TOol for Motif TO Motif comparison (TOMTOM)

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.

Query Motifs  |  Target Databases  |  Matches  |  Program information  |  Explanation

Query Motifs

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Name 

Preview 

Matches 

List 

1
AGATAAGA
6 MA0035.2 (Gata1),  UP00100_1 (Gata6_primary),  UP00032_1 (Gata3_primary),  MA0029.1 (Evi1),  UP00080_1 (Gata5_primary),  MA0140.1 (Tal1::Gata1)
2
GGGCGGCGGGGAGGGGGCGCGGCCGGCGG
12 MA0146.1 (Zfx),  MA0079.2 (SP1),  UP00002_1 (Sp4_primary),  UP00079_2 (Esrra_secondary),  UP00021_1 (Zfp281_primary),  UP00070_2 (Gcm1_secondary),  UP00022_1 (Zfp740_primary),  UP00088_1 (Plagl1_primary),  MA0163.1 (PLAG1),  UP00000_2 (Smad3_secondary)
3
CCCCACCC
14 MA0039.2 (Klf4),  UP00093_1 (Klf7_primary),  UP00099_2 (Ascl2_secondary),  MA0079.1 (SP1),  UP00043_2 (Bcl6b_secondary),  MA0079.2 (SP1),  UP00033_2 (Zfp410_secondary),  UP00002_1 (Sp4_primary),  UP00021_1 (Zfp281_primary),  UP00022_1 (Zfp740_primary)

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

JASPAR_CORE_2009_vertebrates.meme 146 10
uniprobe_mouse.meme 386 18

Matches to Query: 1

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Summary 

Alignment 

Name MA0035.2
Alt. Name Gata1
Database JASPAR_CORE_2009_vertebrates.meme
p-value 1.34787e-07
E-value 7.17067e-05
q-value 0.000143321
Overlap 8
Offset 2
Orientation Normal
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Summary 

Alignment 

Name UP00100_1
Alt. Name Gata6_primary
Database uniprobe_mouse.meme
p-value 3.36967e-07
E-value 0.000179267
q-value 0.000179152
Overlap 8
Offset 5
Orientation Normal
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Summary 

Alignment 

Name UP00032_1
Alt. Name Gata3_primary
Database uniprobe_mouse.meme
p-value 2.87575e-06
E-value 0.0015299
q-value 0.00101928
Overlap 8
Offset 7
Orientation Normal
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Summary 

Alignment 

Name MA0029.1
Alt. Name Evi1
Database JASPAR_CORE_2009_vertebrates.meme
p-value 2.93904e-05
E-value 0.0156357
q-value 0.00781282
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name UP00080_1
Alt. Name Gata5_primary
Database uniprobe_mouse.meme
p-value 0.000175899
E-value 0.0935781
q-value 0.0374072
Overlap 8
Offset 5
Orientation Normal
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Summary 

Alignment 

Name MA0140.1
Alt. Name Tal1::Gata1
Database JASPAR_CORE_2009_vertebrates.meme
p-value 0.000615497
E-value 0.327444
q-value 0.109078
Overlap 7
Offset 11
Orientation Normal
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Matches to Query: 2

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Summary 

Alignment 

Name MA0146.1
Alt. Name Zfx
Database JASPAR_CORE_2009_vertebrates.meme
p-value 1.11295e-06
E-value 0.000592088
q-value 0.00115567
Overlap 14
Offset -12
Orientation Normal
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Summary 

Alignment 

Name MA0079.2
Alt. Name SP1
Database JASPAR_CORE_2009_vertebrates.meme
p-value 6.46564e-06
E-value 0.00343972
q-value 0.00265762
Overlap 10
Offset -6
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00002_1
Alt. Name Sp4_primary
Database uniprobe_mouse.meme
p-value 1.02375e-05
E-value 0.00544637
q-value 0.00265762
Overlap 17
Offset -7
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00079_2
Alt. Name Esrra_secondary
Database uniprobe_mouse.meme
p-value 9.06866e-05
E-value 0.0482453
q-value 0.0188335
Overlap 17
Offset -7
Orientation Normal
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Summary 

Alignment 

Name UP00021_1
Alt. Name Zfp281_primary
Database uniprobe_mouse.meme
p-value 0.000178679
E-value 0.0950573
q-value 0.0272785
Overlap 15
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00070_2
Alt. Name Gcm1_secondary
Database uniprobe_mouse.meme
p-value 0.000183891
E-value 0.0978301
q-value 0.0272785
Overlap 16
Offset 1
Orientation Normal
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Summary 

Alignment 

Name UP00022_1
Alt. Name Zfp740_primary
Database uniprobe_mouse.meme
p-value 0.000494796
E-value 0.263231
q-value 0.0642235
Overlap 16
Offset -3
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00088_1
Alt. Name Plagl1_primary
Database uniprobe_mouse.meme
p-value 0.000661944
E-value 0.352154
q-value 0.0763724
Overlap 16
Offset -10
Orientation Normal
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Summary 

Alignment 

Name MA0163.1
Alt. Name PLAG1
Database JASPAR_CORE_2009_vertebrates.meme
p-value 0.000981383
E-value 0.522096
q-value 0.0947401
Overlap 14
Offset -12
Orientation Normal
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Summary 

Alignment 

Name UP00000_2
Alt. Name Smad3_secondary
Database uniprobe_mouse.meme
p-value 0.00100362
E-value 0.533925
q-value 0.0947401
Overlap 17
Offset -6
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00408_2
Alt. Name Gabpa_secondary
Database uniprobe_mouse.meme
p-value 0.0014032
E-value 0.746503
q-value 0.115202
Overlap 16
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0112.2
Alt. Name ESR1
Database JASPAR_CORE_2009_vertebrates.meme
p-value 0.00144227
E-value 0.767288
q-value 0.115202
Overlap 20
Offset -6
Orientation Reverse Complement
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Matches to Query: 3

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Summary 

Alignment 

Name MA0039.2
Alt. Name Klf4
Database JASPAR_CORE_2009_vertebrates.meme
p-value 6.63138e-11
E-value 3.5279e-08
q-value 6.9596e-08
Overlap 8
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00093_1
Alt. Name Klf7_primary
Database uniprobe_mouse.meme
p-value 6.85149e-07
E-value 0.000364499
q-value 0.000239687
Overlap 8
Offset 4
Orientation Normal
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Summary 

Alignment 

Name UP00099_2
Alt. Name Ascl2_secondary
Database uniprobe_mouse.meme
p-value 6.85149e-07
E-value 0.000364499
q-value 0.000239687
Overlap 8
Offset 4
Orientation Normal
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Summary 

Alignment 

Name MA0079.1
Alt. Name SP1
Database JASPAR_CORE_2009_vertebrates.meme
p-value 1.54122e-05
E-value 0.00819929
q-value 0.00404376
Overlap 8
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00043_2
Alt. Name Bcl6b_secondary
Database uniprobe_mouse.meme
p-value 2.69011e-05
E-value 0.0143114
q-value 0.00564651
Overlap 8
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0079.2
Alt. Name SP1
Database JASPAR_CORE_2009_vertebrates.meme
p-value 7.55493e-05
E-value 0.0401922
q-value 0.0132148
Overlap 8
Offset 0
Orientation Normal
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Summary 

Alignment 

Name UP00033_2
Alt. Name Zfp410_secondary
Database uniprobe_mouse.meme
p-value 0.000155042
E-value 0.0824821
q-value 0.023245
Overlap 8
Offset 3
Orientation Normal
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Summary 

Alignment 

Name UP00002_1
Alt. Name Sp4_primary
Database uniprobe_mouse.meme
p-value 0.000303851
E-value 0.161649
q-value 0.0347885
Overlap 8
Offset 2
Orientation Normal
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Summary 

Alignment 

Name UP00021_1
Alt. Name Zfp281_primary
Database uniprobe_mouse.meme
p-value 0.000324726
E-value 0.172754
q-value 0.0347885
Overlap 8
Offset 3
Orientation Normal
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Summary 

Alignment 

Name UP00022_1
Alt. Name Zfp740_primary
Database uniprobe_mouse.meme
p-value 0.000331478
E-value 0.176347
q-value 0.0347885
Overlap 8
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0073.1
Alt. Name RREB1
Database JASPAR_CORE_2009_vertebrates.meme
p-value 0.00077671
E-value 0.41321
q-value 0.0741049
Overlap 8
Offset 11
Orientation Normal
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Summary 

Alignment 

Name UP00002_2
Alt. Name Sp4_secondary
Database uniprobe_mouse.meme
p-value 0.00104981
E-value 0.558497
q-value 0.0870271
Overlap 8
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00096_2
Alt. Name Sox13_secondary
Database uniprobe_mouse.meme
p-value 0.001078
E-value 0.573494
q-value 0.0870271
Overlap 8
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00048_2
Alt. Name Rara_secondary
Database uniprobe_mouse.meme
p-value 0.00171299
E-value 0.911311
q-value 0.128412
Overlap 8
Offset 7
Orientation Reverse Complement
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TOMTOM version
4.9.1 (Release date: Fri Aug 23 16:49:42 2013 +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 ./background):
A: 0.268   C: 0.232   G: 0.232   T: 0.268

Result calculation took 12.617 seconds
show model parameters...

Explanation of TOMTOM Results

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The TOMTOM results consist of

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.