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_1_0.742
CGTTTCCG
1 STAT1_02_M00492_T
2_re_89_0.737
CCCGCGCCG
1 CNOT3_01_M01253_T
3_e_23_0.691
CTCGCGAGA
0
4_re_66_0.324
CCTGGGCAA
0
5_re_46_0.343
CACCGTGCCTG
0
6_re_30_0.347
GTAGTCCCA
0
7_re_61_0.364
CAGGAGTTCA
1 RPC155_01_M01798_T
8_re_65_0.365
ACTGCACTC
0
9_e_236_0.369
ACCCCATC
0
10_e_306_0.631
AGATCCGTA
0
11_e_140_0.628
AAGCGCACG
1 BZR1_01_M01156_T
12_re_164_0.376
AGTAGCTAG
0
13_h_25_0.617
AACTTAAC
0
14_re_165_0.393
GTGCTAGGA
0
15_re_111_0.403
ACCTCAAG
0
16_re_145_0.406
GTCTCTACA
0
17_h_28_0.590
GGGGAAAAAAAA
0
18_e_343_0.411
CCAGCTGT
13 AP4_Q6_01_M00927_T,  NEUROD_01_M01287_T,  JDP2_6_H,  MEIS3_10_H,  AP4_Q6_M00176_T,  HLH-2_LIN-32_Cell09_U,  hlh-2::lin-32_PL0006.1_J,  HLH-1_Cell09_U,  HLH-2_CND-1_Cell09_U,  hlh-2::cnd-1_PL0003.1_J
19_h_17_0.580
AAGATGGCGG
4 REX1_03_M01744_T,  NFMUE1_Q6_M00651_T,  YY1_Q6_02_M01035_T,  YY1_02_M00069_T
20_e_151_0.552
CTGATTGGC
11 NFYA_MA0060.1_J,  NFY_01_M00287_T,  HAP3_MA0314.1_J,  NFY_Q6_M00185_T,  NFY_C_M00209_T,  CAAT_01_M00254_T,  CCAAT-box_POL004.1_J,  ALPHACP1_01_M00687_T,  HAP5_MA0316.1_J,  HAP4_MA0315.1_J

Target Databases

Previous Next Top

Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 32

Matches to Query: 1_h_1_0.742

Previous Next Top

Summary 

Alignment 

Name STAT1_02_M00492_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.41415e-05
E-value 0.0413074
q-value 0.0496598
Overlap 8
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 2_re_89_0.737

Previous Next Top

Summary 

Alignment 

Name CNOT3_01_M01253_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.49379e-06
E-value 0.0248104
q-value 0.0493664
Overlap 9
Offset 1
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 3_e_23_0.691

Previous Next Top

Matches to Query: 4_re_66_0.324

Previous Next Top

Matches to Query: 5_re_46_0.343

Previous Next Top

Matches to Query: 6_re_30_0.347

Previous Next Top

Matches to Query: 7_re_61_0.364

Previous Next Top

Summary 

Alignment 

Name RPC155_01_M01798_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.24627e-06
E-value 0.00364034
q-value 0.00728068
Overlap 10
Offset 1
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 8_re_65_0.365

Previous Next Top

Matches to Query: 9_e_236_0.369

Previous Next Top

Matches to Query: 10_e_306_0.631

Previous Next Top

Matches to Query: 11_e_140_0.628

Previous Next Top

Summary 

Alignment 

Name BZR1_01_M01156_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.6008e-07
E-value 0.0022202
q-value 0.00444039
Overlap 6
Offset -3
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 12_re_164_0.376

Previous Next Top

Matches to Query: 13_h_25_0.617

Previous Next Top

Matches to Query: 14_re_165_0.393

Previous Next Top

Matches to Query: 15_re_111_0.403

Previous Next Top

Matches to Query: 16_re_145_0.406

Previous Next Top

Matches to Query: 17_h_28_0.590

Previous Next Top

Matches to Query: 18_e_343_0.411

Previous Next Top

Summary 

Alignment 

Name AP4_Q6_01_M00927_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.16134e-06
E-value 0.00923428
q-value 0.00406654
Overlap 8
Offset 1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name NEUROD_01_M01287_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.17179e-06
E-value 0.0151068
q-value 0.00406654
Overlap 6
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name JDP2_6_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.74779e-06
E-value 0.0226313
q-value 0.00406654
Overlap 7
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MEIS3_10_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.74779e-06
E-value 0.0226313
q-value 0.00406654
Overlap 7
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name AP4_Q6_M00176_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.62499e-06
E-value 0.0251936
q-value 0.00406654
Overlap 8
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HLH-2_LIN-32_Cell09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.93841e-06
E-value 0.0261091
q-value 0.00406654
Overlap 8
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name hlh-2::lin-32_PL0006.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.93841e-06
E-value 0.0261091
q-value 0.00406654
Overlap 8
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HLH-1_Cell09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.04017e-05
E-value 0.0303834
q-value 0.00406654
Overlap 8
Offset 5
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HLH-2_CND-1_Cell09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.04017e-05
E-value 0.0303834
q-value 0.00406654
Overlap 8
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name hlh-2::cnd-1_PL0003.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.04017e-05
E-value 0.0303834
q-value 0.00406654
Overlap 8
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name hlh-1_PL0019.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.20532e-05
E-value 0.0352074
q-value 0.00406654
Overlap 8
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name AP4_01_M00005_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.27105e-05
E-value 0.0371275
q-value 0.00406654
Overlap 8
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name AP4_Q5_M00175_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.2744e-05
E-value 0.0372251
q-value 0.00406654
Overlap 8
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 19_h_17_0.580

Previous Next Top

Summary 

Alignment 

Name REX1_03_M01744_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.45635e-07
E-value 0.0018859
q-value 0.0037718
Overlap 10
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name NFMUE1_Q6_M00651_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.72136e-06
E-value 0.00794909
q-value 0.00794909
Overlap 9
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name YY1_Q6_02_M01035_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.25871e-06
E-value 0.0153607
q-value 0.0102405
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name YY1_02_M00069_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.21162e-06
E-value 0.0269071
q-value 0.0134536
Overlap 10
Offset 7
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 20_e_151_0.552

Previous Next Top

Summary 

Alignment 

Name NFYA_MA0060.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.2799e-07
E-value 0.00037386
q-value 0.000479605
Overlap 9
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name NFY_01_M00287_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.64526e-07
E-value 0.000480579
q-value 0.000479605
Overlap 9
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HAP3_MA0314.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.59183e-06
E-value 0.00464975
q-value 0.00309355
Overlap 9
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name NFY_Q6_M00185_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.61918e-06
E-value 0.00765062
q-value 0.00381755
Overlap 9
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name NFY_C_M00209_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.18403e-06
E-value 0.0122216
q-value 0.0048787
Overlap 9
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name CAAT_01_M00254_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.86977e-06
E-value 0.0259086
q-value 0.00738744
Overlap 8
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name CCAAT-box_POL004.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.86977e-06
E-value 0.0259086
q-value 0.00738744
Overlap 8
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ALPHACP1_01_M00687_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.18582e-05
E-value 0.0346378
q-value 0.00816625
Overlap 9
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HAP5_MA0316.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.26902e-05
E-value 0.0370682
q-value 0.00816625
Overlap 9
Offset 6
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HAP4_MA0315.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.40069e-05
E-value 0.0409142
q-value 0.00816625
Overlap 9
Offset 6
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name NFY_Q6_01_M00775_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.62023e-05
E-value 0.0473269
q-value 0.00858744
Overlap 8
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query 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 44.636 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.