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_e_k36me3_1_0.608
CGCCTGTAA
0
2_e_k36me3_20_0.598
CAAGCGATTC
0
3_e_k36me3_51_0.597
GTGAGCCAC
0
4_e_k36me3_88_0.592
CCAAAGTGC
0
5_e_k36me3_89_0.591
ATCCCAGCA
0
6_e_k36me3_21_0.585
CGTCTCTAC
0
7_e_k36me3_13_0.583
CCACCACGCC
1 ING4_01_M01743_T
8_e_k36me3_16_0.582
GATCGCGCC
0
9_e_k36me3_7_0.580
TCCCGAGTAG
0
10_h_k36me3_1_0.568
TACTTACCTG
2 at_AC_acceptor_SD0001.1_J,  AREB6_01_M00412_T
11_e_k36me3_190_0.564
CTCAGGTGA
2 sna_MA0086.1_J,  RAV1_02_M00344_T
12_e_k36me3_8_0.564
ACGCCCGGC
0
13_h_k9me3_20_0.443
GGGTCCCC
0
14_e_k36me3_183_0.555
ACAGGTGCCT
2 SN_01_M00060_T,  TCF4_03_M01769_T
15_e_k36me3_181_0.554
GCGCTACCAC
1 SNT2_MA0384.1_J
16_e_k36me3_230_0.554
GTGGCATGA
0
17_h_k27me3_15_0.448
TCTCTCTCTCTC
1 Trl_MA0205.1_J
18_e_k36me3_335_0.551
ATACATACC
0
19_e_k36me3_179_0.551
AGCCAGGCA
0
20_e_k36me3_110_0.550
GCGTGTGCC
2 hlh-27_PL0004.1_J,  HLH-27_Cell09_U
21_e_k36me3_115_0.548
CTGTCGCCC
0
22_e_k36me3_139_0.546
CTGTGTTGC
0
23_e_k4me3_56_0.454
CGCGGGGGA
1 PTPMT1_7_H
24_h_k36me3_9_0.545
CAGTGTTACTTG
0
25_e_k36me3_151_0.545
CATGATCCGC
0
26_e_k36me3_135_0.544
AGAGTCTCG
0
27_e_k27me3_27_0.456
CCCGCAGCG
0
28_e_k27ac_175_0.541
CAAACAGGCT
0
29_e_k9me3_158_0.460
GGTGGGGACG
3 YPR022C_01_M01647_T,  MZF1_01_M00083_T,  ALFIN1_Q2_M00479_T
30_e_k36me3_208_0.539
AACGTGGCA
0
31_h_k27me3_9_0.463
TTCGCTCCGA
0
32_e_k9me3_286_0.463
AATATCCCA
0
33_h_k27me3_11_0.464
AACTTTCCTCTC
0
34_h_k27me3_14_0.464
CGATTTGCAA
4 NFIX_2_H,  NMI_8_H,  DGCR8_4_H,  IL24_5_H
35_e_k9me3_25_0.464
ATATTTGGAA
0
36_e_k9me3_320_0.467
CCCCTGACCC
0
37_e_k36me3_365_0.532
CGTCACTGAT
0
38_e_k36me3_334_0.531
ACGTAAGAA
0
39_e_k9me3_50_0.469
AAATATCTTC
0
40_e_k9me3_124_0.470
ACGAAGGGA
0
41_e_k27me3_338_0.470
CCCCAAAT
0
42_e_k27me3_38_0.470
CCCCGGACGC
0
43_e_k27ac_370_0.471
GGTGATTAA
0
44_e_k4me3_276_0.529
TCGTTATC
0
45_e_k4me3_36_0.472
GCGCGGAGA
0
46_h_k4me3_12_0.528
GATTCGAAACTG
0
47_e_k27ac_9_0.473
CCTCCTCCC
1 FPM315_01_M01587_T
48_e_k27ac_266_0.526
ATAGCAGGCTG
0
49_h_k9me3_23_0.474
TTCTTTTGAT
0
50_e_k9me3_385_0.474
GGAAATGCC
2 STAT3_01_M00225_T,  SCMH1_9_H
51_e_k9me3_53_0.474
ATGAATGCA
0
52_e_k4me1_202_0.525
AGCTTGGCAG
0
53_h_k9me3_2_0.475
GAAATCACCCGT
0
54_e_k27me3_35_0.475
TCCGAGCCG
0
55_e_k4me1_36_0.476
ATATGCAGA
0
56_e_k9me3_121_0.477
AAATGTCCAG
0
57_h_k27ac_2_0.522
GATGAGTCATCC
23 AP1_01_M00517_T,  Jundm2_secondary_SCI09_U,  GCN4_02_M01555_T,  GCN4_MA0303.1_J,  Gcn4_GR09_U,  AP1_C_M00199_T,  AP1_Q6_M00174_T,  GCN4_01_M00038_T,  BACH1_01_M00495_T,  FRA1_Q5_M01267_T
58_e_k27me3_312_0.478
GCTGGAAAT
2 H1FX_7_H,  MAGEA8_12_H
59_h_k9me3_28_0.522
GAGTGGAATGGA
0
60_e_k9me3_332_0.479
GCCATAAA
0
61_e_k9me3_85_0.479
CACAAAGAA
0
62_e_k27ac_32_0.484
CTCTGAGCCC
0
63_h_k9me3_25_0.487
TGGTGAAAAA
0
64_e_k27ac_162_0.487
AGGAATTTC
0
65_h_k27me3_25_0.488
CTAATTACGC
2 ro_MA0241.1_J,  CG9876_MA0184.1_J
66_e_k4me1_287_0.512
ACAGAATGT
0
67_e_k27ac_327_0.489
CCTTTGTTCT
7 Sox11_primary_SCI09_U,  SOX4_01_M01308_T,  Sox4_primary_SCI09_U,  Sox4_CR09_U,  SMAD1_01_M01590_T,  D_MA00445.1_J,  NANOG_02_M01247_T
68_h_k4me1_31_0.508
GACACCTTTT
0
69_h_k9me3_3_0.493
TCTCGGCAAGGC
0
70_h_k9me3_5_0.497
GCAGATTCTACA
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 56

Matches to Query: 1_e_k36me3_1_0.608

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Matches to Query: 2_e_k36me3_20_0.598

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Matches to Query: 3_e_k36me3_51_0.597

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Matches to Query: 4_e_k36me3_88_0.592

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Matches to Query: 5_e_k36me3_89_0.591

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Matches to Query: 6_e_k36me3_21_0.585

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Matches to Query: 7_e_k36me3_13_0.583

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Summary 

Alignment 

Name ING4_01_M01743_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.54933e-08
E-value 0.000103676
q-value 0.000207003
Overlap 6
Offset 0
Orientation Normal
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Matches to Query: 8_e_k36me3_16_0.582

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Matches to Query: 9_e_k36me3_7_0.580

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Matches to Query: 10_h_k36me3_1_0.568

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Summary 

Alignment 

Name at_AC_acceptor_SD0001.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.57341e-12
E-value 1.62799e-08
q-value 3.25599e-08
Overlap 10
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name AREB6_01_M00412_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.07096e-05
E-value 0.0312826
q-value 0.0312826
Overlap 10
Offset 0
Orientation Normal
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Matches to Query: 11_e_k36me3_190_0.564

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Summary 

Alignment 

Name sna_MA0086.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.33753e-06
E-value 0.00682793
q-value 0.0132409
Overlap 6
Offset -2
Orientation Normal
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Summary 

Alignment 

Name RAV1_02_M00344_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.58018e-06
E-value 0.0133787
q-value 0.0132409
Overlap 9
Offset 2
Orientation Reverse Complement
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Matches to Query: 12_e_k36me3_8_0.564

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Matches to Query: 13_h_k9me3_20_0.443

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Matches to Query: 14_e_k36me3_183_0.555

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Summary 

Alignment 

Name SN_01_M00060_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.07221e-05
E-value 0.0313191
q-value 0.0379576
Overlap 10
Offset 3
Orientation Normal
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Summary 

Alignment 

Name TCF4_03_M01769_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.3675e-05
E-value 0.0399445
q-value 0.0379576
Overlap 7
Offset -1
Orientation Normal
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Matches to Query: 15_e_k36me3_181_0.554

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Summary 

Alignment 

Name SNT2_MA0384.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.64324e-05
E-value 0.0479991
q-value 0.0959981
Overlap 9
Offset 2
Orientation Reverse Complement
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Matches to Query: 16_e_k36me3_230_0.554

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Matches to Query: 17_h_k27me3_15_0.448

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Summary 

Alignment 

Name Trl_MA0205.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.54914e-05
E-value 0.0452503
q-value 0.0905006
Overlap 10
Offset -2
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 18_e_k36me3_335_0.551

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Matches to Query: 19_e_k36me3_179_0.551

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Matches to Query: 20_e_k36me3_110_0.550

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Summary 

Alignment 

Name hlh-27_PL0004.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.13931e-05
E-value 0.0332792
q-value 0.0310638
Overlap 9
Offset 4
Orientation Normal
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Summary 

Alignment 

Name HLH-27_Cell09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.26013e-05
E-value 0.0368083
q-value 0.0310638
Overlap 9
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 21_e_k36me3_115_0.548

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Matches to Query: 22_e_k36me3_139_0.546

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Matches to Query: 23_e_k4me3_56_0.454

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Summary 

Alignment 

Name PTPMT1_7_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.74439e-06
E-value 0.0255424
q-value 0.050735
Overlap 5
Offset -4
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 24_h_k36me3_9_0.545

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Matches to Query: 25_e_k36me3_151_0.545

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Matches to Query: 26_e_k36me3_135_0.544

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Matches to Query: 27_e_k27me3_27_0.456

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Matches to Query: 28_e_k27ac_175_0.541

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Matches to Query: 29_e_k9me3_158_0.460

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Summary 

Alignment 

Name YPR022C_01_M01647_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.64496e-06
E-value 0.0223309
q-value 0.0292855
Overlap 6
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name MZF1_01_M00083_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.40256e-05
E-value 0.0409689
q-value 0.0292855
Overlap 8
Offset 0
Orientation Normal
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Summary 

Alignment 

Name ALFIN1_Q2_M00479_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.51162e-05
E-value 0.0441545
q-value 0.0292855
Overlap 10
Offset 5
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 30_e_k36me3_208_0.539

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Matches to Query: 31_h_k27me3_9_0.463

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Matches to Query: 32_e_k9me3_286_0.463

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Matches to Query: 33_h_k27me3_11_0.464

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Matches to Query: 34_h_k27me3_14_0.464

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Summary 

Alignment 

Name NFIX_2_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.26858e-06
E-value 0.00662651
q-value 0.00993133
Overlap 6
Offset -3
Orientation Reverse Complement
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Summary 

Alignment 

Name NMI_8_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.41513e-06
E-value 0.00997559
q-value 0.00993133
Overlap 8
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name DGCR8_4_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.15333e-05
E-value 0.0336889
q-value 0.0161233
Overlap 7
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name IL24_5_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.61001e-05
E-value 0.0470283
q-value 0.0161233
Overlap 8
Offset -1
Orientation Reverse Complement
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Matches to Query: 35_e_k9me3_25_0.464

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Matches to Query: 36_e_k9me3_320_0.467

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Matches to Query: 37_e_k36me3_365_0.532

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Matches to Query: 38_e_k36me3_334_0.531

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Matches to Query: 39_e_k9me3_50_0.469

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Matches to Query: 40_e_k9me3_124_0.470

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Matches to Query: 41_e_k27me3_338_0.470

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Matches to Query: 42_e_k27me3_38_0.470

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Matches to Query: 43_e_k27ac_370_0.471

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Matches to Query: 44_e_k4me3_276_0.529

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Matches to Query: 45_e_k4me3_36_0.472

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Matches to Query: 46_h_k4me3_12_0.528

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Matches to Query: 47_e_k27ac_9_0.473

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Summary 

Alignment 

Name FPM315_01_M01587_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.93826e-07
E-value 0.000566165
q-value 0.00113062
Overlap 9
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧  [Query Top]

Matches to Query: 48_e_k27ac_266_0.526

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Matches to Query: 49_h_k9me3_23_0.474

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Matches to Query: 50_e_k9me3_385_0.474

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Summary 

Alignment 

Name STAT3_01_M00225_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.83728e-06
E-value 0.0228927
q-value 0.0346743
Overlap 9
Offset 11
Orientation Reverse Complement
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Summary 

Alignment 

Name SCMH1_9_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.31236e-05
E-value 0.0383339
q-value 0.0346743
Overlap 6
Offset -1
Orientation Normal
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Matches to Query: 51_e_k9me3_53_0.474

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Matches to Query: 52_e_k4me1_202_0.525

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Matches to Query: 53_h_k9me3_2_0.475

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Matches to Query: 54_e_k27me3_35_0.475

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Matches to Query: 55_e_k4me1_36_0.476

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Matches to Query: 56_e_k9me3_121_0.477

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Matches to Query: 57_h_k27ac_2_0.522

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Summary 

Alignment 

Name AP1_01_M00517_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.04861e-10
E-value 5.98398e-07
q-value 6.39452e-07
Overlap 12
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name Jundm2_secondary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.8645e-10
E-value 1.12882e-06
q-value 6.39452e-07
Overlap 12
Offset 3
Orientation Normal
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Summary 

Alignment 

Name GCN4_02_M01555_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.72555e-10
E-value 2.25663e-06
q-value 6.39452e-07
Overlap 12
Offset 5
Orientation Normal
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Summary 

Alignment 

Name GCN4_MA0303.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.72555e-10
E-value 2.25663e-06
q-value 6.39452e-07
Overlap 12
Offset 5
Orientation Reverse Complement
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Summary 

Alignment 

Name Gcn4_GR09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.72555e-10
E-value 2.25663e-06
q-value 6.39452e-07
Overlap 12
Offset 5
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_C_M00199_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.66899e-09
E-value 1.65591e-05
q-value 2.986e-06
Overlap 9
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_Q6_M00174_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.29275e-09
E-value 1.83811e-05
q-value 3.03833e-06
Overlap 11
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name GCN4_01_M00038_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.67423e-08
E-value 0.000194954
q-value 2.76216e-05
Overlap 12
Offset 8
Orientation Reverse Complement
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Summary 

Alignment 

Name BACH1_01_M00495_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.46319e-07
E-value 0.0018879
q-value 0.000208166
Overlap 12
Offset 2
Orientation Normal
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Summary 

Alignment 

Name FRA1_Q5_M01267_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.46704e-07
E-value 0.00188902
q-value 0.000208166
Overlap 8
Offset -2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name AP1_Q4_01_M00926_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.18966e-06
E-value 0.00347499
q-value 0.000329019
Overlap 8
Offset -2
Orientation Normal
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Summary 

Alignment 

Name BACH2_01_M00490_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.19252e-06
E-value 0.00348334
q-value 0.000329019
Overlap 11
Offset 0
Orientation Normal
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Summary 

Alignment 

Name NFE2_01_M00037_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.19252e-06
E-value 0.00348334
q-value 0.000329019
Overlap 10
Offset 1
Orientation Normal
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Summary 

Alignment 

Name Fos_MA0099.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.44037e-06
E-value 0.00420732
q-value 0.000362846
Overlap 8
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_Q6_01_M00925_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.58982e-06
E-value 0.00464386
q-value 0.000380023
Overlap 9
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name GCN4_C_M00204_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.4495e-06
E-value 0.010076
q-value 0.000689182
Overlap 10
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_Q4_M00188_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.84129e-06
E-value 0.0112204
q-value 0.000734842
Overlap 11
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name NRF2_Q4_M00821_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.17647e-06
E-value 0.0121995
q-value 0.000756198
Overlap 11
Offset 2
Orientation Normal
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Summary 

Alignment 

Name GCN4_Q2_M01713_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.15863e-06
E-value 0.0179894
q-value 0.0010813
Overlap 11
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MAF_Q6_01_M00983_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.90205e-06
E-value 0.0201609
q-value 0.00117618
Overlap 11
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_Q2_M00173_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.72331e-06
E-value 0.0225598
q-value 0.00124302
Overlap 11
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name AP1_MA0099.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.00393e-06
E-value 0.0233795
q-value 0.00125337
Overlap 7
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name TCF11MAFG_01_M00284_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.21877e-06
E-value 0.026928
q-value 0.00140561
Overlap 12
Offset 7
Orientation Reverse Complement
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Matches to Query: 58_e_k27me3_312_0.478

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Summary 

Alignment 

Name H1FX_7_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.17284e-06
E-value 0.00634686
q-value 0.0125213
Overlap 7
Offset -1
Orientation Normal
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Summary 

Alignment 

Name MAGEA8_12_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.1342e-05
E-value 0.03313
q-value 0.0326799
Overlap 7
Offset -1
Orientation Normal
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Matches to Query: 59_h_k9me3_28_0.522

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Matches to Query: 60_e_k9me3_332_0.479

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Matches to Query: 61_e_k9me3_85_0.479

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Matches to Query: 62_e_k27ac_32_0.484

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Matches to Query: 63_h_k9me3_25_0.487

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Matches to Query: 64_e_k27ac_162_0.487

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Matches to Query: 65_h_k27me3_25_0.488

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Summary 

Alignment 

Name ro_MA0241.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.1283e-06
E-value 0.0208218
q-value 0.0255666
Overlap 7
Offset 0
Orientation Normal
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Summary 

Alignment 

Name CG9876_MA0184.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.70435e-05
E-value 0.0497842
q-value 0.0255666
Overlap 7
Offset 0
Orientation Normal
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Matches to Query: 66_e_k4me1_287_0.512

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Matches to Query: 67_e_k27ac_327_0.489

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Summary 

Alignment 

Name Sox11_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.33077e-07
E-value 0.000388718
q-value 0.00044784
Overlap 10
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name SOX4_01_M01308_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.81294e-07
E-value 0.00052956
q-value 0.00044784
Overlap 8
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name Sox4_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.31883e-07
E-value 0.000677329
q-value 0.00044784
Overlap 10
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name Sox4_CR09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.10701e-06
E-value 0.00323357
q-value 0.00133989
Overlap 10
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name SMAD1_01_M01590_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.15628e-06
E-value 0.00337749
q-value 0.00133989
Overlap 10
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name D_MA00445.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.84971e-06
E-value 0.00832399
q-value 0.00275185
Overlap 10
Offset 1
Orientation Normal
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Summary 

Alignment 

Name NANOG_02_M01247_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.16198e-06
E-value 0.0150781
q-value 0.00427262
Overlap 10
Offset 5
Orientation Reverse Complement
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Matches to Query: 68_h_k4me1_31_0.508

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Matches to Query: 69_h_k9me3_3_0.493

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Matches to Query: 70_h_k9me3_5_0.497

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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 184.026 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.