TOMTOM

Name	Preview	Matches	List
1_re_57_0.355	CTGGGCAACA	0
2_re_40_0.367	AGGCTGAGG	0
3_re_90_0.369	CTCACTGCACC	0
4_re_26_0.370	GTCTCGAACTC	1	RPC155_01_M01798_T
5_re_25_0.374	ACCCCGTCT	0
6_re_124_0.377	TGCACTCCA	0
7_re_118_0.378	GGTGGCTCA	0
8_re_71_0.379	GGAGGTCGA	0
9_re_97_0.380	CCTCCCAAAC	2	IK_Q5_M01169_T, LYF1_01_M00141_T
10_re_139_0.381	CACTTTGGG	0
11_re_53_0.383	GGAGAATCGC	0
12_re_205_0.387	AGGTGATCC	0
13_re_125_0.393	CCTGACCTC	0
14_re_8_0.394	AATTAGCCGG	0
15_re_135_0.397	CGGGTTCA	0
16_re_78_0.397	GAACACGGTG	0
17_re_157_0.398	CAGGTGTGG	3	TCF4_03_M01769_T, sna_MA0086.1_J, Tcfe2a_primary_SCI09_U
18_h_21_0.583	AAAGCCGCTT	0
19_re_240_0.420	ACGTGCCAC	0
20_h_1_0.579	CTTATCTG	3	Gata1_MA0035.2_J, Tal1::Gata1_MA0140.1_J, GATA1_06_M00347_T
21_h_2_0.578	AGTCACTTCCTG	16	ETS_Q4_M00771_T, ETS1_B_M00339_T, FLI1_Q6_M01208_T, NERF_Q2_M00531_T, GABPA_MA0062.2_J, ETS2_B_M00340_T, TEL2_Q6_M00678_T, FEV_MA0156.1_J, E74A_01_M00016_T, Elf2_EMBO10_U
22_re_67_0.423	TACTCGGGA	0
23_e_208_0.569	GAAAACGCCT	0
24_re_165_0.432	GACGTGCAC	1	BZIP911_02_M00359_T
25_e_236_0.434	GACCTGCGT	0
26_re_74_0.437	GAGCGAGACC	0
27_h_25_0.561	GATTTGCA	11	NMI_8_H, NFIX_2_H, OCT1_B_M00342_T, IL24_5_H, OCT1_Q6_M00195_T, SRBD1_3_H, LUZP2_5_H, DGCR8_4_H, OCT1_Q5_01_M00930_T, SNAPC4_9_H
28_h_28_0.553	TTTCGGAACG	0
29_re_209_0.448	GGTGCACAC	0
30_e_310_0.549	GGAATTTCA	0
31_e_357_0.457	ATTACAGTC	0
32_h_20_0.538	CTCAGAAGCTCC	0
33_h_14_0.465	CTGCACCCAGGT	1	RCS1_Q2_M00753_T
34_e_45_0.534	CAAACGCGC	0
35_h_10_0.531	GATGACTCAT	19	AP1_01_M00517_T, Jundm2_secondary_SCI09_U, AP1_C_M00199_T, AP1_Q6_M00174_T, GCN4_02_M01555_T, Gcn4_GR09_U, GCN4_MA0303.1_J, Fos_MA0099.1_J, BACH2_01_M00490_T, NFE2_01_M00037_T
36_h_24_0.527	GCCTTAACCG	0
37_e_100_0.525	GACGGAAAC	0
38_e_270_0.477	GACCACGGC	1	TAF9_2_H
39_h_5_0.523	GGTCGCTTCACA	0
40_e_308_0.483	CTGATGACA	0

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	58

Summary

Alignment

Name	RPC155_01_M01798_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.62254e-07
E-value	0.00193444
q-value	0.00386889
Overlap	11
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	IK_Q5_M01169_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.23876e-07
E-value	0.00123814
q-value	0.00246785
Overlap	9
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	LYF1_01_M00141_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.56856e-06
E-value	0.0104237
q-value	0.0103883
Overlap	9
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	TCF4_03_M01769_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.94068e-07
E-value	0.00202737
q-value	0.00399895
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	sna_MA0086.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.61948e-06
E-value	0.0105725
q-value	0.010427
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	Tcfe2a_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.66577e-05
E-value	0.0486571
q-value	0.0319918
Overlap	9
Offset	5
Orientation	Normal

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Summary

Alignment

Name	Gata1_MA0035.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.52845e-06
E-value	0.0044646
q-value	0.00890495
Overlap	8
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	Tal1::Gata1_MA0140.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.91533e-06
E-value	0.0172787
q-value	0.0172317
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	GATA1_06_M00347_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.36773e-05
E-value	0.0399515
q-value	0.0243898
Overlap	8
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	ETS_Q4_M00771_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.38957e-08
E-value	9.90093e-05
q-value	0.00016224
Overlap	12
Offset	0
Orientation	Normal

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Summary

Alignment

Name	ETS1_B_M00339_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.62763e-08
E-value	0.000164383
q-value	0.00016224
Overlap	12
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	FLI1_Q6_M01208_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.82293e-07
E-value	0.000532478
q-value	0.000350357
Overlap	11
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	NERF_Q2_M00531_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.5708e-07
E-value	0.000750932
q-value	0.000370571
Overlap	12
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	GABPA_MA0062.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.77381e-07
E-value	0.00168653
q-value	0.000665817
Overlap	11
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	ETS2_B_M00340_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.32594e-07
E-value	0.00272411
q-value	0.000896197
Overlap	12
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	TEL2_Q6_M00678_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.25402e-06
E-value	0.00366299
q-value	0.00103292
Overlap	10
Offset	-2
Orientation	Normal

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Summary

Alignment

Name	FEV_MA0156.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.81049e-06
E-value	0.00820943
q-value	0.0020256
Overlap	8
Offset	-4
Orientation	Reverse Complement

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Summary

Alignment

Name	E74A_01_M00016_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.38341e-06
E-value	0.0186459
q-value	0.00370681
Overlap	12
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	Elf2_EMBO10_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.42893e-06
E-value	0.0187789
q-value	0.00370681
Overlap	12
Offset	0
Orientation	Normal

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Summary

Alignment

Name	Elf4_EMBO10_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.61305e-06
E-value	0.0280797
q-value	0.00472813
Overlap	12
Offset	0
Orientation	Normal

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Summary

Alignment

Name	ETS_Q6_M00971_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.84032e-06
E-value	0.0287436
q-value	0.00472813
Overlap	8
Offset	-4
Orientation	Normal

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Summary

Alignment

Name	CETS1P54_03_M01078_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.216e-05
E-value	0.0355194
q-value	0.00539328
Overlap	12
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	ELK1_01_M00007_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.3138e-05
E-value	0.0383761
q-value	0.00541081
Overlap	12
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	SPI1_MA0080.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.50962e-05
E-value	0.0440959
q-value	0.0058028
Overlap	7
Offset	-4
Orientation	Reverse Complement

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Summary

Alignment

Name	GADP_01_M01258_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.70472e-05
E-value	0.049795
q-value	0.00614321
Overlap	9
Offset	-3
Orientation	Normal

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Summary

Alignment

Name	BZIP911_02_M00359_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.75886e-06
E-value	0.0109796
q-value	0.0219593
Overlap	9
Offset	3
Orientation	Normal

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Summary

Alignment

Name	NMI_8_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.46314e-06
E-value	0.00427383
q-value	0.00469352
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	NFIX_2_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.2215e-06
E-value	0.00648902
q-value	0.00469352
Overlap	6
Offset	-2
Orientation	Reverse Complement

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Summary

Alignment

Name	OCT1_B_M00342_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.42265e-06
E-value	0.00707655
q-value	0.00469352
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	IL24_5_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.71009e-06
E-value	0.0137582
q-value	0.00647723
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	OCT1_Q6_M00195_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.6626e-06
E-value	0.0165405
q-value	0.00647723
Overlap	8
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	SRBD1_3_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.8003e-06
E-value	0.0198637
q-value	0.00647723
Overlap	7
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	LUZP2_5_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.80112e-06
E-value	0.0227871
q-value	0.00647723
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	DGCR8_4_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.9748e-06
E-value	0.0291364
q-value	0.00724677
Overlap	7
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	OCT1_Q5_01_M00930_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.1923e-05
E-value	0.034827
q-value	0.0076
Overlap	8
Offset	1
Orientation	Normal

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Summary

Alignment

Name	SNAPC4_9_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.39603e-05
E-value	0.0407781
q-value	0.0076
Overlap	7
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	OCT_Q6_M00795_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.43839e-05
E-value	0.0420153
q-value	0.0076
Overlap	8
Offset	1
Orientation	Normal

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Summary

Alignment

Name	RCS1_Q2_M00753_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.76328e-07
E-value	0.00285185
q-value	0.00570371
Overlap	12
Offset	1
Orientation	Normal

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Summary

Alignment

Name	AP1_01_M00517_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.73861e-09
E-value	2.26045e-05
q-value	4.49151e-05
Overlap	10
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	Jundm2_secondary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.80822e-08
E-value	5.28181e-05
q-value	5.04619e-05
Overlap	10
Offset	3
Orientation	Normal

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Summary

Alignment

Name	AP1_C_M00199_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.65793e-08
E-value	0.000106848
q-value	5.04619e-05
Overlap	9
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_Q6_M00174_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.8217e-08
E-value	0.000111632
q-value	5.04619e-05
Overlap	10
Offset	0
Orientation	Normal

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Summary

Alignment

Name	GCN4_02_M01555_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.95544e-08
E-value	0.000203168
q-value	5.04619e-05
Overlap	10
Offset	5
Orientation	Normal

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Summary

Alignment

Name	Gcn4_GR09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.95544e-08
E-value	0.000203168
q-value	5.04619e-05
Overlap	10
Offset	5
Orientation	Normal

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Summary

Alignment

Name	GCN4_MA0303.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.94768e-08
E-value	0.000261362
q-value	5.64806e-05
Overlap	10
Offset	5
Orientation	Normal

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Summary

Alignment

Name	Fos_MA0099.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.42476e-07
E-value	0.000416172
q-value	6.89111e-05
Overlap	8
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	BACH2_01_M00490_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.69037e-07
E-value	0.00137006
q-value	0.000170144
Overlap	10
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	NFE2_01_M00037_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.42175e-06
E-value	0.00415292
q-value	0.000458436
Overlap	10
Offset	1
Orientation	Normal

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Summary

Alignment

Name	AP1_Q4_01_M00926_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.55262e-06
E-value	0.00453519
q-value	0.000474285
Overlap	8
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_Q6_01_M00925_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.13472e-06
E-value	0.00623552
q-value	0.000589998
Overlap	9
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	GCN4_01_M00038_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.38109e-06
E-value	0.00695517
q-value	0.000628178
Overlap	10
Offset	8
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_Q4_M00188_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.52723e-06
E-value	0.00738205
q-value	0.000637744
Overlap	10
Offset	0
Orientation	Normal

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Summary

Alignment

Name	FRA1_Q5_M01267_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.68681e-06
E-value	0.00784818
q-value	0.000649763
Overlap	8
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_Q2_M00173_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.32995e-06
E-value	0.0126478
q-value	0.000897539
Overlap	10
Offset	0
Orientation	Normal

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Summary

Alignment

Name	AP1_MA0099.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.3622e-06
E-value	0.015663
q-value	0.00107318
Overlap	7
Offset	-2
Orientation	Reverse Complement

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Summary

Alignment

Name	NRF2_Q4_M00821_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.00446e-05
E-value	0.0293403
q-value	0.00175858
Overlap	10
Offset	2
Orientation	Normal

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Summary

Alignment

Name	MAF_Q6_01_M00983_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.03018e-05
E-value	0.0300916
q-value	0.00175858
Overlap	10
Offset	1
Orientation	Normal

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Summary

Alignment

Name	TAF9_2_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.38258e-05
E-value	0.0403851
q-value	0.0807702
Overlap	5
Offset	-2
Orientation	Reverse Complement

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[Query Top]

The TOMTOM results consist of

The query motifs with links to further information on matches. [View]
The target databases with information on the number of matches. [View]
The matches between query motifs and target motifs. [View]
- The summary of match information.
- An alignment of the two motifs.
The program details including:
1. The version of TOMTOM and the date it was released. [View]
2. The reference to cite if you use TOMTOM in your research. [View]
3. The command line summary detailing the parameters with which you ran TOMTOM. [View]
This explanation of how to interpret TOMTOM results.

Inputs

The important inputs to TOMTOM.

Query Motifs

The query motifs section lists the motifs that were searched for in the target databases as well as links to matches found.

Name: The motif name.
Alt. Name: The alternative motif name. This column may be hidden if no query motifs have an alternate name.
Website: A link to a website which has more information on the motif. This column may be hidden if no query motifs have website information.
Preview: The motif preview. On supporting browsers this will display as a motif logo, otherwise the consensus sequence will be displayed.
Matches: The number of significant matches.
List: Links to the first 20 matches

Target Databases

The target motifs section lists details on the motif databases that were specifed to search.

Database: The database name.
Number of Motifs: The number of motifs read from the motif database minus the number that had to be discarded due to conflicting ids.
Motifs Matched: The number of motifs that had a match with at least one of the query motifs.

Matches

The matches section list the group of motifs that match each query motif. For each query-target match the following information is given:

Summary Table

The summary gives the important statistics about the motif match.

Name: The name of the matched motif.
Alt. Name: The alternative name of the matched motif.
p-value: The probability that the match occurred by random chance according to the null model.
E-value: The expected number of false positives in the matches up to this point.
q-value: The minimum False Discovery Rate required to include the match.
Overlap: The number of letters that overlaped in the optimal alignment.
Offset: The offset of the query motif to the matched motif in the optimal alignment.
Orientation: The orientation of the matched motif that gave the optimal alignment. A value of "normal" means that the matched motif is as it appears in the database otherwise the matched motif has been reverse complemented.

Alignment

The image shows the alignment of the two motifs. The matched motif is shown on the top and the query motif is shown on the bottom.

Create custom LOGO

By clicking the link "Create custom LOGO ↧" a form to make custom logos will be displayed. The download button can then be clicked to generate a motif matching the selected specifications.

Image Type: Two image formats, png and eps, are avaliable. The pixel based portable network graphic (png) format is commonly used on the Internet and the Encapsulated PostScript (eps) format is more suitable for publications that might require scaling.
Error bars: Toggle error bars indicating the confidence of a motif based on the number of sites used in its creation.
SSC: Toggle adding pseudocounts for Small Sample Correction.
Flip: Toggle a full reverse complement of the alignment.
Width: Specify the width of the generated motif.
Height: Specify the height of the generated motif.

Query Motifs

Name

Preview

Matches

List

Target Databases

Database

Number of Motifs

Motifs Matched

Matches to Query: 1_re_57_0.355

Matches to Query: 2_re_40_0.367

Matches to Query: 3_re_90_0.369

Matches to Query: 4_re_26_0.370

Summary

Alignment

Matches to Query: 5_re_25_0.374

Matches to Query: 6_re_124_0.377

Matches to Query: 7_re_118_0.378

Matches to Query: 8_re_71_0.379

Matches to Query: 9_re_97_0.380

Summary

Alignment

Summary

Alignment

Matches to Query: 10_re_139_0.381

Matches to Query: 11_re_53_0.383

Matches to Query: 12_re_205_0.387

Matches to Query: 13_re_125_0.393

Matches to Query: 14_re_8_0.394

Matches to Query: 15_re_135_0.397

Matches to Query: 16_re_78_0.397

Matches to Query: 17_re_157_0.398

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 18_h_21_0.583

Matches to Query: 19_re_240_0.420

Matches to Query: 20_h_1_0.579

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 21_h_2_0.578

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment