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 

1_e_k36me3_1_0.408
CGCCTGTAA
0
2_e_k4me3_10_0.410
GTCGCCGCGC
0
3_e_k36me3_20_0.411
CAAGCGATTC
0
4_h_k4me3_12_0.413
GATTCGAAACTG
0
5_e_k4me3_73_0.420
CGTCATCGCG
1 CREB_Q3_M00801_T
6_e_k4me3_296_0.426
CGGTGTTTA
0
7_e_k36me3_16_0.427
GATCGCGCC
0
8_e_k36me3_95_0.428
CTGGGCAAC
0
9_h_k4me3_9_0.428
CTTTCGCG
2 SWI4_MA0401.1_J,  E2F_Q3_M00425_T
10_e_k36me3_69_0.431
AGCCTGGGC
0
11_e_k27me3_33_0.432
GACGCGCGA
0
12_e_k36me3_64_0.432
AGGAGTTCG
0
13_e_k4me3_336_0.434
AACGAAAC
0
14_e_k36me3_261_0.434
ACGTAAGTC
0
15_h_k4me3_4_0.436
CGGTAGTG
0
16_h_k27me3_13_0.438
TTCGGAAA
2 BORG2_01_M01544_T,  Cep3_GR09_U
17_e_k4me3_157_0.439
ACACGTACT
0
18_h_k4me3_10_0.440
CGTTTTCG
0
19_e_k36me3_181_0.442
GCGCTACCAC
1 SNT2_MA0384.1_J
20_e_k27ac_176_0.554
CCCACTGAG
1 AP2REP_01_M00468_T
21_e_k27me3_235_0.447
TACGTCGTT
0
22_e_k9me3_188_0.551
CCCCACCCAC
3 CACCCBINDINGFACTOR_Q6_M00721_T,  Klf4_MA0039.2_J,  GKLF_02_M01588_T
23_e_k9me3_320_0.550
CCCCTGACCC
0
24_e_k9me3_189_0.549
CAGCTCCCAG
0
25_e_k9me3_180_0.549
GAAATCACCC
0
26_e_k9me3_73_0.547
TAGGCCTCA
0
27_e_k27ac_11_0.547
AGAGAGAGAC
0
28_e_k9me3_25_0.546
ATATTTGGAA
0
29_e_k9me3_184_0.546
GCCATGTGA
0
30_e_k9me3_237_0.544
CTCATGAGA
0
31_e_k4me3_313_0.457
AAATAAACG
0
32_e_k9me3_121_0.542
AAATGTCCAG
0
33_e_k9me3_85_0.541
CACAAAGAA
0
34_e_k9me3_132_0.540
ATGGTGGAAAG
1 ING4_01_M01743_T
35_e_k9me3_281_0.539
AGCTGTAGA
0
36_e_k27me3_35_0.461
TCCGAGCCG
0
37_e_k9me3_385_0.538
GGAAATGCC
2 STAT3_01_M00225_T,  SCMH1_9_H
38_e_k4me3_342_0.463
AAATACGGT
0
39_e_k36me3_269_0.463
CCGTAACAC
0
40_e_k9me3_114_0.536
TCTCAGAAAG
0
41_h_k36me3_2_0.466
CAGTGCCGAC
0
42_e_k9me3_310_0.534
TGTTGTGGG
0
43_e_k27ac_327_0.530
CCTTTGTTCT
7 Sox11_primary_SCI09_U,  SOX4_01_M01308_T,  Sox4_primary_SCI09_U,  Sox4_CR09_U,  SMAD1_01_M01590_T,  D_MA00445.1_J,  NANOG_02_M01247_T
44_e_k9me3_56_0.529
ATATCTTCA
0
45_e_k27ac_392_0.524
CTGAGATAA
0
46_e_k9me3_53_0.523
ATGAATGCA
0
47_e_k9me3_332_0.522
GCCATAAA
0
48_h_k27ac_16_0.518
ATGGCTTAGCTT
0
49_h_k4me3_22_0.512
AAACTTTC
0
50_h_k36me3_25_0.500
GCACCACATGCA
0

Target Databases

Previous Next Top

Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 20

Matches to Query: 1_e_k36me3_1_0.408

Previous Next Top

Matches to Query: 2_e_k4me3_10_0.410

Previous Next Top

Matches to Query: 3_e_k36me3_20_0.411

Previous Next Top

Matches to Query: 4_h_k4me3_12_0.413

Previous Next Top

Matches to Query: 5_e_k4me3_73_0.420

Previous Next Top

Summary 

Alignment 

Name CREB_Q3_M00801_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.53653e-06
E-value 0.0044882
q-value 0.00892577
Overlap 6
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 6_e_k4me3_296_0.426

Previous Next Top

Matches to Query: 7_e_k36me3_16_0.427

Previous Next Top

Matches to Query: 8_e_k36me3_95_0.428

Previous Next Top

Matches to Query: 9_h_k4me3_9_0.428

Previous Next Top

Summary 

Alignment 

Name SWI4_MA0401.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.88018e-06
E-value 0.020097
q-value 0.0235262
Overlap 7
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name E2F_Q3_M00425_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.07272e-06
E-value 0.0265014
q-value 0.0235262
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 10_e_k36me3_69_0.431

Previous Next Top

Matches to Query: 11_e_k27me3_33_0.432

Previous Next Top

Matches to Query: 12_e_k36me3_64_0.432

Previous Next Top

Matches to Query: 13_e_k4me3_336_0.434

Previous Next Top

Matches to Query: 14_e_k36me3_261_0.434

Previous Next Top

Matches to Query: 15_h_k4me3_4_0.436

Previous Next Top

Matches to Query: 16_h_k27me3_13_0.438

Previous Next Top

Summary 

Alignment 

Name BORG2_01_M01544_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.22908e-05
E-value 0.0359015
q-value 0.0325303
Overlap 8
Offset 6
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Cep3_GR09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.22908e-05
E-value 0.0359015
q-value 0.0325303
Overlap 8
Offset 6
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 17_e_k4me3_157_0.439

Previous Next Top

Matches to Query: 18_h_k4me3_10_0.440

Previous Next Top

Matches to Query: 19_e_k36me3_181_0.442

Previous Next Top

Summary 

Alignment 

Name SNT2_MA0384.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.64324e-05
E-value 0.0479991
q-value 0.0959981
Overlap 9
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 20_e_k27ac_176_0.554

Previous Next Top

Summary 

Alignment 

Name AP2REP_01_M00468_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.61198e-06
E-value 0.0134716
q-value 0.0269432
Overlap 7
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 21_e_k27me3_235_0.447

Previous Next Top

Matches to Query: 22_e_k9me3_188_0.551

Previous Next Top

Summary 

Alignment 

Name CACCCBINDINGFACTOR_Q6_M00721_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.09126e-06
E-value 0.00610858
q-value 0.00992715
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Klf4_MA0039.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.67947e-06
E-value 0.0136687
q-value 0.00992715
Overlap 9
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GKLF_02_M01588_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.14543e-06
E-value 0.0150298
q-value 0.00992715
Overlap 10
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 23_e_k9me3_320_0.550

Previous Next Top

Matches to Query: 24_e_k9me3_189_0.549

Previous Next Top

Matches to Query: 25_e_k9me3_180_0.549

Previous Next Top

Matches to Query: 26_e_k9me3_73_0.547

Previous Next Top

Matches to Query: 27_e_k27ac_11_0.547

Previous Next Top

Matches to Query: 28_e_k9me3_25_0.546

Previous Next Top

Matches to Query: 29_e_k9me3_184_0.546

Previous Next Top

Matches to Query: 30_e_k9me3_237_0.544

Previous Next Top

Matches to Query: 31_e_k4me3_313_0.457

Previous Next Top

Matches to Query: 32_e_k9me3_121_0.542

Previous Next Top

Matches to Query: 33_e_k9me3_85_0.541

Previous Next Top

Matches to Query: 34_e_k9me3_132_0.540

Previous Next Top

Summary 

Alignment 

Name ING4_01_M01743_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.66152e-06
E-value 0.0253003
q-value 0.0506006
Overlap 6
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 35_e_k9me3_281_0.539

Previous Next Top

Matches to Query: 36_e_k27me3_35_0.461

Previous Next Top

Matches to Query: 37_e_k9me3_385_0.538

Previous Next Top

Summary 

Alignment 

Name STAT3_01_M00225_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.83728e-06
E-value 0.0228927
q-value 0.0347559
Overlap 9
Offset 11
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name SCMH1_9_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.31236e-05
E-value 0.0383339
q-value 0.0347559
Overlap 6
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 38_e_k4me3_342_0.463

Previous Next Top

Matches to Query: 39_e_k36me3_269_0.463

Previous Next Top

Matches to Query: 40_e_k9me3_114_0.536

Previous Next Top

Matches to Query: 41_h_k36me3_2_0.466

Previous Next Top

Matches to Query: 42_e_k9me3_310_0.534

Previous Next Top

Matches to Query: 43_e_k27ac_327_0.530

Previous Next Top

Summary 

Alignment 

Name Sox11_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.33077e-07
E-value 0.000388718
q-value 0.00044784
Overlap 10
Offset 4
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name SOX4_01_M01308_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.81294e-07
E-value 0.00052956
q-value 0.00044784
Overlap 8
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Sox4_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.31883e-07
E-value 0.000677329
q-value 0.00044784
Overlap 10
Offset 4
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Sox4_CR09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.10701e-06
E-value 0.00323357
q-value 0.00133989
Overlap 10
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name SMAD1_01_M01590_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.15628e-06
E-value 0.00337749
q-value 0.00133989
Overlap 10
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name D_MA00445.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.84971e-06
E-value 0.00832399
q-value 0.00275185
Overlap 10
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name NANOG_02_M01247_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.16198e-06
E-value 0.0150781
q-value 0.00427262
Overlap 10
Offset 5
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 44_e_k9me3_56_0.529

Previous Next Top

Matches to Query: 45_e_k27ac_392_0.524

Previous Next Top

Matches to Query: 46_e_k9me3_53_0.523

Previous Next Top

Matches to Query: 47_e_k9me3_332_0.522

Previous Next Top

Matches to Query: 48_h_k27ac_16_0.518

Previous Next Top

Matches to Query: 49_h_k4me3_22_0.512

Previous Next Top

Matches to Query: 50_h_k36me3_25_0.500

Previous Next 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 119.228 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.