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 

1_e_7_0.844
CGCGCGCCG
0
2_e_1_0.830
CCGCCGCCG
2 ERF2_01_M01057_T,  ADF1_Q6_M00171_T
3_h_8_0.812
TGCGCATGCG
0
4_h_10_0.756
CATTCTCGCGAC
0
5_e_32_0.726
AGCGGGCGG
0
6_h_3_0.722
TTAACGTT
0
7_re_74_0.308
GTGCACACA
1 Zscan4_primary_SCI09_U
8_re_14_0.317
CTCTGTGCC
0
9_re_48_0.324
CCTGGCACA
0
10_e_64_0.671
CTGCGACG
0
11_re_11_0.344
ACGTGGCCCCA
1 ABF_Q2_M00442_T
12_re_52_0.355
GCAAGGTCAC
8 ERR2_01_M01589_T,  DAX1_01_M01248_T,  NR4A2_MA0160.1_J,  SF1_Q6_M00727_T,  GTF3C5_2_H,  ESR1_MA0112.2_J,  NUR77_Q5_M01217_T,  SF1_Q6_01_M01132_T
13_re_50_0.360
TGGGCAGGGAT
0
14_e_239_0.627
AAACGGAAAC
0
15_e_278_0.618
GTACGTAG
0
16_e_85_0.615
AGACGCGCA
1 GZF1_01_M01069_T
17_e_193_0.610
CGGACTAC
0
18_e_228_0.571
GCTTTTCTC
0
19_e_211_0.528
AGAGTCGGG
0
20_h_14_0.512
ACTACAATTCCC
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 13

Matches to Query: 1_e_7_0.844

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Matches to Query: 2_e_1_0.830

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Summary 

Alignment 

Name ERF2_01_M01057_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.30244e-06
E-value 0.00380443
q-value 0.00756463
Overlap 7
Offset -1
Orientation Normal
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Summary 

Alignment 

Name ADF1_Q6_M00171_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.11628e-05
E-value 0.0326066
q-value 0.0324171
Overlap 9
Offset 0
Orientation Normal
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Matches to Query: 3_h_8_0.812

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Matches to Query: 4_h_10_0.756

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Matches to Query: 5_e_32_0.726

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Matches to Query: 6_h_3_0.722

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Matches to Query: 7_re_74_0.308

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Summary 

Alignment 

Name Zscan4_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.57236e-06
E-value 0.0221189
q-value 0.0442377
Overlap 9
Offset 5
Orientation Normal
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Matches to Query: 8_re_14_0.317

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Matches to Query: 9_re_48_0.324

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Matches to Query: 10_e_64_0.671

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Matches to Query: 11_re_11_0.344

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Summary 

Alignment 

Name ABF_Q2_M00442_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.43882e-05
E-value 0.042028
q-value 0.0446567
Overlap 11
Offset 6
Orientation Normal
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Matches to Query: 12_re_52_0.355

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Summary 

Alignment 

Name ERR2_01_M01589_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.03868e-06
E-value 0.003034
q-value 0.00470245
Overlap 10
Offset 0
Orientation Normal
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Summary 

Alignment 

Name DAX1_01_M01248_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.24673e-06
E-value 0.00656269
q-value 0.00470245
Overlap 10
Offset 5
Orientation Normal
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Summary 

Alignment 

Name NR4A2_MA0160.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.42893e-06
E-value 0.00709491
q-value 0.00470245
Overlap 8
Offset -2
Orientation Normal
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Summary 

Alignment 

Name SF1_Q6_M00727_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.61542e-06
E-value 0.0105606
q-value 0.00524963
Overlap 8
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name GTF3C5_2_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.16502e-05
E-value 0.0340303
q-value 0.0111261
Overlap 6
Offset -4
Orientation Reverse Complement
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Summary 

Alignment 

Name ESR1_MA0112.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.32448e-05
E-value 0.0386882
q-value 0.0111261
Overlap 10
Offset 2
Orientation Normal
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Summary 

Alignment 

Name NUR77_Q5_M01217_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.34094e-05
E-value 0.0391689
q-value 0.0111261
Overlap 10
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name SF1_Q6_01_M01132_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.6507e-05
E-value 0.0482169
q-value 0.0119842
Overlap 9
Offset 0
Orientation Reverse Complement
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Matches to Query: 13_re_50_0.360

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Matches to Query: 14_e_239_0.627

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Matches to Query: 15_e_278_0.618

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Matches to Query: 16_e_85_0.615

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Summary 

Alignment 

Name GZF1_01_M01069_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.61411e-06
E-value 0.00763581
q-value 0.0152716
Overlap 9
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 17_e_193_0.610

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Matches to Query: 18_e_228_0.571

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Matches to Query: 19_e_211_0.528

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Matches to Query: 20_h_14_0.512

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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 48.081 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.