TOMTOM

Name	Preview	Matches	List
1_h_k27ac-h1_0.601	TTGTTATGCAAA	6	OCT4_01_M01125_T, Pou5f1_MA0142.1_J, Sox2_MA0143.1_J, OCT4_02_M01124_T, OCT1_04_M00138_T, NFIX_2_H
2_h_k27ac-tro_0.563	TGTCTGGA	0
3_h_k27ac-tro_0.561	AATGACTCAT	17	AP1_C_M00199_T, AP1_01_M00517_T, GCN4_02_M01555_T, Jundm2_secondary_SCI09_U, GCN4_MA0303.1_J, Gcn4_GR09_U, AP1_Q6_M00174_T, FRA1_Q5_M01267_T, GCN4_01_M00038_T, AP1_Q4_01_M00926_T
4_h_k27ac-h1_0.560	CCCCCCCCCC	14	Zfp281_primary_SCI09_U, ZNF219_01_M01122_T, MAZR_01_M00491_T, SP1_MA0079.2_J, Zfp740_primary_SCI09_U, ZFP281_01_M01597_T, SP1SP3_Q4_M01219_T, SP1_Q2_01_M00933_T, UF1H3BETA_Q6_M01068_T, KROX_Q6_M00982_T
5_e_k27ac-tro_0.537	CAGGACAGA	0
6_e_k27ac-tro_0.536	GTCACTGGA	0
7_e_k27ac-h1_0.533	GCATAATAA	0
8_h_k27ac-tro_0.533	CCCTCAGGCAAA	3	Tcfap2c_primary_SCI09_U, Tcfap2a_primary_SCI09_U, Tcfap2e_primary_SCI09_U
9_e_k27ac-h1_0.531	CAATTAGCA	0
10_e_k27ac-tro_0.531	ATGATGTCA	0
11_e_k27ac-h1_0.531	CATAACAAAG	7	Sox2_MA0143.1_J, Pou5f1_MA0142.1_J, SOX_Q6_M01014_T, SOX2_Q6_M01272_T, TCF3_01_M01594_T, SMAD1_01_M01590_T, OCT4_01_M01125_T
12_h_k27ac-tro_0.530	GACGTCTG	0
13_e_k27ac-h1_0.529	ACATAGCG	0
14_h_k27ac-h1_0.529	TGCTCGGTGGGG	1	YPR022C_01_M01647_T
15_e_k27ac-h1_0.529	TAACAAACG	1	Foxa2_secondary_SCI09_U
16_e_k27ac-h1_0.527	TGAAATAAA	1	CSTF2_5_H
17_e_k27ac-tro_0.526	CTGACTCCAG	0
18_e_k27ac-tro_0.525	GCGTCTAGA	1	GZF1_01_M01069_T
19_e_k27ac-h1_0.524	ACACCTCGT	0
20_e_k27ac-tro_0.524	CCAGAAACC	0
21_e_k27ac-tro_0.523	GACAGTCTCC	0
22_e_k27ac-tro_0.522	ATCGTAGAA	0
23_e_k27ac-h1_0.522	ATGCGCGTCG	0
24_e_k27ac-tro_0.521	CTGATAAGA	1	Gata5_primary_SCI09_U
25_e_k27ac-h1_0.517	TACCCAAAT	0
26_e_k27ac-h1_0.517	AATAAACCT	0
27_h_k27ac-h1_0.516	CCTTTCAG	0
28_e_k27ac-tro_0.515	GTCAGGGTA	0
29_e_k27ac-h1_0.511	AAATCGTGG	0
30_e_k27ac-h1_0.507	TGAAGCCTC	0

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	49

Summary

Alignment

Name	OCT4_01_M01125_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.29591e-16
E-value	2.13113e-12
q-value	4.23529e-12
Overlap	12
Offset	2
Orientation	Normal

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Summary

Alignment

Name	Pou5f1_MA0142.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.2452e-12
E-value	9.47922e-09
q-value	9.41923e-09
Overlap	12
Offset	2
Orientation	Normal

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Summary

Alignment

Name	Sox2_MA0143.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.17216e-08
E-value	3.42387e-05
q-value	2.26813e-05
Overlap	12
Offset	3
Orientation	Normal

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Summary

Alignment

Name	OCT4_02_M01124_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.30599e-08
E-value	0.000154988
q-value	7.70035e-05
Overlap	12
Offset	1
Orientation	Normal

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Summary

Alignment

Name	OCT1_04_M00138_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.12618e-05
E-value	0.0328957
q-value	0.013075
Overlap	12
Offset	3
Orientation	Normal

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Summary

Alignment

Name	NFIX_2_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.44732e-05
E-value	0.0422761
q-value	0.0140029
Overlap	6
Offset	-6
Orientation	Normal

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Summary

Alignment

Name	AP1_C_M00199_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.16225e-08
E-value	9.23694e-05
q-value	0.000142883
Overlap	9
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	AP1_01_M00517_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.94608e-08
E-value	0.000232105
q-value	0.000142883
Overlap	10
Offset	1
Orientation	Normal

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Summary

Alignment

Name	GCN4_02_M01555_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.50594e-07
E-value	0.000439884
q-value	0.000142883
Overlap	10
Offset	5
Orientation	Reverse Complement

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Summary

Alignment

Name	Jundm2_secondary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.13312e-07
E-value	0.000623084
q-value	0.000142883
Overlap	10
Offset	3
Orientation	Normal

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Summary

Alignment

Name	GCN4_MA0303.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.37646e-07
E-value	0.000694165
q-value	0.000142883
Overlap	10
Offset	5
Orientation	Reverse Complement

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Summary

Alignment

Name	Gcn4_GR09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.37646e-07
E-value	0.000694165
q-value	0.000142883
Overlap	10
Offset	5
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_Q6_M00174_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.91405e-07
E-value	0.000851193
q-value	0.000142883
Overlap	10
Offset	0
Orientation	Normal

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Summary

Alignment

Name	FRA1_Q5_M01267_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.49884e-07
E-value	0.00131411
q-value	0.000200857
Overlap	8
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	GCN4_01_M00038_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.20044e-06
E-value	0.00350647
q-value	0.000424686
Overlap	10
Offset	8
Orientation	Normal

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Summary

Alignment

Name	AP1_Q4_01_M00926_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.24391e-06
E-value	0.00363345
q-value	0.000424686
Overlap	8
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_Q6_01_M00925_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.73656e-06
E-value	0.00507249
q-value	0.000559946
Overlap	9
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	BACH2_01_M00490_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.92345e-06
E-value	0.00561841
q-value	0.000587567
Overlap	10
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	NRF2_Q4_M00821_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.45327e-06
E-value	0.010087
q-value	0.000954421
Overlap	10
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	Fos_MA0099.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.97942e-06
E-value	0.0116239
q-value	0.0010042
Overlap	8
Offset	-2
Orientation	Reverse Complement

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Summary

Alignment

Name	GCN4_Q2_M01713_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.43107e-06
E-value	0.0158642
q-value	0.00121239
Overlap	10
Offset	0
Orientation	Normal

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Summary

Alignment

Name	AP1_MA0099.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.33851e-06
E-value	0.0185148
q-value	0.00133789
Overlap	7
Offset	-2
Orientation	Normal

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Summary

Alignment

Name	BACH1_01_M00495_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.45429e-06
E-value	0.018853
q-value	0.00133789
Overlap	10
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	Zfp281_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.26247e-09
E-value	2.70557e-05
q-value	5.37223e-05
Overlap	10
Offset	2
Orientation	Normal

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Summary

Alignment

Name	ZNF219_01_M01122_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.62479e-08
E-value	0.00025193
q-value	0.000222328
Overlap	10
Offset	2
Orientation	Normal

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Summary

Alignment

Name	MAZR_01_M00491_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.14997e-07
E-value	0.000335907
q-value	0.000222328
Overlap	10
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	SP1_MA0079.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.55183e-07
E-value	0.00074539
q-value	0.000370016
Overlap	10
Offset	0
Orientation	Normal

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Summary

Alignment

Name	Zfp740_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.59505e-07
E-value	0.00134221
q-value	0.000533025
Overlap	10
Offset	1
Orientation	Normal

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Summary

Alignment

Name	ZFP281_01_M01597_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.39435e-06
E-value	0.0040729
q-value	0.00134787
Overlap	10
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	SP1SP3_Q4_M01219_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.7162e-06
E-value	0.00793401
q-value	0.00199295
Overlap	10
Offset	1
Orientation	Normal

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Summary

Alignment

Name	SP1_Q2_01_M00933_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.7489e-06
E-value	0.00802954
q-value	0.00199295
Overlap	10
Offset	0
Orientation	Normal

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Summary

Alignment

Name	UF1H3BETA_Q6_M01068_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.44032e-06
E-value	0.0158912
q-value	0.00350598
Overlap	10
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	KROX_Q6_M00982_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.48723e-06
E-value	0.0247912
q-value	0.00492259
Overlap	10
Offset	4
Orientation	Normal

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Summary

Alignment

Name	SP4_Q5_M01273_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.0629e-05
E-value	0.0310474
q-value	0.00560441
Overlap	10
Offset	1
Orientation	Normal

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Summary

Alignment

Name	SP1_Q6_M00196_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.26458e-05
E-value	0.0369382
q-value	0.00611211
Overlap	10
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	SP1_Q4_01_M00932_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.42515e-05
E-value	0.0416286
q-value	0.00623349
Overlap	10
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	SP1_02_M01303_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.50464e-05
E-value	0.0439504
q-value	0.00623349
Overlap	10
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	Tcfap2c_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.63203e-06
E-value	0.0135301
q-value	0.0109884
Overlap	12
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	Tcfap2a_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.71941e-06
E-value	0.0167064
q-value	0.0109884
Overlap	12
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	Tcfap2e_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.63505e-06
E-value	0.025223
q-value	0.0109884
Overlap	12
Offset	3
Orientation	Normal

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Summary

Alignment

Name	Sox2_MA0143.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.93048e-07
E-value	0.000855994
q-value	0.00157854
Overlap	10
Offset	4
Orientation	Reverse Complement

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Summary

Alignment

Name	Pou5f1_MA0142.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.41137e-07
E-value	0.00158066
q-value	0.00157854
Overlap	10
Offset	5
Orientation	Reverse Complement

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Summary

Alignment

Name	SOX_Q6_M01014_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.41546e-06
E-value	0.00705556
q-value	0.00450721
Overlap	10
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	SOX2_Q6_M01272_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.09021e-06
E-value	0.00902651
q-value	0.00450721
Overlap	10
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	TCF3_01_M01594_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.79868e-06
E-value	0.0169379
q-value	0.00676609
Overlap	10
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	SMAD1_01_M01590_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.16127e-06
E-value	0.0238391
q-value	0.00793571
Overlap	10
Offset	0
Orientation	Normal

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Summary

Alignment

Name	OCT4_01_M01125_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.34698e-05
E-value	0.0393452
q-value	0.0112264
Overlap	10
Offset	5
Orientation	Reverse Complement

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Summary

Alignment

Name	YPR022C_01_M01647_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.7382e-06
E-value	0.0226033
q-value	0.0451926
Overlap	6
Offset	-6
Orientation	Reverse Complement

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Summary

Alignment

Name	Foxa2_secondary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.39802e-05
E-value	0.0408361
q-value	0.0816722
Overlap	9
Offset	5
Orientation	Normal

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Summary

Alignment

Name	CSTF2_5_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.09711e-06
E-value	0.00612566
q-value	0.0122497
Overlap	7
Offset	-2
Orientation	Normal

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Summary

Alignment

Name	GZF1_01_M01069_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.12862e-06
E-value	0.0266647
q-value	0.0533294
Overlap	9
Offset	3
Orientation	Normal

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Summary

Alignment

Name	Gata5_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.54216e-05
E-value	0.0450465
q-value	0.0900929
Overlap	9
Offset	4
Orientation	Normal

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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_h_k27ac-h1_0.601

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 2_h_k27ac-tro_0.563

Matches to Query: 3_h_k27ac-tro_0.561

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

Summary

Alignment

Matches to Query: 4_h_k27ac-h1_0.560

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary