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_1_0.606
GATGAGTCATTC
20 Jundm2_secondary_SCI09_U,  GCN4_MA0303.1_J,  Gcn4_GR09_U,  GCN4_02_M01555_T,  AP1_01_M00517_T,  GCN4_01_M00038_T,  AP1_C_M00199_T,  AP1_Q6_M00174_T,  Fos_MA0099.1_J,  FRA1_Q5_M01267_T
2_e_k27ac_104_0.556
ACAGGAAAT
2 FEV_MA0156.1_J,  ESE1_Q3_M01214_T
3_e_k4me1_1_0.446
CACGTGCACC
7 CBF1_02_M01699_T,  Mycn_MA0104.1_J,  Arnt_MA0004.1_J,  USF1_7_H,  MYC_Q2_M00799_T,  PHO4_02_M01564_T,  Pho4_GR09_U
4_e_k27ac_36_0.550
GACTCATGCT
1 BACH1_01_M00495_T
5_h_k36me3_5_0.451
GACAGGTAAG
2 AREB6_01_M00412_T,  at_AC_acceptor_SD0001.1_J
6_h_k4me1_4_0.543
GTTAATGATTAA
6 HNF1_Q6_M00790_T,  HNF1_C_M00206_T,  HNF1_01_M00132_T,  HNF1A_MA0046.1_J,  HNF1_Q6_01_M01011_T,  HNF1B_MA0153.1_J
7_e_k27me3_37_0.542
CTCTCTCTC
0
8_h_k36me3_24_0.463
GATGCCGTAC
0
9_e_k27ac_123_0.536
GAGTCAGAC
0
10_h_k27ac_16_0.533
AAAGGCCT
0
11_e_k4me1_150_0.469
GCTGTCACC
0
12_e_k36me3_96_0.469
GATGCCGACGAT
1 MSRA_2_H
13_e_k27ac_332_0.530
CTGAATTCCG
0
14_e_k4me3_210_0.472
AAGTACCGG
0
15_e_k27ac_357_0.528
GAAATTCCA
0
16_e_k36me3_253_0.473
AGTATCGT
0
17_e_k4me1_15_0.475
GTGCGTGCA
0
18_e_k27ac_82_0.524
AGAAACCACAG
4 MET28_01_M01674_T,  MET28_MA0332.1_J,  RUNX1_MA0002.2_J,  COREBINDINGFACTOR_Q6_M00722_T
19_e_k4me3_228_0.522
CGGAAAGAA
0
20_h_k9me3_18_0.479
GGTGATCAGTGC
0
21_e_k36me3_121_0.479
GCCACCACC
0
22_h_k36me3_15_0.479
GCACCGAGGACC
0
23_h_k9me3_11_0.479
TTATGTGAAGAT
0
24_e_k27ac_89_0.518
ACTGAGGCCCG
0
25_e_k36me3_185_0.482
GCCATGGCC
0
26_e_k4me3_19_0.517
CACTTCCGGG
16 GADP_01_M01258_T,  GABP_B_M00341_T,  GABPA_MA0062.2_J,  E74A_01_M00016_T,  ELF2_10_H,  ETV4_13_H,  Eip74EF_MA0026.1_J,  EHF_01_M01751_T,  Ehf_primary_SCI09_U,  GABPA_MA0062.1_J
27_e_k36me3_243_0.483
ACGATGTGA
0
28_h_k36me3_29_0.483
CGGTCCAG
0
29_e_k27me3_342_0.517
GTTTGGGGA
0
30_e_k36me3_133_0.484
GGCAACATAT
1 P4HB_2_H
31_h_k9me3_26_0.485
AGGTGATGTAAC
0
32_e_k36me3_271_0.486
TATACAACG
0
33_e_k4me3_179_0.487
TATCGCTGA
0
34_h_k4me3_35_0.513
GCGTTCTCAGAA
0
35_e_k9me3_304_0.507
ATTCATAGG
0
36_e_k4me3_351_0.506
ACGGAGAAA
0
37_h_k9me3_9_0.495
ACATCACAAAGA
0
38_e_k27me3_189_0.504
CGAGCGCTC
0
39_e_k36me3_400_0.497
ACAGCTACC
0
40_h_k9me3_6_0.502
GCTTCTGTCTAG
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 59

Matches to Query: 1_h_k4me1_1_0.606

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Summary 

Alignment 

Name Jundm2_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.68321e-12
E-value 2.82846e-08
q-value 5.61139e-08
Overlap 12
Offset 3
Orientation Normal
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Summary 

Alignment 

Name GCN4_MA0303.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.12044e-11
E-value 1.20358e-07
q-value 7.95927e-08
Overlap 12
Offset 5
Orientation Normal
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Summary 

Alignment 

Name Gcn4_GR09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.12044e-11
E-value 1.20358e-07
q-value 7.95927e-08
Overlap 12
Offset 5
Orientation Normal
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Summary 

Alignment 

Name GCN4_02_M01555_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.8971e-11
E-value 1.72254e-07
q-value 8.54338e-08
Overlap 12
Offset 5
Orientation Normal
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Summary 

Alignment 

Name AP1_01_M00517_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.85055e-09
E-value 2.00105e-05
q-value 4.41098e-06
Overlap 12
Offset 1
Orientation Normal
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Summary 

Alignment 

Name GCN4_01_M00038_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.7869e-08
E-value 5.21955e-05
q-value 1.03551e-05
Overlap 12
Offset 8
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_C_M00199_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.34773e-07
E-value 0.000393672
q-value 6.00775e-05
Overlap 9
Offset -1
Orientation Normal
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Summary 

Alignment 

Name AP1_Q6_M00174_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.4676e-07
E-value 0.000428685
q-value 6.07477e-05
Overlap 11
Offset 0
Orientation Normal
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Summary 

Alignment 

Name Fos_MA0099.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.06805e-07
E-value 0.00235668
q-value 0.000292213
Overlap 8
Offset -1
Orientation Normal
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Summary 

Alignment 

Name FRA1_Q5_M01267_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.43298e-06
E-value 0.00418573
q-value 0.000461337
Overlap 8
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_Q4_01_M00926_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.43994e-06
E-value 0.00712708
q-value 0.000706971
Overlap 8
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name BACH1_01_M00495_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.34786e-06
E-value 0.00977909
q-value 0.000881852
Overlap 12
Offset 2
Orientation Normal
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Summary 

Alignment 

Name AP1_Q6_01_M00925_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.73732e-06
E-value 0.0109167
q-value 0.000941638
Overlap 9
Offset -1
Orientation Normal
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Summary 

Alignment 

Name GCN4_Q2_M01713_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.45597e-06
E-value 0.0130159
q-value 0.000993164
Overlap 11
Offset 0
Orientation Normal
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Summary 

Alignment 

Name GCN4_C_M00204_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.87019e-06
E-value 0.0142258
q-value 0.00100183
Overlap 9
Offset 1
Orientation Normal
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Summary 

Alignment 

Name AP1_Q4_M00188_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.0135e-06
E-value 0.0146444
q-value 0.00100183
Overlap 11
Offset 0
Orientation Normal
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Summary 

Alignment 

Name BACH2_01_M00490_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.90853e-06
E-value 0.0231008
q-value 0.00152766
Overlap 11
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_MA0099.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.27802e-06
E-value 0.0241801
q-value 0.00154745
Overlap 7
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name NFE2_01_M00037_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.21823e-05
E-value 0.0355846
q-value 0.00201704
Overlap 10
Offset 1
Orientation Normal
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Summary 

Alignment 

Name AP1_Q2_M00173_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.35247e-05
E-value 0.0395058
q-value 0.00211826
Overlap 11
Offset 0
Orientation Normal
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Matches to Query: 2_e_k27ac_104_0.556

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Summary 

Alignment 

Name FEV_MA0156.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.17347e-06
E-value 0.00634871
q-value 0.0125974
Overlap 8
Offset -1
Orientation Normal
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Summary 

Alignment 

Name ESE1_Q3_M01214_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.1876e-05
E-value 0.0346897
q-value 0.0344164
Overlap 9
Offset 0
Orientation Reverse Complement
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Matches to Query: 3_e_k4me1_1_0.446

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Summary 

Alignment 

Name CBF1_02_M01699_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.8964e-07
E-value 0.00113814
q-value 0.000737692
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name Mycn_MA0104.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.8964e-07
E-value 0.00113814
q-value 0.000737692
Overlap 6
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name Arnt_MA0004.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.01194e-06
E-value 0.00879786
q-value 0.00342144
Overlap 6
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name USF1_7_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.24336e-06
E-value 0.0123948
q-value 0.00344306
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MYC_Q2_M00799_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.24664e-06
E-value 0.0153254
q-value 0.0034674
Overlap 7
Offset 0
Orientation Normal
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Summary 

Alignment 

Name PHO4_02_M01564_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.70266e-05
E-value 0.0497346
q-value 0.00788862
Overlap 10
Offset 7
Orientation Normal
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Summary 

Alignment 

Name Pho4_GR09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.70266e-05
E-value 0.0497346
q-value 0.00788862
Overlap 10
Offset 7
Orientation Normal
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Matches to Query: 4_e_k27ac_36_0.550

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Summary 

Alignment 

Name BACH1_01_M00495_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.60871e-05
E-value 0.0469905
q-value 0.0526525
Overlap 10
Offset 5
Orientation Reverse Complement
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Matches to Query: 5_h_k36me3_5_0.451

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Summary 

Alignment 

Name AREB6_01_M00412_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.66685e-06
E-value 0.00778988
q-value 0.0155798
Overlap 10
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name at_AC_acceptor_SD0001.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.84663e-06
E-value 0.02292
q-value 0.02292
Overlap 8
Offset -2
Orientation Normal
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Matches to Query: 6_h_k4me1_4_0.543

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Summary 

Alignment 

Name HNF1_Q6_M00790_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.6426e-07
E-value 0.000479803
q-value 0.000365862
Overlap 12
Offset 2
Orientation Normal
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Summary 

Alignment 

Name HNF1_C_M00206_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.70276e-07
E-value 0.000497377
q-value 0.000365862
Overlap 12
Offset 1
Orientation Normal
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Summary 

Alignment 

Name HNF1_01_M00132_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.95525e-07
E-value 0.000571127
q-value 0.000365862
Overlap 12
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name HNF1A_MA0046.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.64486e-07
E-value 0.000772562
q-value 0.000371175
Overlap 12
Offset 1
Orientation Normal
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Summary 

Alignment 

Name HNF1_Q6_01_M01011_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.55463e-07
E-value 0.00279091
q-value 0.000670441
Overlap 12
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name HNF1B_MA0153.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.58481e-06
E-value 0.00462923
q-value 0.000840472
Overlap 12
Offset 0
Orientation Reverse Complement
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Matches to Query: 7_e_k27me3_37_0.542

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Matches to Query: 8_h_k36me3_24_0.463

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Matches to Query: 9_e_k27ac_123_0.536

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Matches to Query: 10_h_k27ac_16_0.533

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Matches to Query: 11_e_k4me1_150_0.469

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Matches to Query: 12_e_k36me3_96_0.469

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Summary 

Alignment 

Name MSRA_2_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.76115e-06
E-value 0.00806533
q-value 0.0161307
Overlap 6
Offset -6
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 13_e_k27ac_332_0.530

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Matches to Query: 14_e_k4me3_210_0.472

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Matches to Query: 15_e_k27ac_357_0.528

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Matches to Query: 16_e_k36me3_253_0.473

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Matches to Query: 17_e_k4me1_15_0.475

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Matches to Query: 18_e_k27ac_82_0.524

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Summary 

Alignment 

Name MET28_01_M01674_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.12286e-06
E-value 0.0120429
q-value 0.0120429
Overlap 6
Offset -5
Orientation Reverse Complement
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Summary 

Alignment 

Name MET28_MA0332.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.12286e-06
E-value 0.0120429
q-value 0.0120429
Overlap 6
Offset -5
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name RUNX1_MA0002.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.23884e-06
E-value 0.0182236
q-value 0.0121491
Overlap 9
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name COREBINDINGFACTOR_Q6_M00722_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.19417e-05
E-value 0.0348816
q-value 0.0174408
Overlap 8
Offset -2
Orientation Reverse Complement
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Matches to Query: 19_e_k4me3_228_0.522

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Matches to Query: 20_h_k9me3_18_0.479

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Matches to Query: 21_e_k36me3_121_0.479

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Matches to Query: 22_h_k36me3_15_0.479

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Matches to Query: 23_h_k9me3_11_0.479

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Matches to Query: 24_e_k27ac_89_0.518

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Matches to Query: 25_e_k36me3_185_0.482

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Matches to Query: 26_e_k4me3_19_0.517

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Summary 

Alignment 

Name GADP_01_M01258_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.0676e-09
E-value 2.64865e-05
q-value 5.21638e-05
Overlap 10
Offset 0
Orientation Normal
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Summary 

Alignment 

Name GABP_B_M00341_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.23418e-08
E-value 6.52605e-05
q-value 6.42636e-05
Overlap 10
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GABPA_MA0062.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.53944e-07
E-value 0.000449671
q-value 0.000295201
Overlap 9
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name E74A_01_M00016_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.84975e-07
E-value 0.00229291
q-value 0.00112894
Overlap 10
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ELF2_10_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.53769e-06
E-value 0.00449159
q-value 0.00172414
Overlap 7
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name ETV4_13_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.79824e-06
E-value 0.00525267
q-value 0.00172414
Overlap 7
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name Eip74EF_MA0026.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.38725e-06
E-value 0.00697317
q-value 0.0019619
Overlap 7
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name EHF_01_M01751_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.88835e-06
E-value 0.00843687
q-value 0.002077
Overlap 9
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name Ehf_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.61308e-06
E-value 0.0105538
q-value 0.00230947
Overlap 10
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name GABPA_MA0062.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.77828e-06
E-value 0.0139573
q-value 0.00249894
Overlap 10
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name NRF2_01_M00108_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.77828e-06
E-value 0.0139573
q-value 0.00249894
Overlap 10
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name FLI1_Q6_M01208_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.40526e-06
E-value 0.0157888
q-value 0.00259127
Overlap 9
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name Elf2_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.10984e-05
E-value 0.0324184
q-value 0.00491127
Overlap 10
Offset 3
Orientation Normal
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Summary 

Alignment 

Name Ehf_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.37008e-05
E-value 0.04002
q-value 0.00545073
Overlap 10
Offset 4
Orientation Normal
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Summary 

Alignment 

Name Elf4_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.42125e-05
E-value 0.0415146
q-value 0.00545073
Overlap 10
Offset 3
Orientation Normal
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Summary 

Alignment 

Name CETS1P54_01_M00032_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.64625e-05
E-value 0.0480869
q-value 0.00591904
Overlap 10
Offset 0
Orientation Reverse Complement
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Matches to Query: 27_e_k36me3_243_0.483

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Matches to Query: 28_h_k36me3_29_0.483

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Matches to Query: 29_e_k27me3_342_0.517

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Matches to Query: 30_e_k36me3_133_0.484

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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
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Matches to Query: 31_h_k9me3_26_0.485

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Matches to Query: 32_e_k36me3_271_0.486

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Matches to Query: 33_e_k4me3_179_0.487

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Matches to Query: 34_h_k4me3_35_0.513

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Matches to Query: 35_e_k9me3_304_0.507

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Matches to Query: 36_e_k4me3_351_0.506

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Matches to Query: 37_h_k9me3_9_0.495

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Matches to Query: 38_e_k27me3_189_0.504

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Matches to Query: 39_e_k36me3_400_0.497

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Matches to Query: 40_h_k9me3_6_0.502

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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 116.875 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.