TOMTOM

Name	Preview	Matches	List
1_h_1_0.530	ATGAGTCATC	15	AP1_Q6_M00174_T, AP1_01_M00517_T, AP1_C_M00199_T, Jundm2_secondary_SCI09_U, AP1_Q6_01_M00925_T, GCN4_MA0303.1_J, Gcn4_GR09_U, GCN4_02_M01555_T, AP1_Q4_01_M00926_T, Fos_MA0099.1_J
2_e_86_0.529	ACATTCCAG	1	HNRPH3_9_H
3_e_229_0.522	GGAATTCCA	0
4_e_402_0.521	GAGGAATGC	0
5_h_2_0.520	CACATTCCTT	0
6_h_34_0.518	CAAAACCGGTTT	0
7_e_31_0.516	AGGAATGTG	2	TEAD1_MA0090.1_J, TEF_01_M01305_T
8_e_391_0.515	AAACCAGGCA	0
9_e_411_0.514	AAACAGCTC	0
10_e_397_0.513	AGGCATTTC	1	TAF1A_8_H
11_e_385_0.513	GGCATTTACG	1	TAF1A_8_H
12_e_308_0.513	AACGTTTAAA	0
13_h_9_0.512	TTCCAAACGC	0
14_e_344_0.512	AAATGCCTGGC	1	TAF1A_8_H
15_e_354_0.511	GCTCAGGAA	0
16_e_162_0.511	AAAATGCAGA	0
17_h_5_0.511	TGCGGAATGC	0
18_e_232_0.510	CGTTTACAG	0
19_e_348_0.510	AAACGCTGA	0
20_e_368_0.510	ATCTGTAAA	0
21_e_260_0.510	CATTCCTGG	0
22_e_361_0.509	TCTGTAAAC	0
23_h_6_0.509	GCTTTGCA	0
24_e_424_0.509	GAATGCTGC	0
25_e_286_0.509	GCAAACAGC	0
26_h_26_0.508	GCGTTGTAAA	0
27_e_12_0.508	GCCACATTCC	0
28_e_200_0.507	AACGCCAGCC	0
29_h_12_0.506	GTAAACCAGA	0
30_h_10_0.506	GCTGTTTACT	0
31_e_415_0.506	GGAAAAGCA	2	FOXP4_6_H, NFAT1_Q6_M01281_T
32_e_383_0.506	AATACCCCG	0
33_e_107_0.505	AAACGTGCTGG	0
34_h_4_0.504	TGCCAGGAAA	0
35_e_163_0.504	CTACGTAGC	0
36_re_64_0.497	GGGGAAAAA	0
37_h_15_0.503	CGGAAATG	1	STAT1_02_M00492_T
38_re_72_0.497	TGCCAGGCA	0
39_e_346_0.503	CTGGAAAACAC	0
40_re_39_0.497	AAAATGTAAAAT	0
41_re_7_0.497	AAAACGTGT	0
42_e_26_0.503	ACAGGAAATGG	3	FEV_MA0156.1_J, ETS1_B_M00339_T, ETS_Q4_M00771_T
43_h_35_0.502	AAACACGC	0
44_e_426_0.502	CGCTTTATC	0
45_h_19_0.502	CCTTTAGGCA	0
46_re_10_0.498	ACGTATGTGC	0
47_e_420_0.502	AAACGGAAAG	0
48_h_11_0.502	CAGAGCTGCTTT	0
49_e_77_0.502	AAACACGGCT	0
50_e_298_0.501	ACCTCTGGC	0
51_re_45_0.499	ACGTTTTCT	0
52_e_204_0.501	AGGTCACTG	3	GTF3C5_2_H, ERALPHA_01_M01801_T, PPARG_02_M00515_T
53_h_33_0.500	TTTTTACCCC	0

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	28

Summary

Alignment

Name	AP1_Q6_M00174_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.32255e-08
E-value	0.000126262
q-value	0.00012016
Overlap	10
Offset	1
Orientation	Normal

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Summary

Alignment

Name	AP1_01_M00517_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.40242e-08
E-value	0.000128595
q-value	0.00012016
Overlap	10
Offset	2
Orientation	Normal

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Summary

Alignment

Name	AP1_C_M00199_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.2426e-07
E-value	0.000362963
q-value	0.00012016
Overlap	9
Offset	0
Orientation	Normal

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Summary

Alignment

Name	Jundm2_secondary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.79009e-07
E-value	0.000814985
q-value	0.000231259
Overlap	10
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_Q6_01_M00925_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.61274e-07
E-value	0.00105528
q-value	0.000262014
Overlap	9
Offset	0
Orientation	Normal

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Summary

Alignment

Name	GCN4_MA0303.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.79573e-07
E-value	0.00169293
q-value	0.000336269
Overlap	10
Offset	6
Orientation	Reverse Complement

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Summary

Alignment

Name	Gcn4_GR09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.79573e-07
E-value	0.00169293
q-value	0.000336269
Overlap	10
Offset	6
Orientation	Reverse Complement

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Summary

Alignment

Name	GCN4_02_M01555_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.98596e-07
E-value	0.0020406
q-value	0.000368478
Overlap	10
Offset	6
Orientation	Reverse Complement

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Summary

Alignment

Name	AP1_Q4_01_M00926_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.51134e-07
E-value	0.00277826
q-value	0.000383173
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	Fos_MA0099.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.17693e-06
E-value	0.00343781
q-value	0.000383173
Overlap	8
Offset	0
Orientation	Normal

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Summary

Alignment

Name	BACH2_01_M00490_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.9091e-06
E-value	0.00557647
q-value	0.000582979
Overlap	10
Offset	1
Orientation	Normal

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Summary

Alignment

Name	FRA1_Q5_M01267_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.46466e-06
E-value	0.0247253
q-value	0.0021353
Overlap	8
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	AP1_MA0099.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.06056e-05
E-value	0.030979
q-value	0.00256391
Overlap	7
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	GCN4_Q2_M01713_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.28627e-05
E-value	0.037572
q-value	0.00287037
Overlap	10
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	GCN4_01_M00038_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.40246e-05
E-value	0.0409659
q-value	0.00301374
Overlap	10
Offset	9
Orientation	Normal

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Summary

Alignment

Name	HNRPH3_9_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.47875e-06
E-value	0.0218454
q-value	0.0436908
Overlap	6
Offset	-3
Orientation	Reverse Complement

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Summary

Alignment

Name	TEAD1_MA0090.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.05426e-06
E-value	0.0030795
q-value	0.0030795
Overlap	9
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	TEF_01_M01305_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.05426e-06
E-value	0.0030795
q-value	0.0030795
Overlap	9
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	TAF1A_8_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.30894e-06
E-value	0.0184284
q-value	0.0368568
Overlap	7
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	TAF1A_8_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.30766e-05
E-value	0.0381967
q-value	0.0763935
Overlap	7
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	TAF1A_8_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.66012e-06
E-value	0.0252962
q-value	0.0505924
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	FOXP4_6_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	9.56506e-06
E-value	0.0279396
q-value	0.0338838
Overlap	9
Offset	0
Orientation	Normal

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Summary

Alignment

Name	NFAT1_Q6_M01281_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.16518e-05
E-value	0.0340348
q-value	0.0338838
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	STAT1_02_M00492_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.6461e-05
E-value	0.0480827
q-value	0.0490874
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	FEV_MA0156.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.13926e-06
E-value	0.0120908
q-value	0.015885
Overlap	8
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	ETS1_B_M00339_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.90424e-06
E-value	0.0201673
q-value	0.015885
Overlap	11
Offset	0
Orientation	Normal

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Summary

Alignment

Name	ETS_Q4_M00771_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.26937e-06
E-value	0.0241548
q-value	0.015885
Overlap	10
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	GTF3C5_2_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.07264e-06
E-value	0.00897518
q-value	0.0128659
Overlap	6
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	ERALPHA_01_M01801_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.44729e-06
E-value	0.0129905
q-value	0.0128659
Overlap	9
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	PPARG_02_M00515_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.3705e-05
E-value	0.0400324
q-value	0.0171313
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_1_0.530

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: 2_e_86_0.529

Summary

Alignment

Matches to Query: 3_e_229_0.522

Matches to Query: 4_e_402_0.521

Matches to Query: 5_h_2_0.520

Matches to Query: 6_h_34_0.518

Matches to Query: 7_e_31_0.516

Summary

Alignment

Summary

Alignment

Matches to Query: 8_e_391_0.515

Matches to Query: 9_e_411_0.514

Matches to Query: 10_e_397_0.513

Summary

Alignment

Matches to Query: 11_e_385_0.513

Summary

Alignment

Matches to Query: 12_e_308_0.513

Matches to Query: 13_h_9_0.512

Matches to Query: 14_e_344_0.512

Summary

Alignment

Matches to Query: 15_e_354_0.511

Matches to Query: 16_e_162_0.511

Matches to Query: 17_h_5_0.511

Matches to Query: 18_e_232_0.510

Matches to Query: 19_e_348_0.510

Matches to Query: 20_e_368_0.510

Matches to Query: 21_e_260_0.510

Matches to Query: 22_e_361_0.509

Matches to Query: 23_h_6_0.509

Matches to Query: 24_e_424_0.509

Matches to Query: 25_e_286_0.509

Matches to Query: 26_h_26_0.508

Matches to Query: 27_e_12_0.508

Matches to Query: 28_e_200_0.507

Matches to Query: 29_h_12_0.506