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_k9me3_25_0.781
CGCGCGGCGC
0
2_h_k4me3_3_0.765
TATCGTCG
0
3_h_k4me3_1_0.721
AACTTCCG
24 ELK1_02_M00025_T,  Elk3_EMBO10_U,  Elk1_EMBO10_U,  SAP1A_01_M01167_T,  Ehf_primary_SCI09_U,  Ets1_EMBO10_U,  Gabpa_primary_SCI09_U,  Elf2_EMBO10_U,  Elk4_EMBO10_U,  GABPA_MA0062.1_J
4_h_k9me3_23_0.720
TCGCGTTT
0
5_e_k4me3_349_0.686
AAATATCG
0
6_e_k4me3_58_0.685
CTCGCGAGA
0
7_e_k4me1_5_0.322
GCACAGCAGG
4 Zic1_secondary_SCI09_U,  Zic3_secondary_SCI09_U,  Zic2_secondary_SCI09_U,  NEUROD_02_M01288_T
8_e_k4me1_48_0.333
CAGAGGCCAG
0
9_e_k4me3_364_0.667
TTCGTTAA
0
10_e_k27ac_3_0.340
GCTGAGTCA
10 NFE2_01_M00037_T,  MAF_Q6_01_M00983_T,  NRF2_Q4_M00821_T,  TCF11MAFG_01_M00284_T,  NFE2L2_MA0150.1_J,  AP1_MA0099.2_J,  VMAF_01_M00035_T,  AP1_01_M00517_T,  AP1_Q6_M00174_T,  AP1_C_M00199_T
11_e_k4me3_357_0.657
ATAATCCG
0
12_e_k27ac_361_0.343
CCCACTGAG
0
13_e_k4me1_192_0.347
ATGTGTGCA
0
14_e_k4me3_57_0.631
AGATGGCGG
2 REX1_03_M01744_T,  NFMUE1_Q6_M00651_T
15_e_k4me3_328_0.630
AAAACTACG
0
16_e_k9me3_117_0.376
AGGCCTATG
0
17_e_k36me3_126_0.431
AAGTGATCC
0
18_e_k36me3_386_0.433
CACACGAGA
0
19_h_k9me3_8_0.438
GAGTTGAATGCA
0
20_e_k36me3_214_0.461
ACAGCGTGG
0

Target Databases

 Previous Next Top

Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 40

Matches to Query: 1_h_k9me3_25_0.781

 Previous Next Top

Matches to Query: 2_h_k4me3_3_0.765

 Previous Next Top

Matches to Query: 3_h_k4me3_1_0.721

 Previous Next Top

Summary 

Alignment 

Name ELK1_02_M00025_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.99486e-06
E-value 0.00582699
q-value 0.00356951
Overlap 8
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Elk3_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.8498e-06
E-value 0.00832427
q-value 0.00356951
Overlap 8
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elk1_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.6477e-06
E-value 0.0106549
q-value 0.00356951
Overlap 8
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name SAP1A_01_M01167_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.9779e-06
E-value 0.0145404
q-value 0.00356951
Overlap 8
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Ehf_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.6325e-06
E-value 0.0164525
q-value 0.00356951
Overlap 8
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Ets1_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.71921e-06
E-value 0.0167058
q-value 0.00356951
Overlap 8
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gabpa_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.71921e-06
E-value 0.0167058
q-value 0.00356951
Overlap 8
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elf2_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.33656e-06
E-value 0.0185091
q-value 0.00356951
Overlap 8
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elk4_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.33656e-06
E-value 0.0185091
q-value 0.00356951
Overlap 8
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GABPA_MA0062.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.4433e-06
E-value 0.0246629
q-value 0.00356951
Overlap 8
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name NRF2_01_M00108_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.4433e-06
E-value 0.0246629
q-value 0.00356951
Overlap 8
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GADP_01_M01258_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.74988e-06
E-value 0.0255584
q-value 0.00356951
Overlap 8
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name RARG_9_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.59774e-06
E-value 0.028035
q-value 0.00356951
Overlap 6
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GABPA_MA0062.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.62872e-06
E-value 0.0281255
q-value 0.00356951
Overlap 8
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ELK4_MA0076.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.02447e-05
E-value 0.0299249
q-value 0.00356951
Overlap 7
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gabpa_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.03796e-05
E-value 0.0303187
q-value 0.00356951
Overlap 8
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elf4_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.11981e-05
E-value 0.0327097
q-value 0.00356951
Overlap 8
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Erg_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.11981e-05
E-value 0.0327097
q-value 0.00356951
Overlap 8
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Fli1_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.33201e-05
E-value 0.0389081
q-value 0.00382134
Overlap 8
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gm5454_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.33201e-05
E-value 0.0389081
q-value 0.00382134
Overlap 8
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ETV4_13_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.41028e-05
E-value 0.0411941
q-value 0.0038532
Overlap 6
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Etv4_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.57345e-05
E-value 0.0459606
q-value 0.00395998
Overlap 8
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ELF2_10_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.68972e-05
E-value 0.0493567
q-value 0.00395998
Overlap 6
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name FLI1_7_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.68972e-05
E-value 0.0493567
q-value 0.00395998
Overlap 7
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 4_h_k9me3_23_0.720

 Previous Next Top

Matches to Query: 5_e_k4me3_349_0.686

 Previous Next Top

Matches to Query: 6_e_k4me3_58_0.685

 Previous Next Top

Matches to Query: 7_e_k4me1_5_0.322

 Previous Next Top

Summary 

Alignment 

Name Zic1_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.46032e-07
E-value 0.000426559
q-value 0.000501206
Overlap 10
Offset 2
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Zic3_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.71587e-07
E-value 0.000501206
q-value 0.000501206
Overlap 10
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Zic2_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.01501e-06
E-value 0.00296483
q-value 0.00197656
Overlap 10
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name NEUROD_02_M01288_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.0083e-06
E-value 0.0146292
q-value 0.00731462
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 8_e_k4me1_48_0.333

 Previous Next Top

Matches to Query: 9_e_k4me3_364_0.667

 Previous Next Top

Matches to Query: 10_e_k27ac_3_0.340

 Previous Next Top

Summary 

Alignment 

Name NFE2_01_M00037_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.69397e-09
E-value 2.83161e-05
q-value 5.6303e-05
Overlap 9
Offset 1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name MAF_Q6_01_M00983_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.41524e-07
E-value 0.000413392
q-value 0.000410989
Overlap 9
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name NRF2_Q4_M00821_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.43622e-07
E-value 0.00100372
q-value 0.000665257
Overlap 9
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name TCF11MAFG_01_M00284_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.34043e-06
E-value 0.0039154
q-value 0.00155825
Overlap 9
Offset 7
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name NFE2L2_MA0150.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.65687e-06
E-value 0.00483972
q-value 0.00155825
Overlap 9
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name AP1_MA0099.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.78734e-06
E-value 0.00522082
q-value 0.00155825
Overlap 7
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name VMAF_01_M00035_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.87804e-06
E-value 0.00548575
q-value 0.00155825
Overlap 9
Offset 4
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name AP1_01_M00517_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.1437e-06
E-value 0.0121037
q-value 0.00300834
Overlap 9
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name AP1_Q6_M00174_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.69929e-06
E-value 0.0166476
q-value 0.00367797
Overlap 9
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name AP1_C_M00199_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.30282e-06
E-value 0.0242525
q-value 0.00482231
Overlap 8
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 11_e_k4me3_357_0.657

 Previous Next Top

Matches to Query: 12_e_k27ac_361_0.343

 Previous Next Top

Matches to Query: 13_e_k4me1_192_0.347

 Previous Next Top

Matches to Query: 14_e_k4me3_57_0.631

 Previous Next Top

Summary 

Alignment 

Name REX1_03_M01744_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.37944e-06
E-value 0.00695035
q-value 0.0139007
Overlap 9
Offset 1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name NFMUE1_Q6_M00651_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.0524e-06
E-value 0.0176791
q-value 0.0176791
Overlap 9
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 15_e_k4me3_328_0.630

 Previous Next Top

Matches to Query: 16_e_k9me3_117_0.376

 Previous Next Top

Matches to Query: 17_e_k36me3_126_0.431

 Previous Next Top

Matches to Query: 18_e_k36me3_386_0.433

 Previous Next Top

Matches to Query: 19_h_k9me3_8_0.438

 Previous Next Top

Matches to Query: 20_e_k36me3_214_0.461

 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 43.635 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.