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 

TTGHGYAA
TTGTGCAA
2 MA0102.3 (CEBPA),  MA0466.1 (CEBPB)
CNGCCTCC
CAGCCTCC
0
GGAYTACA
GGATTACA
2 MA0212.1 (bcd),  MA0234.1 (oc)
TTTWTTTW
TTTTTTTT
0
GGCTCACK
GGCTCACT
0
GCCYGGS
GCCTGGG
0
GTGGCGCR
GTGGCGCA
0
CTCCTSCC
CTCCTGCC
0
AYACAMA
ACACACA
0
DCTCTGTC
GCTCTGTC
0
AGTAGCTG
AGTAGCTG
0
RTGASTCA
GTGACTCA
13 MA0490.1 (JUNB),  MA0478.1 (FOSL2),  MA0303.1 (GCN4),  MA0491.1 (JUND),  MA0489.1 (JUN),  MA0477.1 (FOSL1),  MA0591.1 (Bach1::Mafk),  MA0476.1 (FOS),  MA0501.1 (NFE2::MAF),  MA0150.2 (Nfe2l2)
ATCRCTTG
ATCGCTTG
0
RTAAAYA
GTAAACA
9 MA0297.1 (FKH2),  MA0030.1 (FOXF2),  MA0047.2 (Foxa2),  MA0458.1 (slp1),  MA0593.1 (FOXP2),  MA0031.1 (FOXD1),  MA0157.1 (FOXO3),  MA0148.3 (FOXA1),  MA0317.1 (HCM1)
CCMCDCCC
CCCCTCCC
6 MA0599.1 (KLF5),  MA0039.2 (Klf4),  MA0079.3 (SP1),  MA0162.2 (EGR1),  MA0493.1 (Klf1),  MA0472.1 (EGR2)
GCAYTCCA
GCACTCCA
0
GAGAYGGR
GAGATGGG
0
CRCCCGCC
CGCCCGCC
0
TGWTGCAA
TGTTGCAA
0
TKGTGAAA
TTGTGAAA
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

JASPAR_CORE_2014.meme 593 32

Matches to Query: TTGHGYAA

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Summary 

Alignment 

Name MA0102.3
Alt. Name CEBPA
Database JASPAR_CORE_2014.meme
p-value 2.83521e-05
E-value 0.0168128
q-value 0.0319011
Overlap 8
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0466.1
Alt. Name CEBPB
Database JASPAR_CORE_2014.meme
p-value 5.38907e-05
E-value 0.0319572
q-value 0.0319011
Overlap 8
Offset 1
Orientation Reverse Complement
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Matches to Query: CNGCCTCC

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Matches to Query: GGAYTACA

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Summary 

Alignment 

Name MA0212.1
Alt. Name bcd
Database JASPAR_CORE_2014.meme
p-value 2.33587e-05
E-value 0.0138517
q-value 0.0138517
Overlap 6
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0234.1
Alt. Name oc
Database JASPAR_CORE_2014.meme
p-value 2.33587e-05
E-value 0.0138517
q-value 0.0138517
Overlap 6
Offset 0
Orientation Reverse Complement
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Matches to Query: TTTWTTTW

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Matches to Query: GGCTCACK

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Matches to Query: GCCYGGS

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Matches to Query: GTGGCGCR

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Matches to Query: CTCCTSCC

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Matches to Query: AYACAMA

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Matches to Query: DCTCTGTC

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Matches to Query: AGTAGCTG

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Matches to Query: RTGASTCA

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Summary 

Alignment 

Name MA0490.1
Alt. Name JUNB
Database JASPAR_CORE_2014.meme
p-value 2.70319e-11
E-value 1.60299e-08
q-value 3.13516e-08
Overlap 8
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0478.1
Alt. Name FOSL2
Database JASPAR_CORE_2014.meme
p-value 1.98322e-10
E-value 1.17605e-07
q-value 1.15007e-07
Overlap 8
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0303.1
Alt. Name GCN4
Database JASPAR_CORE_2014.meme
p-value 6.94128e-10
E-value 4.11618e-07
q-value 2.13343e-07
Overlap 8
Offset 6
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0491.1
Alt. Name JUND
Database JASPAR_CORE_2014.meme
p-value 7.35793e-10
E-value 4.36325e-07
q-value 2.13343e-07
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0489.1
Alt. Name JUN
Database JASPAR_CORE_2014.meme
p-value 1.28764e-09
E-value 7.63569e-07
q-value 2.9868e-07
Overlap 8
Offset 5
Orientation Normal
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Summary 

Alignment 

Name MA0477.1
Alt. Name FOSL1
Database JASPAR_CORE_2014.meme
p-value 4.2739e-09
E-value 2.53442e-06
q-value 8.26144e-07
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0591.1
Alt. Name Bach1::Mafk
Database JASPAR_CORE_2014.meme
p-value 2.25921e-07
E-value 0.000133971
q-value 3.27529e-05
Overlap 8
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0476.1
Alt. Name FOS
Database JASPAR_CORE_2014.meme
p-value 3.03182e-07
E-value 0.000179787
q-value 3.907e-05
Overlap 8
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0501.1
Alt. Name NFE2::MAF
Database JASPAR_CORE_2014.meme
p-value 4.39198e-07
E-value 0.000260445
q-value 5.09382e-05
Overlap 8
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0150.2
Alt. Name Nfe2l2
Database JASPAR_CORE_2014.meme
p-value 8.26322e-07
E-value 0.000490009
q-value 7.37206e-05
Overlap 8
Offset 4
Orientation Normal
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Summary 

Alignment 

Name MA0462.1
Alt. Name BATF::JUN
Database JASPAR_CORE_2014.meme
p-value 3.44366e-06
E-value 0.00204209
q-value 0.000221886
Overlap 8
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0099.2
Alt. Name JUN::FOS
Database JASPAR_CORE_2014.meme
p-value 9.5336e-06
E-value 0.00565342
q-value 0.000552853
Overlap 7
Offset -1
Orientation Normal
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Summary 

Alignment 

Name MA0272.1
Alt. Name ARG81
Database JASPAR_CORE_2014.meme
p-value 3.70222e-05
E-value 0.0219542
q-value 0.00204468
Overlap 8
Offset 0
Orientation Normal
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Matches to Query: ATCRCTTG

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Matches to Query: RTAAAYA

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Summary 

Alignment 

Name MA0297.1
Alt. Name FKH2
Database JASPAR_CORE_2014.meme
p-value 2.12274e-05
E-value 0.0125878
q-value 0.00955701
Overlap 7
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0030.1
Alt. Name FOXF2
Database JASPAR_CORE_2014.meme
p-value 2.73882e-05
E-value 0.0162412
q-value 0.00955701
Overlap 7
Offset 5
Orientation Normal
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Summary 

Alignment 

Name MA0047.2
Alt. Name Foxa2
Database JASPAR_CORE_2014.meme
p-value 3.0807e-05
E-value 0.0182686
q-value 0.00955701
Overlap 7
Offset 5
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0458.1
Alt. Name slp1
Database JASPAR_CORE_2014.meme
p-value 4.49716e-05
E-value 0.0266682
q-value 0.00955701
Overlap 7
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0593.1
Alt. Name FOXP2
Database JASPAR_CORE_2014.meme
p-value 4.49716e-05
E-value 0.0266682
q-value 0.00955701
Overlap 7
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0031.1
Alt. Name FOXD1
Database JASPAR_CORE_2014.meme
p-value 4.88906e-05
E-value 0.0289921
q-value 0.00955701
Overlap 7
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0157.1
Alt. Name FOXO3
Database JASPAR_CORE_2014.meme
p-value 6.65936e-05
E-value 0.03949
q-value 0.00989899
Overlap 7
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0148.3
Alt. Name FOXA1
Database JASPAR_CORE_2014.meme
p-value 6.75201e-05
E-value 0.0400394
q-value 0.00989899
Overlap 7
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0317.1
Alt. Name HCM1
Database JASPAR_CORE_2014.meme
p-value 7.71592e-05
E-value 0.0457554
q-value 0.0100553
Overlap 7
Offset 0
Orientation Normal
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Matches to Query: CCMCDCCC

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Summary 

Alignment 

Name MA0599.1
Alt. Name KLF5
Database JASPAR_CORE_2014.meme
p-value 2.76375e-09
E-value 1.63891e-06
q-value 3.21879e-06
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0039.2
Alt. Name Klf4
Database JASPAR_CORE_2014.meme
p-value 5.97007e-07
E-value 0.000354025
q-value 0.000347651
Overlap 8
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0079.3
Alt. Name SP1
Database JASPAR_CORE_2014.meme
p-value 3.72139e-06
E-value 0.00220679
q-value 0.0014447
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0162.2
Alt. Name EGR1
Database JASPAR_CORE_2014.meme
p-value 1.72248e-05
E-value 0.0102143
q-value 0.0050152
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0493.1
Alt. Name Klf1
Database JASPAR_CORE_2014.meme
p-value 3.56407e-05
E-value 0.0211349
q-value 0.00830176
Overlap 8
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0472.1
Alt. Name EGR2
Database JASPAR_CORE_2014.meme
p-value 7.12801e-05
E-value 0.0422691
q-value 0.013836
Overlap 8
Offset 1
Orientation Normal
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Matches to Query: GCAYTCCA

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Matches to Query: GAGAYGGR

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Matches to Query: CRCCCGCC

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Matches to Query: TGWTGCAA

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Matches to Query: TKGTGAAA

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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 5.792 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.