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_k27ac_16_0.411
GCGGGGGGGG
8 MAZR_01_M00491_T,  Zfp281_primary_SCI09_U,  SP1SP3_Q4_M01219_T,  ZNF219_01_M01122_T,  SP1_MA0079.2_J,  WT1_Q6_M01118_T,  Zfp740_primary_SCI09_U,  Egr1_primary_SCI09_U
2_e_k36me3_31_0.586
GATCATCATC
0
3_e_k27me3_5_0.418
CCCGCGCCC
1 ZF5_01_M00716_T
4_e_k27ac_150_0.427
CTAATTGGC
25 PRRX1_16_H,  Dr_MA0188.1_J,  LHX8_01_M01440_T,  Lhx8_2247.2_Cell08_U,  Nobox_MA0125.1_J,  LHX61_02_M01422_T,  Lhx4_1719.2_Cell08_U,  Lhx6_3432.1_Cell08_U,  EVX2_01_M01386_T,  Evx2_2645.3_Cell08_U
5_e_k4me3_78_0.428
ACGCCCCCT
2 btd_MA0443.1_J,  Sp4_primary_SCI09_U
6_e_k36me3_144_0.571
ACAGGTGAG
1 sna_MA0086.1_J
7_h_k4me3_3_0.430
AAACGCGA
0
8_e_k4me3_72_0.433
GGCGGGGAA
2 ZMS1_01_M01617_T,  ZMS1_MA0441.1_J
9_e_k36me3_244_0.566
AACATGGAC
0
10_h_k27ac_22_0.438
GCCGGAAA
0
11_e_k36me3_357_0.560
CAGTGGTACT
0
12_e_k27ac_64_0.443
AAACAAAACCC
0
13_h_k36me3_4_0.556
GATGACCTCCAC
0
14_e_k36me3_215_0.556
CAGGTACTG
0
15_e_k36me3_291_0.556
CACCAGGC
0
16_e_k4me3_86_0.447
GAACGCGGC
0
17_e_k36me3_138_0.553
ACATCGTACC
0
18_e_k27ac_459_0.448
GGAAAATCC
1 NFAT1_Q6_M01281_T
19_e_k4me3_15_0.448
CGGGGACGCG
0
20_e_k36me3_256_0.552
AGGCAGATGA
0
21_e_k36me3_159_0.551
ACCACATCAG
1 AML1_Q6_M00751_T
22_e_k36me3_102_0.551
GGCTCACAC
0
23_e_k36me3_280_0.549
GCTGGACACG
0
24_e_k27me3_262_0.548
GAACACGT
0
25_h_k27ac_19_0.453
ACATTCCGCG
0
26_e_k36me3_84_0.547
GCACAGGCTGT
0
27_e_k36me3_296_0.546
TACCGCACCT
0
28_e_k36me3_162_0.546
GCCAGCACTTA
0
29_e_k4me3_291_0.454
AACGAATGA
0
30_e_k36me3_310_0.543
TCACTGTCA
0
31_e_k36me3_303_0.541
ACCTTGGCC
0
32_e_k36me3_318_0.540
AGGGTGGTAC
0
33_h_k27me3_24_0.462
GAGGATTAAA
1 Ptx1_MA0201.1_J
34_e_k27ac_173_0.462
AAATGCAGCC
0
35_h_k4me3_24_0.464
TTCGAAACCGAA
1 Irf4_primary_SCI09_U
36_e_k27ac_145_0.466
CCCTATTGTC
0
37_h_k9me3_1_0.534
TCACACTGGAGA
0
38_e_k27ac_482_0.469
AATTAGGG
0
39_h_k9me3_7_0.469
AGCGGCAAGG
0
40_e_k9me3_489_0.530
ACCATAGCA
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 43

Matches to Query: 1_h_k27ac_16_0.411

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Summary 

Alignment 

Name MAZR_01_M00491_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.11557e-07
E-value 0.000910059
q-value 0.00179858
Overlap 10
Offset 0
Orientation Normal
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Summary 

Alignment 

Name Zfp281_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.39714e-06
E-value 0.00700204
q-value 0.00465776
Overlap 10
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name SP1SP3_Q4_M01219_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.42051e-06
E-value 0.00707032
q-value 0.00465776
Overlap 10
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name ZNF219_01_M01122_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.37845e-06
E-value 0.00986845
q-value 0.00487583
Overlap 10
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name SP1_MA0079.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.82172e-06
E-value 0.0140842
q-value 0.00548162
Overlap 10
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name WT1_Q6_M01118_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.6973e-06
E-value 0.0166418
q-value 0.00548162
Overlap 9
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name Zfp740_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.44346e-06
E-value 0.0246633
q-value 0.00696327
Overlap 10
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name Egr1_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.75971e-06
E-value 0.0285081
q-value 0.00704268
Overlap 10
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 2_e_k36me3_31_0.586

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Matches to Query: 3_e_k27me3_5_0.418

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Summary 

Alignment 

Name ZF5_01_M00716_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.98925e-06
E-value 0.0145736
q-value 0.0288775
Overlap 8
Offset -1
Orientation Reverse Complement
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Matches to Query: 4_e_k27ac_150_0.427

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Summary 

Alignment 

Name PRRX1_16_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.58638e-08
E-value 0.000192388
q-value 0.000354095
Overlap 7
Offset -1
Orientation Normal
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Summary 

Alignment 

Name Dr_MA0188.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.94559e-07
E-value 0.000568307
q-value 0.000522991
Overlap 7
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name LHX8_01_M01440_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.06364e-06
E-value 0.0060279
q-value 0.0017758
Overlap 9
Offset 4
Orientation Normal
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Summary 

Alignment 

Name Lhx8_2247.2_Cell08_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.06364e-06
E-value 0.0060279
q-value 0.0017758
Overlap 9
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Nobox_MA0125.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.20635e-06
E-value 0.00936575
q-value 0.0017758
Overlap 8
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name LHX61_02_M01422_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.21175e-06
E-value 0.00938151
q-value 0.0017758
Overlap 9
Offset 4
Orientation Normal
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Summary 

Alignment 

Name Lhx4_1719.2_Cell08_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.21175e-06
E-value 0.00938151
q-value 0.0017758
Overlap 9
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Lhx6_3432.1_Cell08_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.21175e-06
E-value 0.00938151
q-value 0.0017758
Overlap 9
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name EVX2_01_M01386_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.68789e-06
E-value 0.0107723
q-value 0.0017758
Overlap 9
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name Evx2_2645.3_Cell08_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.68789e-06
E-value 0.0107723
q-value 0.0017758
Overlap 9
Offset 4
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name LHX4_01_M01421_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.68789e-06
E-value 0.0107723
q-value 0.0017758
Overlap 9
Offset 4
Orientation Normal
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Summary 

Alignment 

Name CHX10_01_M00437_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.28495e-06
E-value 0.0154373
q-value 0.0017758
Overlap 9
Offset 2
Orientation Normal
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Summary 

Alignment 

Name Prrx2_3072.1_Cell08_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.20519e-06
E-value 0.0181253
q-value 0.0017758
Overlap 9
Offset 5
Orientation Reverse Complement
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Summary 

Alignment 

Name S8_02_M01376_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.20519e-06
E-value 0.0181253
q-value 0.0017758
Overlap 9
Offset 5
Orientation Reverse Complement
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Summary 

Alignment 

Name OdsH_MA0198.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.77268e-06
E-value 0.019783
q-value 0.0017758
Overlap 7
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name OdsH_MA0455.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.77268e-06
E-value 0.019783
q-value 0.0017758
Overlap 7
Offset 0
Orientation Normal
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Summary 

Alignment 

Name GBX2_01_M01382_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.92741e-06
E-value 0.023156
q-value 0.0017758
Overlap 9
Offset 4
Orientation Normal
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Summary 

Alignment 

Name Gbx2_3110.1_Cell08_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.92741e-06
E-value 0.023156
q-value 0.0017758
Overlap 9
Offset 4
Orientation Normal
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Summary 

Alignment 

Name NKX11_01_M01334_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.92741e-06
E-value 0.023156
q-value 0.0017758
Overlap 9
Offset 5
Orientation Reverse Complement
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Summary 

Alignment 

Name Nkx1-1_3856.3_Cell08_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.92741e-06
E-value 0.023156
q-value 0.0017758
Overlap 9
Offset 5
Orientation Reverse Complement
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Summary 

Alignment 

Name Hoxd1_3448.1_Cell08_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.25542e-05
E-value 0.0366707
q-value 0.00232736
Overlap 9
Offset 4
Orientation Normal
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Summary 

Alignment 

Name Pdx1_MA0132.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.32475e-05
E-value 0.038696
q-value 0.00235209
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name Prrx2_MA0075.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.36751e-05
E-value 0.0399449
q-value 0.00235209
Overlap 5
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name HOXD1_01_M01448_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.40001e-05
E-value 0.0408943
q-value 0.00235209
Overlap 9
Offset 4
Orientation Normal
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Summary 

Alignment 

Name CG9876_MA0184.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.61524e-05
E-value 0.0471811
q-value 0.00263145
Overlap 7
Offset 0
Orientation Normal
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Matches to Query: 5_e_k4me3_78_0.428

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Summary 

Alignment 

Name btd_MA0443.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.58122e-06
E-value 0.0104608
q-value 0.0208611
Overlap 9
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name Sp4_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.44494e-06
E-value 0.0217467
q-value 0.0216839
Overlap 9
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 6_e_k36me3_144_0.571

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Summary 

Alignment 

Name sna_MA0086.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.42049e-06
E-value 0.0129123
q-value 0.0257371
Overlap 6
Offset -1
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 7_h_k4me3_3_0.430

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Matches to Query: 8_e_k4me3_72_0.433

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Summary 

Alignment 

Name ZMS1_01_M01617_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.01468e-06
E-value 0.00588487
q-value 0.0116669
Overlap 8
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name ZMS1_MA0441.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.23748e-05
E-value 0.0361468
q-value 0.035831
Overlap 9
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 9_e_k36me3_244_0.566

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Matches to Query: 10_h_k27ac_22_0.438

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Matches to Query: 11_e_k36me3_357_0.560

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Matches to Query: 12_e_k27ac_64_0.443

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Matches to Query: 13_h_k36me3_4_0.556

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Matches to Query: 14_e_k36me3_215_0.556

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Matches to Query: 15_e_k36me3_291_0.556

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Matches to Query: 16_e_k4me3_86_0.447

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Matches to Query: 17_e_k36me3_138_0.553

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Matches to Query: 18_e_k27ac_459_0.448

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Summary 

Alignment 

Name NFAT1_Q6_M01281_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.62135e-05
E-value 0.0473598
q-value 0.0536057
Overlap 6
Offset 0
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 19_e_k4me3_15_0.448

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Matches to Query: 20_e_k36me3_256_0.552

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Matches to Query: 21_e_k36me3_159_0.551

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Summary 

Alignment 

Name AML1_Q6_M00751_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.34657e-05
E-value 0.0393332
q-value 0.0786664
Overlap 6
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 22_e_k36me3_102_0.551

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Matches to Query: 23_e_k36me3_280_0.549

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Matches to Query: 24_e_k27me3_262_0.548

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Matches to Query: 25_h_k27ac_19_0.453

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Matches to Query: 26_e_k36me3_84_0.547

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Matches to Query: 27_e_k36me3_296_0.546

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Matches to Query: 28_e_k36me3_162_0.546

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Matches to Query: 29_e_k4me3_291_0.454

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Matches to Query: 30_e_k36me3_310_0.543

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Matches to Query: 31_e_k36me3_303_0.541

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Matches to Query: 32_e_k36me3_318_0.540

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Matches to Query: 33_h_k27me3_24_0.462

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Summary 

Alignment 

Name Ptx1_MA0201.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.18045e-05
E-value 0.0344809
q-value 0.0689049
Overlap 7
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 34_e_k27ac_173_0.462

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Matches to Query: 35_h_k4me3_24_0.464

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Summary 

Alignment 

Name Irf4_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.32519e-05
E-value 0.0387087
q-value 0.0774173
Overlap 12
Offset 3
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 36_e_k27ac_145_0.466

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Matches to Query: 37_h_k9me3_1_0.534

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Matches to Query: 38_e_k27ac_482_0.469

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Matches to Query: 39_h_k9me3_7_0.469

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Matches to Query: 40_e_k9me3_489_0.530

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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 103.313 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.