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

 Next Top

Name 

Preview 

Matches 

List 

h117-k4me3-4_h_k4me3_12_0.710
CTGCGCATGCGC
4 ZFP206_01_M01742_T,  NRF1_dimeric_0_P,  NRF1_Q6_M00652_T,  HIST1H2BN_4_H
msc15-k27ac-7_e_55_0.544
ACGCAGGCG
1 TRIM69_7_H
msc15-k4me3-7_h_15_0.719
TGCGCATGCG
4 NRF1_dimeric_0_P,  NRF1_Q6_M00652_T,  ZFP206_01_M01742_T,  HIST1H2BN_4_H
msc20-k4me3-5_e_4_0.690
CGCATGCGCAA
4 NRF1_Q6_M00652_T,  NRF1_dimeric_0_P,  ZFP206_01_M01742_T,  HIST1H2BN_4_H
npc15-k27ac-21_e_5_0.564
CGCCTGCGC
3 HIST1H2BN_4_H,  ZFP206_01_M01742_T,  TRIM69_7_H
npc15-k4me3-4_h_10_0.757
CGCAAGCG
6 DNMT3A_5_H,  NRF1_Q6_M00652_T,  ZFP206_01_M01742_T,  TRIM69_7_H,  HIST1H2BN_4_H,  NRF1_dimeric_0_P
npc17-k4me3-4_e_k4me3_7_0.707
CGCAGGCGC
2 ZFP206_01_M01742_T,  TRIM69_7_H
npc20-k27ac-50_e_45_0.521
ACGCAGACG
1 TRIM69_7_H
tro15-k27ac-33_e_27_0.528
CGCGCAGGC
1 ZFP206_01_M01742_T

Target Databases

 Previous Next Top

Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiTaipaleCmbned.meme 3764 6

Matches to Query: h117-k4me3-4_h_k4me3_12_0.710

 Previous Next Top

Summary 

Alignment 

Name ZFP206_01_M01742_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.80105e-10
E-value 1.80712e-06
q-value 3.61357e-06
Overlap 11
Offset -1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name NRF1_dimeric_0_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.55223e-09
E-value 9.60661e-06
q-value 9.60486e-06
Overlap 11
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name NRF1_Q6_M00652_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 3.50288e-07
E-value 0.00131848
q-value 0.000527298
Overlap 10
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HIST1H2BN_4_H
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 5.34724e-07
E-value 0.0020127
q-value 0.000670778
Overlap 9
Offset -3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: msc15-k27ac-7_e_55_0.544

 Previous Next Top

Summary 

Alignment 

Name TRIM69_7_H
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.82228e-06
E-value 0.00685906
q-value 0.0137181
Overlap 8
Offset -1
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: msc15-k4me3-7_h_15_0.719

 Previous Next Top

Summary 

Alignment 

Name NRF1_dimeric_0_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.62019e-09
E-value 6.09841e-06
q-value 1.21968e-05
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name NRF1_Q6_M00652_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 3.98454e-08
E-value 0.000149978
q-value 7.7207e-05
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ZFP206_01_M01742_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.10239e-08
E-value 0.000154414
q-value 7.7207e-05
Overlap 10
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HIST1H2BN_4_H
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.20283e-06
E-value 0.00452747
q-value 0.00150916
Overlap 9
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: msc20-k4me3-5_e_4_0.690

 Previous Next Top

Summary 

Alignment 

Name NRF1_Q6_M00652_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.93956e-10
E-value 1.85925e-06
q-value 3.71634e-06
Overlap 10
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name NRF1_dimeric_0_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.01169e-08
E-value 3.80801e-05
q-value 3.8058e-05
Overlap 10
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ZFP206_01_M01742_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 3.25447e-08
E-value 0.000122498
q-value 7.29213e-05
Overlap 10
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HIST1H2BN_4_H
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 5.76139e-07
E-value 0.00216859
q-value 0.000722442
Overlap 9
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: npc15-k27ac-21_e_5_0.564

 Previous Next Top

Summary 

Alignment 

Name HIST1H2BN_4_H
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 6.17852e-07
E-value 0.00232559
q-value 0.00281261
Overlap 9
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ZFP206_01_M01742_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 7.47275e-07
E-value 0.00281274
q-value 0.00281261
Overlap 9
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name TRIM69_7_H
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.48449e-06
E-value 0.00558761
q-value 0.0037249
Overlap 8
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: npc15-k4me3-4_h_10_0.757

 Previous Next Top

Summary 

Alignment 

Name DNMT3A_5_H
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.53602e-06
E-value 0.00578157
q-value 0.0115631
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name NRF1_Q6_M00652_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.02788e-06
E-value 0.0151609
q-value 0.0150183
Overlap 8
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ZFP206_01_M01742_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 5.98498e-06
E-value 0.0225275
q-value 0.0150183
Overlap 8
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name TRIM69_7_H
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 9.10948e-06
E-value 0.0342881
q-value 0.017144
Overlap 8
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HIST1H2BN_4_H
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.55421e-05
E-value 0.0585006
q-value 0.0211186
Overlap 8
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name NRF1_dimeric_0_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.96373e-05
E-value 0.073915
q-value 0.0211186
Overlap 8
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: npc17-k4me3-4_e_k4me3_7_0.707

 Previous Next Top

Summary 

Alignment 

Name ZFP206_01_M01742_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 6.93936e-07
E-value 0.00261198
q-value 0.00520836
Overlap 9
Offset 2
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name TRIM69_7_H
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.52451e-06
E-value 0.00573825
q-value 0.00572112
Overlap 8
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: npc20-k27ac-50_e_45_0.521

 Previous Next Top

Summary 

Alignment 

Name TRIM69_7_H
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.61602e-05
E-value 0.0984672
q-value 0.196934
Overlap 8
Offset -1
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: tro15-k27ac-33_e_27_0.528

 Previous Next Top

Summary 

Alignment 

Name ZFP206_01_M01742_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.17159e-05
E-value 0.0440987
q-value 0.0881974
Overlap 9
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]
Previous Next Top
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 29.137 seconds
show model parameters...

Explanation of TOMTOM Results

 Previous Top

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.