The name of the query motif.

[close ]

The alternate name of the query motif.

[close ]

A link to more information about the query motif.

[close ]

The motif preview. On supporting browsers this will display as a motif logo, otherwise the consensus sequence will be displayed.

[close ]

The number of significant matches of the query motif to a motif in the target database.

[close ]

Links to the first 20 matches of the query motif to a motif in the target database.

[close ]

The database name.

[close ]

The number of motifs read from the motif database minus the number that had to be discarded due to conflicting IDs.

[close ]

The number of motifs that had a match with at least one of the query motifs.

[close ]

The summary gives information about the matched motif. Mouse over each row to show further help buttons for each specific title.

[close ]

The name of the matched motif.

[close ]

The alternative name of the matched motif.

[close ]

The database containing the matched motif.

[close ]

The probability that the match occurred by random chance according to the null model.

[close ]

The expected number of false positives in the matches up to this point.

[close ]

The minimum False Discovery Rate required to include the match.

[close ]

The number of letters that overlaped in the optimal alignment.

[close ]

The offset of the query motif to the matched motif in the optimal alignment.

[close ]

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.

[close ]

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.

[close ]

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.

[close ]

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.

[close ]

Toggle error bars indicating the confidence of a motif based on the number of sites used in its creation.

[close ]

Toggle adding pseudocounts for Small Sample Correction.

[close ]

Toggle a full reverse complement of the alignment.

[close ]

Specify the width of the generated logo.

[close ]

Specify the height of the generated logo.

[close ]

[close ]

[close ]

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org.

If you use TOMTOM in your research, please cite the following paper:
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007. [full text]

Query Motifs  |  Target Databases  |  Matches  |  Program information

Query Motifs

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Name 

Preview 

Matches 

List 

STRGGTCAN
GTAGGTCAC
24 MA0066.1 (PPARG),  MA0072.1 (RORA_2),  MA0160.1 (NR4A2),  MA0592.1 (ESRRA),  MA0071.1 (RORA_1),  MA0451.1 (kni),  MA0065.2 (PPARG::RXRA),  MA0580.1 (DYT1),  MA0552.1 (PIL5),  MA0258.2 (ESR2)

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

JASPAR_CORE_2014.meme 593 24

Matches to Query Motif STRGGTCAN

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Summary 

Alignment 

Name 
MA0066.1
Alt. Name 
PPARG
Database 
JASPAR_CORE_2014.meme
p-value 
1.23179e-11
E-value 
7.30452e-09
q-value 
1.45215e-08
Overlap 
9
Offset 
0
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0072.1
Alt. Name 
RORA_2
Database 
JASPAR_CORE_2014.meme
p-value 
0.000227628
E-value 
0.134983
q-value 
0.0894496
Overlap 
9
Offset 
5
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0160.1
Alt. Name 
NR4A2
Database 
JASPAR_CORE_2014.meme
p-value 
0.000387209
E-value 
0.229615
q-value 
0.11412
Overlap 
8
Offset 
-1
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0592.1
Alt. Name 
ESRRA
Database 
JASPAR_CORE_2014.meme
p-value 
0.000556165
E-value 
0.329806
q-value 
0.131132
Overlap 
9
Offset 
1
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0071.1
Alt. Name 
RORA_1
Database 
JASPAR_CORE_2014.meme
p-value 
0.00248655
E-value 
1.47452
q-value 
0.376386
Overlap 
8
Offset 
2
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0451.1
Alt. Name 
kni
Database 
JASPAR_CORE_2014.meme
p-value 
0.00284845
E-value 
1.68913
q-value 
0.376386
Overlap 
9
Offset 
3
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0065.2
Alt. Name 
PPARG::RXRA
Database 
JASPAR_CORE_2014.meme
p-value 
0.0031861
E-value 
1.88936
q-value 
0.376386
Overlap 
9
Offset 
0
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0580.1
Alt. Name 
DYT1
Database 
JASPAR_CORE_2014.meme
p-value 
0.00335545
E-value 
1.98978
q-value 
0.376386
Overlap 
9
Offset 
1
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0552.1
Alt. Name 
PIL5
Database 
JASPAR_CORE_2014.meme
p-value 
0.00335545
E-value 
1.98978
q-value 
0.376386
Overlap 
9
Offset 
1
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0258.2
Alt. Name 
ESR2
Database 
JASPAR_CORE_2014.meme
p-value 
0.00351198
E-value 
2.0826
q-value 
0.376386
Overlap 
7
Offset 
-2
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0129.1
Alt. Name 
TGA1A
Database 
JASPAR_CORE_2014.meme
p-value 
0.00389035
E-value 
2.30698
q-value 
0.382193
Overlap 
7
Offset 
-1
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0112.2
Alt. Name 
ESR1
Database 
JASPAR_CORE_2014.meme
p-value 
0.00483913
E-value 
2.86961
q-value 
0.425465
Overlap 
9
Offset 
3
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0434.1
Alt. Name 
YPR013C
Database 
JASPAR_CORE_2014.meme
p-value 
0.00505263
E-value 
2.99621
q-value 
0.425465
Overlap 
8
Offset 
1
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0016.1
Alt. Name 
usp
Database 
JASPAR_CORE_2014.meme
p-value 
0.00687354
E-value 
4.07601
q-value 
0.540212
Overlap 
8
Offset 
-1
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0141.2
Alt. Name 
Esrrb
Database 
JASPAR_CORE_2014.meme
p-value 
0.00793159
E-value 
4.70343
q-value 
0.584407
Overlap 
8
Offset 
4
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0589.1
Alt. Name 
ZAP1
Database 
JASPAR_CORE_2014.meme
p-value 
0.0106133
E-value 
6.29368
q-value 
0.733799
Overlap 
9
Offset 
2
Orientation 
Reverse Complement
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Summary 

Alignment 

Name 
MA0286.1
Alt. Name 
CST6
Database 
JASPAR_CORE_2014.meme
p-value 
0.0115472
E-value 
6.84749
q-value 
0.733799
Overlap 
9
Offset 
0
Orientation 
Reverse Complement
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Summary 

Alignment 

Name 
MA0272.1
Alt. Name 
ARG81
Database 
JASPAR_CORE_2014.meme
p-value 
0.01247
E-value 
7.39469
q-value 
0.733799
Overlap 
8
Offset 
-1
Orientation 
Reverse Complement
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Summary 

Alignment 

Name 
MA0093.2
Alt. Name 
USF1
Database 
JASPAR_CORE_2014.meme
p-value 
0.012561
E-value 
7.44868
q-value 
0.733799
Overlap 
6
Offset 
-3
Orientation 
Reverse Complement
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Summary 

Alignment 

Name 
MA0513.1
Alt. Name 
SMAD2::SMAD3::SMAD4
Database 
JASPAR_CORE_2014.meme
p-value 
0.0130714
E-value 
7.75133
q-value 
0.733799
Overlap 
9
Offset 
2
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0478.1
Alt. Name 
FOSL2
Database 
JASPAR_CORE_2014.meme
p-value 
0.0142225
E-value 
8.43394
q-value 
0.762128
Overlap 
9
Offset 
0
Orientation 
Reverse Complement
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Summary 

Alignment 

Name 
MA0477.1
Alt. Name 
FOSL1
Database 
JASPAR_CORE_2014.meme
p-value 
0.0160748
E-value 
9.53238
q-value 
0.766791
Overlap 
9
Offset 
1
Orientation 
Reverse Complement
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Summary 

Alignment 

Name 
MA0526.1
Alt. Name 
USF2
Database 
JASPAR_CORE_2014.meme
p-value 
0.0160748
E-value 
9.53238
q-value 
0.766791
Overlap 
6
Offset 
-3
Orientation 
Reverse Complement
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Summary 

Alignment 

Name 
MA0389.1
Alt. Name 
SRD1
Database 
JASPAR_CORE_2014.meme
p-value 
0.0164092
E-value 
9.73066
q-value 
0.766791
Overlap 
8
Offset 
0
Orientation 
Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]
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TOMTOM version
4.10.2 (Release date: Thu Aug 06 17:34:33 2015 -0700)
Reference
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.
Command line summary

Background letter frequencies (from first motif database):
A: 0.250   C: 0.250   G: 0.250   T: 0.250

Result calculation took 1.024 seconds
show model parameters...