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 

h115-dmv-2_e_2_0.799
CCGCCGCCG
2 ERF2_01_M01057_T,  ETF_Q6_M00695_T
h115-k27ac-1_e_2_0.573
CCGCCGCCG
2 ERF2_01_M01057_T,  ADF1_Q6_M00171_T
h117-k4me3-1_e_k4me3_2_0.782,h117-k9me3-1_e_k4me3_2_0.390
CCGCCGCCG
3 ERF2_01_M01057_T,  ADF1_Q6_M00171_T,  ETF_Q6_M00695_T
h120-k4me3-1_re_13_0.776
CCGCCGCCGG
3 ERF2_01_M01057_T,  ADF1_Q6_M00171_T,  ODC1_3_H
mes20-k4me3-1_e_0_0.789
GCGCGGCGGCG
1 ERF2_01_M01057_T
msc15-dmv-1_h_5_0.862
CGCCGCCGGCGA
1 ERF2_01_M01057_T
msc15-k27ac-4_e_0_0.552
CCGCCGCCG
2 ERF2_01_M01057_T,  ADF1_Q6_M00171_T
msc15-k4me3-1_e_1_0.779
CGCCGCCGC
2 ERF2_01_M01057_T,  ETF_Q6_M00695_T
msc20-k4me3-2_e_1_0.750
CGCCGCCGC
2 ERF2_01_M01057_T,  ETF_Q6_M00695_T
npc15-k27me3-2_e_0_0.808
CGCCGCCGC
1 ERF2_01_M01057_T
npc15-k4me3-1_e_1_0.844
CCGCCGCCG
2 ERF2_01_M01057_T,  ADF1_Q6_M00171_T
npc17-k4me3-1_e_k4me3_2_0.786
CCGCCGCCG
2 ERF2_01_M01057_T,  ADF1_Q6_M00171_T
npc17-k9me3-2_e_k4me3_1_0.393
ACGCGGCGGC
0
npc20-k9me3-1_e_135_0.383
CCGCCGCCG
2 ERF2_01_M01057_T,  ADF1_Q6_M00171_T
tro15-dmv-2_e_1_0.847
CCGCCGCCG
2 ERF2_01_M01057_T,  ETF_Q6_M00695_T
tro15-k27ac-12_h_10_0.541
CCGCCGCCGCCG
5 ADF1_Q6_M00171_T,  ERF2_01_M01057_T,  ADF1_Q6_01_M00923_T,  SP1SP3_Q4_M01219_T,  KROX_Q6_M00982_T
tro15-k27me3-2_e_0_0.724
CGCCGCCGC
2 ERF2_01_M01057_T,  ETF_Q6_M00695_T
tro15-k4me3-2_e_1_0.830
CCGCCGCCG
2 ERF2_01_M01057_T,  ADF1_Q6_M00171_T

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiTaipaleCmbned.meme 3764 7

Matches to Query: h115-dmv-2_e_2_0.799

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 9.36637e-07
E-value 0.0035255
q-value 0.00700548
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ETF_Q6_M00695_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.37433e-05
E-value 0.0893699
q-value 0.0803146
Overlap 7
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: h115-k27ac-1_e_2_0.573

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.72241e-06
E-value 0.00648317
q-value 0.0129069
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ADF1_Q6_M00171_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.79592e-05
E-value 0.0675986
q-value 0.0672885
Overlap 9
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: h117-k4me3-1_e_k4me3_2_0.782,h117-k9me3-1_e_k4me3_2_0.390

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.64162e-06
E-value 0.00994306
q-value 0.0197763
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ADF1_Q6_M00171_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.36133e-05
E-value 0.0512406
q-value 0.04083
Overlap 9
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ETF_Q6_M00695_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.63616e-05
E-value 0.061585
q-value 0.04083
Overlap 7
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: h120-k4me3-1_re_13_0.776

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.0049e-06
E-value 0.00378243
q-value 0.00749058
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ADF1_Q6_M00171_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.085e-05
E-value 0.0408392
q-value 0.0404382
Overlap 10
Offset 0
Orientation Normal
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Summary 

Alignment 

Name ODC1_3_H
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.94396e-05
E-value 0.0731707
q-value 0.0483015
Overlap 6
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: mes20-k4me3-1_e_0_0.789

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.23359e-07
E-value 0.000464325
q-value 0.000919837
Overlap 7
Offset -4
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: msc15-dmv-1_h_5_0.862

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 7.57126e-07
E-value 0.00284982
q-value 0.00567274
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: msc15-k27ac-4_e_0_0.552

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.64302e-06
E-value 0.00994832
q-value 0.0198027
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ADF1_Q6_M00171_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.8388e-05
E-value 0.0692126
q-value 0.0688859
Overlap 9
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: msc15-k4me3-1_e_1_0.779

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.27604e-07
E-value 0.000856702
q-value 0.00170051
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ETF_Q6_M00695_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.17206e-05
E-value 0.0817565
q-value 0.0648497
Overlap 7
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: msc20-k4me3-2_e_1_0.750

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 6.4749e-07
E-value 0.00243715
q-value 0.00483893
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ETF_Q6_M00695_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.57277e-05
E-value 0.0968389
q-value 0.0756951
Overlap 7
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: npc15-k27me3-2_e_0_0.808

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 3.82847e-07
E-value 0.00144104
q-value 0.00286077
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: npc15-k4me3-1_e_1_0.844

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.98082e-07
E-value 0.00187478
q-value 0.00372986
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ADF1_Q6_M00171_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.65176e-05
E-value 0.0621722
q-value 0.0618455
Overlap 9
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: npc17-k4me3-1_e_k4me3_2_0.786

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 3.00642e-06
E-value 0.0113162
q-value 0.0225285
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ADF1_Q6_M00171_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.26979e-05
E-value 0.047795
q-value 0.0475758
Overlap 9
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: npc17-k9me3-2_e_k4me3_1_0.393

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Matches to Query: npc20-k9me3-1_e_135_0.383

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.18991e-07
E-value 0.000447882
q-value 0.000890817
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ADF1_Q6_M00171_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.93349e-05
E-value 0.0727765
q-value 0.0723746
Overlap 9
Offset 6
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: tro15-dmv-2_e_1_0.847

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 5.64462e-08
E-value 0.000212463
q-value 0.000422183
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ETF_Q6_M00695_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.33999e-05
E-value 0.0880772
q-value 0.0683007
Overlap 7
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: tro15-k27ac-12_h_10_0.541

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Summary 

Alignment 

Name ADF1_Q6_M00171_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.25768e-07
E-value 0.000849792
q-value 0.00168642
Overlap 12
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 7.31532e-07
E-value 0.00275349
q-value 0.00273216
Overlap 7
Offset -4
Orientation Normal
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Summary 

Alignment 

Name ADF1_Q6_01_M00923_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.40642e-06
E-value 0.0165858
q-value 0.0109715
Overlap 12
Offset 0
Orientation Normal
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Summary 

Alignment 

Name SP1SP3_Q4_M01219_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 9.48812e-06
E-value 0.0357133
q-value 0.0152312
Overlap 11
Offset 0
Orientation Normal
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Summary 

Alignment 

Name KROX_Q6_M00982_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.01953e-05
E-value 0.0383753
q-value 0.0152312
Overlap 12
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: tro15-k27me3-2_e_0_0.724

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.10742e-08
E-value 0.000154603
q-value 0.000306921
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ETF_Q6_M00695_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.96726e-05
E-value 0.0740476
q-value 0.0626228
Overlap 7
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: tro15-k4me3-2_e_1_0.830

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.07362e-06
E-value 0.00780509
q-value 0.0155386
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ADF1_Q6_M00171_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.2242e-05
E-value 0.0460788
q-value 0.0458675
Overlap 9
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]
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TOMTOM version
4.8.1 (Release date: Tue Feb 7 14:03:40 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: 0.295   C: 0.205   G: 0.205   T: 0.295

Result calculation took 59.156 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.