TOMTOM

Name	Preview	Matches	List
1_e_6_0.818	CGCGCCCCG	0
2_e_0_0.808	CGCCGCCGC	1	ERF2_01_M01057_T
3_h_1_0.790	TACCCGCG	0
4_e_69_0.729	CGTCTACGC	0
5_h_28_0.660	GAACGCGTTG	0
6_h_10_0.646	AACTCCGCGGAC	4	PDR3_MA0353.1_J, PDR3_Q2_M00752_T, PDR1_MA0352.1_J, PDR1_02_M01633_T
7_e_165_0.645	AAACGCAC	0
8_re_60_0.362	CAGGCACTG	0
9_re_72_0.373	ACACAGCTG	0
10_re_65_0.379	CAGCCCTGCC	0
11_e_275_0.620	CGTTTTAAA	0
12_re_50_0.387	CCTGGCACA	0
13_re_1_0.389	CACGTGGCCA	6	ABF1_02_M00400_T, GBF_Q2_M00441_T, PIF3_02_M00435_T, PIF3_01_M00434_T, CG1_Q6_M00440_T, CMYC_02_M01154_T
14_re_64_0.411	CAAGGTCAC	5	NR4A2_MA0160.1_J, ERR2_01_M01589_T, SF1_Q6_M00727_T, GTF3C5_2_H, DAX1_01_M01248_T
15_h_18_0.587	ACCGGTAAAG	0
16_re_22_0.423	TCGTGGCTGC	0
17_re_28_0.427	AGCACCTAC	0
18_re_91_0.439	ATGCACGTA	0
19_re_43_0.442	CCTCCCCAC	2	MZF1_Q5_M01733_T, YPR022C_01_M01647_T
20_h_27_0.526	CTCTCTCTCTCT	0

Database	Number of Motifs	Motifs Matched
trnsfcJsprUnprobHpdiCmbned3.meme	2921	18

Summary

Alignment

Name	ERF2_01_M01057_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.78416e-07
E-value	0.00110535
q-value	0.00219367
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	PDR3_MA0353.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.77459e-07
E-value	0.00168676
q-value	0.00154733
Overlap	8
Offset	-3
Orientation	Normal

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Summary

Alignment

Name	PDR3_Q2_M00752_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	7.9648e-07
E-value	0.00232652
q-value	0.00154733
Overlap	8
Offset	-3
Orientation	Reverse Complement

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Summary

Alignment

Name	PDR1_MA0352.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.93e-06
E-value	0.00563752
q-value	0.00209371
Overlap	8
Offset	-3
Orientation	Normal

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Summary

Alignment

Name	PDR1_02_M01633_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.45631e-06
E-value	0.0100959
q-value	0.0028777
Overlap	7
Offset	-4
Orientation	Reverse Complement

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Summary

Alignment

Name	ABF1_02_M00400_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.65345e-06
E-value	0.00482973
q-value	0.00830693
Overlap	10
Offset	10
Orientation	Normal

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Summary

Alignment

Name	GBF_Q2_M00441_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.96402e-06
E-value	0.0115789
q-value	0.00830693
Overlap	9
Offset	3
Orientation	Normal

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Summary

Alignment

Name	PIF3_02_M00435_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	4.42619e-06
E-value	0.0129289
q-value	0.00830693
Overlap	10
Offset	6
Orientation	Reverse Complement

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Summary

Alignment

Name	PIF3_01_M00434_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	8.52281e-06
E-value	0.0248951
q-value	0.00998469
Overlap	10
Offset	6
Orientation	Reverse Complement

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Summary

Alignment

Name	CG1_Q6_M00440_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.23575e-05
E-value	0.0360962
q-value	0.00998469
Overlap	9
Offset	2
Orientation	Normal

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Summary

Alignment

Name	CMYC_02_M01154_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.53255e-05
E-value	0.0447659
q-value	0.00998469
Overlap	9
Offset	3
Orientation	Normal

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Summary

Alignment

Name	NR4A2_MA0160.1_J
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.5343e-07
E-value	0.00161657
q-value	0.00195152
Overlap	8
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	ERR2_01_M01589_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	6.73289e-07
E-value	0.00196668
q-value	0.00195152
Overlap	9
Offset	1
Orientation	Normal

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Summary

Alignment

Name	SF1_Q6_M00727_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	2.10154e-06
E-value	0.00613859
q-value	0.00406086
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	GTF3C5_2_H
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	5.80405e-06
E-value	0.0169536
q-value	0.0084115
Overlap	6
Offset	-3
Orientation	Reverse Complement

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Summary

Alignment

Name	DAX1_01_M01248_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.24499e-05
E-value	0.036366
q-value	0.0144343
Overlap	9
Offset	6
Orientation	Normal

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Summary

Alignment

Name	MZF1_Q5_M01733_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	3.76525e-06
E-value	0.0109983
q-value	0.0219293
Overlap	7
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	YPR022C_01_M01647_T
Database	trnsfcJsprUnprobHpdiCmbned3.meme
p-value	1.35821e-05
E-value	0.0396734
q-value	0.039552
Overlap	6
Offset	-3
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_e_6_0.818

Matches to Query: 2_e_0_0.808

Summary

Alignment

Matches to Query: 3_h_1_0.790

Matches to Query: 4_e_69_0.729

Matches to Query: 5_h_28_0.660

Matches to Query: 6_h_10_0.646

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 7_e_165_0.645

Matches to Query: 8_re_60_0.362

Matches to Query: 9_re_72_0.373

Matches to Query: 10_re_65_0.379

Matches to Query: 11_e_275_0.620

Matches to Query: 12_re_50_0.387

Matches to Query: 13_re_1_0.389

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 14_re_64_0.411

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: 15_h_18_0.587

Matches to Query: 16_re_22_0.423

Matches to Query: 17_re_28_0.427

Matches to Query: 18_re_91_0.439

Matches to Query: 19_re_43_0.442

Summary

Alignment

Summary

Alignment

Matches to Query: 20_h_27_0.526

TOMTOM version

Reference

Command line summary

Model parameters

Explanation of TOMTOM Results

The TOMTOM results consist of

Inputs

Query Motifs

Target Databases

Matches

Summary Table

Alignment

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