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.nbcr.net.

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
20 MA0066.1 (PPARG),  MA0072.1 (RORA_2),  MA0160.1 (NR4A2),  MA0258.1 (ESR2),  MA0071.1 (RORA_1),  MA0112.1 (ESR1),  MA0451.1 (kni),  MA0065.2 (PPARG::RXRA),  MA0129.1 (TGA1A),  MA0112.2 (ESR1)

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

JASPAR_CORE_2009.meme 476 20

Matches to Query: STRGGTCAN

Previous Next Top

Summary 

Alignment 

Name 
MA0066.1
Alt. Name 
PPARG
Database 
JASPAR_CORE_2009.meme
p-value 
9.00728e-10
E-value 
4.28746e-07
q-value 
8.50939e-07
Overlap 
9
Offset 
0
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0072.1
Alt. Name 
RORA_2
Database 
JASPAR_CORE_2009.meme
p-value 
0.000225683
E-value 
0.107425
q-value 
0.0710692
Overlap 
9
Offset 
5
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0160.1
Alt. Name 
NR4A2
Database 
JASPAR_CORE_2009.meme
p-value 
0.000425494
E-value 
0.202535
q-value 
0.100493
Overlap 
8
Offset 
-1
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0258.1
Alt. Name 
ESR2
Database 
JASPAR_CORE_2009.meme
p-value 
0.0012322
E-value 
0.586525
q-value 
0.232817
Overlap 
9
Offset 
0
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0071.1
Alt. Name 
RORA_1
Database 
JASPAR_CORE_2009.meme
p-value 
0.00241632
E-value 
1.15017
q-value 
0.325291
Overlap 
8
Offset 
2
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0112.1
Alt. Name 
ESR1
Database 
JASPAR_CORE_2009.meme
p-value 
0.0024236
E-value 
1.15363
q-value 
0.325291
Overlap 
9
Offset 
0
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0451.1
Alt. Name 
kni
Database 
JASPAR_CORE_2009.meme
p-value 
0.00275791
E-value 
1.31276
q-value 
0.325291
Overlap 
9
Offset 
3
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0065.2
Alt. Name 
PPARG::RXRA
Database 
JASPAR_CORE_2009.meme
p-value 
0.00309891
E-value 
1.47508
q-value 
0.325291
Overlap 
9
Offset 
0
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0129.1
Alt. Name 
TGA1A
Database 
JASPAR_CORE_2009.meme
p-value 
0.00358711
E-value 
1.70747
q-value 
0.338883
Overlap 
7
Offset 
-1
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0112.2
Alt. Name 
ESR1
Database 
JASPAR_CORE_2009.meme
p-value 
0.00450089
E-value 
2.14243
q-value 
0.366079
Overlap 
9
Offset 
3
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0434.1
Alt. Name 
YPR013C
Database 
JASPAR_CORE_2009.meme
p-value 
0.00464999
E-value 
2.21339
q-value 
0.366079
Overlap 
8
Offset 
1
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0099.1
Alt. Name 
Fos
Database 
JASPAR_CORE_2009.meme
p-value 
0.00623632
E-value 
2.96849
q-value 
0.4532
Overlap 
8
Offset 
0
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0016.1
Alt. Name 
usp
Database 
JASPAR_CORE_2009.meme
p-value 
0.00726528
E-value 
3.45827
q-value 
0.490263
Overlap 
8
Offset 
-1
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0141.1
Alt. Name 
Esrrb
Database 
JASPAR_CORE_2009.meme
p-value 
0.00848823
E-value 
4.0404
q-value 
0.518083
Overlap 
8
Offset 
4
Orientation 
Normal
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Summary 

Alignment 

Name 
MA0286.1
Alt. Name 
CST6
Database 
JASPAR_CORE_2009.meme
p-value 
0.011501
E-value 
5.47447
q-value 
0.613296
Overlap 
9
Offset 
0
Orientation 
Reverse Complement
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Summary 

Alignment 

Name 
MA0150.1
Alt. Name 
NFE2L2
Database 
JASPAR_CORE_2009.meme
p-value 
0.0116852
E-value 
5.56218
q-value 
0.613296
Overlap 
9
Offset 
2
Orientation 
Reverse Complement
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Summary 

Alignment 

Name 
MA0018.1
Alt. Name 
CREB1
Database 
JASPAR_CORE_2009.meme
p-value 
0.0124753
E-value 
5.93822
q-value 
0.614505
Overlap 
8
Offset 
-1
Orientation 
Reverse Complement
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Summary 

Alignment 

Name 
MA0272.1
Alt. Name 
ARG81
Database 
JASPAR_CORE_2009.meme
p-value 
0.0130092
E-value 
6.19238
q-value 
0.614505
Overlap 
8
Offset 
-1
Orientation 
Reverse Complement
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Summary 

Alignment 

Name 
MA0389.1
Alt. Name 
SRD1
Database 
JASPAR_CORE_2009.meme
p-value 
0.0156012
E-value 
7.42615
q-value 
0.669944
Overlap 
8
Offset 
0
Orientation 
Reverse Complement
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Summary 

Alignment 

Name 
MA0159.1
Alt. Name 
RXR::RAR_DR5
Database 
JASPAR_CORE_2009.meme
p-value 
0.0166394
E-value 
7.92038
q-value 
0.683464
Overlap 
7
Offset 
-2
Orientation 
Normal
Create custom LOGO ↧ [Previous Match] [Query Top]
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TOMTOM version
4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000)
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 0.825 seconds
show model parameters...