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.

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

Query Motifs

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Name 

Alt. Name 

Preview 

Matches 

List 

ACAAWGV 2.9e-024
ACAAAGG
5 Sox11_primary, Sox4_primary, MA0442.1 (SOX10) , MA0143.1 (Sox2) , Sox12_secondary
ATGYWAA 1.0e-013
ATGCAAA
4 Pou2f3_3986.2, Pou2f2_3748.1, MA0142.1 (Pou5f1) , MA0143.1 (Sox2)
AAGGDCA 3.5e-010
AAGGTCA
7 MA0141.1 (Esrrb) , MA0160.1 (NR4A2) , Esrra_primary, MA0115.1 (NR1H2::RXRA) , MA0065.1 (PPARG::RXRA) , Rara_primary, Nr2f2_primary
CAGCWGG 2.0e-008
CAGCAGG
3 Zic1_secondary, Zic2_secondary, Zic3_secondary
AAAGRM 1.5e-005
AAAGAA
2 Sox12_secondary, Sox4_primary
GGGTGK 4.9e-004
GGGTGG
2 MA0073.1 (RREB1) , MA0039.2 (Klf4)
BAGGAA 7.3e-003
CAGGAA
2 MA0156.1 (FEV) , MA0080.2 (SPI1)
ACAATAS 1.3e-002
ACAATAG
1 MA0087.1 (Sox5)
CCCGS 3.6e-002
CCCGG
1 Zfp740_secondary

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

jaspar_vertebrates.meme 146 12
uniprobe_mouse.meme 386 12

Matches to Query: ACAAWGV (2.9e-024)

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Summary 

Alignment 

Name Sox11_primary
Database uniprobe_mouse.meme
p-value 4.44589e-07
E-value 0.000236522
q-value 0.000466037
Overlap 7
Offset 6
Orientation Normal
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Summary 

Alignment 

Name Sox4_primary
Database uniprobe_mouse.meme
p-value 1.55356e-06
E-value 0.000826496
q-value 0.000814255
Overlap 7
Offset 6
Orientation Normal
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Summary 

Alignment 

Name MA0442.1
Alt. Name SOX10
Database jaspar_vertebrates.meme
p-value 3.27342e-06
E-value 0.00174146
q-value 0.00105622
Overlap 6
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0143.1
Alt. Name Sox2
Database jaspar_vertebrates.meme
p-value 4.67822e-06
E-value 0.00248881
q-value 0.00105622
Overlap 7
Offset 8
Orientation Reverse Complement
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Summary 

Alignment 

Name Sox12_secondary
Database uniprobe_mouse.meme
p-value 5.03808e-06
E-value 0.00268026
q-value 0.00105622
Overlap 7
Offset 6
Orientation Normal
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Matches to Query: ATGYWAA (1.0e-013)

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Summary 

Alignment 

Name Pou2f3_3986.2
Database uniprobe_mouse.meme
p-value 2.07025e-06
E-value 0.00110137
q-value 0.00178493
Overlap 7
Offset 4
Orientation Normal
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Summary 

Alignment 

Name Pou2f2_3748.1
Database uniprobe_mouse.meme
p-value 3.36047e-06
E-value 0.00178777
q-value 0.00178493
Overlap 7
Offset 4
Orientation Normal
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Summary 

Alignment 

Name MA0142.1
Alt. Name Pou5f1
Database jaspar_vertebrates.meme
p-value 7.60536e-06
E-value 0.00404605
q-value 0.00269309
Overlap 7
Offset 7
Orientation Normal
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Summary 

Alignment 

Name MA0143.1
Alt. Name Sox2
Database jaspar_vertebrates.meme
p-value 6.23397e-05
E-value 0.0331647
q-value 0.016556
Overlap 7
Offset 8
Orientation Normal
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Matches to Query: AAGGDCA (3.5e-010)

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Summary 

Alignment 

Name MA0141.1
Alt. Name Esrrb
Database jaspar_vertebrates.meme
p-value 1.39268e-05
E-value 0.00740905
q-value 0.00911079
Overlap 7
Offset 5
Orientation Normal
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Summary 

Alignment 

Name MA0160.1
Alt. Name NR4A2
Database jaspar_vertebrates.meme
p-value 2.59749e-05
E-value 0.0138186
q-value 0.00911079
Overlap 7
Offset 0
Orientation Normal
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Summary 

Alignment 

Name Esrra_primary
Database uniprobe_mouse.meme
p-value 3.81106e-05
E-value 0.0202749
q-value 0.00911079
Overlap 7
Offset 5
Orientation Normal
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Summary 

Alignment 

Name MA0115.1
Alt. Name NR1H2::RXRA
Database jaspar_vertebrates.meme
p-value 4.26776e-05
E-value 0.0227045
q-value 0.00911079
Overlap 7
Offset 8
Orientation Normal
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Summary 

Alignment 

Name MA0065.1
Alt. Name PPARG::RXRA
Database jaspar_vertebrates.meme
p-value 5.12131e-05
E-value 0.0272454
q-value 0.00911079
Overlap 7
Offset 10
Orientation Normal
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Summary 

Alignment 

Name Rara_primary
Database uniprobe_mouse.meme
p-value 5.48589e-05
E-value 0.0291849
q-value 0.00911079
Overlap 7
Offset 5
Orientation Normal
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Summary 

Alignment 

Name Nr2f2_primary
Database uniprobe_mouse.meme
p-value 6.0608e-05
E-value 0.0322435
q-value 0.00911079
Overlap 7
Offset 5
Orientation Normal
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Matches to Query: CAGCWGG (2.0e-008)

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Summary 

Alignment 

Name Zic1_secondary
Database uniprobe_mouse.meme
p-value 5.47867e-06
E-value 0.00291465
q-value 0.00580353
Overlap 7
Offset 5
Orientation Normal
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Summary 

Alignment 

Name Zic2_secondary
Database uniprobe_mouse.meme
p-value 1.4731e-05
E-value 0.00783688
q-value 0.00749278
Overlap 7
Offset 5
Orientation Normal
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Summary 

Alignment 

Name Zic3_secondary
Database uniprobe_mouse.meme
p-value 2.12201e-05
E-value 0.0112891
q-value 0.00749278
Overlap 7
Offset 5
Orientation Normal
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Matches to Query: AAAGRM (1.5e-005)

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Summary 

Alignment 

Name Sox12_secondary
Database uniprobe_mouse.meme
p-value 4.0302e-05
E-value 0.0214407
q-value 0.0337191
Overlap 6
Offset 8
Orientation Normal
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Summary 

Alignment 

Name Sox4_primary
Database uniprobe_mouse.meme
p-value 6.53855e-05
E-value 0.0347851
q-value 0.0337191
Overlap 6
Offset 8
Orientation Normal
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Matches to Query: GGGTGK (4.9e-004)

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Summary 

Alignment 

Name MA0073.1
Alt. Name RREB1
Database jaspar_vertebrates.meme
p-value 3.09286e-05
E-value 0.016454
q-value 0.0170213
Overlap 6
Offset 7
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0039.2
Alt. Name Klf4
Database jaspar_vertebrates.meme
p-value 3.24371e-05
E-value 0.0172566
q-value 0.0170213
Overlap 6
Offset 1
Orientation Normal
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Matches to Query: BAGGAA (7.3e-003)

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Summary 

Alignment 

Name MA0156.1
Alt. Name FEV
Database jaspar_vertebrates.meme
p-value 5.74837e-05
E-value 0.0305813
q-value 0.0467864
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0080.2
Alt. Name SPI1
Database jaspar_vertebrates.meme
p-value 8.85027e-05
E-value 0.0470835
q-value 0.0467864
Overlap 5
Offset -1
Orientation Normal
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Matches to Query: ACAATAS (1.3e-002)

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Summary 

Alignment 

Name MA0087.1
Alt. Name Sox5
Database jaspar_vertebrates.meme
p-value 3.27069e-05
E-value 0.0174001
q-value 0.0345477
Overlap 5
Offset 2
Orientation Normal
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Matches to Query: CCCGS (3.6e-002)

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Summary 

Alignment 

Name Zfp740_secondary
Database uniprobe_mouse.meme
p-value 5.39499e-05
E-value 0.0287014
q-value 0.0565112
Overlap 5
Offset 8
Orientation Normal
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TOMTOM version
4.5.0 (Release date: Wed Oct 20 15:18:53 EST 2010)
Reference
Shobhit Gupta, John A. Stamatoyannopoulos, Timothy L. Bailey and William Stafford Noble, "Quantifying similarity between motifs",
Genome Biology, 8: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 3.754 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.