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_k27me3-h1_0.549
AGCCGCGCT
0
2_e_k27me3-h1_0.549
CGCCGAGCG
1 RAB7A_5_H
3_e_k27me3-h1_0.547
TAGCGCGTT
0
4_e_k27me3-h1_0.547
CCGCCCGCG
2 DAL81_01_M01690_T,  DAL81_MA0290.1_J
5_e_k27me3-h1_0.543
CGGAGACCGA
0
6_e_k27me3-mes_0.543
ACCTCTCTG
0
7_e_k27me3-h1_0.543
CGTTTAGAA
0
8_h_k27me3-h1_0.538
CGTTTTCC
0
9_e_k27me3-h1_0.537
CAAGAGCGA
0
10_e_k27me3-mes_0.536
CATCATCCC
0
11_e_k27me3-mes_0.536
CATCTGTAAG
0
12_e_k27me3-mes_0.536
AGTGACACCA
0
13_e_k27me3-h1_0.535
ACGACGGCG
0
14_e_k27me3-h1_0.535
ACACCGTAA
0
15_e_k27me3-h1_0.535
GATCGTTT
0
16_h_k27me3-h1_0.535
AAGCATTG
0
17_h_k27me3-h1_0.534
TTCCCGGAAA
10 STAT1STAT1_Q3_M01212_T,  STAT_01_M00259_T,  STAT_01_M00223_T,  STAT1_MA0137.2_J,  STAT1_05_M01260_T,  STAT3_01_M00225_T,  STAT1_01_M00224_T,  STAT3STAT3_Q3_M01220_T,  STAT3_03_M01595_T,  Sp100_primary_SCI09_U
18_e_k27me3-mes_0.534
GATGGAGAA
0
19_e_k27me3-h1_0.534
AGTTAGGAA
0
20_e_k27me3-h1_0.532
AACGAGAAA
0
21_e_k27me3-mes_0.532
TCCCAAGGTC
0
22_e_k27me3-mes_0.532
AGCACCTACA
0
23_e_k27me3-mes_0.531
ATATTCTCC
0
24_e_k27me3-mes_0.530
CCACCCTGA
0
25_e_k27me3-h1_0.529
AAGACTCGCG
0
26_e_k27me3-mes_0.529
GGGTCTCAC
0
27_e_k27me3-mes_0.525
CACATAGTA
0
28_e_k27me3-mes_0.525
AGTGTCTA
0
29_e_k27me3-h1_0.525
CCTACGATGA
0
30_e_k27me3-h1_0.524
TAATTAAC
0
31_e_k27me3-h1_0.523
AACGCCTTTT
1 APOLYA_B_M00310_T
32_e_k27me3-mes_0.522
CAGAAGTCA
0
33_e_k27me3-mes_0.522
GATACCTG
0
34_e_k27me3-h1_0.521
CGGACATT
0
35_e_k27me3-mes_0.521
TGATTCCAA
0
36_e_k27me3-h1_0.520
AAATGCCAC
1 TAF1A_8_H
37_e_k27me3-h1_0.518
GTATGCCGA
0
38_e_k27me3-h1_0.516
ACCGTTAAC
0
39_e_k27me3-h1_0.516
CACGTGCAGT
0
40_e_k27me3-mes_0.513
AGCATTCGC
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 15

Matches to Query: 1_e_k27me3-h1_0.549

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Matches to Query: 2_e_k27me3-h1_0.549

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Summary 

Alignment 

Name RAB7A_5_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.55008e-05
E-value 0.0452778
q-value 0.0861228
Overlap 6
Offset -2
Orientation Reverse Complement
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Matches to Query: 3_e_k27me3-h1_0.547

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Matches to Query: 4_e_k27me3-h1_0.547

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Summary 

Alignment 

Name DAL81_01_M01690_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.06498e-07
E-value 0.000311079
q-value 0.000307762
Overlap 9
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name DAL81_MA0290.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.06498e-07
E-value 0.000311079
q-value 0.000307762
Overlap 9
Offset 4
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 5_e_k27me3-h1_0.543

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Matches to Query: 6_e_k27me3-mes_0.543

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Matches to Query: 7_e_k27me3-h1_0.543

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Matches to Query: 8_h_k27me3-h1_0.538

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Matches to Query: 9_e_k27me3-h1_0.537

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Matches to Query: 10_e_k27me3-mes_0.536

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Matches to Query: 11_e_k27me3-mes_0.536

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Matches to Query: 12_e_k27me3-mes_0.536

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Matches to Query: 13_e_k27me3-h1_0.535

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Matches to Query: 14_e_k27me3-h1_0.535

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Matches to Query: 15_e_k27me3-h1_0.535

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Matches to Query: 16_h_k27me3-h1_0.535

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Matches to Query: 17_h_k27me3-h1_0.534

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Summary 

Alignment 

Name STAT1STAT1_Q3_M01212_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.04955e-07
E-value 0.000890774
q-value 0.00176261
Overlap 10
Offset 2
Orientation Normal
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Summary 

Alignment 

Name STAT_01_M00259_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.09569e-07
E-value 0.00207265
q-value 0.00205062
Overlap 10
Offset 6
Orientation Normal
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Summary 

Alignment 

Name STAT_01_M00223_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.36222e-06
E-value 0.00397904
q-value 0.00245003
Overlap 9
Offset 0
Orientation Normal
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Summary 

Alignment 

Name STAT1_MA0137.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.69555e-06
E-value 0.0049527
q-value 0.00245003
Overlap 10
Offset 3
Orientation Normal
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Summary 

Alignment 

Name STAT1_05_M01260_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.72403e-06
E-value 0.00795691
q-value 0.00280003
Overlap 10
Offset 10
Orientation Reverse Complement
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Summary 

Alignment 

Name STAT3_01_M00225_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.07457e-06
E-value 0.00898083
q-value 0.00280003
Overlap 10
Offset 6
Orientation Reverse Complement
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Summary 

Alignment 

Name STAT1_01_M00224_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.50931e-06
E-value 0.0131717
q-value 0.00325792
Overlap 10
Offset 6
Orientation Reverse Complement
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Summary 

Alignment 

Name STAT3STAT3_Q3_M01220_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.64394e-06
E-value 0.0281699
q-value 0.0055741
Overlap 10
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name STAT3_03_M01595_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.08069e-05
E-value 0.0315668
q-value 0.00567841
Overlap 10
Offset 5
Orientation Reverse Complement
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Summary 

Alignment 

Name Sp100_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.59057e-05
E-value 0.0464606
q-value 0.00766111
Overlap 10
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 18_e_k27me3-mes_0.534

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Matches to Query: 19_e_k27me3-h1_0.534

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Matches to Query: 20_e_k27me3-h1_0.532

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Matches to Query: 21_e_k27me3-mes_0.532

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Matches to Query: 22_e_k27me3-mes_0.532

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Matches to Query: 23_e_k27me3-mes_0.531

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Matches to Query: 24_e_k27me3-mes_0.530

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Matches to Query: 25_e_k27me3-h1_0.529

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Matches to Query: 26_e_k27me3-mes_0.529

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Matches to Query: 27_e_k27me3-mes_0.525

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Matches to Query: 28_e_k27me3-mes_0.525

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Matches to Query: 29_e_k27me3-h1_0.525

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Matches to Query: 30_e_k27me3-h1_0.524

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Matches to Query: 31_e_k27me3-h1_0.523

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Summary 

Alignment 

Name APOLYA_B_M00310_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.16908e-06
E-value 0.0267829
q-value 0.0535658
Overlap 10
Offset 4
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 32_e_k27me3-mes_0.522

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Matches to Query: 33_e_k27me3-mes_0.522

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Matches to Query: 34_e_k27me3-h1_0.521

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Matches to Query: 35_e_k27me3-mes_0.521

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Matches to Query: 36_e_k27me3-h1_0.520

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Summary 

Alignment 

Name TAF1A_8_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.25112e-05
E-value 0.0365451
q-value 0.0730903
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 37_e_k27me3-h1_0.518

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Matches to Query: 38_e_k27me3-h1_0.516

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Matches to Query: 39_e_k27me3-h1_0.516

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Matches to Query: 40_e_k27me3-mes_0.513

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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 82.500 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.