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 

Alt. Name 

Preview 

Matches 

List 
1 MEME
TGTTTTTTTGTTTTTTTTTGT
9 MA0041.1 (Foxd3),  MA0481.1 (FOXP1),  MA0042.1 (FOXI1),  UP00039_1 (Foxj3_primary),  UP00037_1 (Zfp105_primary),  UP00061_2 (Foxl1_secondary),  UP00097_2 (Mtf1_secondary),  UP00041_1 (Foxj1_primary),  MA0511.1 (RUNX2)
2 MEME
GATTCTGGGAA
5 MA0519.1 (Stat5a::Stat5b),  MA0137.3 (STAT1),  MA0144.2 (STAT3),  MA0518.1 (Stat4),  MA0463.1 (Bcl6)
3 MEME
TTTTCCTGGAA
6 MA0137.3 (STAT1),  MA0463.1 (Bcl6),  MA0144.2 (STAT3),  MA0519.1 (Stat5a::Stat5b),  MA0518.1 (Stat4),  UP00180_1 (Hoxd13_2356.1)

Target Databases

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Database 

Number of Motifs 

Motifs Matched 
JASPAR_CORE_2014_vertebrates.meme 205 9
uniprobe_mouse.meme 386 6

Matches to Query: 1 (MEME)

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Summary 

Alignment 
Name 
 MA0041.1
Alt. Name 
 Foxd3
Database 
 JASPAR_CORE_2014_vertebrates.meme
p-value 
 1.33586e-05
E-value 
 0.00789495
q-value 
 0.0156544
Overlap 
 12
Offset 
 -1
Orientation 
 Normal
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Summary 

Alignment 
Name 
 MA0481.1
Alt. Name 
 FOXP1
Database 
 JASPAR_CORE_2014_vertebrates.meme
p-value 
 0.000227128
E-value 
 0.134233
q-value 
 0.124587
Overlap 
 15
Offset 
 -5
Orientation 
 Reverse Complement
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Summary 

Alignment 
Name 
 MA0042.1
Alt. Name 
 FOXI1
Database 
 JASPAR_CORE_2014_vertebrates.meme
p-value 
 0.000392188
E-value 
 0.231783
q-value 
 0.124587
Overlap 
 12
Offset 
 -1
Orientation 
 Normal
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Summary 

Alignment 
Name 
 UP00039_1
Alt. Name 
 Foxj3_primary
Database 
 uniprobe_mouse.meme
p-value 
 0.000425261
E-value 
 0.25133
q-value 
 0.124587
Overlap 
 17
Offset 
 -3
Orientation 
 Reverse Complement
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Summary 

Alignment 
Name 
 UP00037_1
Alt. Name 
 Zfp105_primary
Database 
 uniprobe_mouse.meme
p-value 
 0.000962328
E-value 
 0.568736
q-value 
 0.162283
Overlap 
 15
Offset 
 -4
Orientation 
 Reverse Complement
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Summary 

Alignment 
Name 
 UP00061_2
Alt. Name 
 Foxl1_secondary
Database 
 uniprobe_mouse.meme
p-value 
 0.00103751
E-value 
 0.613166
q-value 
 0.162283
Overlap 
 16
Offset 
 -3
Orientation 
 Reverse Complement
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Summary 

Alignment 
Name 
 UP00097_2
Alt. Name 
 Mtf1_secondary
Database 
 uniprobe_mouse.meme
p-value 
 0.00109831
E-value 
 0.649102
q-value 
 0.162283
Overlap 
 14
Offset 
 -1
Orientation 
 Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 
Name 
 UP00041_1
Alt. Name 
 Foxj1_primary
Database 
 uniprobe_mouse.meme
p-value 
 0.00110787
E-value 
 0.654751
q-value 
 0.162283
Overlap 
 14
Offset 
 2
Orientation 
 Reverse Complement
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Summary 

Alignment 
Name 
 MA0511.1
Alt. Name 
 RUNX2
Database 
 JASPAR_CORE_2014_vertebrates.meme
p-value 
 0.001646
E-value 
 0.972789
q-value 
 0.199855
Overlap 
 15
Offset 
 0
Orientation 
 Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 2 (MEME)

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Summary 

Alignment 
Name 
 MA0519.1
Alt. Name 
 Stat5a::Stat5b
Database 
 JASPAR_CORE_2014_vertebrates.meme
p-value 
 1.73035e-05
E-value 
 0.0102263
q-value 
 0.0101995
Overlap 
 9
Offset 
 -2
Orientation 
 Reverse Complement
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Summary 

Alignment 
Name 
 MA0137.3
Alt. Name 
 STAT1
Database 
 JASPAR_CORE_2014_vertebrates.meme
p-value 
 1.73035e-05
E-value 
 0.0102263
q-value 
 0.0101995
Overlap 
 10
Offset 
 -1
Orientation 
 Normal
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Summary 

Alignment 
Name 
 MA0144.2
Alt. Name 
 STAT3
Database 
 JASPAR_CORE_2014_vertebrates.meme
p-value 
 7.09994e-05
E-value 
 0.0419607
q-value 
 0.0279003
Overlap 
 10
Offset 
 -1
Orientation 
 Normal
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Summary 

Alignment 
Name 
 MA0518.1
Alt. Name 
 Stat4
Database 
 JASPAR_CORE_2014_vertebrates.meme
p-value 
 0.00021519
E-value 
 0.127177
q-value 
 0.0634216
Overlap 
 10
Offset 
 -1
Orientation 
 Normal
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Summary 

Alignment 
Name 
 MA0463.1
Alt. Name 
 Bcl6
Database 
 JASPAR_CORE_2014_vertebrates.meme
p-value 
 0.000702133
E-value 
 0.41496
q-value 
 0.165548
Overlap 
 11
Offset 
 2
Orientation 
 Reverse Complement
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Matches to Query: 3 (MEME)

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Summary 

Alignment 
Name 
 MA0137.3
Alt. Name 
 STAT1
Database 
 JASPAR_CORE_2014_vertebrates.meme
p-value 
 2.22268e-05
E-value 
 0.0131361
q-value 
 0.013485
Overlap 
 10
Offset 
 -1
Orientation 
 Reverse Complement
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Summary 

Alignment 
Name 
 MA0463.1
Alt. Name 
 Bcl6
Database 
 JASPAR_CORE_2014_vertebrates.meme
p-value 
 2.30345e-05
E-value 
 0.0136134
q-value 
 0.013485
Overlap 
 10
Offset 
 -1
Orientation 
 Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 
Name 
 MA0144.2
Alt. Name 
 STAT3
Database 
 JASPAR_CORE_2014_vertebrates.meme
p-value 
 5.21289e-05
E-value 
 0.0308082
q-value 
 0.0152588
Overlap 
 10
Offset 
 -1
Orientation 
 Normal
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Summary 

Alignment 
Name 
 MA0519.1
Alt. Name 
 Stat5a::Stat5b
Database 
 JASPAR_CORE_2014_vertebrates.meme
p-value 
 0.000105674
E-value 
 0.0624532
q-value 
 0.0247457
Overlap 
 9
Offset 
 -2
Orientation 
 Reverse Complement
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Summary 

Alignment 
Name 
 MA0518.1
Alt. Name 
 Stat4
Database 
 JASPAR_CORE_2014_vertebrates.meme
p-value 
 0.000197469
E-value 
 0.116704
q-value 
 0.0385345
Overlap 
 11
Offset 
 2
Orientation 
 Reverse Complement
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Summary 

Alignment 
Name 
 UP00180_1
Alt. Name 
 Hoxd13_2356.1
Database 
 uniprobe_mouse.meme
p-value 
 0.00110528
E-value 
 0.653218
q-value 
 0.129412
Overlap 
 11
Offset 
 4
Orientation 
 Reverse Complement
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 Dynamic_Male-biased_Output/background):
A: 0.282   C: 0.218   G: 0.218   T: 0.282

Result calculation took 5.109 seconds
show model parameters...