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 

CACGTG
CACGTG
19 MA0281.1 (CBF1),  MA0569.1 (MYC4),  MA0409.1 (TYE7),  MA0004.1 (Arnt),  MA0059.1 (MYC::MAX),  MA0104.3 (Mycn),  MA0561.1 (PIF4),  MA0550.1 (BZR1),  MA0580.1 (DYT1),  MA0357.1 (PHO4)
RGGCGGGR
GGGCGGGG
6 MA0516.1 (SP2),  MA0079.3 (SP1),  MA0162.2 (EGR1),  MA0599.1 (KLF5),  MA0039.2 (Klf4),  MA0471.1 (E2F6)
CGCABGCG
CGCAGGCG
2 MA0506.1 (NRF1),  MA0565.1 (FUS3)
RGRAAA
GGGAAA
0
CMGGAAG
CCGGAAG
6 MA0026.1 (Eip74EF),  MA0076.2 (ELK4),  MA0062.2 (GABPA),  MA0473.1 (ELF1),  MA0475.1 (FLI1),  MA0323.1 (IXR1)
AAVATGGC
AAGATGGC
1 MA0095.2 (YY1)
RGCCAATS
GGCCAATC
2 MA0314.1 (HAP3),  MA0502.1 (NFYB)
TGABGTCA
TGACGTCA
3 MA0018.2 (CREB1),  MA0492.1 (JUND),  MA0286.1 (CST6)
DTAAAW
TTAAAA
0
GGRAGGR
GGGAGGG
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

JASPAR_CORE_2014.meme 593 39

Matches to Query: CACGTG

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Summary 

Alignment 

Name MA0281.1
Alt. Name CBF1
Database JASPAR_CORE_2014.meme
p-value 5.38052e-06
E-value 0.00319065
q-value 0.000878556
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0569.1
Alt. Name MYC4
Database JASPAR_CORE_2014.meme
p-value 5.38052e-06
E-value 0.00319065
q-value 0.000878556
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0409.1
Alt. Name TYE7
Database JASPAR_CORE_2014.meme
p-value 7.54126e-06
E-value 0.00447197
q-value 0.000878556
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0004.1
Alt. Name Arnt
Database JASPAR_CORE_2014.meme
p-value 7.58397e-06
E-value 0.00449729
q-value 0.000878556
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0059.1
Alt. Name MYC::MAX
Database JASPAR_CORE_2014.meme
p-value 1.0761e-05
E-value 0.00638128
q-value 0.000878556
Overlap 6
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0104.3
Alt. Name Mycn
Database JASPAR_CORE_2014.meme
p-value 1.13119e-05
E-value 0.00670793
q-value 0.000878556
Overlap 6
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0561.1
Alt. Name PIF4
Database JASPAR_CORE_2014.meme
p-value 1.13119e-05
E-value 0.00670793
q-value 0.000878556
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0550.1
Alt. Name BZR1
Database JASPAR_CORE_2014.meme
p-value 1.61415e-05
E-value 0.00957189
q-value 0.000878556
Overlap 6
Offset 4
Orientation Normal
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Summary 

Alignment 

Name MA0580.1
Alt. Name DYT1
Database JASPAR_CORE_2014.meme
p-value 1.61415e-05
E-value 0.00957189
q-value 0.000878556
Overlap 6
Offset 7
Orientation Normal
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Summary 

Alignment 

Name MA0357.1
Alt. Name PHO4
Database JASPAR_CORE_2014.meme
p-value 1.70796e-05
E-value 0.0101282
q-value 0.000878556
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0566.1
Alt. Name MYC2
Database JASPAR_CORE_2014.meme
p-value 1.70796e-05
E-value 0.0101282
q-value 0.000878556
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0551.1
Alt. Name HY5
Database JASPAR_CORE_2014.meme
p-value 1.97284e-05
E-value 0.011699
q-value 0.000930243
Overlap 6
Offset 5
Orientation Normal
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Summary 

Alignment 

Name MA0549.1
Alt. Name BES1
Database JASPAR_CORE_2014.meme
p-value 2.26236e-05
E-value 0.0134158
q-value 0.000984699
Overlap 6
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0552.1
Alt. Name PIL5
Database JASPAR_CORE_2014.meme
p-value 3.39352e-05
E-value 0.0201236
q-value 0.00137154
Overlap 6
Offset 7
Orientation Normal
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Summary 

Alignment 

Name MA0568.1
Alt. Name MYC3
Database JASPAR_CORE_2014.meme
p-value 4.04596e-05
E-value 0.0239925
q-value 0.00152621
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0464.1
Alt. Name Bhlhe40
Database JASPAR_CORE_2014.meme
p-value 4.55029e-05
E-value 0.0269832
q-value 0.00157925
Overlap 6
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0560.1
Alt. Name PIF3
Database JASPAR_CORE_2014.meme
p-value 4.74475e-05
E-value 0.0281364
q-value 0.00157925
Overlap 6
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0562.1
Alt. Name PIF5
Database JASPAR_CORE_2014.meme
p-value 5.97201e-05
E-value 0.035414
q-value 0.0018773
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0570.1
Alt. Name ABF1
Database JASPAR_CORE_2014.meme
p-value 7.97021e-05
E-value 0.0472634
q-value 0.00237357
Overlap 6
Offset 3
Orientation Normal
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Matches to Query: RGGCGGGR

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Summary 

Alignment 

Name MA0516.1
Alt. Name SP2
Database JASPAR_CORE_2014.meme
p-value 2.59431e-07
E-value 0.000153842
q-value 0.000302712
Overlap 8
Offset 6
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0079.3
Alt. Name SP1
Database JASPAR_CORE_2014.meme
p-value 1.98234e-06
E-value 0.00117553
q-value 0.00115653
Overlap 8
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0162.2
Alt. Name EGR1
Database JASPAR_CORE_2014.meme
p-value 1.08358e-05
E-value 0.00642565
q-value 0.00371657
Overlap 8
Offset 5
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0599.1
Alt. Name KLF5
Database JASPAR_CORE_2014.meme
p-value 1.27407e-05
E-value 0.00755524
q-value 0.00371657
Overlap 8
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0039.2
Alt. Name Klf4
Database JASPAR_CORE_2014.meme
p-value 4.813e-05
E-value 0.0285411
q-value 0.011232
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0471.1
Alt. Name E2F6
Database JASPAR_CORE_2014.meme
p-value 6.78006e-05
E-value 0.0402058
q-value 0.0131853
Overlap 8
Offset 0
Orientation Normal
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Matches to Query: CGCABGCG

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Summary 

Alignment 

Name MA0506.1
Alt. Name NRF1
Database JASPAR_CORE_2014.meme
p-value 1.29912e-07
E-value 7.70379e-05
q-value 0.000152412
Overlap 8
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0565.1
Alt. Name FUS3
Database JASPAR_CORE_2014.meme
p-value 5.46189e-05
E-value 0.032389
q-value 0.0228517
Overlap 8
Offset 0
Orientation Normal
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Matches to Query: RGRAAA

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Matches to Query: CMGGAAG

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Summary 

Alignment 

Name MA0026.1
Alt. Name Eip74EF
Database JASPAR_CORE_2014.meme
p-value 1.33841e-06
E-value 0.000793679
q-value 0.00112465
Overlap 7
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0076.2
Alt. Name ELK4
Database JASPAR_CORE_2014.meme
p-value 1.92769e-06
E-value 0.00114312
q-value 0.00112465
Overlap 7
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0062.2
Alt. Name GABPA
Database JASPAR_CORE_2014.meme
p-value 4.49956e-06
E-value 0.00266824
q-value 0.00175008
Overlap 7
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0473.1
Alt. Name ELF1
Database JASPAR_CORE_2014.meme
p-value 2.3409e-05
E-value 0.0138815
q-value 0.0068286
Overlap 7
Offset 4
Orientation Normal
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Summary 

Alignment 

Name MA0475.1
Alt. Name FLI1
Database JASPAR_CORE_2014.meme
p-value 3.79748e-05
E-value 0.0225191
q-value 0.00886207
Overlap 7
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0323.1
Alt. Name IXR1
Database JASPAR_CORE_2014.meme
p-value 7.64023e-05
E-value 0.0453065
q-value 0.0148581
Overlap 7
Offset 3
Orientation Normal
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Matches to Query: AAVATGGC

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Summary 

Alignment 

Name MA0095.2
Alt. Name YY1
Database JASPAR_CORE_2014.meme
p-value 1.46903e-07
E-value 8.71135e-05
q-value 0.000174227
Overlap 8
Offset 1
Orientation Normal
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Matches to Query: RGCCAATS

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Summary 

Alignment 

Name MA0314.1
Alt. Name HAP3
Database JASPAR_CORE_2014.meme
p-value 7.19389e-06
E-value 0.00426598
q-value 0.00851699
Overlap 8
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0502.1
Alt. Name NFYB
Database JASPAR_CORE_2014.meme
p-value 1.68073e-05
E-value 0.00996672
q-value 0.00994924
Overlap 8
Offset 5
Orientation Normal
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Matches to Query: TGABGTCA

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Summary 

Alignment 

Name MA0018.2
Alt. Name CREB1
Database JASPAR_CORE_2014.meme
p-value 1.32358e-06
E-value 0.000784881
q-value 0.00108834
Overlap 8
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0492.1
Alt. Name JUND
Database JASPAR_CORE_2014.meme
p-value 2.19633e-05
E-value 0.0130242
q-value 0.00861607
Overlap 8
Offset 5
Orientation Normal
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Summary 

Alignment 

Name MA0286.1
Alt. Name CST6
Database JASPAR_CORE_2014.meme
p-value 6.76749e-05
E-value 0.0401312
q-value 0.016886
Overlap 8
Offset 0
Orientation Reverse Complement
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Matches to Query: DTAAAW

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Matches to Query: GGRAGGR

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TOMTOM version
4.9.0 (Release date: Wed Oct 3 11:07:26 EST 2012)
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 2.591 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.