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 

h120-k27ac-28_e_382_0.565
CCTTTGTTA
1 SOX4_01_M01308_T
h1v10msc-k27ac-3_h_k27ac-h1_0.559
TGACAAAGGG
10 SMAD1_01_M01590_T,  NANOG_02_M01247_T,  Sox4_CR09_U,  SOX2_Q6_M01272_T,  Sox4_primary_SCI09_U,  Sox2_MA0143.1_J,  SOX9_Q4_M01284_T,  SOX4_01_M01308_T,  D_MA00445.1_J,  Sox11_primary_SCI09_U
npc17-k27ac-11_e_k27ac_401_0.558
TCTTTGTTA
6 SOX_Q6_M01014_T,  SOX4_01_M01308_T,  Sox4_CR09_U,  Sox4_primary_SCI09_U,  MAT1MC_01_M00275_T,  Sox11_primary_SCI09_U
npc17-k4me3-11_e_k27ac_226_0.379
CACAAAGGG
1 SOX10_MA0442.1_J
npc20-k27ac-15_h_1_0.606
AGCACAAAGGCA
8 SOX9_Q4_M01284_T,  Sox4_primary_SCI09_U,  SMAD1_01_M01590_T,  Sox4_CR09_U,  Sox11_primary_SCI09_U,  NANOG_02_M01247_T,  Sox12_secondary_SCI09_U,  Sox14_secondary_SCI09_U
npc20-k4me1-25_h_1_0.594
CACAAAGGCC
3 SOX9_Q4_M01284_T,  SMAD1_01_M01590_T,  Sox14_secondary_SCI09_U

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiTaipaleCmbned.meme 3764 15

Matches to Query: h120-k27ac-28_e_382_0.565

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Summary 

Alignment 

Name SOX4_01_M01308_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.1329e-05
E-value 0.0802823
q-value 0.0837287
Overlap 8
Offset 0
Orientation Reverse Complement
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Matches to Query: h1v10msc-k27ac-3_h_k27ac-h1_0.559

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Summary 

Alignment 

Name SMAD1_01_M01590_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.57828e-09
E-value 5.94064e-06
q-value 1.18537e-05
Overlap 10
Offset 2
Orientation Normal
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Summary 

Alignment 

Name NANOG_02_M01247_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.34979e-07
E-value 0.00163726
q-value 0.0011254
Overlap 10
Offset 6
Orientation Normal
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Summary 

Alignment 

Name Sox4_CR09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.49526e-07
E-value 0.00169202
q-value 0.0011254
Overlap 10
Offset 2
Orientation Normal
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Summary 

Alignment 

Name SOX2_Q6_M01272_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.19217e-06
E-value 0.0157793
q-value 0.00787137
Overlap 10
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name Sox4_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 7.47344e-06
E-value 0.02813
q-value 0.0109697
Overlap 10
Offset 4
Orientation Normal
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Summary 

Alignment 

Name Sox2_MA0143.1_J
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.0062e-05
E-value 0.0378733
q-value 0.0109697
Overlap 9
Offset 6
Orientation Reverse Complement
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Summary 

Alignment 

Name SOX9_Q4_M01284_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.0224e-05
E-value 0.038483
q-value 0.0109697
Overlap 10
Offset 0
Orientation Normal
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Summary 

Alignment 

Name SOX4_01_M01308_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.28011e-05
E-value 0.0858233
q-value 0.0189723
Overlap 8
Offset -1
Orientation Normal
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Summary 

Alignment 

Name D_MA00445.1_J
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.43922e-05
E-value 0.0918123
q-value 0.0189723
Overlap 10
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name Sox11_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.52608e-05
E-value 0.0950817
q-value 0.0189723
Overlap 10
Offset 4
Orientation Normal
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Matches to Query: npc17-k27ac-11_e_k27ac_401_0.558

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Summary 

Alignment 

Name SOX_Q6_M01014_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.74308e-06
E-value 0.00656094
q-value 0.0131072
Overlap 9
Offset 1
Orientation Normal
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Summary 

Alignment 

Name SOX4_01_M01308_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 5.53735e-06
E-value 0.0208426
q-value 0.0203589
Overlap 8
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name Sox4_CR09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 8.12232e-06
E-value 0.0305724
q-value 0.0203589
Overlap 9
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name Sox4_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.56245e-05
E-value 0.0588106
q-value 0.0293725
Overlap 9
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name MAT1MC_01_M00275_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.2103e-05
E-value 0.0831957
q-value 0.0300025
Overlap 9
Offset 5
Orientation Normal
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Summary 

Alignment 

Name Sox11_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.5203e-05
E-value 0.0948642
q-value 0.0300025
Overlap 9
Offset 4
Orientation Reverse Complement
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Matches to Query: npc17-k4me3-11_e_k27ac_226_0.379

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Summary 

Alignment 

Name SOX10_MA0442.1_J
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.80202e-06
E-value 0.00678282
q-value 0.0135656
Overlap 6
Offset -1
Orientation Reverse Complement
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Matches to Query: npc20-k27ac-15_h_1_0.606

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Summary 

Alignment 

Name SOX9_Q4_M01284_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 3.75192e-07
E-value 0.00141222
q-value 0.0011863
Overlap 11
Offset -1
Orientation Normal
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Summary 

Alignment 

Name Sox4_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.07443e-07
E-value 0.00153361
q-value 0.0011863
Overlap 12
Offset 3
Orientation Normal
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Summary 

Alignment 

Name SMAD1_01_M01590_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 5.51961e-07
E-value 0.00207758
q-value 0.0011863
Overlap 11
Offset 1
Orientation Normal
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Summary 

Alignment 

Name Sox4_CR09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 6.32903e-07
E-value 0.00238225
q-value 0.0011863
Overlap 12
Offset 1
Orientation Normal
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Summary 

Alignment 

Name Sox11_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.1558e-06
E-value 0.00435043
q-value 0.00173312
Overlap 12
Offset 3
Orientation Normal
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Summary 

Alignment 

Name NANOG_02_M01247_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.89496e-06
E-value 0.00713264
q-value 0.00236791
Overlap 12
Offset 5
Orientation Normal
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Summary 

Alignment 

Name Sox12_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.35629e-06
E-value 0.0163971
q-value 0.00466589
Overlap 12
Offset 3
Orientation Normal
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Summary 

Alignment 

Name Sox14_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.29459e-05
E-value 0.0863683
q-value 0.0215046
Overlap 12
Offset 2
Orientation Normal
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Matches to Query: npc20-k4me1-25_h_1_0.594

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Summary 

Alignment 

Name SOX9_Q4_M01284_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 6.14095e-06
E-value 0.0231145
q-value 0.0461836
Overlap 10
Offset 1
Orientation Normal
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Summary 

Alignment 

Name SMAD1_01_M01590_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.88879e-05
E-value 0.0710941
q-value 0.0576171
Overlap 9
Offset 3
Orientation Normal
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Summary 

Alignment 

Name Sox14_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.29837e-05
E-value 0.0865107
q-value 0.0576171
Overlap 10
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [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 21.139 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.