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-msc_0.568
TGACTCATCA
18 AP1_01_M00517_T,  Jundm2_secondary_SCI09_U,  GCN4_02_M01555_T,  GCN4_MA0303.1_J,  Gcn4_GR09_U,  AP1_C_M00199_T,  FRA1_Q5_M01267_T,  AP1_Q4_01_M00926_T,  Fos_MA0099.1_J,  GCN4_01_M00038_T
2_h_k4me1-msc_0.563
TTAATCATTAAC
6 HNF1_C_M00206_T,  HNF1_Q6_M00790_T,  HNF1_01_M00132_T,  HNF1A_MA0046.1_J,  HNF1_Q6_01_M01011_T,  HNF1B_MA0153.1_J
3_e_k4me1-msc_0.560
CAGCACAGCC
0
4_h_k4me1-msc_0.559
CCGTGCAG
0
5_e_k4me1-msc_0.552
GCCAGGCCAC
0
6_e_k4me1-msc_0.549
ACAGCCACC
0
7_h_k4me1-h1_0.547
GGGGGAAA
0
8_e_k4me1-msc_0.546
GTCGGCTGC
0
9_e_k4me1-msc_0.542
CGCTGCTGGA
0
10_e_k4me1-msc_0.541
AGGCCACACC
0
11_e_k4me1-msc_0.538
AGCACTGGCT
0
12_e_k4me1-msc_0.536
AGCAGCCTC
0
13_h_k4me1-msc_0.535
CACCGAGGGC
0
14_e_k4me1-msc_0.534
CCGCACCAA
0
15_e_k4me1-h1_0.534
GCAAATTCT
0
16_e_k4me1-msc_0.534
CGGGTGTCA
0
17_e_k4me1-h1_0.534
ATTCTACCC
0
18_h_k4me1-msc_0.533
TTTCGGAAAA
1 HNRPA1_7_H
19_e_k4me1-h1_0.533
CGTTAGCGA
0
20_e_k4me1-msc_0.532
CCTGGGACATG
0
21_e_k4me1-h1_0.531
GCATTGTTA
0
22_e_k4me1-msc_0.531
CATGAGAGC
0
23_e_k4me1-h1_0.530
AACAAAGGA
5 SOX4_01_M01308_T,  Sox11_primary_SCI09_U,  Sox4_primary_SCI09_U,  D_MA00445.1_J,  SMAD1_01_M01590_T
24_e_k4me1-msc_0.529
ACAGCAGTG
0
25_e_k4me1-msc_0.529
CTGTGAAGC
0
26_e_k4me1-msc_0.528
CACACATGG
0
27_e_k4me1-h1_0.528
GAATCTGAA
0
28_e_k4me1-h1_0.528
AAATGGGGA
0
29_e_k4me1-msc_0.527
GCAGGATGCA
0
30_e_k4me1-h1_0.527
GGTAGTGTAA
0
31_e_k4me1-msc_0.527
ACACAGATGG
0
32_e_k4me1-msc_0.526
AAATATTTCA
0
33_e_k4me1-h1_0.526
AAATCCCCT
0
34_e_k4me1-msc_0.526
CACTGAACA
0
35_e_k4me1-msc_0.525
CAAGGGCAGT
0
36_e_k4me1-msc_0.525
CGGGCCACATTCC
0
37_h_k4me1-msc_0.525
TATTTAAA
0
38_e_k4me1-h1_0.524
TATTACCC
0
39_e_k4me1-msc_0.524
GCCACATCA
0
40_e_k4me1-msc_0.524
AGGTCTGCA
0
41_e_k4me1-msc_0.524
AGATGCCAT
0
42_e_k4me1-h1_0.524
ACAGTAGGAG
0
43_e_k4me1-msc_0.524
CCCGTGAGC
0
44_e_k4me1-msc_0.524
AACACGTCA
0
45_e_k4me1-h1_0.523
GGAGGATTA
0
46_e_k4me1-msc_0.522
TGACTGGAC
0
47_e_k4me1-h1_0.522
AATAACTGG
0
48_e_k4me1-h1_0.522
CCCGTATCT
0
49_e_k4me1-msc_0.522
GACCCCGCT
0
50_h_k4me1-h1_0.521
GAAAGCTA
0
51_h_k4me1-h1_0.521
GCATTTAGCA
1 MRPS25_4_H
52_e_k4me1-msc_0.520
ACAGTGAAG
0
53_e_k4me1-h1_0.520
CACTTACAG
0
54_e_k4me1-h1_0.520
CAACCGATA
0
55_e_k4me1-h1_0.520
CATTACGAC
0
56_e_k4me1-h1_0.520
CCCTGATTTC
0
57_e_k4me1-h1_0.519
CGATTGGTA
0
58_e_k4me1-msc_0.519
AAAATAACGTA
0
59_e_k4me1-h1_0.519
AGATGCGTCT
0
60_e_k4me1-h1_0.517
TAGAGGACA
0
61_e_k4me1-h1_0.517
GAAGATAAA
0
62_e_k4me1-h1_0.517
GGACGCTA
0
63_e_k4me1-h1_0.516
GAATGAGCA
0
64_e_k4me1-msc_0.516
AACAGAAAC
0
65_e_k4me1-h1_0.515
CCCCCACCA
0
66_e_k4me1-h1_0.515
AGCTGGGGAT
1 FHL2_6_H
67_e_k4me1-h1_0.514
ATCTTTAGC
0
68_e_k4me1-h1_0.512
ACATGAATAC
1 BAT4_2_H
69_e_k4me1-h1_0.508
CAAAGTGTC
0
70_e_k4me1-h1_0.503
AAAACGTGGC
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 33

Matches to Query: 1_h_k4me1-msc_0.568

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Summary 

Alignment 

Name AP1_01_M00517_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.34457e-10
E-value 1.26905e-06
q-value 2.51854e-06
Overlap 10
Offset 3
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Jundm2_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.69847e-09
E-value 1.08032e-05
q-value 4.59428e-06
Overlap 10
Offset 5
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GCN4_02_M01555_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.41102e-09
E-value 1.28846e-05
q-value 4.59428e-06
Overlap 10
Offset 7
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GCN4_MA0303.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.41102e-09
E-value 1.28846e-05
q-value 4.59428e-06
Overlap 10
Offset 7
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gcn4_GR09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.41102e-09
E-value 1.28846e-05
q-value 4.59428e-06
Overlap 10
Offset 7
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name AP1_C_M00199_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.26268e-07
E-value 0.00036883
q-value 7.31975e-05
Overlap 8
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name FRA1_Q5_M01267_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.60953e-07
E-value 0.00163854
q-value 0.000250141
Overlap 8
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name AP1_Q4_01_M00926_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.46458e-07
E-value 0.0024725
q-value 0.000350493
Overlap 8
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Fos_MA0099.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.0338e-06
E-value 0.00301974
q-value 0.00039953
Overlap 8
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GCN4_01_M00038_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.14174e-06
E-value 0.00333504
q-value 0.000413667
Overlap 10
Offset 10
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name NFE2_01_M00037_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.52212e-06
E-value 0.0044461
q-value 0.000519041
Overlap 10
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name BACH1_01_M00495_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.43125e-06
E-value 0.00710169
q-value 0.000782996
Overlap 10
Offset 4
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name AP1_Q6_M00174_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.64203e-06
E-value 0.00771736
q-value 0.000806094
Overlap 9
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MAF_Q6_01_M00983_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.02383e-06
E-value 0.0146746
q-value 0.00126622
Overlap 10
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name AP1_Q6_01_M00925_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.24421e-06
E-value 0.0153183
q-value 0.00126669
Overlap 8
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name BACH2_01_M00490_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.68008e-06
E-value 0.0165915
q-value 0.00131709
Overlap 9
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name AP1_MA0099.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.04957e-06
E-value 0.0176708
q-value 0.00134882
Overlap 7
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name AP1_Q2_01_M00924_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.02428e-05
E-value 0.0299191
q-value 0.00204749
Overlap 10
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 2_h_k4me1-msc_0.563

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Summary 

Alignment 

Name HNF1_C_M00206_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.88292e-08
E-value 0.00028868
q-value 0.00036562
Overlap 12
Offset 4
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name HNF1_Q6_M00790_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.30432e-07
E-value 0.000380992
q-value 0.00036562
Overlap 12
Offset 4
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HNF1_01_M00132_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.12225e-07
E-value 0.00120411
q-value 0.000601997
Overlap 12
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HNF1A_MA0046.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.36895e-07
E-value 0.00156827
q-value 0.000601997
Overlap 12
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HNF1_Q6_01_M01011_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.70809e-07
E-value 0.00225153
q-value 0.000617339
Overlap 12
Offset 5
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HNF1B_MA0153.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.46413e-05
E-value 0.0427672
q-value 0.00746211
Overlap 12
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 3_e_k4me1-msc_0.560

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Matches to Query: 4_h_k4me1-msc_0.559

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Matches to Query: 5_e_k4me1-msc_0.552

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Matches to Query: 6_e_k4me1-msc_0.549

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Matches to Query: 7_h_k4me1-h1_0.547

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Matches to Query: 8_e_k4me1-msc_0.546

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Matches to Query: 9_e_k4me1-msc_0.542

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Matches to Query: 10_e_k4me1-msc_0.541

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Matches to Query: 11_e_k4me1-msc_0.538

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Matches to Query: 12_e_k4me1-msc_0.536

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Matches to Query: 13_h_k4me1-msc_0.535

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Matches to Query: 14_e_k4me1-msc_0.534

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Matches to Query: 15_e_k4me1-h1_0.534

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Matches to Query: 16_e_k4me1-msc_0.534

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Matches to Query: 17_e_k4me1-h1_0.534

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Matches to Query: 18_h_k4me1-msc_0.533

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Summary 

Alignment 

Name HNRPA1_7_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.30615e-06
E-value 0.0271832
q-value 0.0543498
Overlap 9
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 19_e_k4me1-h1_0.533

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Matches to Query: 20_e_k4me1-msc_0.532

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Matches to Query: 21_e_k4me1-h1_0.531

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Matches to Query: 22_e_k4me1-msc_0.531

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Matches to Query: 23_e_k4me1-h1_0.530

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Summary 

Alignment 

Name SOX4_01_M01308_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.48063e-06
E-value 0.00432493
q-value 0.00688272
Overlap 8
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Sox11_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.36884e-06
E-value 0.00691937
q-value 0.00688272
Overlap 9
Offset 5
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Sox4_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.96671e-06
E-value 0.0232708
q-value 0.0153694
Overlap 9
Offset 5
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name D_MA00445.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.16416e-05
E-value 0.0340052
q-value 0.0153694
Overlap 9
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name SMAD1_01_M01590_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.5522e-05
E-value 0.0453398
q-value 0.0153694
Overlap 9
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 24_e_k4me1-msc_0.529

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Matches to Query: 25_e_k4me1-msc_0.529

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Matches to Query: 26_e_k4me1-msc_0.528

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Matches to Query: 27_e_k4me1-h1_0.528

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Matches to Query: 28_e_k4me1-h1_0.528

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Matches to Query: 29_e_k4me1-msc_0.527

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Matches to Query: 30_e_k4me1-h1_0.527

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Matches to Query: 31_e_k4me1-msc_0.527

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Matches to Query: 32_e_k4me1-msc_0.526

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Matches to Query: 33_e_k4me1-h1_0.526

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Matches to Query: 34_e_k4me1-msc_0.526

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Matches to Query: 35_e_k4me1-msc_0.525

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Matches to Query: 36_e_k4me1-msc_0.525

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Matches to Query: 37_h_k4me1-msc_0.525

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Matches to Query: 38_e_k4me1-h1_0.524

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Matches to Query: 39_e_k4me1-msc_0.524

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Matches to Query: 40_e_k4me1-msc_0.524

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Matches to Query: 41_e_k4me1-msc_0.524

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Matches to Query: 42_e_k4me1-h1_0.524

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Matches to Query: 43_e_k4me1-msc_0.524

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Matches to Query: 44_e_k4me1-msc_0.524

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Matches to Query: 45_e_k4me1-h1_0.523

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Matches to Query: 46_e_k4me1-msc_0.522

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Matches to Query: 47_e_k4me1-h1_0.522

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Matches to Query: 48_e_k4me1-h1_0.522

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Matches to Query: 49_e_k4me1-msc_0.522

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Matches to Query: 50_h_k4me1-h1_0.521

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Matches to Query: 51_h_k4me1-h1_0.521

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Summary 

Alignment 

Name MRPS25_4_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.22455e-06
E-value 0.00649791
q-value 0.0129958
Overlap 9
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 52_e_k4me1-msc_0.520

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Matches to Query: 53_e_k4me1-h1_0.520

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Matches to Query: 54_e_k4me1-h1_0.520

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Matches to Query: 55_e_k4me1-h1_0.520

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Matches to Query: 56_e_k4me1-h1_0.520

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Matches to Query: 57_e_k4me1-h1_0.519

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Matches to Query: 58_e_k4me1-msc_0.519

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Matches to Query: 59_e_k4me1-h1_0.519

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Matches to Query: 60_e_k4me1-h1_0.517

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Matches to Query: 61_e_k4me1-h1_0.517

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Matches to Query: 62_e_k4me1-h1_0.517

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Matches to Query: 63_e_k4me1-h1_0.516

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Matches to Query: 64_e_k4me1-msc_0.516

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Matches to Query: 65_e_k4me1-h1_0.515

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Matches to Query: 66_e_k4me1-h1_0.515

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Summary 

Alignment 

Name FHL2_6_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.56053e-05
E-value 0.045583
q-value 0.0909497
Overlap 8
Offset -1
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 67_e_k4me1-h1_0.514

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Matches to Query: 68_e_k4me1-h1_0.512

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Summary 

Alignment 

Name BAT4_2_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 0
E-value 0
q-value 0
Overlap 5
Offset -4
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 69_e_k4me1-h1_0.508

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Matches to Query: 70_e_k4me1-h1_0.503

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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 168.827 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.