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 

RACTACR
AACTACA
0
TCCCAGVR
TCCCAGCA
1 MA0144.2 (STAT3)
ACTHCCG
ACTTCCG
2 MA0062.2 (GABPA),  MA0076.2 (ELK4)
CVGGAAR
CCGGAAG
5 MA0026.1 (Eip74EF),  MA0076.2 (ELK4),  MA0028.1 (ELK1),  MA0156.1 (FEV),  MA0062.2 (GABPA)
TGGGARW
TGGGAGT
0
AASATGGC
AAGATGGC
1 MA0095.2 (YY1)
CCCCRCCC
CCCCGCCC
5 MA0599.1 (KLF5),  MA0079.3 (SP1),  MA0039.2 (Klf4),  MA0162.2 (EGR1),  MA0516.1 (SP2)
CGCAKGCG
CGCAGGCG
2 MA0506.1 (NRF1),  MA0565.1 (FUS3)
RCGTCAY
GCGTCAC
3 MA0588.1 (TGA1),  MA0097.1 (bZIP911),  MA0286.1 (CST6)
ACTACHA
ACTACCA
0
GGACTYCA
GGACTCCA
0
GCGGMGSC
GCGGCGGC
0
CYGGRA
CCGGGA
0
CGCGGBGC
CGCGGGGC
1 MA0399.1 (SUT1)
CCCASAA
CCCAGAA
0
ATGGCGYC
ATGGCGCC
0
ATTGGCY
ATTGGCT
0

Target Databases

 Previous Next Top

Database 

Number of Motifs 

Motifs Matched 

JASPAR_CORE_2014.meme 593 18

Matches to Query: RACTACR

 Previous Next Top

Matches to Query: TCCCAGVR

 Previous Next Top

Summary 

Alignment 

Name MA0144.2
Alt. Name STAT3
Database JASPAR_CORE_2014.meme
p-value 4.47392e-05
E-value 0.0265304
q-value 0.0529677
Overlap 8
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: ACTHCCG

 Previous Next Top

Summary 

Alignment 

Name MA0062.2
Alt. Name GABPA
Database JASPAR_CORE_2014.meme
p-value 2.53348e-05
E-value 0.0150235
q-value 0.0298416
Overlap 7
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name MA0076.2
Alt. Name ELK4
Database JASPAR_CORE_2014.meme
p-value 6.46528e-05
E-value 0.0383391
q-value 0.0380769
Overlap 7
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: CVGGAAR

 Previous Next Top

Summary 

Alignment 

Name MA0026.1
Alt. Name Eip74EF
Database JASPAR_CORE_2014.meme
p-value 5.0754e-07
E-value 0.000300971
q-value 0.000585978
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name MA0076.2
Alt. Name ELK4
Database JASPAR_CORE_2014.meme
p-value 7.81106e-06
E-value 0.00463196
q-value 0.00308785
Overlap 7
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0028.1
Alt. Name ELK1
Database JASPAR_CORE_2014.meme
p-value 8.02354e-06
E-value 0.00475796
q-value 0.00308785
Overlap 7
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0156.1
Alt. Name FEV
Database JASPAR_CORE_2014.meme
p-value 2.19199e-05
E-value 0.0129985
q-value 0.00632688
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0062.2
Alt. Name GABPA
Database JASPAR_CORE_2014.meme
p-value 3.37699e-05
E-value 0.0200255
q-value 0.00779777
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: TGGGARW

 Previous Next Top

Matches to Query: AASATGGC

 Previous Next Top

Summary 

Alignment 

Name MA0095.2
Alt. Name YY1
Database JASPAR_CORE_2014.meme
p-value 4.95515e-06
E-value 0.0029384
q-value 0.00587681
Overlap 8
Offset 1
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: CCCCRCCC

 Previous Next Top

Summary 

Alignment 

Name MA0599.1
Alt. Name KLF5
Database JASPAR_CORE_2014.meme
p-value 3.41537e-06
E-value 0.00202532
q-value 0.00224363
Overlap 8
Offset 1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name MA0079.3
Alt. Name SP1
Database JASPAR_CORE_2014.meme
p-value 3.85231e-06
E-value 0.00228442
q-value 0.00224363
Overlap 8
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0039.2
Alt. Name Klf4
Database JASPAR_CORE_2014.meme
p-value 8.30558e-06
E-value 0.00492521
q-value 0.00317979
Overlap 8
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0162.2
Alt. Name EGR1
Database JASPAR_CORE_2014.meme
p-value 1.09194e-05
E-value 0.0064752
q-value 0.00317979
Overlap 8
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0516.1
Alt. Name SP2
Database JASPAR_CORE_2014.meme
p-value 1.5613e-05
E-value 0.00925852
q-value 0.00363729
Overlap 8
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: CGCAKGCG

 Previous Next Top

Summary 

Alignment 

Name MA0506.1
Alt. Name NRF1
Database JASPAR_CORE_2014.meme
p-value 1.90119e-06
E-value 0.0011274
q-value 0.00225481
Overlap 8
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name MA0565.1
Alt. Name FUS3
Database JASPAR_CORE_2014.meme
p-value 6.31321e-05
E-value 0.0374373
q-value 0.0263069
Overlap 8
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: RCGTCAY

 Previous Next Top

Summary 

Alignment 

Name MA0588.1
Alt. Name TGA1
Database JASPAR_CORE_2014.meme
p-value 6.57901e-05
E-value 0.0390135
q-value 0.030882
Overlap 7
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name MA0097.1
Alt. Name bZIP911
Database JASPAR_CORE_2014.meme
p-value 6.77987e-05
E-value 0.0402046
q-value 0.030882
Overlap 7
Offset 4
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0286.1
Alt. Name CST6
Database JASPAR_CORE_2014.meme
p-value 7.92261e-05
E-value 0.0469811
q-value 0.030882
Overlap 7
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: ACTACHA

 Previous Next Top

Matches to Query: GGACTYCA

 Previous Next Top

Matches to Query: GCGGMGSC

 Previous Next Top

Matches to Query: CYGGRA

 Previous Next Top

Matches to Query: CGCGGBGC

 Previous Next Top

Summary 

Alignment 

Name MA0399.1
Alt. Name SUT1
Database JASPAR_CORE_2014.meme
p-value 3.60196e-05
E-value 0.0213596
q-value 0.042419
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: CCCASAA

 Previous Next Top

Matches to Query: ATGGCGYC

 Previous Next Top

Matches to Query: ATTGGCY

 Previous Next Top
Previous Next Top
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 4.345 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.