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_h_k4me1_2_0.555
ATGAGTCATA
17 GCN4_MA0303.1_J,  Gcn4_GR09_U,  Jundm2_secondary_SCI09_U,  GCN4_02_M01555_T,  AP1_C_M00199_T,  AP1_01_M00517_T,  GCN4_01_M00038_T,  Fos_MA0099.1_J,  AP1_Q6_M00174_T,  AP1_Q6_01_M00925_T
2_h_k4me1_1_0.548
ACAGGAATTC
0
3_e_k27ac_304_0.542
TTCCAGAAA
1 HNRPH3_9_H
4_e_k36me3_367_0.465
GACGGTAC
0
5_e_k27ac_105_0.533
AAACAAAACGCT
0
6_e_k4me3_269_0.530
CCGGGAAA
1 STAT3STAT3_Q3_M01220_T
7_e_k4me3_77_0.472
CGCGGTAC
0
8_e_k36me3_129_0.472
CGGATCACC
0
9_e_k4me3_280_0.473
CGTAGGTA
0
10_e_k27ac_22_0.527
AGGCCTGGG
0
11_h_k36me3_2_0.474
CGTCGACG
0
12_h_k27me3_14_0.476
CGCGATGCAA
0
13_h_k9me3_1_0.524
TCTCAGCAAGGC
0
14_e_k27me3_70_0.476
AGCGCGCA
0
15_e_k27me3_321_0.476
ATAATAACG
0
16_e_k27ac_326_0.523
AGTCTGGAG
1 UGP2_3_H
17_e_k27ac_360_0.522
AAACCAGGC
0
18_e_k27ac_399_0.522
GCCTGAGAAT
1 ALX4_01_M00619_T
19_h_k36me3_3_0.478
AGCTGCTGCTGC
3 MYF_01_M01302_T,  Myf_MA0055.1_J,  Ascl2_primary_SCI09_U
20_e_k27ac_204_0.522
GAAGGGAAGG
0
21_e_k27ac_197_0.520
AGGTCAGGCA
0
22_e_k9me3_299_0.519
ATGGACTCA
0
23_e_k4me3_180_0.483
CTACTCGTA
0
24_e_k9me3_7_0.516
CCAACGAAA
0
25_e_k27ac_406_0.516
AAAATGCTG
1 Mafk_primary_SCI09_U
26_h_k9me3_19_0.484
TTTGTGATGT
0
27_e_k27me3_277_0.487
AAATAACCG
0
28_e_k9me3_315_0.488
AGATTTGGGG
0
29_h_k4me3_32_0.490
CGCCTTAACCAC
0
30_h_k4me3_24_0.494
GTTCATGAATGG
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 25

Matches to Query: 1_h_k4me1_2_0.555

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Summary 

Alignment 

Name GCN4_MA0303.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.55909e-10
E-value 4.55409e-07
q-value 3.92303e-07
Overlap 10
Offset 6
Orientation Normal
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Summary 

Alignment 

Name Gcn4_GR09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.55909e-10
E-value 4.55409e-07
q-value 3.92303e-07
Overlap 10
Offset 6
Orientation Normal
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Summary 

Alignment 

Name Jundm2_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.63295e-10
E-value 7.69086e-07
q-value 3.92303e-07
Overlap 10
Offset 4
Orientation Normal
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Summary 

Alignment 

Name GCN4_02_M01555_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.70413e-10
E-value 7.89877e-07
q-value 3.92303e-07
Overlap 10
Offset 6
Orientation Normal
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Summary 

Alignment 

Name AP1_C_M00199_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.63903e-08
E-value 4.78762e-05
q-value 1.18892e-05
Overlap 9
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_01_M00517_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.30281e-08
E-value 0.000125685
q-value 2.49693e-05
Overlap 10
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name GCN4_01_M00038_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.17225e-08
E-value 0.000267921
q-value 4.83879e-05
Overlap 10
Offset 9
Orientation Reverse Complement
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Summary 

Alignment 

Name Fos_MA0099.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.35437e-07
E-value 0.000395612
q-value 6.54953e-05
Overlap 8
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_Q6_M00174_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.16648e-07
E-value 0.000632829
q-value 9.67087e-05
Overlap 10
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_Q6_01_M00925_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.46911e-07
E-value 0.00159753
q-value 0.00018669
Overlap 9
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_Q4_01_M00926_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.03066e-07
E-value 0.00176156
q-value 0.000194422
Overlap 8
Offset -1
Orientation Normal
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Summary 

Alignment 

Name FRA1_Q5_M01267_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.13014e-06
E-value 0.00330115
q-value 0.00034517
Overlap 8
Offset -1
Orientation Normal
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Summary 

Alignment 

Name BACH2_01_M00490_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.35211e-06
E-value 0.00394951
q-value 0.000362399
Overlap 10
Offset 1
Orientation Normal
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Summary 

Alignment 

Name AP1_MA0099.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.89353e-06
E-value 0.014294
q-value 0.00105175
Overlap 7
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name GCN4_Q2_M01713_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.0884e-06
E-value 0.0177842
q-value 0.00121831
Overlap 10
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name NFE2_01_M00037_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.0884e-06
E-value 0.0177842
q-value 0.00121831
Overlap 9
Offset 2
Orientation Normal
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Summary 

Alignment 

Name BACH1_01_M00495_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.21529e-06
E-value 0.0239969
q-value 0.00153785
Overlap 10
Offset 3
Orientation Reverse Complement
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Matches to Query: 2_h_k4me1_1_0.548

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Matches to Query: 3_e_k27ac_304_0.542

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Summary 

Alignment 

Name HNRPH3_9_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.63263e-05
E-value 0.047689
q-value 0.0950533
Overlap 6
Offset 0
Orientation Reverse Complement
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Matches to Query: 4_e_k36me3_367_0.465

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Matches to Query: 5_e_k27ac_105_0.533

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Matches to Query: 6_e_k4me3_269_0.530

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Summary 

Alignment 

Name STAT3STAT3_Q3_M01220_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.49327e-06
E-value 0.0160458
q-value 0.0316044
Overlap 8
Offset 3
Orientation Normal
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Matches to Query: 7_e_k4me3_77_0.472

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Matches to Query: 8_e_k36me3_129_0.472

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Matches to Query: 9_e_k4me3_280_0.473

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Matches to Query: 10_e_k27ac_22_0.527

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Matches to Query: 11_h_k36me3_2_0.474

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Matches to Query: 12_h_k27me3_14_0.476

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Matches to Query: 13_h_k9me3_1_0.524

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Matches to Query: 14_e_k27me3_70_0.476

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Matches to Query: 15_e_k27me3_321_0.476

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Matches to Query: 16_e_k27ac_326_0.523

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Summary 

Alignment 

Name UGP2_3_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.16991e-05
E-value 0.0341731
q-value 0.0683463
Overlap 6
Offset -3
Orientation Normal
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Matches to Query: 17_e_k27ac_360_0.522

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Matches to Query: 18_e_k27ac_399_0.522

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Summary 

Alignment 

Name ALX4_01_M00619_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.46518e-05
E-value 0.0427978
q-value 0.0855956
Overlap 9
Offset -1
Orientation Normal
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Matches to Query: 19_h_k36me3_3_0.478

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Summary 

Alignment 

Name MYF_01_M01302_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.38712e-06
E-value 0.0157358
q-value 0.00796136
Overlap 10
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name Myf_MA0055.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.38712e-06
E-value 0.0157358
q-value 0.00796136
Overlap 10
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name Ascl2_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.82422e-06
E-value 0.0199336
q-value 0.00796136
Overlap 12
Offset 3
Orientation Normal
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Matches to Query: 20_e_k27ac_204_0.522

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Matches to Query: 21_e_k27ac_197_0.520

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Matches to Query: 22_e_k9me3_299_0.519

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Matches to Query: 23_e_k4me3_180_0.483

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Matches to Query: 24_e_k9me3_7_0.516

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Matches to Query: 25_e_k27ac_406_0.516

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Summary 

Alignment 

Name Mafk_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.58716e-06
E-value 0.0250831
q-value 0.0501662
Overlap 9
Offset 2
Orientation Normal
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Matches to Query: 26_h_k9me3_19_0.484

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Matches to Query: 27_e_k27me3_277_0.487

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Matches to Query: 28_e_k9me3_315_0.488

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Matches to Query: 29_h_k4me3_32_0.490

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Matches to Query: 30_h_k4me3_24_0.494

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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 75.734 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.