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_k36me3_1_0.394
ACAGGCGTG
0
2_e_k36me3_5_0.394
GCGTGAGCC
0
3_h_k27me3_5_0.601
TCGGAGCG
0
4_e_k4me3_2_0.600
CCCCGCCCC
18 SP1_Q6_01_M00931_T,  SP1_Q2_01_M00933_T,  SP1_Q6_M00196_T,  SP4_Q5_M01273_T,  SP1_02_M01303_T,  SP1_Q4_01_M00932_T,  SP1_MA0079.2_J,  GC-box_POL003.1_J,  GC_01_M00255_T,  SP1_01_M00008_T
5_e_k36me3_13_0.410
CAGCCTGGCC
0
6_e_k36me3_126_0.414
AAGTGATCC
0
7_e_k36me3_133_0.417
GGCAACATAT
1 P4HB_2_H
8_e_k27me3_37_0.575
CTCTCTCTC
0
9_e_k36me3_208_0.426
AGCTCGGCC
0
10_h_k27me3_7_0.571
TAGGGCGC
0
11_e_k27ac_3_0.430
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
12_e_k36me3_351_0.431
GTCACTGCA
0
13_e_k36me3_254_0.434
CAGGCCACA
0
14_e_k27me3_149_0.566
CCCCCTTTCC
0
15_e_k36me3_144_0.435
AACATGGCG
0
16_e_k27me3_286_0.564
TCCCCAAATCCC
0
17_e_k27me3_53_0.564
ATCGCGGCG
0
18_e_k9me3_117_0.438
AGGCCTATG
0
19_e_k4me3_192_0.558
CGCGATTTA
0
20_h_k4me3_14_0.557
GATATCCGCG
0
21_e_k36me3_185_0.444
GCCATGGCC
0
22_e_k27me3_179_0.555
CCATTCATTC
1 Hbp1_primary_SCI09_U
23_e_k27me3_269_0.553
CCCCCTAC
0
24_e_k27me3_270_0.552
AATAAACGAT
0
25_e_k36me3_173_0.449
AGACCTCATC
0
26_e_k36me3_75_0.451
AAGACGGTGTT
0
27_e_k27me3_191_0.549
GCGGGAATAA
1 YRR1_MA0439.1_J
28_e_k27me3_235_0.546
AAATGGGGAA
0
29_e_k4me1_184_0.456
GACATG
1 P53_05_M01655_T
30_h_k4me3_18_0.539
ACGCGTAAAG
0
31_e_k27ac_182_0.463
ACTGCATTC
0
32_e_k27me3_275_0.537
CATTTCAC
0
33_e_k9me3_17_0.464
TCCAGTATGA
0
34_e_k36me3_201_0.466
AACGTGCGT
0
35_e_k9me3_30_0.467
CATCACAAAG
0
36_e_k4me1_375_0.467
CAGTGCACA
0
37_e_k27me3_278_0.531
GACGCTTCC
0
38_e_k36me3_347_0.474
GGTACTCAC
0
39_h_k4me3_31_0.525
TCAACTTT
0
40_e_k36me3_206_0.477
TCTCGAAGG
1 XBP1_Q2_M00683_T

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 33

Matches to Query: 1_e_k36me3_1_0.394

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Matches to Query: 2_e_k36me3_5_0.394

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Matches to Query: 3_h_k27me3_5_0.601

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Matches to Query: 4_e_k4me3_2_0.600

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Summary 

Alignment 

Name SP1_Q6_01_M00931_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.58846e-08
E-value 4.63989e-05
q-value 4.71201e-05
Overlap 9
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name SP1_Q2_01_M00933_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.94189e-08
E-value 5.67227e-05
q-value 4.71201e-05
Overlap 9
Offset 0
Orientation Normal
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Summary 

Alignment 

Name SP1_Q6_M00196_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.45126e-08
E-value 7.16014e-05
q-value 4.71201e-05
Overlap 9
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name SP4_Q5_M01273_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.49822e-08
E-value 0.000102183
q-value 5.04342e-05
Overlap 9
Offset 1
Orientation Normal
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Summary 

Alignment 

Name SP1_02_M01303_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.06928e-07
E-value 0.000312335
q-value 0.00010303
Overlap 9
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name SP1_Q4_01_M00932_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.07196e-07
E-value 0.000313119
q-value 0.00010303
Overlap 9
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name SP1_MA0079.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.51569e-07
E-value 0.000442732
q-value 0.000124867
Overlap 9
Offset 0
Orientation Normal
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Summary 

Alignment 

Name GC-box_POL003.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.11269e-07
E-value 0.00120132
q-value 0.000261038
Overlap 9
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name GC_01_M00255_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.11269e-07
E-value 0.00120132
q-value 0.000261038
Overlap 9
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name SP1_01_M00008_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.52653e-07
E-value 0.0013222
q-value 0.000261038
Overlap 9
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name KROX_Q6_M00982_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.69756e-07
E-value 0.00195636
q-value 0.000351125
Overlap 9
Offset 5
Orientation Normal
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Summary 

Alignment 

Name SP1_MA0079.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.07766e-06
E-value 0.00314784
q-value 0.000517889
Overlap 9
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name Zfp410_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.71992e-06
E-value 0.00502388
q-value 0.000762959
Overlap 9
Offset 3
Orientation Normal
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Summary 

Alignment 

Name Klf7_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.13605e-06
E-value 0.00623939
q-value 0.000861058
Overlap 9
Offset 4
Orientation Normal
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Summary 

Alignment 

Name PGAM2_4_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.23968e-06
E-value 0.00654211
q-value 0.000861058
Overlap 8
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name Bcl6b_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.18224e-06
E-value 0.00929532
q-value 0.00114697
Overlap 9
Offset 2
Orientation Normal
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Summary 

Alignment 

Name CKROX_Q2_M01175_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.78661e-06
E-value 0.0110607
q-value 0.00128452
Overlap 9
Offset 0
Orientation Normal
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Summary 

Alignment 

Name ZFP281_01_M01597_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.2201e-06
E-value 0.0269319
q-value 0.00295393
Overlap 9
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 5_e_k36me3_13_0.410

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Matches to Query: 6_e_k36me3_126_0.414

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Matches to Query: 7_e_k36me3_133_0.417

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Summary 

Alignment 

Name P4HB_2_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.35775e-05
E-value 0.0396598
q-value 0.0793197
Overlap 6
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 8_e_k27me3_37_0.575

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Matches to Query: 9_e_k36me3_208_0.426

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Matches to Query: 10_h_k27me3_7_0.571

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Matches to Query: 11_e_k27ac_3_0.430

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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Matches to Query: 12_e_k36me3_351_0.431

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Matches to Query: 13_e_k36me3_254_0.434

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Matches to Query: 14_e_k27me3_149_0.566

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Matches to Query: 15_e_k36me3_144_0.435

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Matches to Query: 16_e_k27me3_286_0.564

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Matches to Query: 17_e_k27me3_53_0.564

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Matches to Query: 18_e_k9me3_117_0.438

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Matches to Query: 19_e_k4me3_192_0.558

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Matches to Query: 20_h_k4me3_14_0.557

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Matches to Query: 21_e_k36me3_185_0.444

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Matches to Query: 22_e_k27me3_179_0.555

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Summary 

Alignment 

Name Hbp1_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.56646e-07
E-value 0.00221016
q-value 0.00442033
Overlap 10
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 23_e_k27me3_269_0.553

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Matches to Query: 24_e_k27me3_270_0.552

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Matches to Query: 25_e_k36me3_173_0.449

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Matches to Query: 26_e_k36me3_75_0.451

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Matches to Query: 27_e_k27me3_191_0.549

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Summary 

Alignment 

Name YRR1_MA0439.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.00839e-05
E-value 0.0294549
q-value 0.0530585
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 28_e_k27me3_235_0.546

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Matches to Query: 29_e_k4me1_184_0.456

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Summary 

Alignment 

Name P53_05_M01655_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.87362e-06
E-value 0.0171568
q-value 0.0343137
Overlap 6
Offset 11
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 30_h_k4me3_18_0.539

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Matches to Query: 31_e_k27ac_182_0.463

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Matches to Query: 32_e_k27me3_275_0.537

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Matches to Query: 33_e_k9me3_17_0.464

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Matches to Query: 34_e_k36me3_201_0.466

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Matches to Query: 35_e_k9me3_30_0.467

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Matches to Query: 36_e_k4me1_375_0.467

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Matches to Query: 37_e_k27me3_278_0.531

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Matches to Query: 38_e_k36me3_347_0.474

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Matches to Query: 39_h_k4me3_31_0.525

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Matches to Query: 40_e_k36me3_206_0.477

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Summary 

Alignment 

Name XBP1_Q2_M00683_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.54644e-06
E-value 0.00451715
q-value 0.00903429
Overlap 7
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]
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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 92.793 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.