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_h_k27ac_10_0.580
CAGGAAATGCCT
3 FEV_MA0156.1_J,  ETS_Q4_M00771_T,  ETS1_B_M00339_T
2_e_k27ac_162_0.579
AGGAATTTC
0
3_h_k27ac_1_0.579
CTTATCTGAC
8 Tal1::Gata1_MA0140.1_J,  Gata1_MA0035.2_J,  GATA1_04_M00128_T,  GATA2_02_M00348_T,  GATA2_03_M00349_T,  Gata6_primary_SCI09_U,  SIRT6_01_M01797_T,  Gata3_primary_SCI09_U
4_e_k4me3_10_0.436
GTCGCCGCGC
0
5_e_k27ac_56_0.561
AGGAGAGGAA
0
6_e_k36me3_16_0.441
GATCGCGCC
0
7_e_k27ac_249_0.559
CAAAGCCTGG
1 NONO_4_H
8_h_k36me3_3_0.442
GTACGTCGAC
0
9_e_k36me3_181_0.443
GCGCTACCAC
1 SNT2_MA0384.1_J
10_e_k27ac_98_0.557
CTCCAGGAA
0
11_h_k27ac_30_0.556
TTAACAGCTC
0
12_e_k4me3_66_0.445
CTCGCGAT
0
13_e_k9me3_243_0.553
CTCCCTCTC
0
14_h_k4me1_9_0.552
TTCCCCCCCCCA
3 Zfp740_primary_SCI09_U,  MAZR_01_M00491_T,  Zfp281_primary_SCI09_U
15_e_k4me3_87_0.448
GACGACGAC
0
16_e_k27ac_86_0.551
GAGGCCTCTG
0
17_e_k36me3_110_0.450
GCGTGTGCC
2 hlh-27_PL0004.1_J,  HLH-27_Cell09_U
18_h_k27ac_25_0.550
AAGGCAGATT
0
19_e_k27ac_217_0.550
GCCAGAGAA
0
20_e_k27ac_129_0.550
CTATCTCCC
0
21_e_k36me3_40_0.451
CGGTGGCTC
0
22_e_k27ac_175_0.546
CAAACAGGCT
0
23_e_k36me3_131_0.454
CAGTGGTGC
0
24_e_k4me3_174_0.454
AGAACCGCG
0
25_h_k36me3_1_0.455
TACTTACCTG
2 at_AC_acceptor_SD0001.1_J,  AREB6_01_M00412_T
26_e_k27ac_406_0.544
AGGAATGCA
0
27_e_k27ac_82_0.543
CCACATTCC
0
28_e_k36me3_302_0.457
CATCGTGG
0
29_e_k4me3_330_0.458
AACGTTAGT
0
30_e_k9me3_313_0.542
ACTTCCCAG
0
31_h_k4me1_11_0.540
TTCACACCTCCC
2 TBR2_01_M01774_T,  Eomes_primary_SCI09_U
32_e_k36me3_244_0.461
TGCACCGTA
0
33_e_k27ac_404_0.539
ATTAGCATA
2 OCT1_07_M00248_T,  POU3F2_02_M00464_T
34_e_k27ac_291_0.538
GGAGGGAAA
0
35_h_k4me1_19_0.538
CTGCCACTCTCC
0
36_e_k36me3_105_0.463
ATGTTGGCC
0
37_e_k27me3_88_0.463
CGCCGGTCC
0
38_e_k27ac_392_0.536
CTGAGATAA
0
39_e_k27ac_372_0.535
TCTCATTAG
4 zen_MA0256.1_J,  IPF1_02_M01234_T,  eve_MA0221.1_J,  LHX4_8_H
40_e_k27me3_318_0.465
TAAAAACGAA
2 HOMEZ_01_M01429_T,  Homez_1063.2_Cell08_U
41_e_k27ac_182_0.534
CAGGGACAG
0
42_e_k27ac_25_0.532
CAGCCCTGCT
0
43_e_k4me3_332_0.469
TAAATCGTA
0
44_e_k36me3_46_0.472
ACATGGTGAC
0
45_e_k4me3_75_0.475
CGACTCGGAC
0
46_e_k27me3_327_0.476
ATATGTGCG
0
47_h_k9me3_13_0.477
GGTACCTCAG
0
48_e_k4me3_218_0.478
CGCCACTTA
0
49_e_k36me3_139_0.481
CTGTGTTGC
0
50_h_k4me1_35_0.482
ACTTTACTAC
0
51_e_k9me3_364_0.518
TCATGGACA
0
52_e_k27me3_301_0.483
AATACGCGT
0
53_h_k36me3_13_0.484
CGGATGTGCTGC
0
54_h_k9me3_18_0.488
CCGTTTCCAACG
0
55_h_k9me3_27_0.511
CCCATGGG
1 GPAM_2_H
56_e_k4me1_346_0.490
CACGTCATG
0
57_h_k9me3_23_0.504
TTCTTTTGAT
0
58_h_k9me3_14_0.496
TCCAAATATCCA
0
59_e_k9me3_100_0.503
CCCCCGATAC
0
60_h_k4me1_31_0.503
GACACCTTTT
0

Target Databases

Previous Next Top

Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 31

Matches to Query: 1_h_k27ac_10_0.580

Previous Next Top

Summary 

Alignment 

Name FEV_MA0156.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.17285e-07
E-value 0.000926789
q-value 0.00182487
Overlap 8
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ETS_Q4_M00771_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.2844e-06
E-value 0.00667272
q-value 0.00656937
Overlap 12
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ETS1_B_M00339_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.80525e-06
E-value 0.0286411
q-value 0.0187984
Overlap 12
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 2_e_k27ac_162_0.579

Previous Next Top

Matches to Query: 3_h_k27ac_1_0.579

Previous Next Top

Summary 

Alignment 

Name Tal1::Gata1_MA0140.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.4808e-08
E-value 4.3254e-05
q-value 8.63029e-05
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Gata1_MA0035.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.31838e-07
E-value 0.000969298
q-value 0.000966999
Overlap 9
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA1_04_M00128_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.63829e-06
E-value 0.00478545
q-value 0.00318273
Overlap 10
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA2_02_M00348_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.14131e-06
E-value 0.00917577
q-value 0.004577
Overlap 9
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA2_03_M00349_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.76754e-06
E-value 0.016847
q-value 0.00611247
Overlap 9
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gata6_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.29271e-06
E-value 0.018381
q-value 0.00611247
Overlap 10
Offset 5
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name SIRT6_01_M01797_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.22632e-05
E-value 0.0358208
q-value 0.0102102
Overlap 7
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gata3_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.46516e-05
E-value 0.0427973
q-value 0.010674
Overlap 10
Offset 8
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 4_e_k4me3_10_0.436

Previous Next Top

Matches to Query: 5_e_k27ac_56_0.561

Previous Next Top

Matches to Query: 6_e_k36me3_16_0.441

Previous Next Top

Matches to Query: 7_e_k27ac_249_0.559

Previous Next Top

Summary 

Alignment 

Name NONO_4_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.5916e-05
E-value 0.0464908
q-value 0.0929815
Overlap 7
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 8_h_k36me3_3_0.442

Previous Next Top

Matches to Query: 9_e_k36me3_181_0.443

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: 10_e_k27ac_98_0.557

Previous Next Top

Matches to Query: 11_h_k27ac_30_0.556

Previous Next Top

Matches to Query: 12_e_k4me3_66_0.445

Previous Next Top

Matches to Query: 13_e_k9me3_243_0.553

Previous Next Top

Matches to Query: 14_h_k4me1_9_0.552

Previous Next Top

Summary 

Alignment 

Name Zfp740_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.4411e-06
E-value 0.0129725
q-value 0.018369
Overlap 12
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name MAZR_01_M00491_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.33415e-06
E-value 0.0185021
q-value 0.018369
Overlap 12
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Zfp281_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.658e-05
E-value 0.0484302
q-value 0.0320547
Overlap 12
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 15_e_k4me3_87_0.448

Previous Next Top

Matches to Query: 16_e_k27ac_86_0.551

Previous Next Top

Matches to Query: 17_e_k36me3_110_0.450

Previous Next Top

Summary 

Alignment 

Name hlh-27_PL0004.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.13931e-05
E-value 0.0332792
q-value 0.0310638
Overlap 9
Offset 4
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name HLH-27_Cell09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.26013e-05
E-value 0.0368083
q-value 0.0310638
Overlap 9
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 18_h_k27ac_25_0.550

Previous Next Top

Matches to Query: 19_e_k27ac_217_0.550

Previous Next Top

Matches to Query: 20_e_k27ac_129_0.550

Previous Next Top

Matches to Query: 21_e_k36me3_40_0.451

Previous Next Top

Matches to Query: 22_e_k27ac_175_0.546

Previous Next Top

Matches to Query: 23_e_k36me3_131_0.454

Previous Next Top

Matches to Query: 24_e_k4me3_174_0.454

Previous Next Top

Matches to Query: 25_h_k36me3_1_0.455

Previous Next Top

Summary 

Alignment 

Name at_AC_acceptor_SD0001.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.57341e-12
E-value 1.62799e-08
q-value 3.25599e-08
Overlap 10
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name AREB6_01_M00412_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.07096e-05
E-value 0.0312826
q-value 0.0312826
Overlap 10
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 26_e_k27ac_406_0.544

Previous Next Top

Matches to Query: 27_e_k27ac_82_0.543

Previous Next Top

Matches to Query: 28_e_k36me3_302_0.457

Previous Next Top

Matches to Query: 29_e_k4me3_330_0.458

Previous Next Top

Matches to Query: 30_e_k9me3_313_0.542

Previous Next Top

Matches to Query: 31_h_k4me1_11_0.540

Previous Next Top

Summary 

Alignment 

Name TBR2_01_M01774_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.31531e-07
E-value 0.000968401
q-value 0.0019368
Overlap 9
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Eomes_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.29043e-06
E-value 0.0242163
q-value 0.0242163
Overlap 12
Offset 4
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 32_e_k36me3_244_0.461

Previous Next Top

Matches to Query: 33_e_k27ac_404_0.539

Previous Next Top

Summary 

Alignment 

Name OCT1_07_M00248_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.89819e-06
E-value 0.0143076
q-value 0.017753
Overlap 9
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name POU3F2_02_M00464_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.1069e-06
E-value 0.0178383
q-value 0.017753
Overlap 9
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 34_e_k27ac_291_0.538

Previous Next Top

Matches to Query: 35_h_k4me1_19_0.538

Previous Next Top

Matches to Query: 36_e_k36me3_105_0.463

Previous Next Top

Matches to Query: 37_e_k27me3_88_0.463

Previous Next Top

Matches to Query: 38_e_k27ac_392_0.536

Previous Next Top

Matches to Query: 39_e_k27ac_372_0.535

Previous Next Top

Summary 

Alignment 

Name zen_MA0256.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.74439e-06
E-value 0.00509537
q-value 0.00972255
Overlap 7
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name IPF1_02_M01234_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.1026e-06
E-value 0.0149047
q-value 0.0142199
Overlap 8
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name eve_MA0221.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.28764e-05
E-value 0.037612
q-value 0.0193917
Overlap 7
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name LHX4_8_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.39168e-05
E-value 0.0406509
q-value 0.0193917
Overlap 6
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 40_e_k27me3_318_0.465

Previous Next Top

Summary 

Alignment 

Name HOMEZ_01_M01429_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.51116e-06
E-value 0.0131771
q-value 0.0147905
Overlap 10
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Homez_1063.2_Cell08_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.06352e-06
E-value 0.0147905
q-value 0.0147905
Overlap 10
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 41_e_k27ac_182_0.534

Previous Next Top

Matches to Query: 42_e_k27ac_25_0.532

Previous Next Top

Matches to Query: 43_e_k4me3_332_0.469

Previous Next Top

Matches to Query: 44_e_k36me3_46_0.472

Previous Next Top

Matches to Query: 45_e_k4me3_75_0.475

Previous Next Top

Matches to Query: 46_e_k27me3_327_0.476

Previous Next Top

Matches to Query: 47_h_k9me3_13_0.477

Previous Next Top

Matches to Query: 48_e_k4me3_218_0.478

Previous Next Top

Matches to Query: 49_e_k36me3_139_0.481

Previous Next Top

Matches to Query: 50_h_k4me1_35_0.482

Previous Next Top

Matches to Query: 51_e_k9me3_364_0.518

Previous Next Top

Matches to Query: 52_e_k27me3_301_0.483

Previous Next Top

Matches to Query: 53_h_k36me3_13_0.484

Previous Next Top

Matches to Query: 54_h_k9me3_18_0.488

Previous Next Top

Matches to Query: 55_h_k9me3_27_0.511

Previous Next Top

Summary 

Alignment 

Name GPAM_2_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.16269e-05
E-value 0.0339623
q-value 0.0679246
Overlap 5
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 56_e_k4me1_346_0.490

Previous Next Top

Matches to Query: 57_h_k9me3_23_0.504

Previous Next Top

Matches to Query: 58_h_k9me3_14_0.496

Previous Next Top

Matches to Query: 59_e_k9me3_100_0.503

Previous Next Top

Matches to Query: 60_h_k4me1_31_0.503

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 155.855 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.