at 3543, TGGTTT at 3531, TGGTGT at 3294, TTTTTT at 3167, TGATAT at 3121, TTTTTT at 3067, TCCTCT at 3030, TAGTTT at 3021, TCGTTT at 3016, TAGTTT at 2955, TCTTTT at 2811, TTGTCT at 2808, TTGTTT at 2783, TAATTT at 2615, TATTCT at 2606, TGCTTT at 2469, TCATTT at 2326, TCCTAT at 2283, TTGTTT at 2266, TACTTT at 2223, TAGTGT at 2204, TCGTGT at 2199, TGCTTT at 2025, TGATTT at 2018, TTTTTT at 1914, TTTTTT at 1913, TCTTAT at 1872, TCCTTT at 1847, TCCTAT at 1637, TAGTGT at 1572, TTATGT at 1562, TCATTT at 1558, TTCTTT at 1541, TAGTCT at 1266, TGCTCT at 1152, TCATGT at 1133, TGATCT at 1126, TGGTTT at 1110, TGATTT at 1087, TTGTTT at 1029, TTTTGT at 1027, TCTTTT at 1025, TTCTTT at 1024, TCTTCT at 1022, TCTTCT at 988, TCATTT at 924, TAATTT at 919, TTATCT at 771, TCCTTT at 733, TGTTGT at 639, TCGTCT at 614, TCATGT at 577, TTGTTT at 531, TGCTCT at 467, TTGTTT at 449, TAATTT at 408, TCCTGT at 350, TTCTGT at 334, TCTTCT at 332, TGCTTT at 316, TGCTTT at 287, TATTTT at 170, TCTTTT at 148, TGGTCT at 26.
  8. HboxMr5ci: TAGTCT at 4009, TGATGT at 3711, TTTTTT at 3706, TATTTT at 3704, TTCTTT at 3694, TTATTT at 3655, TTATTT at 3628, TTTTCT at 3439, TTTTTT at 3357, TTTTTT at 3356, TGGTTT at 3269, TTCTTT at 3222, TCTTCT at 3195, TAGTAT at 3050, TTTTTT at 2954, TCTTGT at 2853, TTGTGT at 2837, TATTGT at 2835, TGATGT at 2782, TGGTGT at 2732, TTTTAT at 2708, TTCTTT at 2559, TCGTTT at 2543, TTCTTT at 2527, TGTTCT at 2442, TTATAT at 2179, TTGTCT at 2173, TGTTTT at 2074, TAATCT at 2062, TTCTTT at 1980, TTTTCT at 1978, TACTCT at 1622, TGATTT at 1447, TTTTTT at 1416, TAGTTT at 1413, TAATCT at 1317, TCTTTT at 1265, TAGTCT at 1262, TGTTTT at 1149, TAATGT at 1146, TAATTT at 1109, TCGTTT at 1093, TCGTCT at 1019, TGGTCT at 1014, TTATGT at 975, TGTTCT at 958, TCGTTT at 947, TGGTTT at 932, TATTTT at 860, TTATTT at 859, TTATTT at 855, TGTTTT at 831, TGCTGT at 724, TTGTGT at 323, TTTTGT at 321, TAGTTT at 318, TATTTT at 273, TTATTT at 272, TTTTAT at 270, TACTGT at 169, TGCTGT at 164, TTCTAT at 148, TATTTT at 111, TGGTAT at 90.
  9. HboxMr7ci: TACTTT at 3927, TAATTT at 3913, TGGTTT at 3727, TATTGT at 3600, TCCTAT at 3585, TCCTTT at 3579, TGGTAT at 3474, TTTTTT at 3459, TTTTTT at 3458, TTTTTT at 3457, TTTTTT at 3456, TTTTTT at 3455, TAATTT at 3452, TCCTTT at 3275, TCCTAT at 3224, TCCTTT at 3173, TGGTCT at 3122, TGCTTT at 2837, TGTTTT at 2821, TATTTT at 2517, TTGTTT at 2449, TAATTT at 2253, TAATTT at 2242, TCCTCT at 2126, TAGTTT at 2118, TCATTT at 1893, TTCTTT at 1888, TGTTCT at 1886, TTATTT at 1808, TCCTCT at 1627, TAGTGT at 1531, TCGTGT at 1401, TCTTCT at 1359, TTATGT at 1326, TCATCT at 1158, TCGTTT at 1088, TGATCT at 1003, TGCTGT at 876, TAGTTT at 766, TTCTAT at 737, TAGTCT at 719, TTCTGT at 714, TTTTCT at 712, TGGTTT at 608, TTTTGT at 492, TTTTTT at 349, TATTAT at 309, TAATGT at 246, TCATAT at 205, TGATTT at 110.
  10. Hboxr9ci: TTATAT at 3989, TCATGT at 3778, TCGTTT at 3594, TTGTTT at 3413, TCTTGT at 3411, TTTTTT at 3387, TTGTAT at 3317, TAATGT at 3296, TACTTT at 3255, TTGTTT at 3168, TGATTT at 3115, TCTTCT at 3106, TCGTTT at 3027, TATTCT at 2970, TCGTTT at 2898, TGCTAT at 2815, TTCTCT at 2753, TGGTTT at 2706, TCCTAT at 2618, TCTTAT at 2580, TTTTGT at 2513, TTCTAT at 2347, TTTTCT at 2345, TCATTT at 2341, TCTTTT at 2313, TTCTTT at 2312, TACTGT at 2253, TTGTTT at 2248, TGGTGT at 2203, TTATAT at 2123, TTATCT at 1991, TCGTAT at 1983, TCATGT at 1974, TTCTTT at 1942, TTGTAT at 1925, TCCTTT at 1907, TGATTT at 1741, TTGTTT at 1734, TCCTTT at 1542, TCTTCT at 1537, TGTTCT at 1534, TCATGT at 1531, TTTTCT at 1353, TGTTTT at 1124, TGTTTT at 1078, TTGTAT at 1073, TTCTCT at 1052, TTATTT at 967, TGGTCT at 926, TTTTTT at 902, TGGTGT at 850, TTTTTT at 836, TATTTT at 834, TTATTT at 808, TGTTTT at 717, TTCTGT at 714, TCGTTT at 705, TTGTAT at 620, TACTGT at 551, TGGTAT at 474, TTTTGT at 469, TATTTT at 467, TTATTT at 466, TGCTAT at 440, TTCTAT at 353, TTTTCT at 351, TCGTTT at 347, TTTTAT at 161, TATTTT at 159, TGCTAT at 156, TTGTTT at 96, TGGTTT at 92, TTGTCT at 24, TAGTGT at 18.

HboxM Alternate Distal positives

  1. HboxMr0: AAAGTA at 3758, ACAACA at 3729, AGAAAA at 3657, ACAGAA at 3655, ATATAA at 3602, AAAGCA at 3597, ACAATA at 3577, AAAGTA at 3484, AAAGTA at 3340, ACAAAA at 3171, AGAATA at 3150, ATAGGA at 2939, AGACGA at 2908, ATATTA at 2852, AAATCA at 2809, ATAGGA at 2799, AAACGA at 2779, ATAAAA at 2737, AAAATA at 2697, AGAATA at 2677, ACACTA at 2555, AGAGGA at 2529, ATATTA at 2374, ACAAAA at 2333, AGACAA at 2331, ATAATA at 2263, AAATAA at 2261, AAAATA at 2260, AGACAA at 2183, ACACCA at 2165, AAAACA at 2086, ATACTA at 1964, AGAATA at 1961, AGAGAA at 1959, AGAGTA at 1872, AGATCA at 1853, AAATAA at 1790, AAACAA at 1576, AAAGGA at 1530, AAACGA at 1502, ATAAAA at 1499, AAATAA at 1497, ATAATA at 1492, ACAAGA at 1436, AAACCA at 1324, AAACCA at 1244, AGACGA at 1237, AGATGA at 1126, AAACCA at 1088, AAACTA at 833, AGAAAA at 634, AAAGAA at 632, AAAAGA at 593, ACAGCA at 579, AAATTA at 546, ATAGAA at 542, AAACAA at 502, AAACCA at 284, ATAAAA at 199, AAATAA at 197, AAAATA at 196, ATAATA at 146, AAATAA at 144.
  2. HboxMr2: ATAGTA at 4029, ATAATA at 3946, AGATAA at 3944, ATATAA at 3855, AAATGA at 3800, AAATTA at 3788, ACATTA at 3723, ATAGTA at 3689, ACAGCA at 3622, AGATTA at 3613, ATATTA at 3519, ACATAA at 3252, AAACCA at 3210, AAACCA at 3172, AAACAA at 3168, AAAGCA at 3151, ATAGGA at 3132, AGAGGA at 3038, AAAGAA at 2939, AAAGCA at 2915, AGACGA at 2904, ACAACA at 2832, AAAATA at 2666, ATATCA at 2481, AAACCA at 2443, AAATCA at 2384, AAAAGA at 2341, AGAAAA at 2339, AGAGCA at 2208, AAACAA at 2191, AAAACA at 2190, ACAAGA at 2029, AAACTA at 1852, AGAAAA at 1849, AAAGAA at 1847, AAAAGA at 1846, AGAAAA at 1844, ATAGAA at 1842, ATAATA at 1839, ACATAA at 1837, ACAGTA at 1832, AGATGA at 1827, ACAGCA at 1800, ATACCA at 1784, ACATTA at 1779, ATATGA at 1758, AAACCA at 1631, AAATTA at 1553, ATAGCA at 1432, ATATTA at 1327, AGACTA at 1115, ACAGTA at 1090, ACAGCA at 1042, ATAATA at 990, ACAGAA at 944, AAAACA at 941, AAAAAA at 939, AAAAAA at 938, AAAAAA at 937, AGAACA at 908, ACACAA at 510, AGAAAA at 472, AAATGA at 371, AGAAAA at 368, AGATTA at 337, AAACTA at 312, ATAAAA at 309, AAAGGA at 253, ACACAA at 60.
  3. HboxMr4: AAACCA at 3907, AAAAAA at 3879, ACAGTA at 3479, AAACCA at 3447, AAAAAA at 3444, AAACTA at 3417, ACATTA at 3370, ACACTA at 3039, ATAAGA at 2995, AAAGAA at 2951, AGACGA at 2881, AAAGCA at 2876, AAAGGA at 2698, ACACCA at 2656, AAAAAA at 2514, AGAAAA at 2512, AAAAAA at 2339, AGAAAA at 2337, ACAAGA at 2306, ATATTA at 2297, ATACGA at 2230, AAAGTA at 2182, AGAAAA at 2179, AAACGA at 2137, AAAAGA at 1998, ACAAAA at 1971, ACACAA at 1969, AGAGCA at 1805, AAAATA at 1778, ACAAAA at 1776, ACACAA at 1774, AGAATA at 1694, ACAAGA at 1691, ATATGA at 1686, AAAGTA at 1643, AGAAAA at 1612, ATAGCA at 1592, AGACCA at 1574, ACAATA at 1569, AAAACA at 1251, AAAAAA at 1249, ATAGAA at 1098, AGATTA at 946, AAACTA at 602, AAACGA at 535, AAACAA at 531, AAATTA at 479, ATATTA at 164, AGAATA at 151, ATATCA at 116, AAACCA at 56.
  4. HboxMr6: AGAGGA at 4031, ATAGAA at 3949, AAATTA at 3865, ACAACA at 3773, AAATGA at 3699, ATAAAA at 3696, AAATTA at 3683, ATAGAA at 3504, AAACCA at 3303, ATACGA at 3219, ACAGTA at 3209, AAATGA at 3190, AAAGCA at 2864, AAAAAA at 2861, ATAACA at 2725, ACATAA at 2723, ACATGA at 2602, ACAGGA at 2593, ACAAGA at 2588, ATACAA at 2586, ACAGAA at 2567, AGAGCA at 2506, ACAGTA at 2380, ATACTA at 2374, AGAGCA at 2326, ACATAA at 2315, ATATAA at 2239, ATAACA at 2206, AAAGTA at 2183, ATAACA at 2169, ACAATA at 2051, AGATAA at 2000, ATACAA at 1915, AGATAA at 1815, AAATTA at 1783, ACAAAA at 1779, ACAACA at 1608, AAAGGA at 1501, AAAGCA at 1444, AAAAAA at 1441, AAAAGA at 1239, AGACTA at 1204, ACAGAA at 1102, AAAGGA at 973, ACAAAA at 970, AGAGTA at 799, ACATCA at 794, ATAGGA at 778, AAACTA at 773, AAAAAA at 770, AAAAAA at 769, AAAAAA at 768, AAATGA at 749, AGAGTA at 711, AGAACA at 646, ATATCA at 627, AGAGGA at 372, ATATGA at 246, ATACAA at 180, AGAAAA at 69, ACAACA at 41.
  5. HboxMr8: ATATAA at 3982, ATATTA at 3912, AAAGAA at 3874, ATACGA at 3700, AAAGTA at 3685, AGATAA at 3578, ATATTA at 3557, ATATTA at 3506, AGAGGA at 3479, AAAAAA at 3103, AAAGTA at 3098, AAAGAA at 3079, AAATCA at 2981, ACACCA at 2711, AAAAAA at 2699, AAACAA at 2656, AAAACA at 2409, AGACCA at 2229, ATATGA at 2190, ACATTA at 2185, AGAATA at 2169, AAAGAA at 2167, AAAAGA at 2166, ACAAAA at 2132, AAACAA at 2130, AGAGAA at 2116, AAAAGA at 2113, AAACAA at 2103, AAAACA at 2102, AAATTA at 2083, AAATTA at 1959, ACACCA at 1949, ATAACA at 1842, ATACCA at 1798, AAAGAA at 1686, AAAAGA at 1685, ACATTA at 1506, AGATCA at 1501, AAAAAA at 1476, AGAGAA at 1293, AAACGA at 1037, AAAAAA at 1034, ATAAAA at 1032, ACAATA at 990, AAATGA at 964, ATAAAA at 926, AAAGAA at 883, ATATTA at 878, AGATCA at 865, ATACTA at 850, ATAATA at 783, AAACTA at 724, ATAAAA at 707, AAACCA at 558, ACACCA at 493, AAACAA at 479, ACATAA at 434, AAAAAA at 388, ATAGGA at 335, AGATGA at 326, AAAGAA at 312, AAAAGA at 311, AGAAAA at 282, ACAACA at 232, ACACTA at 200, AAATCA at 141.
  6. HboxMr0ci: TGCTAT at 4014, TTTTAT at 4005, TCATAT at 3962, TCTTTT at 3942, TTCTGT at 3930, TAATTT at 3694, TTCTGT at 3668, TTATCT at 3618, TCGTAT at 3562, TGTTAT at 3471, TTATGT at 3375, TCTTCT at 3266, TCATCT at 3263, TGTTTT at 3182, TTGTTT at 3181, TGGTTT at 3177, TCATGT at 3098, TGTTTT at 3080, TAGTTT at 3030, TGATTT at 3023, TCGTCT at 2985, TTTTTT at 2955, TACTTT at 2952, TTGTAT at 2935, TCATAT at 2850, TCTTCT at 2830, TGATTT at 2825, TCATCT at 2812, TTTTCT at 2569, TCTTCT at 2542, TTATAT at 2372, TAGTTT at 2343, TCCTGT at 2253, TTGTAT at 2244, TGTTAT at 2177, TCATAT at 2150, TATTTT at 2145, TTATAT at 2142, TTATGT at 2113, TACTTT at 2109, TCCTAT at 2060, TTATGT at 2054, TCTTAT at 2052, TGGTGT at 2025, TGCTCT at 1998, TGTTCT at 1979, TTCTCT at 1974, TTTTCT at 1972, TGTTTT at 1970, TACTAT at 1965, TGGTGT at 1939, TACTCT at 1906, TGGTTT at 1901, TTATGT at 1824, TTTTAT at 1822, TGATTT at 1819, TCGTTT at 1755, TTTTCT at 1673, TGTTTT at 1671, TTGTTT at 1670, TTATTT at 1642, TGGTTT at 1638, TATTTT at 1569, TCCTGT at 1551, TCGTAT at 1543, TGATTT at 1459, TTTTTT at 1454, TTTTTT at 1453, TACTCT at 1427, TTTTCT at 1195, TCCTCT at 1134, TACTTT at 1020, TCCTGT at 1009, TTGTAT at 987, TGCTTT at 983, TACTCT at 853, TTTTTT at 656, TCTTTT at 654, TTCTTT at 653, TGTTTT at 605, TAATGT at 602, TAGTTT at 563, TTTTAT at 496, TATTTT at 494, TAATTT at 474, TCTTAT at 338, TTTTAT at 226, TTTTTT at 224, TTTTTT at 223, TTGTAT at 155, TGTTGT at 153, TAATGT at 150, TGTTGT at 17.
  7. HboxMr2ci: TAGTAT at 4030, TCCTCT at 3967, TGATCT at 3762, TCCTCT at 3628, TTATTT at 3616, TTATCT at 3576, TTCTTT at 3572, TGATAT at 3535, TGGTTT at 3492, TCGTCT at 3386, TCCTCT at 3234, TCATCT at 3225, TGCTTT at 3188, TAATTT at 3115, TTGTCT at 3099, TGGTCT at 2962, TCCTGT at 2879, TCTTAT at 2852, TTTTTT at 2825, TTCTCT at 2740, TTGTCT at 2535, TGTTGT at 2533, TTTTGT at 2530, TTCTTT at 2466, TGGTTT at 2462, TACTAT at 2411, TCGTAT at 2355, TTGTTT at 2348, TCATCT at 2169, TGCTCT at 2164, TCGTGT at 1998, TCCTCT at 1977, TAGTCT at 1899, TTTTTT at 1681, TAGTTT at 1653, TTATGT at 1584, TTCTGT at 1513, TGGTAT at 1387, TATTTT at 1374, TGGTCT at 1338, TTGTAT at 1272, TCTTGT at 1270, TGATTT at 1245, TCCTGT at 1204, TGATCT at 1193, TCATCT at 1061, TGGTTT at 1056, TGGTTT at 1026, TTATGT at 862, TTTTAT at 860, TAATCT at 828, TAGTCT at 783, TCGTTT at 738, TCCTGT at 725, TCGTTT at 717, TGATGT at 701, TCTTCT at 696, TCGTTT at 445, TATTTT at 262, TGTTTT at 245, TAATGT at 242, TCCTTT at 223, TCATCT at 202, TATTTT at 34.
  8. HboxMr4ci: TGCTGT at 4039, TACTGT at 3992, TCTTCT at 3987, TAATCT at 3984, TCTTTT at 3926, TTATGT at 3866, TACTCT at 3852, TTGTCT at 3797, TTATAT at 3720, TAATTT at 3672, TTATGT at 3538, TTTTAT at 3536, TGTTTT at 3533, TTGTTT at 3532, TTTTGT at 3517, TATTTT at 3515, TTATTT at 3514, TCTTAT at 3512, TATTTT at 3354, TGGTGT at 3325, TGGTTT at 3205, TTATTT at 3017, TAGTAT at 3007, TGGTGT at 2759, TGGTTT at 2591, TAGTGT at 2485, TTGTTT at 2437, TAGTTT at 2398, TTATAT at 2295, TTTTGT at 2257, TATTTT at 2255, TTATTT at 2254, TTGTCT at 2163, TACTTT at 2127, TACTTT at 2018, TCCTTT at 2012, TGATGT at 1822, TTGTAT at 1794, TTTTGT at 1792, TCTTTT at 1790, TTCTTT at 1789, TCTTGT at 1766, TCCTTT at 1731, TCTTCT at 1701, TAATCT at 1698, TCATAT at 1684, TTATCT at 1679, TCATTT at 1675, TTCTAT at 1588, TCATCT at 1533, TCTTTT at 1423, TTTTAT at 1407, TTGTCT at 1353, TATTGT at 1351, TTTTAT at 1348, TAATGT at 1315, TGCTGT at 1310, TTATAT at 1262, TCGTTT at 1186, TGCTCT at 1066, TGGTAT at 973, TTTTTT at 846, TTTTTT at 845, TTTTTT at 844, TCCTTT at 827, TCCTGT at 801, TAGTCT at 609, TCCTTT at 593, TCTTTT at 472, TTCTTT at 471, TTCTTT at 365, TTTTCT at 363, TCGTTT at 360, TTATCT at 167, TATTAT at 165, TGATAT at 114, TTTTCT at 44.
  9. HboxMr6ci: TTCTCT at 4004, TCTTCT at 4002, TCCTTT at 3956, TGCTTT at 3923, TTATTT at 3857, TCATTT at 3760, TGCTGT at 3566, TTCTTT at 3474, TATTCT at 3472, TGCTTT at 3352, TCCTTT at 3294, TCCTTT at 3281, TCCTCT at 3269, TTCTAT at 3180, TCCTCT at 3124, TGATCT at 3048, TCGTTT at 3013, TGGTGT at 2946, TCCTAT at 2854, TTATCT at 2808, TTTTGT at 2652, TCGTAT at 2513, TTCTCT at 2444, TATTGT at 2420, TTTTAT at 2417, TCTTTT at 2394, TAGTTT at 2344, TAATGT at 2102, TAGTTT at 2077, TAATAT at 2036, TAATGT at 2003, TACTTT at 1993, TCTTCT at 1988, TTGTCT at 1985, TGTTAT at 1749, TTGTGT at 1746, TCTTGT at 1744, TACTCT at 1728, TTTTGT at 1702, TAATTT at 1654, TAGTTT at 1631, TTCTTT at 1530, TTCTCT at 1517, TCTTTT at 1372, TCTTCT at 1356, TCATGT at 1341, TAGTTT at 1317, TACTGT at 1312, TTATGT at 1289, TGCTTT at 1259, TTATTT at 1143, TCGTCT at 1085, TGCTGT at 997, TTGTAT at 913, TGATCT at 880, TAGTTT at 875, TATTGT at 860, TTATAT at 832, TCTTAT at 830, TGTTCT at 827, TGCTGT at 824, TAATTT at 815, TAGTCT at 803, TTATGT at 472, TGGTAT at 434, TAATTT at 402, TTCTGT at 262, TTATTT at 186, TGGTGT at 99.
  10. HboxMr8ci: TACTCT at 3947, TGGTTT at 3923, TATTGT at 3510, TATTAT at 3507, TCCTGT at 3449, TAGTTT at 3396, TGCTTT at 3380, TCATTT at 3334, TGGTTT at 3120, TTCTAT at 3068, TATTGT at 2967, TAGTAT at 2964, TAATCT at 2927, TTTTTT at 2543, TGATTT at 2540, TTGTTT at 2382, TTATTT at 2331, TCTTAT at 2329, TCCTAT at 2324, TTTTAT at 2293, TTTTTT at 2291, TGATCT at 2193, TTATAT at 2188, TCGTAT at 2140, TTGTCT at 2035, TAGTTT at 1924, TCGTCT at 1876, TAGTTT at 1850, TCGTTT at 1832, TACTCT at 1772, TCTTCT at 1397, TTATCT at 1366, TACTTT at 1350, TTATCT at 1337, TTCTGT at 1283, TTGTTT at 1230, TCCTAT at 1198, TTATGT at 1171, TGTTAT at 1169, TGCTTT at 1164, TAGTTT at 981, TTTTGT at 955, TCATAT at 876, TATTTT at 740, TTATTT at 739, TAATTT at 728, TTCTTT at 651, TTGTAT at 568, TGGTGT at 535, TCTTGT at 402, TTCTAT at 264, TGTTCT at 217, TATTTT at 166, TTTTAT at 77, TCGTCT at 63, TTGTTT at 44, TATTCT at 34.

H boxes (Mitchell) analysis and results

Main article: Complex locus A1BG and ZNF497 § H boxes (Mitchell)

They "have the consensus H box sequence (5'-ANANNA-3') but have no other primary sequence identity."[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 145 2 72.5 72.5 ± 3.5 (--69,+-76)
Randoms UTR arbitrary negative 265 10 26.5 28.55
Randoms UTR alternate negative 306 10 30.6 28.55
Reals Core negative 21 2 10.5 10.5 ± 5.5 (--5,+-16)
Randoms Core arbitrary negative 5 10 0.5 0.6
Randoms Core alternate negative 7 10 0.7 0.6
Reals Core positive 5 2 2.5 2.5 ± 1.5 (-+4,++1)
Randoms Core arbitrary positive 36 10 3.6 3.45
Randoms Core alternate positive 33 10 3.3 3.45
Reals Proximal negative 21 2 10.5 10.5 ± 2.5 (--8,+-13)
Randoms Proximal arbitrary negative 19 10 1.9 2.65
Randoms Proximal alternate negative 34 10 3.4 2.65
Reals Proximal positive 17 2 8.5 8.5 ± 0.5 (-+8,++9)
Randoms Proximal arbitrary positive 40 10 4.0 3.8
Randoms Proximal alternate positive 36 10 3.6 3.8
Reals Distal negative 288 2 144.0 144.0 ± 34 (--110,+-178)
Randoms Distal arbitrary negative 478 10 47.8 44.0
Randoms Distal alternate negative 402 10 40.2 44.0
Reals Distal positive 130 2 65.0 65.0 ± 4.0 (-+61,++69)
Randoms Distal arbitrary positive 659 10 65.9 66.45
Randoms Distal alternate positive 670 10 67.0 66.45

Comparison:

For the occurrences of real H boxes (Mitchell), the UTRs, negative cores, proximals and distals are greater than the randoms, the positive cores are outside the randoms. This suggests that the real H boxes (Mitchell) are likely active or activable.

H boxes (Rozhdestvensky)

An H box has a consensus sequence of 3'-ACACCA-5'.[4]

H boxes (Rozhdestvensky) in promoters of A1BG

For the Basic programs (starting with SuccessablesHACA.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesHACA--.bas, looking for 3'-ACACCA-5', 4, 3'-ACACCA-5', 788, 3'-ACACCA-5', 2659, 3'-ACACCA-5', 3187, 3'-ACACCA-5', 3811,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesHACA-+.bas, looking for 3'-ACACCA-5', 1, 3'-ACACCA-5', 386,
  3. positive strand in the negative direction is SuccessablesHACA+-.bas, looking for 3'-ACACCA-5', 2, 3'-ACACCA-5', 883, 3'-ACACCA-5', 2419,
  4. positive strand in the positive direction is SuccessablesHACA++.bas, looking for 3'-ACACCA-5', 2, 3'-ACACCA-5', 204, 3'-ACACCA-5', 528,
  5. complement, negative strand, negative direction is SuccessablesHACAc--.bas, looking for 3'-TGTGGT-5', 2, 3'-TGTGGT-5', 883, 3'-TGTGGT-5', 2419,
  6. complement, negative strand, positive direction is SuccessablesHACAc-+.bas, looking for 3'-TGTGGT-5', 2, 3'-TGTGGT-5', 204, 3'-TGTGGT-5', 528,
  7. complement, positive strand, negative direction is SuccessablesHACAc+-.bas, looking for 3'-TGTGGT-5', 4, 3'-TGTGGT-5', 788, 3'-TGTGGT-5', 2659, 3'-TGTGGT-5', 3187, 3'-TGTGGT-5', 3811,
  8. complement, positive strand, positive direction is SuccessablesHACAc++.bas, looking for 3'-TGTGGT-5', 1, 3'-TGTGGT-5', 386,
  9. inverse complement, negative strand, negative direction is SuccessablesHACAci--.bas, looking for 3'-TGGTGT-5', 1, 3'-TGGTGT-5', 3764,
  10. inverse complement, negative strand, positive direction is SuccessablesHACAci-+.bas, looking for 3'-TGGTGT-5', 2, 3'-TGGTGT-5', 511, 3'-TGGTGT-5', 530,
  11. inverse complement, positive strand, negative direction is SuccessablesHACAci+-.bas, looking for 3'-TGGTGT-5', 3, 3'-TGGTGT-5', 608, 3'-TGGTGT-5', 793, 3'-TGGTGT-5', 1477,
  12. inverse complement, positive strand, positive direction is SuccessablesHACAci++.bas, looking for 3'-TGGTGT-5', 1, 3'-TGGTGT-5', 420,
  13. inverse, negative strand, negative direction, is SuccessablesHACAi--.bas, looking for 3'-ACCACA-5', 3, 3'-ACCACA-5', 608, 3'-ACCACA-5', 793, 3'-ACCACA-5', 1477,
  14. inverse, negative strand, positive direction, is SuccessablesHACAi-+.bas, looking for 3'-ACCACA-5', 1, 3'-ACCACA-5', 420,
  15. inverse, positive strand, negative direction, is SuccessablesHACAi+-.bas, looking for 3'-ACCACA-5', 1, 3'-ACCACA-5', 3764,
  16. inverse, positive strand, positive direction, is SuccessablesHACAi++.bas, looking for 3'-ACCACA-5', 2, 3'-ACCACA-5', 511, 3'-ACCACA-5', 530.

UTRs (Rozhdestvensky)

  1. Negative strand, negative direction: ACACCA at 3811, TGGTGT at 3764, ACACCA at 3187.

Proximal promoters (Rozhdestvensky)

  1. Negative strand, negative direction: ACACCA at 2659.

Distal promoters (Rozhdestvensky)

  1. Negative strand, negative direction: ACACCA at 788.
  2. Positive strand, negative direction: ACACCA at 2419, TGGTGT at 1477, ACACCA at 883, TGGTGT at 793, TGGTGT at 608.


  1. Negative strand, positive direction: TGGTGT at 530, TGGTGT at 511, ACACCA at 386.
  2. Positive strand, positive direction: ACACCA at 528, TGGTGT at 420, ACACCA at 204.

H boxes (Rozhdestvensky) random dataset samplings

  1. HboxRr0: 1, ACACCA at 2165.
  2. HboxRr1: 0.
  3. HboxRr2: 0.
  4. HboxRr3: 0.
  5. HboxRr4: 1, ACACCA at 2656.
  6. HboxRr5: 0.
  7. HboxRr6: 0.
  8. HboxRr7: 1, ACACCA at 1207.
  9. HboxRr8: 3, ACACCA at 2711, ACACCA at 1949, ACACCA at 493.
  10. HboxRr9: 1, ACACCA at 3187.
  11. HboxRr0ci: 2, TCCTCT at 4371, TCCTCT at 1134.
  12. HboxRr1ci: 1, TGGTGT at 1743.
  13. HboxRr2ci: 0.
  14. HboxRr3ci: 1, TGGTGT at 3294.
  15. HboxRr4ci: 2, TGGTGT at 3325, TGGTGT at 2759.
  16. HboxRr5ci: 1, TGGTGT at 2732.
  17. HboxRr6ci: 2, TGGTGT at 2946, TGGTGT at 99.
  18. HboxRr7ci: 0.
  19. HboxRr8ci: 1, TGGTGT at 535.
  20. HboxRr9ci: 2, TGGTGT at 2203, TGGTGT at 850.

HboxRr UTRs

  1. HboxRr0ci: TCCTCT at 4371.
  2. HboxRr4ci: TGGTGT at 3325.
  3. HboxRr6ci: TGGTGT at 2946.

HboxRr proximal promoters

  1. HboxRr4: ACACCA at 2656.
  2. HboxRr8: ACACCA at 2711.
  3. HboxRr4ci: TGGTGT at 2759.

HboxRr distal promoters

  1. HboxRr0: ACACCA at 2165.
  2. HboxRr8: ACACCA at 1949, ACACCA at 493.
  3. HboxRr0ci: TCCTCT at 1134.
  4. HboxRr6ci: TGGTGT at 99.
  5. HboxRr8ci: TGGTGT at 535.


  1. HboxRr7: ACACCA at 1207.
  2. HboxRr9: ACACCA at 3187.
  3. HboxRr1ci: TGGTGT at 1743.
  4. HboxRr3ci: TGGTGT at 3294.
  5. HboxRr5ci: TGGTGT at 2732.
  6. HboxRr9ci: TGGTGT at 2203, TGGTGT at 850.

H boxes (Rozhdestvensky) analysis and results

Main article: Complex locus A1BG and ZNF497 § H boxes (Rozhdestvensky)

An H box has a consensus sequence of 3'-ACACCA-5'.[4]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 3 2 1.5 1.5
Randoms UTR arbitrary negative 3 10 0.3 0.25
Randoms UTR alternate negative 2 10 0.2 0.25
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 1 2 0.5 0.5
Randoms Proximal arbitrary negative 3 10 0.3 0.2
Randoms Proximal alternate negative 1 10 0.1 0.2
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 6 2 3.0 3.0
Randoms Distal arbitrary negative 6 10 0.6 0.5
Randoms Distal alternate negative 4 10 0.4 0.5
Reals Distal positive 6 2 3.0 3.0
Randoms Distal arbitrary positive 7 10 0.7 0.9
Randoms Distal alternate positive 11 10 1.1 0.9

Comparison:

The occurrences of real H boxes (Rozhdestvensky) are greater than the randoms. This suggests that the real H boxes (Rozhdestvensky) are likely active or activable.

H-boxes (Grandbastien)

"Two distinct sequence elements, the H-box (consensus CCTACC(N)7CT) and the G-box (CACGTG), are required for stimulation of the chs15 promoter by 4-CA."[5]

H-box consensus sequences

The earlier H-box consensus sequence is CCTACC(N)7CT.[5]

H box in Solanaceae has the following consensus sequence 3'-CC(A/T)ACCNNNNNNN(A/C)T-5'.[6]

H-box (Grandbastien) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence CCTACCTGGCGGAT and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or CCTACC finds none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CC(A/T)ACCNNNNNNN(A/C)T (starting with SuccessablesH-box.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for CC(A/T)ACCNNNNNNN(A/C)T, 0.
  2. positive strand, negative direction, looking for CC(A/T)ACCNNNNNNN(A/C)T, 0.
  3. positive strand, positive direction, looking for CC(A/T)ACCNNNNNNN(A/C)T, 0.
  4. negative strand, positive direction, looking for CC(A/T)ACCNNNNNNN(A/C)T, 0.
  5. complement, negative strand, negative direction, looking for GG(A/T)TGGNNNNNNN(G/T)A, 0.
  6. complement, positive strand, negative direction, looking for GG(A/T)TGGNNNNNNN(G/T)A, 0.
  7. complement, positive strand, positive direction, looking for GG(A/T)TGGNNNNNNN(G/T)A, 0.
  8. complement, negative strand, positive direction, looking for GG(A/T)TGGNNNNNNN(G/T)A, 0.
  9. inverse complement, negative strand, negative direction, looking for A(G/T)NNNNNNNGGT(A/T)GG, 0.
  10. inverse complement, positive strand, negative direction, looking for A(G/T)NNNNNNNGGT(A/T)GG, 1, AGAAGTGTTGGTTGG at 3946.
  11. inverse complement, positive strand, positive direction, looking for A(G/T)NNNNNNNGGT(A/T)GG, 0.
  12. inverse complement, negative strand, positive direction, looking for A(G/T)NNNNNNNGGT(A/T)GG, 0.
  13. inverse negative strand, negative direction, looking for T(A/C)NNNNNNNCCA(A/T)CC, 1, TCTTCACAACCAACC at 3946.
  14. inverse positive strand, negative direction, looking for T(A/C)NNNNNNNCCA(A/T)CC, 0.
  15. inverse positive strand, positive direction, looking for T(A/C)NNNNNNNCCA(A/T)CC, 0.
  16. inverse negative strand, positive direction, looking for T(A/C)NNNNNNNCCA(A/T)CC, 0.

H-box (Grandbastien) UTRs

Main article: UTR promoter gene transcriptions

Positive strand, negative direction: AGAAGTGTTGGTTGG at 3946.

H-box (Grandbastien) random dataset samplings

  1. H-boxGr0: 0.
  2. H-boxGr1: 1, CCTACCCCGGCGCAT at 4300.
  3. H-boxGr2: 1, CCTACCCTAGGTACT at 2304.
  4. H-boxGr3: 0.
  5. H-boxGr4: 0.
  6. H-boxGr5: 0.
  7. H-boxGr6: 0.
  8. H-boxGr7: 0.
  9. H-boxGr8: 1, CCAACCGTCCTTACT at 4305.
  10. H-boxGr9: 0.
  11. H-boxGr0ci: 0.
  12. H-boxGr1ci: 0.
  13. H-boxGr2ci: 0.
  14. H-boxGr3ci: 0.
  15. H-boxGr4ci: 0.
  16. H-boxGr5ci: 1, ATGGTCCGCGGTAGG at 404.
  17. H-boxGr6ci: 0.
  18. H-boxGr7ci: 0.
  19. H-boxGr8ci: 0.
  20. H-boxGr9ci: 0.

H-boxGr UTRs

  1. H-boxGr8: CCAACCGTCCTTACT at 4305.

H-boxGr core promoters

  1. H-boxGr1: CCTACCCCGGCGCAT at 4300.

H-boxGr distal promoters

  1. H-boxGr2: CCTACCCTAGGTACT at 2304.


  1. H-boxGr5ci: ATGGTCCGCGGTAGG at 404.

H-boxes (Grandbastien) analysis and results

Main article: Complex locus A1BG and ZNF497 § H-boxes (Grandbastien)

H box in Solanaceae has the following consensus sequence 3'-CC(A/T)ACCNNNNNNN(A/C)T-5'.[6]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms UTR arbitrary negative 1 10 0.1 0.1
Randoms UTR alternate negative 1 10 0.1 0.1
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 1 10 0.1 0.1
Randoms Core alternate positive 1 10 0.1 0.1
Reals Proximal negative 0 2 0 0
Randoms Proximal negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 1 10 0.1 0.1
Randoms Distal alternate negative 1 10 0.1 0.1
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 1 10 0.1 0.1
Randoms Distal alternate positive 1 10 0.1 0.1

Comparison:

The occurrences of real H-box (Grandbastien) is greater than the randoms. This suggests that the real H-box (Grandbastien) is likely active or activable.

H-box (Lindsay) samplings

Main article: Model samplings

Copying a responsive element consensus sequence CCTACC and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or one between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CCTACC (starting with SuccessablesHL-box.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:

  1. negative strand, negative direction, looking for CCTACC, 0.
  2. positive strand, negative direction, looking for CCTACC, 0.
  3. positive strand, positive direction, looking for CCTACC, 1, CCTACC at 1879.
  4. negative strand, positive direction, looking for CCTACC, 1, CCTACC at 1196.
  5. complement, negative strand, negative direction, looking for GGATGG, 0.
  6. complement, positive strand, negative direction, looking for GGATGG, 0.
  7. complement, positive strand, positive direction, looking for GGATGG, 1, GGATGG at 1196.
  8. complement, negative strand, positive direction, looking for GGATGG, 1, GGATGG at 1879.
  9. inverse complement, negative strand, negative direction, looking for GGTAGG, 2, GGTAGG at 4456, GGTAGG at 1838.
  10. inverse complement, positive strand, negative direction, looking for GGTAGG, 1, GGTAGG at 119.
  11. inverse complement, positive strand, positive direction, looking for GGTAGG, 2, GGTAGG at 3629, GGTAGG at 3108.
  12. inverse complement, negative strand, positive direction, looking for GGTAGG, 1, GGTAGG at 3753.
  13. inverse negative strand, negative direction, looking for CCATCC, 1, CCATCC at 119.
  14. inverse positive strand, negative direction, looking for CCATCC, 2, CCATCC at 4456, CCATCC at 1838.
  15. inverse positive strand, positive direction, looking for CCATCC, 1, CCATCC at 3753.
  16. inverse negative strand, positive direction, looking for CCATCC, 2, CCATCC at 3629, CCATCC at 3108.

H-box (Lindsay) UTRs

Main article: UTR promoter gene transcriptions
  1. Negative strand, negative direction: GGTAGG at 4456.

H-box (Lindsay) distal promoters

Main article: Distal promoter gene transcriptions
  1. Negative strand, negative direction: GGTAGG at 1838.
  2. Positive strand, negative direction:, GGTAGG at 119.
  1. Negative strand, positive direction: GGTAGG at 3753, CCTACC at 1196.
  2. Positive strand, positive direction: GGTAGG at 3629, GGTAGG at 3108. CCTACC at 1879.

H-box (Lindsay) random dataset samplings

  1. HboxLr0: 0.
  2. HboxLr1: 1, CCTACC at 4291.
  3. HboxLr2: 3, CCTACC at 3716, CCTACC at 2295, CCTACC at 1943.
  4. HboxLr3: 0.
  5. HboxLr4: 2, CCTACC at 4554, CCTACC at 1036.
  6. HboxLr5: 1, CCTACC at 4408.
  7. HboxLr6: 2, CCTACC at 2434, CCTACC at 620.
  8. HboxLr7: 1, CCTACC at 4340.
  9. HboxLr8: 0.
  10. HboxLr9: 1, CCTACC at 130.
  11. HboxLr0ci: 1, GGTAGG at 3868.
  12. HboxLr1ci: 0.
  13. HboxLr2ci: 1, GGTAGG at 3202.
  14. HboxLr3ci: 0.
  15. HboxLr4ci: 4, GGTAGG at 4125, GGTAGG at 1206, GGTAGG at 687, GGTAGG at 32.
  16. HboxLr5ci: 3, GGTAGG at 4149, GGTAGG at 3890, GGTAGG at 404.
  17. HboxLr6ci: 2, GGTAGG at 3023, GGTAGG at 1478.
  18. HboxLr7ci: 2, GGTAGG at 3507, GGTAGG at 3182.
  19. HboxLr8ci: 3, GGTAGG at 3247, GGTAGG at 2739, GGTAGG at 575.
  20. HboxLr9ci: 2, GGTAGG at 1275, GGTAGG at 606.

HboxLr arbitrary UTRs

  1. HboxLr2: CCTACC at 3716.
  2. HboxLr4: CCTACC at 4554.
  3. HboxLr0ci: GGTAGG at 3868.
  4. HboxLr2ci: GGTAGG at 3202.
  5. HboxLr4ci: GGTAGG at 4125.
  6. HboxLr6ci: GGTAGG at 3023.
  7. HboxLr8ci: 3GGTAGG at 3247.

HboxLr alternate UTRs

  1. HboxLr1: CCTACC at 4291.
  2. HboxLr5: CCTACC at 4408.
  3. HboxLr7: CCTACC at 4340.
  4. HboxLr5ci: GGTAGG at 4149, GGTAGG at 3890.
  5. HboxLr7ci: GGTAGG at 3507, GGTAGG at 3182.

HboxLr arbitrary positive direction core promoters

  1. HboxLr1: CCTACC at 4291.
  2. HboxLr5: CCTACC at 4408.
  3. HboxLr7: CCTACC at 4340.

HboxLr arbitrary negative direction proximal promoters

  1. HboxLr8ci: GGTAGG at 2739.

HboxLr arbitrary positive direction proximal promoters

  1. HboxLr5ci: GGTAGG at 4149.

HboxLr alternate positive direction proximal promoters

  1. HboxLr4ci: GGTAGG at 4125.

HboxLr arbitrary negative direction distal promoters

  1. HboxLr2: CCTACC at 2295, CCTACC at 1943.
  2. HboxLr4: CCTACC at 1036.
  3. HboxLr6: CCTACC at 2434, CCTACC at 620.
  4. HboxLr4ci: GGTAGG at 1206, GGTAGG at 687, GGTAGG at 32.
  5. HboxLr6ci: GGTAGG at 1478.
  6. HboxLr8ci: GGTAGG at 575.

HboxLr alternate negative direction distal promoters

  1. HboxLr9: CCTACC at 130.
  2. HboxLr5ci: GGTAGG at 404.
  3. HboxLr9ci: GGTAGG at 1275, GGTAGG at 606.

HboxLr arbitrary positive direction distal promoters

  1. HboxLr9: CCTACC at 130.
  2. HboxLr5ci: GGTAGG at 3890, GGTAGG at 404.
  3. HboxLr7ci: GGTAGG at 3507, GGTAGG at 3182.
  4. HboxLr9ci: GGTAGG at 1275, GGTAGG at 606.

HboxLr alternate positive direction distal promoters

  1. HboxLr2: CCTACC at 3716, CCTACC at 2295, CCTACC at 1943.
  2. HboxLr4: CCTACC at 1036.
  3. HboxLr6: CCTACC at 2434, CCTACC at 620.
  4. HboxLr0ci: GGTAGG at 3868.
  5. HboxLr2ci: GGTAGG at 3202.
  6. HboxLr4ci: GGTAGG at 1206, GGTAGG at 687, GGTAGG at 32.
  7. HboxLr6ci: GGTAGG at 3023, GGTAGG at 1478.
  8. HboxLr8ci: GGTAGG at 3247, GGTAGG at 2739, GGTAGG at 575.

H-boxes (Lindsay) analysis and results

Main article: Complex locus A1BG and ZNF497 § H-boxes (Lindsay)

"The KAP-2 protein [...] binds to the H-box (CCTACC) element in the bean CHS15 chalcone synthase promoter".[7]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--1,+-0)
Randoms UTR arbitrary negative 7 10 0.7 0.7
Randoms UTR alternate negative 7 10 0.7 0.7
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 3 10 0.3 0.15
Randoms Core alternate positive 0 10 0 0.15
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 1 10 0.1 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 1 10 0.1 0.1
Randoms Proximal alternate positive 1 10 0.1 0.1
Reals Distal negative 2 2 1 1 ± 1 (--1,+-1)
Randoms Distal arbitrary negative 10 10 1 0.7
Randoms Distal alternate negative 4 10 0.4 0.7
Reals Distal positive 5 2 2.5 2.5 ± 0.5 (-+2,++3)
Randoms Distal arbitrary positive 7 10 0.7 1.15
Randoms Distal alternate positive 16 10 1.6 1.15

Comparison:

The occurrences of real H-boxes (Lindsay) are greater than the randoms for the UTRs and positive distals, the negative distals are equal to the high randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Paul J Rushton and Imre E Somssich (August 1998). "Transcriptional control of plant genes responsive to pathogens" (PDF). Current Opinion in Plant Biology. 1 (4): 311–5. doi:10.1016/1369-5266(88)80052-9. Retrieved 5 November 2018.
  2. ↑ Jun Zhong, Antoine H.F.M. Peters, Kathy Kafer, Robert E. Braun (1 June 2001). "A Highly Conserved Sequence Essential for Translational Repression of the Protamine 1 Messenger RNA in Murine Spermatids". Biology of Reproduction. 64 (6): 1784–1789. doi:10.1095/biolreprod64.6.1784. Retrieved 5 November 2018.
  3. ↑ 3.0 3.1 3.2 3.3 James R. Mitchell, Jeffrey Cheng, and Kathleen Collins (January 1999). "A Box H/ACA Small Nucleolar RNA-Like Domain at the Human Telomerase RNA 3' End" (PDF). Molecular and Cellular Biology. 19 (1): 567–576. Retrieved 5 November 2018.
  4. ↑ 4.0 4.1 Timofey S. Rozhdestvensky, Thean Hock Tang, Inna V. Tchirkova, Jürgen Brosius, Jean‐Pierre Bachellerie and Alexander Hüttenhofer (2003). "Binding of L7Ae protein to the K‐turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea". Nucleic Acids Research. 31 (3): 869–77. doi:10.1093/nar/gkg175. Retrieved 2014-06-08.
  5. ↑ 5.0 5.1 Gary J. Loake, Ouriel Faktor, Christopher J. Lamb, and Richard A. Dixon (October 1992). "Combination of H-box [CCTACC(N)7CT] and G-box (CACGTG) cis elements is necessary for feed-forward stimulation of a chalcone synthase promoter by the phenylpropanoid-pathway intermediate p-coumaricacid" (PDF). Proceedings of the National Academy of Sciences USA. 89 (19): 9230–9234. doi:10.1073/pnas.89.19.9230. Retrieved 16 March 2021.
  6. ↑ 6.0 6.1 M.-A. Grandbastien, C. Audeon, E. Bonnivard, J.M. Casacuberta, B. Chalhoub, A.-P.P. Costa, Q.H. Le, D. Melayah, M. Petit, C. Poncet, S.M. Tam, M.-A. Van Sluys, C. Mhiri (July 2005). "Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae" (PDF). Cytogenetic and Genomic Research. 110 (1–4): 229–41. doi:10.1159/000084957. Retrieved 5 November 2018.
  7. ↑ William P. Lindsay, Fiona M. McAlister, Qun Zhu, Xian-Zhi He, Wolfgang Dröge-Laser, Susie Hedrick, Peter Doerner, Chris Lamb and Richard A. Dixon (July 2002). "KAP-2, a protein that binds to the H-box in a bean chalcone synthase promoter, is a novel plant transcription factor with sequence identity to the large subunit of human Ku autoantigen". Plant Molecular Biology. 49 (5): 503–514. doi:10.1023/A:1015505316379. Retrieved 5 October 2019.

External links


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