TOMTOM

Name	Preview	Matches	List
1_re_13_0.776	CCGCCGCCGG	3	ERF2_01_M01057_T, ADF1_Q6_M00171_T, ODC1_3_H
2_h_2_0.768	TTTTCGCG	0
3_h_7_0.759	CGCGACGTAA	0
4_h_10_0.749	CGTTCCCG	0
5_h_12_0.727	CGCGAGAG	0
6_h_8_0.722	TCGGACCG	0
7_h_3_0.717	TACTTCCG	21	SAP1A_01_M01167_T, Ets1_EMBO10_U, ELK1_02_M00025_T, Ehf_primary_SCI09_U, ELF2_10_H, CETS1P54_01_M00032_T, Elk4_EMBO10_U, ELK4_MA0076.1_J, ETV4_13_H, Ehf_EMBO10_U
8_re_156_0.315	CAGGTGTGA	3	sna_MA0086.1_J, TBX5_Q5_M01044_T, TBR2_01_M01774_T
9_re_109_0.315	CCAAAGTGC	0
10_re_152_0.319	ATGTTGGCC	0
11_re_82_0.332	AGGCAGGAG	0
12_re_94_0.334	GAGGTTGCA	0
13_re_162_0.349	CAGGAGCCA	0
14_re_63_0.359	CGGGTTCAA	0
15_re_112_0.361	ATGGTCTCG	0
16_re_137_0.368	ACCTCAGGT	0
17_re_61_0.380	AATCGCTTG	0
18_h_17_0.619	AGTACTTTCCCG	0
19_h_21_0.598	GGGGGAAAAAAA	0
20_h_25_0.572	AAGCTTTA	0

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	27

Summary

Alignment

Name	ERF2_01_M01057_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.53395e-07
E-value	0.00190857
q-value	0.00377502
Overlap	7
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	ADF1_Q6_M00171_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.05645e-05
E-value	0.0308588
q-value	0.0273399
Overlap	10
Offset	0
Orientation	Normal

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Summary

Alignment

Name	ODC1_3_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.41963e-05
E-value	0.0414673
q-value	0.0273399
Overlap	6
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	SAP1A_01_M01167_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.4837e-07
E-value	0.00072549
q-value	0.00124501
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	Ets1_EMBO10_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.35272e-07
E-value	0.00127143
q-value	0.00124501
Overlap	8
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	ELK1_02_M00025_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.28292e-07
E-value	0.00241944
q-value	0.00157944
Overlap	8
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	Ehf_primary_SCI09_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.52182e-06
E-value	0.0102872
q-value	0.00399844
Overlap	8
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	ELF2_10_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.33756e-06
E-value	0.01267
q-value	0.00399844
Overlap	6
Offset	-2
Orientation	Reverse Complement

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Summary

Alignment

Name	CETS1P54_01_M00032_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.48735e-06
E-value	0.0160285
q-value	0.00399844
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	Elk4_EMBO10_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.1466e-06
E-value	0.0179542
q-value	0.00399844
Overlap	8
Offset	3
Orientation	Normal

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Summary

Alignment

Name	ELK4_MA0076.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.58539e-06
E-value	0.0221569
q-value	0.00399844
Overlap	7
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	ETV4_13_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.73423e-06
E-value	0.0225917
q-value	0.00399844
Overlap	6
Offset	-2
Orientation	Reverse Complement

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Summary

Alignment

Name	Ehf_EMBO10_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.38745e-06
E-value	0.0244997
q-value	0.00399844
Overlap	8
Offset	4
Orientation	Normal

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Summary

Alignment

Name	Elk3_EMBO10_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.38745e-06
E-value	0.0244997
q-value	0.00399844
Overlap	8
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	Etv1_EMBO10_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.38745e-06
E-value	0.0244997
q-value	0.00399844
Overlap	8
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	GADP_01_M01258_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.07146e-05
E-value	0.0312974
q-value	0.00416033
Overlap	8
Offset	0
Orientation	Normal

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Summary

Alignment

Name	Eip74EF_MA0026.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.11764e-05
E-value	0.0326462
q-value	0.00416033
Overlap	6
Offset	-2
Orientation	Reverse Complement

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Summary

Alignment

Name	ELK1_04_M01165_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.21281e-05
E-value	0.0354261
q-value	0.00416033
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	ERG_01_M01752_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.22551e-05
E-value	0.0357972
q-value	0.00416033
Overlap	7
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	Etv6_EMBO10_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.23633e-05
E-value	0.0361133
q-value	0.00416033
Overlap	8
Offset	4
Orientation	Normal

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Summary

Alignment

Name	FLI1_7_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.33156e-05
E-value	0.038895
q-value	0.00423186
Overlap	7
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	Gabpa_EMBO10_U
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.48576e-05
E-value	0.043399
q-value	0.00428346
Overlap	8
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	EHF_01_M01751_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.49756e-05
E-value	0.0437436
q-value	0.00428346
Overlap	7
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	GABPA_MA0062.2_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.66976e-05
E-value	0.0487738
q-value	0.00435076
Overlap	8
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	sna_MA0086.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.37859e-06
E-value	0.00402687
q-value	0.00799584
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	TBX5_Q5_M01044_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.28959e-05
E-value	0.037669
q-value	0.025656
Overlap	9
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	TBR2_01_M01774_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.32703e-05
E-value	0.0387626
q-value	0.025656
Overlap	8
Offset	-1
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_re_13_0.776

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 2_h_2_0.768

Matches to Query: 3_h_7_0.759

Matches to Query: 4_h_10_0.749

Matches to Query: 5_h_12_0.727

Matches to Query: 6_h_8_0.722

Matches to Query: 7_h_3_0.717

Summary

Alignment

Summary

Alignment

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Alignment

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Alignment

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Alignment

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Alignment

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Alignment

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Alignment

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Alignment

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Alignment

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Alignment

Matches to Query: 8_re_156_0.315

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 9_re_109_0.315

Matches to Query: 10_re_152_0.319

Matches to Query: 11_re_82_0.332

Matches to Query: 12_re_94_0.334

Matches to Query: 13_re_162_0.349

Matches to Query: 14_re_63_0.359

Matches to Query: 15_re_112_0.361

Matches to Query: 16_re_137_0.368

Matches to Query: 17_re_61_0.380