Homeobox gene transcriptions
"Transcription factors Pax-4 and Pax-6 are known to be key regulators of pancreatic cell differentiation and development.  The gene-targeting experiments revealed that Pax-4 and Pax-6 cannot substitute for each other in tissue with overlapping expression of both genes.  DNA-binding specificities of Pax-4 and Pax-6 are similar. The Pax-4 homeodomain  was shown to preferentially dimerize on DNA sequences consisting of an inverted TAAT motif, separated by 4-nucleotide spacing."
The "crucial difference between the binding sites of Antennapedia class and TTF-1 HDs is in the motifs 5'-TAAT-3', recognized by Antennapedia , and 5'-CAAG-3', preferentially bound by TTF-1.  binding of wild type and mutants TTF-1 HD to oligonucleotides containing either 5'-TAAT-3' or 5'-CAAG-3' indicate that only in the presence of the latter motif the Gln50 in TTF-1 HD is utilized for DNA recognition."

# Human genes

# Interactions

# Consensus sequences
An apparent consensus sequence is 5'-CAAG-3'.

# Hypotheses
- A1BG has no homeoboxes in either promoter.
- A1BG is not transcribed by a homeobox.
- No homeobox participates in the transcription of A1BG.

# Homeobox samplings
Copying a portion of the homeobox motif of CAAG and putting it in "F" finds eight located between ZSCAN22 and A1BG and 21 between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence CAAG (starting with SuccessablesHome.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:
- negative strand, negative direction, looking for CAAG, 8, CAAG at 4417, CAAG at 4175, CAAG at 4024, CAAG at 1177, CAAG at 719, CAAG at 344, CAAG at 253, CAAG at 44.
- negative strand, positive direction, looking for CAAG, 21, CAAG at 2692, CAAG at 2615, CAAG at 2593, CAAG at 2508, CAAG at 2398, CAAG at 2189, CAAG at 1947, CAAG at 1525, CAAG at 1510, CAAG at 1426, CAAG at 1326, CAAG at 1258, CAAG at 1006, CAAG at 922, CAAG at 822, CAAG at 754, CAAG at 670, CAAG at 586, CAAG at 502, CAAG at 338, CAAG at 177.
- positive strand, negative direction, looking for CAAG, 24, CAAG at 4183, CAAG at 4178, CAAG at 4027, CAAG at 4019, CAAG at 3844, CAAG at 3758, CAAG at 3634, CAAG at 3373, CAAG at 3339, CAAG at 3306, CAAG at 3273, CAAG at 3140, CAAG at 2963, CAAG at 2244, CAAG at 2022, CAAG at 1817, CAAG at 1496, CAAG at 874, CAAG at 692, CAAG at 556, CAAG at 454, CAAG at 419, CAAG at 114, CAAG at 70.
- positive strand, positive direction, looking for CAAG, 14, CAAG at 4200, CAAG at 4073, CAAG at 3624, CAAG at 3351, CAAG at 2954, CAAG at 2933, CAAG at 2922, CAAG at 1987, CAAG at 1926, CAAG at 1489, CAAG at 1389, CAAG at 508, CAAG at 305, CAAG at 107.
- inverse complement, negative strand, negative direction, looking for CTTG, 15, CTTG at 4450, CTTG at 3783, CTTG at 3723, CTTG at 3667, CTTG at 3459, CTTG at 3244, CTTG at 2716, CTTG at 2381, CTTG at 1955, CTTG at 1684, CTTG at 1551, CTTG at 1302, CTTG at 1011, CTTG at 845, CTTG at 286.
- inverse complement, negative strand, positive direction, looking for CTTG, 13, CTTG at 4388, CTTG at 4299, CTTG at 4130, CTTG at 4015, CTTG at 3373, CTTG at 3001, CTTG at 2741, CTTG at 2418, CTTG at 1798, CTTG at 1578, CTTG at 654, CTTG at 526, CTTG at 129.
- inverse complement, positive strand, negative direction, looking for CTTG, 24, CTTG at 4293, CTTG at 4267, CTTG at 4187, CTTG at 4011, CTTG at 3792, CTTG at 3570, CTTG at 3400, CTTG at 3241, CTTG at 3102, CTTG at 2920, CTTG at 2713, CTTG at 2579, CTTG at 2378, CTTG at 2126, CTTG at 1972, CTTG at 1926, CTTG at 1648, CTTG at 1618, CTTG at 1606, CTTG at 1299, CTTG at 1008, CTTG at 842, CTTG at 327, CTTG at 280.
- inverse complement, positive strand, positive direction, looking for CTTG, 13, CTTG at 4443, CTTG at 4067, CTTG at 4047, CTTG at 3936, CTTG at 3855, CTTG at 3837, CTTG at 3093, CTTG at 2775, CTTG at 2578, CTTG at 2224, CTTG at 1950, CTTG at 1810, CTTG at 362.

## Homeobox (4560-2846) UTRs
- Negative strand, negative direction: CTTG at 4450, CAAG at 4417, CAAG at 4175, CAAG at 4024, CTTG at 3783, CTTG at 3723, CTTG at 3667, CTTG at 3459, CTTG at 3244.
- Positive strand, negative direction: CTTG at 4293, CTTG at 4267, CTTG at 4187, CAAG at 4183, CAAG at 4178, CAAG at 4027, CAAG at 4019, CTTG at 4011, CAAG at 3844, CTTG at 3792, CAAG at 3758, CAAG at 3634, CTTG at 3570, CTTG at 3400, CAAG at 3373, CAAG at 3339, CAAG at 3306, CAAG at 3273, CTTG at 3241, CAAG at 3140, CTTG at 3102, CAAG at 2963, CTTG at 2920.

## Homeobox positive direction (4445-4265) core promoters
- Negative strand, positive direction: CTTG at 4388, CTTG at 4299.
- Positive strand, positive direction: CTTG at 4443.

## Homeobox negative direction (2811-2596) proximal promoters
- Negative strand, negative direction: CTTG at 2716.
- Positive strand, negative direction: CTTG at 2713.

## Homeobox positive direction (4265-4050) proximal promoters
- Negative strand, positive direction: CTTG at 4130.
- Positive strand, positive direction: CAAG at 4200, CAAG at 4073, CTTG at 4067.

## Homeobox negative direction (2596-1) distal promoters
- Negative strand, negative direction: CTTG at 2381, CTTG at 1955, CTTG at 1684, CTTG at 1551, CTTG at 1302, CAAG at 1177, CTTG at 1011, CTTG at 845, CAAG at 719, CAAG at 344, CTTG at 286, CAAG at 253, CAAG at 44.
- Positive strand, negative direction: CTTG at 2579, CTTG at 2378, CAAG at 2244, CTTG at 2126, CAAG at 2022, CTTG at 1972, CTTG at 1926, CAAG at 1817, CTTG at 1648, CTTG at 1618, CTTG at 1606, CAAG at 1496, CTTG at 1299, CTTG at 1008, CAAG at 874, CTTG at 842, CAAG at 692, CAAG at 556, CAAG at 454, CAAG at 419, CTTG at 327, CTTG at 280, CAAG at 114, CAAG at 70.

## Homeobox positive direction (4050-1) distal promoters
- Negative strand, positive direction: CTTG at 4015, CTTG at 3373, CTTG at 3001, CTTG at 2741, CAAG at 2692, CAAG at 2615, CAAG at 2593, CAAG at 2508, CTTG at 2418, CAAG at 2398, CAAG at 2189, CAAG at 1947, CTTG at 1798, CTTG at 1578, CAAG at 1525, CAAG at 1510, CAAG at 1426, CAAG at 1326, CAAG at 1258, CAAG at 1006, CAAG at 922, CAAG at 822, CAAG at 754, CAAG at 670, CTTG at 654, CAAG at 586, CTTG at 526, CAAG at 502, CAAG at 338, CAAG at 177, CTTG at 129.
- Positive strand, positive direction: CTTG at 4047, CTTG at 3936, CTTG at 3855, CTTG at 3837, CAAG at 3624, CAAG at 3351, CTTG at 3093, CAAG at 2954, CAAG at 2933, CAAG at 2922, CTTG at 2775, CTTG at 2578, CTTG at 2224, CTTG at 1950, CAAG at 1987, CAAG at 1926, CTTG at 1810, CAAG at 1489, CAAG at 1389, CAAG at 508, CTTG at 362, CAAG at 305, CAAG at 107.

# Homeoboxes random dataset samplings
- Homer0: 16, CAAG at 4274, CAAG at 4155, CAAG at 4069, CAAG at 4045, CAAG at 4040, CAAG at 3490, CAAG at 2196, CAAG at 2184, CAAG at 1849, CAAG at 1435, CAAG at 1294, CAAG at 1122, CAAG at 1031, CAAG at 915, CAAG at 523, CAAG at 328.
- Homer1: 21, CAAG at 4525, CAAG at 4485, CAAG at 4462, CAAG at 3996, CAAG at 3572, CAAG at 3393, CAAG at 3326, CAAG at 3313, CAAG at 3199, CAAG at 2992, CAAG at 2888, CAAG at 2419, CAAG at 2225, CAAG at 2218, CAAG at 1946, CAAG at 1031, CAAG at 1016, CAAG at 843, CAAG at 622, CAAG at 563, CAAG at 99.
- Homer2: 19, CAAG at 4466, CAAG at 4249, CAAG at 4198, CAAG at 4090, CAAG at 3899, CAAG at 3889, CAAG at 3609, CAAG at 3602, CAAG at 3509, CAAG at 3307, CAAG at 2602, CAAG at 2567, CAAG at 2445, CAAG at 2386, CAAG at 2028, CAAG at 1786, CAAG at 1642, CAAG at 1519, CAAG at 1391.
- Homer3: 18, CAAG at 4556, CAAG at 4308, CAAG at 4163, CAAG at 3930, CAAG at 3859, CAAG at 3666, CAAG at 3643, CAAG at 3303, CAAG at 3237, CAAG at 3106, CAAG at 1905, CAAG at 1839, CAAG at 1807, CAAG at 1614, CAAG at 1310, CAAG at 898, CAAG at 675, CAAG at 264.
- Homer4: 23, CAAG at 4403, CAAG at 4396, CAAG at 4319, CAAG at 3967, CAAG at 3611, CAAG at 3565, CAAG at 3462, CAAG at 3432, CAAG at 3269, CAAG at 3241, CAAG at 3044, CAAG at 2673, CAAG at 2407, CAAG at 2305, CAAG at 2215, CAAG at 2063, CAAG at 1690, CAAG at 1594, CAAG at 1333, CAAG at 791, CAAG at 628, CAAG at 552, CAAG at 329.
- Homer5: 12, CAAG at 4129, CAAG at 3802, CAAG at 3609, CAAG at 3418, CAAG at 3255, CAAG at 2147, CAAG at 1996, CAAG at 1630, CAAG at 1436, CAAG at 1237, CAAG at 1049, CAAG at 81.
- Homer6: 19, CAAG at 4547, CAAG at 4437, CAAG at 4381, CAAG at 3368, CAAG at 3115, CAAG at 2959, CAAG at 2866, CAAG at 2587, CAAG at 2543, CAAG at 1897, CAAG at 1090, CAAG at 1036, CAAG at 989, CAAG at 787, CAAG at 707, CAAG at 594, CAAG at 163, CAAG at 125, CAAG at 55.
- Homer7: 15, CAAG at 4346, CAAG at 4206, CAAG at 3818, CAAG at 3762, CAAG at 3744, CAAG at 3151, CAAG at 2691, CAAG at 2582, CAAG at 2368, CAAG at 2302, CAAG at 2163, CAAG at 1821, CAAG at 770, CAAG at 704, CAAG at 274.
- Homer8: 12, CAAG at 4389, CAAG at 3972, CAAG at 3369, CAAG at 3169, CAAG at 3039, CAAG at 2576, CAAG at 2225, CAAG at 1726, CAAG at 1413, CAAG at 861, CAAG at 234, CAAG at 152.
- Homer9: 17, CAAG at 4128, CAAG at 3899, CAAG at 3460, CAAG at 2730, CAAG at 2535, CAAG at 2435, CAAG at 2318, CAAG at 2065, CAAG at 1834, CAAG at 1822, CAAG at 1656, CAAG at 1420, CAAG at 1114, CAAG at 950, CAAG at 638, CAAG at 338, CAAG at 209.
- Homer0ci: 13, CTTG at 4514, CTTG at 4104, CTTG at 4051, CTTG at 4028, CTTG at 3550, CTTG at 2427, CTTG at 1925, CTTG at 1695, CTTG at 1675, CTTG at 1375, CTTG at 1041, CTTG at 717, CTTG at 75.
- Homer1ci: 22, CTTG at 4374, CTTG at 4188, CTTG at 4159, CTTG at 4104, CTTG at 4083, CTTG at 3863, CTTG at 3805, CTTG at 2939, CTTG at 2934, CTTG at 2325, CTTG at 2159, CTTG at 2032, CTTG at 2005, CTTG at 1599, CTTG at 1502, CTTG at 1138, CTTG at 1117, CTTG at 1063, CTTG at 869, CTTG at 388, CTTG at 351, CTTG at 42.
- Homer2ci: 14, CTTG at 3781, CTTG at 3503, CTTG at 2345, CTTG at 2255, CTTG at 1524, CTTG at 1269, CTTG at 1258, CTTG at 1161, CTTG at 1063, CTTG at 873, CTTG at 621, CTTG at 229, CTTG at 211, CTTG at 79.
- Homer3ci: 18, CTTG at 4390, CTTG at 4300, CTTG at 4221, CTTG at 4097, CTTG at 4008, CTTG at 3872, CTTG at 3631, CTTG at 3290, CTTG at 2980, CTTG at 2860, CTTG at 2805, CTTG at 2780, CTTG at 2513, CTTG at 2294, CTTG at 2039, CTTG at 1501, CTTG at 283, CTTG at 22.
- Homer4ci: 22, CTTG at 4448, CTTG at 4287, CTTG at 4102, CTTG at 4058, CTTG at 3973, CTTG at 3544, CTTG at 3382, CTTG at 3185, CTTG at 2958, CTTG at 2845, CTTG at 2084, CTTG at 1894, CTTG at 1765, CTTG at 1703, CTTG at 1633, CTTG at 1442, CTTG at 1392, CTTG at 1162, CTTG at 646, CTTG at 373, CTTG at 269, CTTG at 176.
- Homer5ci: 21, CTTG at 4555, CTTG at 4420, CTTG at 4199, CTTG at 4191, CTTG at 3937, CTTG at 3922, CTTG at 3466, CTTG at 3319, CTTG at 2997, CTTG at 2852, CTTG at 2431, CTTG at 2119, CTTG at 2064, CTTG at 1911, CTTG at 1731, CTTG at 1010, CTTG at 548, CTTG at 483, CTTG at 477, CTTG at 353, CTTG at 212.
- Homer6ci: 20, CTTG at 4512, CTTG at 4411, CTTG at 4160, CTTG at 3633, CTTG at 3574, CTTG at 3398, CTTG at 3309, CTTG at 3271, CTTG at 3197, CTTG at 3173, CTTG at 3166, CTTG at 3066, CTTG at 2151, CTTG at 2062, CTTG at 2040, CTTG at 1870, CTTG at 1743, CTTG at 455, CTTG at 366, CTTG at 15.
- Homer7ci: 16, CTTG at 4416, CTTG at 3970, CTTG at 3890, CTTG at 3723, CTTG at 3363, CTTG at 3296, CTTG at 3118, CTTG at 2574, CTTG at 2553, CTTG at 2477, CTTG at 2463, CTTG at 1981, CTTG at 1633, CTTG at 1024, CTTG at 721, CTTG at 321.
- Homer8ci: 16, CTTG at 4433, CTTG at 4159, CTTG at 3765, CTTG at 3322, CTTG at 3260, CTTG at 2929, CTTG at 2849, CTTG at 2636, CTTG at 2452, CTTG at 2195, CTTG at 2032, CTTG at 1627, CTTG at 1254, CTTG at 565, CTTG at 498, CTTG at 401.
- Homer9ci: 23, CTTG at 4112, CTTG at 3835, CTTG at 3668, CTTG at 3646, CTTG at 3410, CTTG at 3165, CTTG at 3108, CTTG at 3049, CTTG at 2988, CTTG at 2947, CTTG at 2902, CTTG at 2797, CTTG at 2734, CTTG at 2292, CTTG at 2165, CTTG at 2104, CTTG at 1891, CTTG at 1363, CTTG at 1070, CTTG at 910, CTTG at 846, CTTG at 490, CTTG at 267.

## Homeoboxr arbitrary (evens) (4560-2846) UTRs
- Homer0: CAAG at 4274, CAAG at 4155, CAAG at 4069, CAAG at 4045, CAAG at 4040, CAAG at 3490.
- Homer2: CAAG at 4466, CAAG at 4249, CAAG at 4198, CAAG at 4090, CAAG at 3899, CAAG at 3889, CAAG at 3609, CAAG at 3602, CAAG at 3509, CAAG at 3307.
- Homer4: CAAG at 4403, CAAG at 4396, CAAG at 4319, CAAG at 3967, CAAG at 3611, CAAG at 3565, CAAG at 3462, CAAG at 3432, CAAG at 3269, CAAG at 3241, CAAG at 3044.
- Homer6: CAAG at 4547, CAAG at 4437, CAAG at 4381, CAAG at 3368, CAAG at 3115, CAAG at 2959, CAAG at 2866.
- Homer8: CAAG at 4389, CAAG at 3972, CAAG at 3369, CAAG at 3169, CAAG at 3039.
- Homer0ci: CTTG at 4514, CTTG at 4104, CTTG at 4051, CTTG at 4028, CTTG at 3550.
- Homer2ci: CTTG at 3781, CTTG at 3503.
- Homer4ci: CTTG at 4448, CTTG at 4287, CTTG at 4102, CTTG at 4058, CTTG at 3973, CTTG at 3544, CTTG at 3382, CTTG at 3185, CTTG at 2958.
- Homer6ci: CTTG at 4512, CTTG at 4411, CTTG at 4160, CTTG at 3633, CTTG at 3574, CTTG at 3398, CTTG at 3309, CTTG at 3271, CTTG at 3197, CTTG at 3173, CTTG at 3166, CTTG at 3066.
- Homer8ci: CTTG at 4433, CTTG at 4159, CTTG at 3765, CTTG at 3322, CTTG at 3260, CTTG at 2929, CTTG at 2849.

## Homeoboxr alternate (odds) (4560-2846) UTRs
- Homer1: CAAG at 4525, CAAG at 4485, CAAG at 4462, CAAG at 3996, CAAG at 3572, CAAG at 3393, CAAG at 3326, CAAG at 3313, CAAG at 3199, CAAG at 2992, CAAG at 2888.
- Homer3: CAAG at 4556, CAAG at 4308, CAAG at 4163, CAAG at 3930, CAAG at 3859, CAAG at 3666, CAAG at 3643, CAAG at 3303, CAAG at 3237, CAAG at 3106.
- Homer5: CAAG at 4129, CAAG at 3802, CAAG at 3609, CAAG at 3418, CAAG at 3255.
- Homer7: CAAG at 4346, CAAG at 4206, CAAG at 3818, CAAG at 3762, CAAG at 3744, CAAG at 3151.
- Homer9: CAAG at 4128, CAAG at 3899, CAAG at 3460.
- Homer3ci: CTTG at 4390, CTTG at 4300, CTTG at 4221, CTTG at 4097, CTTG at 4008, CTTG at 3872, CTTG at 3631, CTTG at 3290, CTTG at 2980, CTTG at 2860.
- Homer5ci: CTTG at 4555, CTTG at 4420, CTTG at 4199, CTTG at 4191, CTTG at 3937, CTTG at 3922, CTTG at 3466, CTTG at 3319, CTTG at 2997, CTTG at 2852.
- Homer7ci: CTTG at 4416, CTTG at 3970, CTTG at 3890, CTTG at 3723, CTTG at 3363, CTTG at 3296, CTTG at 3118.
- Homer9ci: CTTG at 4112, CTTG at 3835, CTTG at 3668, CTTG at 3646, CTTG at 3410, CTTG at 3165, CTTG at 3108, CTTG at 3049, CTTG at 2988, CTTG at 2947, CTTG at 2902.

## Homeoboxr arbitrary negative direction (evens) (2846-2811) core promoters
- Homer4ci: CTTG at 2845.

## Homeoboxr arbitrary positive direction (odds) (4445-4265) core promoters
- Homer3: CAAG at 4308.
- Homer7: CAAG at 4346.
- Homer3ci: CTTG at 4390, CTTG at 4300.
- Homer5ci: CTTG at 4420.
- Homer7ci: CTTG at 4416.

## Homeoboxr alternate positive direction (evens) (4445-4265) core promoters
- Homer0: CAAG at 4274.
- Homer4: CAAG at 4403, CAAG at 4396, CAAG at 4319.
- Homer6: CAAG at 4437, CAAG at 4381.
- Homer8: CAAG at 4389.
- Homer4ci: CTTG at 4287.
- Homer6ci: CTTG at 4411.
- Homer8ci: CTTG at 4433.

## Homeoboxr arbitrary negative direction (evens) (2811-2596) proximal promoters
- Homer2: CAAG at 2602.
- Homer4: CAAG at 2673.
- Homer8ci: CTTG at 2636.

## Homeoboxr alternate negative direction (odds) (2811-2596) proximal promoters
- Homer7: CAAG at 2691.
- Homer9: CAAG at 2730.
- Homer3ci: CTTG at 2805, CTTG at 2780.
- Homer9ci: CTTG at 2797, CTTG at 2734.

## Homeoboxr arbitrary positive direction (odds) (4265-4050) proximal promoters
- Homer3: CAAG at 4163.
- Homer5: CAAG at 4129.
- Homer7: CAAG at 4206.
- Homer9: CAAG at 4128.
- Homer3ci: CTTG at 4221, CTTG at 4097.
- Homer5ci: CTTG at 4199, CTTG at 4191.
- Homer9ci: CTTG at 4112.

## Homeoboxr alternate positive direction (evens) (4265-4050) proximal promoters
- Homer0: CAAG at 4155, CAAG at 4069.
- Homer2: CAAG at 4249, CAAG at 4198, CAAG at 4090.
- Homer4ci: CTTG at 4102, CTTG at 4058.
- Homer6ci: CTTG at 4160.
- Homer8ci: CTTG at 4159.

## Homeoboxr arbitrary negative direction (evens) (2596-1) distal promoters
- Homer0: CAAG at 2196, CAAG at 2184, CAAG at 1849, CAAG at 1435, CAAG at 1294, CAAG at 1122, CAAG at 1031, CAAG at 915, CAAG at 523, CAAG at 328.
- Homer2: CAAG at 2567, CAAG at 2445, CAAG at 2386, CAAG at 2028, CAAG at 1786, CAAG at 1642, CAAG at 1519, CAAG at 1391.
- Homer4: CAAG at 2407, CAAG at 2305, CAAG at 2215, CAAG at 2063, CAAG at 1690, CAAG at 1594, CAAG at 1333, CAAG at 791, CAAG at 628, CAAG at 552, CAAG at 329.
- Homer6: CAAG at 2587, CAAG at 2543, CAAG at 1897, CAAG at 1090, CAAG at 1036, CAAG at 989, CAAG at 787, CAAG at 707, CAAG at 594, CAAG at 163, CAAG at 125, CAAG at 55.
- Homer8: CAAG at 2576, CAAG at 2225, CAAG at 1726, CAAG at 1413, CAAG at 861, CAAG at 234, CAAG at 152.
- Homer2ci: CTTG at 2345, CTTG at 2255, CTTG at 1524, CTTG at 1269, CTTG at 1258, CTTG at 1161, CTTG at 1063, CTTG at 873, CTTG at 621, CTTG at 229, CTTG at 211, CTTG at 79.
- Homer4ci: CTTG at 2084, CTTG at 1894, CTTG at 1765, CTTG at 1703, CTTG at 1633, CTTG at 1442, CTTG at 1392, CTTG at 1162, CTTG at 646, CTTG at 373, CTTG at 269, CTTG at 176.
- Homer6ci: CTTG at 2151, CTTG at 2062, CTTG at 2040, CTTG at 1870, CTTG at 1743, CTTG at 455, CTTG at 366, CTTG at 15.
- Homer8ci: CTTG at 2452, CTTG at 2195, CTTG at 2032, CTTG at 1627, CTTG at 1254, CTTG at 565, CTTG at 498, CTTG at 401.

## Homeoboxr alternate negative direction (odds) (2596-1) distal promoters
- Homer1: CAAG at 2419, CAAG at 2225, CAAG at 2218, CAAG at 1946, CAAG at 1031, CAAG at 1016, CAAG at 843, CAAG at 622, CAAG at 563, CAAG at 99.
- Homer3: CAAG at 1905, CAAG at 1839, CAAG at 1807, CAAG at 1614, CAAG at 1310, CAAG at 898, CAAG at 675, CAAG at 264.
- Homer5: CAAG at 3802, CAAG at 3609, CAAG at 3418, CAAG at 3255, CAAG at 2147, CAAG at 1996, CAAG at 1630, CAAG at 1436, CAAG at 1237, CAAG at 1049, CAAG at 81.
- Homer7: CAAG at 2582, CAAG at 2368, CAAG at 2302, CAAG at 2163, CAAG at 1821, CAAG at 770, CAAG at 704, CAAG at 274.
- Homer9: CAAG at 2535, CAAG at 2435, CAAG at 2318, CAAG at 2065, CAAG at 1834, CAAG at 1822, CAAG at 1656, CAAG at 1420, CAAG at 1114, CAAG at 950, CAAG at 638, CAAG at 338, CAAG at 209.
- Homer3ci: 18, CTTG at 4390, CTTG at 4300, CTTG at 4221, CTTG at 4097, CTTG at 4008, CTTG at 3872, CTTG at 3631, CTTG at 3290, CTTG at 2980, CTTG at 2860, CTTG at 2805, CTTG at 2780, CTTG at 2513, CTTG at 2294, CTTG at 2039, CTTG at 1501, CTTG at 283, CTTG at 22.
- Homer5ci: CTTG at 2431, CTTG at 2119, CTTG at 2064, CTTG at 1911, CTTG at 1731, CTTG at 1010, CTTG at 548, CTTG at 483, CTTG at 477, CTTG at 353, CTTG at 212.
- Homer7ci: CTTG at 2574, CTTG at 2553, CTTG at 2477, CTTG at 2463, CTTG at 1981, CTTG at 1633, CTTG at 1024, CTTG at 721, CTTG at 321.
- Homer9ci: CTTG at 2292, CTTG at 2165, CTTG at 2104, CTTG at 1891, CTTG at 1363, CTTG at 1070, CTTG at 910, CTTG at 846, CTTG at 490, CTTG at 267.

## Homeoboxr arbitrary positive direction (odds) (4050-1) distal promoters
- Homer1: CAAG at 3996, CAAG at 3572, CAAG at 3393, CAAG at 3326, CAAG at 3313, CAAG at 3199, CAAG at 2992, CAAG at 2888, CAAG at 2419, CAAG at 2225, CAAG at 2218, CAAG at 1946, CAAG at 1031, CAAG at 1016, CAAG at 843, CAAG at 622, CAAG at 563, CAAG at 99.
- Homer3: CAAG at 3930, CAAG at 3859, CAAG at 3666, CAAG at 3643, CAAG at 3303, CAAG at 3237, CAAG at 3106, CAAG at 1905, CAAG at 1839, CAAG at 1807, CAAG at 1614, CAAG at 1310, CAAG at 898, CAAG at 675, CAAG at 264.
- Homer5: CAAG at 3802, CAAG at 3609, CAAG at 3418, CAAG at 3255, CAAG at 2147, CAAG at 1996, CAAG at 1630, CAAG at 1436, CAAG at 1237, CAAG at 1049, CAAG at 81.
- Homer7: CAAG at 3818, CAAG at 3762, CAAG at 3744, CAAG at 3151, CAAG at 2691, CAAG at 2582, CAAG at 2368, CAAG at 2302, CAAG at 2163, CAAG at 1821, CAAG at 770, CAAG at 704, CAAG at 274.
- Homer9: CAAG at 2535, CAAG at 2435, CAAG at 2318, CAAG at 2065, CAAG at 1834, CAAG at 1822, CAAG at 1656, CAAG at 1420, CAAG at 1114, CAAG at 950, CAAG at 638, CAAG at 338, CAAG at 209.
- Homer5ci: CTTG at 3937, CTTG at 3922, CTTG at 3466, CTTG at 3319, CTTG at 2997, CTTG at 2852, CTTG at 2431, CTTG at 2119, CTTG at 2064, CTTG at 1911, CTTG at 1731, CTTG at 1010, CTTG at 548, CTTG at 483, CTTG at 477, CTTG at 353, CTTG at 212.
- Homer7ci: CTTG at 3970, CTTG at 3890, CTTG at 3723, CTTG at 3363, CTTG at 3296, CTTG at 3118, CTTG at 2574, CTTG at 2553, CTTG at 2477, CTTG at 2463, CTTG at 1981, CTTG at 1633, CTTG at 1024, CTTG at 721, CTTG at 321.
- Homer9ci: CTTG at 3835, CTTG at 3668, CTTG at 3646, CTTG at 3410, CTTG at 3165, CTTG at 3108, CTTG at 3049, CTTG at 2988, CTTG at 2947, CTTG at 2902, CTTG at 2797, CTTG at 2734, CTTG at 2292, CTTG at 2165, CTTG at 2104, CTTG at 1891, CTTG at 1363, CTTG at 1070, CTTG at 910, CTTG at 846, CTTG at 490, CTTG at 267.

## Homeoboxr alternate positive direction (evens) (4050-1) distal promoters
- Homer0: CAAG at 4045, CAAG at 4040, CAAG at 3490, CAAG at 2196, CAAG at 2184, CAAG at 1849, CAAG at 1435, CAAG at 1294, CAAG at 1122, CAAG at 1031, CAAG at 915, CAAG at 523, CAAG at 328.
- Homer2: CAAG at 2567, CAAG at 2445, CAAG at 2386, CAAG at 2028, CAAG at 1786, CAAG at 1642, CAAG at 1519, CAAG at 1391.
- Homer6: CAAG at 3368, CAAG at 3115, CAAG at 2959, CAAG at 2866, CAAG at 2587, CAAG at 2543, CAAG at 1897, CAAG at 1090, CAAG at 1036, CAAG at 989, CAAG at 787, CAAG at 707, CAAG at 594, CAAG at 163, CAAG at 125, CAAG at 55.
- Homer8: CAAG at 3972, CAAG at 3369, CAAG at 3169, CAAG at 3039, CAAG at 2576, CAAG at 2225, CAAG at 1726, CAAG at 1413, CAAG at 861, CAAG at 234, CAAG at 152.
- Homer2ci: CTTG at 3781, CTTG at 3503, CTTG at 2345, CTTG at 2255, CTTG at 1524, CTTG at 1269, CTTG at 1258, CTTG at 1161, CTTG at 1063, CTTG at 873, CTTG at 621, CTTG at 229, CTTG at 211, CTTG at 79.
- Homer4ci: CTTG at 3973, CTTG at 3544, CTTG at 3382, CTTG at 3185, CTTG at 2958, CTTG at 2845, CTTG at 2084, CTTG at 1894, CTTG at 1765, CTTG at 1703, CTTG at 1633, CTTG at 1442, CTTG at 1392, CTTG at 1162, CTTG at 646, CTTG at 373, CTTG at 269, CTTG at 176.
- Homer6ci: CTTG at 3633, CTTG at 3574, CTTG at 3398, CTTG at 3309, CTTG at 3271, CTTG at 3197, CTTG at 3173, CTTG at 3166, CTTG at 3066, CTTG at 2151, CTTG at 2062, CTTG at 2040, CTTG at 1870, CTTG at 1743, CTTG at 455, CTTG at 366, CTTG at 15.
- Homer8ci: CTTG at 3765, CTTG at 3322, CTTG at 3260, CTTG at 2929, CTTG at 2849, CTTG at 2636, CTTG at 2452, CTTG at 2195, CTTG at 2032, CTTG at 1627, CTTG at 1254, CTTG at 565, CTTG at 498, CTTG at 401.

# Homeobox analysis and results
The "binding of wild type and mutants TTF-1 HD to oligonucleotides containing either 5'-TAAT-3' or 5'-CAAG-3' indicate that only in the presence of the latter motif the Gln50 in TTF-1 HD is utilized for DNA recognition."
Comparison:
The occurrences of real homeoboxes are greater than the randoms. This suggests that the real homeoboxes are likely active or activable.

# Homeodomain samplings
For the Basic programs testing consensus sequence TAAT (starting with SuccessablesTAAT.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:
- negative strand, negative direction, looking for TAAT, 19, TAAT at 4538, TAAT at 4227, TAAT at 3468, TAAT at 3454, TAAT at 3436, TAAT at 3175, TAAT at 2998, TAAT at 2977, TAAT at 2951, TAAT at 1886, TAAT at 1723, TAAT at 1695, TAAT at 1295, TAAT at 1233, TAAT at 776, TAAT at 498, TAAT at 236, TAAT at 173, TAAT at 153.
- Positive strand, negative direction: 23, TAAT at 4540, TAAT at 4225, TAAT at 4222, TAAT at 4076, TAAT at 3973, TAAT at 3657, TAAT at 3537, TAAT at 3064, TAAT at 2675, TAAT at 2088, TAAT at 1914, TAAT at 1779, TAAT at 1707, TAAT at 1261, TAAT at 1134, TAAT at 980, TAAT at 804, TAAT at 670, TAAT at 601, TAAT at 534, TAAT at 397, TAAT at 270, TAAT at 248.
- Negative strand, positive direction: 3, TAAT at 4168, TAAT at 4145, TAAT at 2438.
- Positive strand, positive direction: 4, TAAT at 4164, TAAT at 4157, TAAT at 4143, TAAT at 2546.
- inverse complement, negative strand, negative direction, looking for ATTA, 23, ATTA at 4540, ATTA at 4225, ATTA at 4222, ATTA at 4076, ATTA at 3973, ATTA at 3657, ATTA at 3537, ATTA at 3064, ATTA at 2675, ATTA at 2088, ATTA at 1914, ATTA at 1779, ATTA at 1707, ATTA at 1261, ATTA at 1134, ATTA at 980, ATTA at 804, ATTA at 670, ATTA at 601, ATTA at 534, ATTA at 397, ATTA at 270, ATTA at 248.
- inverse complement, positive strand, negative direction: 19, ATTA at 4538, ATTA at 4227, ATTA at 3468, ATTA at 3454, ATTA at 3436, ATTA at 3175, ATTA at 2998, ATTA at 2977, ATTA at 2951, ATTA at 1886, ATTA at 1723, ATTA at 1695, ATTA at 1295, ATTA at 1233, ATTA at 776, ATTA at 498, ATTA at 236, ATTA at 173, ATTA at 153.
- inverse complement, negative strand, positive direction: 4, ATTA at 4164, ATTA at 4157, ATTA at 4143, ATTA at 2546.
- inverse complement, positive strand, positive direction: 3, ATTA at 4168, ATTA at 4145, ATTA at 2438.

## TAAT (4560-2846) UTRs
- Negative strand, negative direction: TAAT at 4538, TAAT at 4227, TAAT at 3468, TAAT at 3454, TAAT at 3436, TAAT at 3175, TAAT at 2998, TAAT at 2977, TAAT at 2951.
- Positive strand, negative direction: TAAT at 4540, TAAT at 4225, TAAT at 4222, TAAT at 4076, TAAT at 3973, TAAT at 3657, TAAT at 3537, TAAT at 3064.

## TAAT negative direction (2811-2596) proximal promoters
- Positive strand, negative direction: TAAT at 2675.

## TAAT positive direction (4265-4050) proximal promoters
- Negative strand, positive direction: TAAT at 4168, TAAT at 4145.
- Positive strand, positive direction: TAAT at 4164, TAAT at 4157, TAAT at 4143.

## TAAT negative direction (2596-1) distal promoters
- Negative strand, negative direction: TAAT at 1886, TAAT at 1723, TAAT at 1695, TAAT at 1295, TAAT at 1233, TAAT at 776, TAAT at 498, TAAT at 236, TAAT at 173, TAAT at 153.
- Positive strand, negative direction: TAAT at 2088, TAAT at 1914, TAAT at 1779, TAAT at 1707, TAAT at 1261, TAAT at 1134, TAAT at 980, TAAT at 804, TAAT at 670, TAAT at 601, TAAT at 534, TAAT at 397, TAAT at 270, TAAT at 248.

## TAAT positive direction (4050-1) distal promoters
- Negative strand, positive direction: TAAT at 2438.
- Positive strand, positive direction: TAAT at 2546.

# Homeodomain random dataset samplings
- TAATr0: 14, TAAT at 4151, TAAT at 3692, TAAT at 3603, TAAT at 3579, TAAT at 3125, TAAT at 2578, TAAT at 2505, TAAT at 2262, TAAT at 1491, TAAT at 600, TAAT at 472, TAAT at 409, TAAT at 148, TAAT at 145.
- TAATr1: 15, TAAT at 4335, TAAT at 3937, TAAT at 3458, TAAT at 3330, TAAT at 3083, TAAT at 2900, TAAT at 2525, TAAT at 2474, TAAT at 2375, TAAT at 1241, TAAT at 1045, TAAT at 1006, TAAT at 825, TAAT at 805, TAAT at 538.
- TAATr2: 20, TAAT at 4025, TAAT at 3983, TAAT at 3980, TAAT at 3945, TAAT at 3447, TAAT at 3237, TAAT at 3229, TAAT at 3113, TAAT at 3032, TAAT at 2510, TAAT at 2502, TAAT at 1958, TAAT at 1838, TAAT at 1555, TAAT at 1449, TAAT at 989, TAAT at 845, TAAT at 826, TAAT at 793, TAAT at 240.
- TAATr3: 23, TAAT at 4367, TAAT at 4347, TAAT at 4149, TAAT at 4114, TAAT at 4091, TAAT at 4048, TAAT at 3879, TAAT at 3866, TAAT at 3798, TAAT at 3274, TAAT at 2775, TAAT at 2613, TAAT at 2591, TAAT at 2230, TAAT at 1794, TAAT at 1695, TAAT at 1350, TAAT at 1249, TAAT at 1217, TAAT at 917, TAAT at 824, TAAT at 784, TAAT at 406.
- TAATr4: 20, TAAT at 4375, TAAT at 4165, TAAT at 4159, TAAT at 4116, TAAT at 4113, TAAT at 4051, TAAT at 3982, TAAT at 3892, TAAT at 3670, TAAT at 3404, TAAT at 3217, TAAT at 2440, TAAT at 2035, TAAT at 1696, TAAT at 1313, TAAT at 1211, TAAT at 948, TAAT at 775, TAAT at 705, TAAT at 254.
- TAATr5: 24, TAAT at 4548, TAAT at 4182, TAAT at 3851, TAAT at 3631, TAAT at 3565, TAAT at 3518, TAAT at 3213, TAAT at 3203, TAAT at 2658, TAAT at 2646, TAAT at 2517, TAAT at 2089, TAAT at 2060, TAAT at 2011, TAAT at 1315, TAAT at 1243, TAAT at 1144, TAAT at 1107, TAAT at 850, TAAT at 645, TAAT at 467, TAAT at 429, TAAT at 313, TAAT at 114.
- TAATr6: 19, TAAT at 4442, TAAT at 4425, TAAT at 4096, TAAT at 4089, TAAT at 3612, TAAT at 3127, TAAT at 3002, TAAT at 2316, TAAT at 2100, TAAT at 2034, TAAT at 2001, TAAT at 1652, TAAT at 1386, TAAT at 1185, TAAT at 813, TAAT at 664, TAAT at 631, TAAT at 400, TAAT at 33.
- TAATr7: 19, TAAT at 4443, TAAT at 4084, TAAT at 3911, TAAT at 3842, TAAT at 3450, TAAT at 3235, TAAT at 3106, TAAT at 2454, TAAT at 2251, TAAT at 2240, TAAT at 1861, TAAT at 1736, TAAT at 905, TAAT at 372, TAAT at 292, TAAT at 244, TAAT at 209, TAAT at 81, TAAT at 29.
- TAATr8: 23, TAAT at 3983, TAAT at 3579, TAAT at 3563, TAAT at 3352, TAAT at 3071, TAAT at 2925, TAAT at 2818, TAAT at 2663, TAAT at 2619, TAAT at 2435, TAAT at 1747, TAAT at 1431, TAAT at 1345, TAAT at 1319, TAAT at 922, TAAT at 852, TAAT at 785, TAAT at 782, TAAT at 726, TAAT at 718, TAAT at 637, TAAT at 406, TAAT at 274.
- TAATr9: 14, TAAT at 4169, TAAT at 3957, TAAT at 3611, TAAT at 3556, TAAT at 3365, TAAT at 3294, TAAT at 3084, TAAT at 2848, TAAT at 2392, TAAT at 2043, TAAT at 1491, TAAT at 1228, TAAT at 1000, TAAT at 242.
- TAATr0ci: 15, ATTA at 4463, ATTA at 4225, ATTA at 4099, ATTA at 3974, ATTA at 3776, ATTA at 3721, ATTA at 3605, ATTA at 2852, ATTA at 2374, ATTA at 1663, ATTA at 1185, ATTA at 812, ATTA at 546, ATTA at 482, ATTA at 275.
- TAATr1ci: 22, ATTA at 4266, ATTA at 4042, ATTA at 3417, ATTA at 3159, ATTA at 3144, ATTA at 2911, ATTA at 2898, ATTA at 2850, ATTA at 2601, ATTA at 1701, ATTA at 1541, ATTA at 1263, ATTA at 1260, ATTA at 1231, ATTA at 1143, ATTA at 1026, ATTA at 584, ATTA at 367, ATTA at 362, ATTA at 336, ATTA at 250, ATTA at 141.
- TAATr2ci: 20, ATTA at 4069, ATTA at 4032, ATTA at 3884, ATTA at 3788, ATTA at 3723, ATTA at 3613, ATTA at 3519, ATTA at 3030, ATTA at 2910, ATTA at 2753, ATTA at 2242, ATTA at 2177, ATTA at 1949, ATTA at 1779, ATTA at 1707, ATTA at 1581, ATTA at 1553, ATTA at 1327, ATTA at 847, ATTA at 337.
- TAATr3ci: 15, ATTA at 4345, ATTA at 4214, ATTA at 3918, ATTA at 3915, ATTA at 3889, ATTA at 2973, ATTA at 2732, ATTA at 1646, ATTA at 1466, ATTA at 1348, ATTA at 1066, ATTA at 936, ATTA at 709, ATTA at 322, ATTA at 208.
- TAATr4ci: 24, ATTA at 4373, ATTA at 4163, ATTA at 4147, ATTA at 3752, ATTA at 3406, ATTA at 3370, ATTA at 2933, ATTA at 2917, ATTA at 2646, ATTA at 2349, ATTA at 2327, ATTA at 2297, ATTA at 2251, ATTA at 2234, ATTA at 2033, ATTA at 1539, ATTA at 975, ATTA at 950, ATTA at 946, ATTA at 620, ATTA at 617, ATTA at 605, ATTA at 479, ATTA at 164.
- TAATr5ci: 16, ATTA at 4454, ATTA at 4203, ATTA at 4062, ATTA at 3930, ATTA at 3783, ATTA at 3625, ATTA at 3147, ATTA at 2509, ATTA at 1559, ATTA at 1272, ATTA at 1136, ATTA at 1065, ATTA at 892, ATTA at 852, ATTA at 691, ATTA at 647.
- TAATr6ci: 21, ATTA at 4494, ATTA at 4262, ATTA at 3865, ATTA at 3754, ATTA at 3727, ATTA at 3683, ATTA at 3610, ATTA at 3392, ATTA at 2912, ATTA at 2889, ATTA at 2525, ATTA at 2461, ATTA at 2293, ATTA at 2178, ATTA at 1783, ATTA at 919, ATTA at 717, ATTA at 469, ATTA at 329, ATTA at 183, ATTA at 31.
- TAATr7ci: 19, ATTA at 4524, ATTA at 4516, ATTA at 4164, ATTA at 4147, ATTA at 3621, ATTA at 3596, ATTA at 3411, ATTA at 3375, ATTA at 2957, ATTA at 2403, ATTA at 2334, ATTA at 1660, ATTA at 1653, ATTA at 1650, ATTA at 1638, ATTA at 1571, ATTA at 308, ATTA at 242, ATTA at 207.
- TAATr8ci: 27, ATTA at 4361, ATTA at 3966, ATTA at 3912, ATTA at 3675, ATTA at 3557, ATTA at 3506, ATTA at 3482, ATTA at 3124, ATTA at 3049, ATTA at 2960, ATTA at 2855, ATTA at 2715, ATTA at 2433, ATTA at 2185, ATTA at 2090, ATTA at 2083, ATTA at 1959, ATTA at 1846, ATTA at 1819, ATTA at 1722, ATTA at 1506, ATTA at 1363, ATTA at 1074, ATTA at 878, ATTA at 606, ATTA at 355, ATTA at 227.
- TAATr9ci: 10, ATTA at 4277, ATTA at 4055, ATTA at 3502, ATTA at 1230, ATTA at 1167, ATTA at 1160, ATTA at 1157, ATTA at 1002, ATTA at 805, ATTA at 240.

## TAATr arbitrary (evens) (4560-2846) UTRs
- TAATr0: TAAT at 4151, TAAT at 3692, TAAT at 3603, TAAT at 3579, TAAT at 3125.
- TAATr2: TAAT at 4025, TAAT at 3983, TAAT at 3980, TAAT at 3945, TAAT at 3447, TAAT at 3237, TAAT at 3229, TAAT at 3113, TAAT at 3032.
- TAATr4: TAAT at 4375, TAAT at 4165, TAAT at 4159, TAAT at 4116, TAAT at 4113, TAAT at 4051, TAAT at 3982, TAAT at 3892, TAAT at 3670, TAAT at 3404, TAAT at 3217.
- TAATr6: TAAT at 4442, TAAT at 4425, TAAT at 4096, TAAT at 4089, TAAT at 3612, TAAT at 3127, TAAT at 3002.
- TAATr8: TAAT at 3983, TAAT at 3579, TAAT at 3563, TAAT at 3352, TAAT at 3071, TAAT at 2925.
- TAATr0ci: ATTA at 4463, ATTA at 4225, ATTA at 4099, ATTA at 3974, ATTA at 3776, ATTA at 3721, ATTA at 3605, ATTA at 2852.
- TAATr2ci: ATTA at 4069, ATTA at 4032, ATTA at 3884, ATTA at 3788, ATTA at 3723, ATTA at 3613, ATTA at 3519, ATTA at 3030, ATTA at 2910.
- TAATr4ci: ATTA at 4373, ATTA at 4163, ATTA at 4147, ATTA at 3752, ATTA at 3406, ATTA at 3370, ATTA at 2933, ATTA at 2917.
- TAATr6ci: ATTA at 4494, ATTA at 4262, ATTA at 3865, ATTA at 3754, ATTA at 3727, ATTA at 3683, ATTA at 3610, ATTA at 3392, ATTA at 2912, ATTA at 2889.
- TAATr8ci: ATTA at 4361, ATTA at 3966, ATTA at 3912, ATTA at 3675, ATTA at 3557, ATTA at 3506, ATTA at 3482, ATTA at 3124, ATTA at 3049, ATTA at 2960, ATTA at 2855.

## TAATr alternate (odds) (4560-2846) UTRs
- TAATr1: TAAT at 4335, TAAT at 3937, TAAT at 3458, TAAT at 3330, TAAT at 3083, TAAT at 2900.
- TAATr3: TAAT at 4367, TAAT at 4347, TAAT at 4149, TAAT at 4114, TAAT at 4091, TAAT at 4048, TAAT at 3879, TAAT at 3866, TAAT at 3798, TAAT at 3274.
- TAATr5: TAAT at 4548, TAAT at 4182, TAAT at 3851, TAAT at 3631, TAAT at 3565, TAAT at 3518, TAAT at 3213, TAAT at 3203.
- TAATr7: TAAT at 4443, TAAT at 4084, TAAT at 3911, TAAT at 3842, TAAT at 3450, TAAT at 3235, TAAT at 3106.
- TAATr9: TAAT at 4169, TAAT at 3957, TAAT at 3611, TAAT at 3556, TAAT at 3365, TAAT at 3294, TAAT at 3084, TAAT at 2848.
- TAATr1ci: ATTA at 4266, ATTA at 4042, ATTA at 3417, ATTA at 3159, ATTA at 3144, ATTA at 2911, ATTA at 2898, ATTA at 2850.
- TAATr3ci: ATTA at 4345, ATTA at 4214, ATTA at 3918, ATTA at 3915, ATTA at 3889, ATTA at 2973.
- TAATr5ci: ATTA at 4454, ATTA at 4203, ATTA at 4062, ATTA at 3930, ATTA at 3783, ATTA at 3625, ATTA at 3147.
- TAATr7ci: ATTA at 4524, ATTA at 4516, ATTA at 4164, ATTA at 4147, ATTA at 3621, ATTA at 3596, ATTA at 3411, ATTA at 3375, ATTA at 2957.
- TAATr9ci: ATTA at 4277, ATTA at 4055, ATTA at 3502.

## TAATr arbitrary negative direction (evens) (2846-2811) core promoters
- TAATr8: TAAT at 2818.

## TAATr arbitrary positive direction (odds) (4445-4265) core promoters
- TAATr1: TAAT at 4335.
- TAATr3: TAAT at 4367, TAAT at 4347.
- TAATr7: TAAT at 4443.
- TAATr1ci: ATTA at 4266.
- TAATr3ci: ATTA at 4345.
- TAATr9ci: ATTA at 4277.

## TAATr alternate positive direction (evens) (4445-4265) core promoters
- TAATr4: TAAT at 4375.
- TAATr6: TAAT at 4442, TAAT at 4425.
- TAATr4ci: ATTA at 4373.
- TAATr8ci: ATTA at 4361.

## TAATr arbitrary negative direction (evens) (2811-2596) proximal promoters
- TAATr8: TAAT at 2663, TAAT at 2619.
- TAATr2ci: ATTA at 2753.
- TAATr4ci: ATTA at 2646.
- TAATr6ci: ATTA at 2525.
- TAATr8ci: ATTA at 2715.

## TAATr alternate negative direction (odds) (2811-2596) proximal promoters
- TAATr3: TAAT at 2775, TAAT at 2613.
- TAATr5: TAAT at 2658, TAAT at 2646.
- TAATr1ci: ATTA at 2601.
- TAATr3ci: ATTA at 2732.

## TAATr arbitrary positive direction (odds) (4265-4050) proximal promoters
- TAATr3: TAAT at 4149, TAAT at 4114, TAAT at 4091.
- TAATr5: TAAT at 4182.
- TAATr7: TAAT at 4084.
- TAATr9: TAAT at 4169.
- TAATr3ci: ATTA at 4214.
- TAATr5ci: ATTA at 4203, ATTA at 4062.
- TAATr7ci: ATTA at 4164, ATTA at 4147.
- TAATr9ci: ATTA at 4055.

## TAATr alternate positive direction (evens) (4265-4050) proximal promoters
- TAATr0: TAAT at 4151.
- TAATr4: TAAT at 4165, TAAT at 4159, TAAT at 4116, TAAT at 4113, TAAT at 4051.
- TAATr6: TAAT at 4096, TAAT at 4089.
- TAATr0ci: ATTA at 4225, ATTA at 4099.
- TAATr2ci: ATTA at 4069.
- TAATr4ci: ATTA at 4163, ATTA at 4147.
- TAATr6ci: ATTA at 4262.

## TAATr arbitrary negative direction (evens) (2596-1) distal promoters
- TAATr0: TAAT at 2578, TAAT at 2505, TAAT at 2262, TAAT at 1491, TAAT at 600, TAAT at 472, TAAT at 409, TAAT at 148, TAAT at 145.
- TAATr2: TAAT at 2510, TAAT at 2502, TAAT at 1958, TAAT at 1838, TAAT at 1555, TAAT at 1449, TAAT at 989, TAAT at 845, TAAT at 826, TAAT at 793, TAAT at 240.
- TAATr4: TAAT at 2440, TAAT at 2035, TAAT at 1696, TAAT at 1313, TAAT at 1211, TAAT at 948, TAAT at 775, TAAT at 705, TAAT at 254.
- TAATr6: TAAT at 2316, TAAT at 2100, TAAT at 2034, TAAT at 2001, TAAT at 1652, TAAT at 1386, TAAT at 1185, TAAT at 813, TAAT at 664, TAAT at 631, TAAT at 400, TAAT at 33.
- TAATr8: TAAT at 2435, TAAT at 1747, TAAT at 1431, TAAT at 1345, TAAT at 1319, TAAT at 922, TAAT at 852, TAAT at 785, TAAT at 782, TAAT at 726, TAAT at 718, TAAT at 637, TAAT at 406, TAAT at 274.
- TAATr0ci: ATTA at 2374, ATTA at 1663, ATTA at 1185, ATTA at 812, ATTA at 546, ATTA at 482, ATTA at 275.
- TAATr2ci: ATTA at 2242, ATTA at 2177, ATTA at 1949, ATTA at 1779, ATTA at 1707, ATTA at 1581, ATTA at 1553, ATTA at 1327, ATTA at 847, ATTA at 337.
- TAATr4ci: ATTA at 2349, ATTA at 2327, ATTA at 2297, ATTA at 2251, ATTA at 2234, ATTA at 2033, ATTA at 1539, ATTA at 975, ATTA at 950, ATTA at 946, ATTA at 620, ATTA at 617, ATTA at 605, ATTA at 479, ATTA at 164.
- TAATr6ci: ATTA at 2525, ATTA at 2461, ATTA at 2293, ATTA at 2178, ATTA at 1783, ATTA at 919, ATTA at 717, ATTA at 469, ATTA at 329, ATTA at 183, ATTA at 31.
- TAATr8ci: ATTA at 2433, ATTA at 2185, ATTA at 2090, ATTA at 2083, ATTA at 1959, ATTA at 1846, ATTA at 1819, ATTA at 1722, ATTA at 1506, ATTA at 1363, ATTA at 1074, ATTA at 878, ATTA at 606, ATTA at 355, ATTA at 227.

## TAATr alternate negative direction (odds) (2596-1) distal promoters
- TAATr1: TAAT at 2525, TAAT at 2474, TAAT at 2375, TAAT at 1241, TAAT at 1045, TAAT at 1006, TAAT at 825, TAAT at 805, TAAT at 538.
- TAATr3: TAAT at 2591, TAAT at 2230, TAAT at 1794, TAAT at 1695, TAAT at 1350, TAAT at 1249, TAAT at 1217, TAAT at 917, TAAT at 824, TAAT at 784, TAAT at 406.
- TAATr5: TAAT at 2517, TAAT at 2089, TAAT at 2060, TAAT at 2011, TAAT at 1315, TAAT at 1243, TAAT at 1144, TAAT at 1107, TAAT at 850, TAAT at 645, TAAT at 467, TAAT at 429, TAAT at 313, TAAT at 114.
- TAATr7: TAAT at 2454, TAAT at 2251, TAAT at 2240, TAAT at 1861, TAAT at 1736, TAAT at 905, TAAT at 372, TAAT at 292, TAAT at 244, TAAT at 209, TAAT at 81, TAAT at 29.
- TAATr9: TAAT at 2392, TAAT at 2043, TAAT at 1491, TAAT at 1228, TAAT at 1000, TAAT at 242.
- TAATr1ci: ATTA at 1701, ATTA at 1541, ATTA at 1263, ATTA at 1260, ATTA at 1231, ATTA at 1143, ATTA at 1026, ATTA at 584, ATTA at 367, ATTA at 362, ATTA at 336, ATTA at 250, ATTA at 141.
- TAATr3ci: ATTA at 1646, ATTA at 1466, ATTA at 1348, ATTA at 1066, ATTA at 936, ATTA at 709, ATTA at 322, ATTA at 208.
- TAATr5ci: ATTA at 2509, ATTA at 1559, ATTA at 1272, ATTA at 1136, ATTA at 1065, ATTA at 892, ATTA at 852, ATTA at 691, ATTA at 647.
- TAATr7ci: ATTA at 2403, ATTA at 2334, ATTA at 1660, ATTA at 1653, ATTA at 1650, ATTA at 1638, ATTA at 1571, ATTA at 308, ATTA at 242, ATTA at 207.
- TAATr9ci: ATTA at 1230, ATTA at 1167, ATTA at 1160, ATTA at 1157, ATTA at 1002, ATTA at 805, ATTA at 240.

## TAATr arbitrary positive direction (odds) (4050-1) distal promoters
- TAATr1: TAAT at 3937, TAAT at 3458, TAAT at 3330, TAAT at 3083, TAAT at 2900, TAAT at 2525, TAAT at 2474, TAAT at 2375, TAAT at 1241, TAAT at 1045, TAAT at 1006, TAAT at 825, TAAT at 805, TAAT at 538.
- TAATr3: TAAT at 4048, TAAT at 3879, TAAT at 3866, TAAT at 3798, TAAT at 3274, TAAT at 2775, TAAT at 2613, TAAT at 2591, TAAT at 2230, TAAT at 1794, TAAT at 1695, TAAT at 1350, TAAT at 1249, TAAT at 1217, TAAT at 917, TAAT at 824, TAAT at 784, TAAT at 406.
- TAATr5: TAAT at 3851, TAAT at 3631, TAAT at 3565, TAAT at 3518, TAAT at 3213, TAAT at 3203, TAAT at 2658, TAAT at 2646, TAAT at 2517, TAAT at 2089, TAAT at 2060, TAAT at 2011, TAAT at 1315, TAAT at 1243, TAAT at 1144, TAAT at 1107, TAAT at 850, TAAT at 645, TAAT at 467, TAAT at 429, TAAT at 313, TAAT at 114.
- TAATr7: TAAT at 3911, TAAT at 3842, TAAT at 3450, TAAT at 3235, TAAT at 3106, TAAT at 2454, TAAT at 2251, TAAT at 2240, TAAT at 1861, TAAT at 1736, TAAT at 905, TAAT at 372, TAAT at 292, TAAT at 244, TAAT at 209, TAAT at 81, TAAT at 29.
- TAATr9: TAAT at 3957, TAAT at 3611, TAAT at 3556, TAAT at 3365, TAAT at 3294, TAAT at 3084, TAAT at 2848, TAAT at 2392, TAAT at 2043, TAAT at 1491, TAAT at 1228, TAAT at 1000, TAAT at 242.
- TAATr1ci: ATTA at 4042, ATTA at 3417, ATTA at 3159, ATTA at 3144, ATTA at 2911, ATTA at 2898, ATTA at 2850, ATTA at 2601, ATTA at 1701, ATTA at 1541, ATTA at 1263, ATTA at 1260, ATTA at 1231, ATTA at 1143, ATTA at 1026, ATTA at 584, ATTA at 367, ATTA at 362, ATTA at 336, ATTA at 250, ATTA at 141.
- TAATr3ci: ATTA at 3918, ATTA at 3915, ATTA at 3889, ATTA at 2973, ATTA at 2732, ATTA at 1646, ATTA at 1466, ATTA at 1348, ATTA at 1066, ATTA at 936, ATTA at 709, ATTA at 322, ATTA at 208.
- TAATr5ci: ATTA at 3930, ATTA at 3783, ATTA at 3625, ATTA at 3147, ATTA at 2509, ATTA at 1559, ATTA at 1272, ATTA at 1136, ATTA at 1065, ATTA at 892, ATTA at 852, ATTA at 691, ATTA at 647.
- TAATr7ci: ATTA at 3621, ATTA at 3596, ATTA at 3411, ATTA at 3375, ATTA at 2957, ATTA at 2403, ATTA at 2334, ATTA at 1660, ATTA at 1653, ATTA at 1650, ATTA at 1638, ATTA at 1571, ATTA at 308, ATTA at 242, ATTA at 207.
- TAATr9ci: ATTA at 3502, ATTA at 1230, ATTA at 1167, ATTA at 1160, ATTA at 1157, ATTA at 1002, ATTA at 805, ATTA at 240.

## TAATr alternate positive direction (evens) (4050-1) distal promoters
- TAATr0: TAAT at 3692, TAAT at 3603, TAAT at 3579, TAAT at 3125, TAAT at 2578, TAAT at 2505, TAAT at 2262, TAAT at 1491, TAAT at 600, TAAT at 472, TAAT at 409, TAAT at 148, TAAT at 145.
- TAATr2: TAAT at 4025, TAAT at 3983, TAAT at 3980, TAAT at 3945, TAAT at 3447, TAAT at 3237, TAAT at 3229, TAAT at 3113, TAAT at 3032, TAAT at 2510, TAAT at 2502, TAAT at 1958, TAAT at 1838, TAAT at 1555, TAAT at 1449, TAAT at 989, TAAT at 845, TAAT at 826, TAAT at 793, TAAT at 240.
- TAATr4: TAAT at 3982, TAAT at 3892, TAAT at 3670, TAAT at 3404, TAAT at 3217, TAAT at 2440, TAAT at 2035, TAAT at 1696, TAAT at 1313, TAAT at 1211, TAAT at 948, TAAT at 775, TAAT at 705, TAAT at 254.
- TAATr6: TAAT at 3612, TAAT at 3127, TAAT at 3002, TAAT at 2316, TAAT at 2100, TAAT at 2034, TAAT at 2001, TAAT at 1652, TAAT at 1386, TAAT at 1185, TAAT at 813, TAAT at 664, TAAT at 631, TAAT at 400, TAAT at 33.
- TAATr8: TAAT at 3983, TAAT at 3579, TAAT at 3563, TAAT at 3352, TAAT at 3071, TAAT at 2925, TAAT at 2818, TAAT at 2663, TAAT at 2619, TAAT at 2435, TAAT at 1747, TAAT at 1431, TAAT at 1345, TAAT at 1319, TAAT at 922, TAAT at 852, TAAT at 785, TAAT at 782, TAAT at 726, TAAT at 718, TAAT at 637, TAAT at 406, TAAT at 274.
- TAATr0ci: ATTA at 3974, ATTA at 3776, ATTA at 3721, ATTA at 3605, ATTA at 2852, ATTA at 2374, ATTA at 1663, ATTA at 1185, ATTA at 812, ATTA at 546, ATTA at 482, ATTA at 275.
- TAATr2ci: ATTA at 4032, ATTA at 3884, ATTA at 3788, ATTA at 3723, ATTA at 3613, ATTA at 3519, ATTA at 3030, ATTA at 2910, ATTA at 2753, ATTA at 2242, ATTA at 2177, ATTA at 1949, ATTA at 1779, ATTA at 1707, ATTA at 1581, ATTA at 1553, ATTA at 1327, ATTA at 847, ATTA at 337.
- TAATr4ci: ATTA at 3752, ATTA at 3406, ATTA at 3370, ATTA at 2933, ATTA at 2917, ATTA at 2646, ATTA at 2349, ATTA at 2327, ATTA at 2297, ATTA at 2251, ATTA at 2234, ATTA at 2033, ATTA at 1539, ATTA at 975, ATTA at 950, ATTA at 946, ATTA at 620, ATTA at 617, ATTA at 605, ATTA at 479, ATTA at 164.
- TAATr8ci: ATTA at 3966, ATTA at 3912, ATTA at 3675, ATTA at 3557, ATTA at 3506, ATTA at 3482, ATTA at 3124, ATTA at 3049, ATTA at 2960, ATTA at 2855, ATTA at 2715, ATTA at 2433, ATTA at 2185, ATTA at 2090, ATTA at 2083, ATTA at 1959, ATTA at 1846, ATTA at 1819, ATTA at 1722, ATTA at 1506, ATTA at 1363, ATTA at 1074, ATTA at 878, ATTA at 606, ATTA at 355, ATTA at 227.

# Homeodomain analysis and results
The Pax-4 homeodomain  was shown to preferentially dimerize on DNA sequences consisting of an inverted TAAT motif, separated by 4-nucleotide spacing."
Comparison:
The occurrences of real UTR homeodomains are generally greater than the randoms, but overlap the high randoms, negative direction proximals are less than the randoms, positive direction proximals are greater than the randoms, the negative direction distals are generally greater than the randoms, but overlap the high end of the randoms, and the positive direction distals are less than the randoms. This suggests that the real homeodomains are likely active or activable.

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