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_k27me3_1_0.762
CCCCGCGCGC
6 RSC30_01_M01520_T,  Rsc30_GR09_U,  RSC30_MA0375.1_J,  ZF5_01_M00716_T,  SUT1_01_M01677_T,  SUT1_MA0399.1_J
2_h_k4me3_4_0.660
TCGCGTTT
0
3_h_k4me3_10_0.659
TATTTCGCGG
0
4_e_k36me3_125_0.354
ATGTTGGCC
0
5_e_k36me3_61_0.354
GTGAGCCAC
0
6_e_k36me3_30_0.367
CCAAAGTGCTG
0
7_e_k36me3_83_0.368
CAGGAGTTCA
1 RPC155_01_M01798_T
8_e_k36me3_21_0.393
AACCCCGTC
0
9_e_k36me3_121_0.412
CCGTGTTAG
0
10_e_k4me3_338_0.585
AATCGTTAAT
0
11_e_k4me3_313_0.583
TTAATTCGT
0
12_h_k4me3_22_0.570
AAAACGTACG
0
13_e_k4me3_159_0.567
GGATTCGAA
2 BRF1_01_M01747_T,  BDP1_01_M01796_T
14_e_k27me3_251_0.565
CGATTTGCA
4 DGCR8_4_H,  NFIX_2_H,  NOC2L_4_H,  NMI_8_H
15_h_k9me3_17_0.439
CATAGGCCTCAA
0
16_h_k36me3_24_0.440
GCCTCATCATAG
0
17_h_k4me3_1_0.555
CACTTCCGGG
43 GADP_01_M01258_T,  Ehf_primary_SCI09_U,  Ehf_EMBO10_U,  ELF2_10_H,  Elf2_EMBO10_U,  E74A_01_M00016_T,  GABPA_MA0062.2_J,  CETS1P54_01_M00032_T,  ELK1_02_M00025_T,  ETV4_13_H
18_e_k4me3_280_0.542
CGTAGGTA
0
19_h_k36me3_21_0.533
CAGTATGCGCTC
0
20_h_k36me3_11_0.522
AAGCTCTTGCCG
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 56

Matches to Query: 1_h_k27me3_1_0.762

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Summary 

Alignment 

Name RSC30_01_M01520_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.77945e-06
E-value 0.00519778
q-value 0.00517204
Overlap 10
Offset 5
Orientation Reverse Complement
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Summary 

Alignment 

Name Rsc30_GR09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.77945e-06
E-value 0.00519778
q-value 0.00517204
Overlap 10
Offset 5
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name RSC30_MA0375.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.65619e-06
E-value 0.0223637
q-value 0.00958599
Overlap 8
Offset -1
Orientation Normal
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Summary 

Alignment 

Name ZF5_01_M00716_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.14646e-05
E-value 0.0334882
q-value 0.00958599
Overlap 8
Offset -2
Orientation Reverse Complement
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Summary 

Alignment 

Name SUT1_01_M01677_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.31923e-05
E-value 0.0385348
q-value 0.00958599
Overlap 7
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name SUT1_MA0399.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.31923e-05
E-value 0.0385348
q-value 0.00958599
Overlap 7
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 2_h_k4me3_4_0.660

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Matches to Query: 3_h_k4me3_10_0.659

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Matches to Query: 4_e_k36me3_125_0.354

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Matches to Query: 5_e_k36me3_61_0.354

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Matches to Query: 6_e_k36me3_30_0.367

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Matches to Query: 7_e_k36me3_83_0.368

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Summary 

Alignment 

Name RPC155_01_M01798_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.78308e-06
E-value 0.0139714
q-value 0.0279427
Overlap 10
Offset 1
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 8_e_k36me3_21_0.393

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Matches to Query: 9_e_k36me3_121_0.412

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Matches to Query: 10_e_k4me3_338_0.585

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Matches to Query: 11_e_k4me3_313_0.583

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Matches to Query: 12_h_k4me3_22_0.570

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Matches to Query: 13_e_k4me3_159_0.567

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Summary 

Alignment 

Name BRF1_01_M01747_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.36646e-07
E-value 0.00185964
q-value 0.00371929
Overlap 9
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name BDP1_01_M01796_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.49257e-05
E-value 0.0435979
q-value 0.0435979
Overlap 9
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 14_e_k27me3_251_0.565

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Summary 

Alignment 

Name DGCR8_4_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.47605e-07
E-value 0.00189165
q-value 0.00376652
Overlap 7
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name NFIX_2_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.14132e-06
E-value 0.00917578
q-value 0.00913507
Overlap 6
Offset -3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name NOC2L_4_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.22732e-05
E-value 0.03585
q-value 0.0185799
Overlap 6
Offset -3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name NMI_8_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.27783e-05
E-value 0.0373254
q-value 0.0185799
Overlap 8
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 15_h_k9me3_17_0.439

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Matches to Query: 16_h_k36me3_24_0.440

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Matches to Query: 17_h_k4me3_1_0.555

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Summary 

Alignment 

Name GADP_01_M01258_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.51115e-09
E-value 7.33508e-06
q-value 1.43678e-05
Overlap 10
Offset 0
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Ehf_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.23886e-08
E-value 6.53972e-05
q-value 4.74156e-05
Overlap 10
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Ehf_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.98515e-08
E-value 8.71963e-05
q-value 4.74156e-05
Overlap 10
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ELF2_10_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.62588e-08
E-value 0.000105912
q-value 4.74156e-05
Overlap 7
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elf2_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.35074e-08
E-value 0.000127085
q-value 4.74156e-05
Overlap 10
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name E74A_01_M00016_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.97227e-08
E-value 0.00014524
q-value 4.74156e-05
Overlap 10
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GABPA_MA0062.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.97055e-08
E-value 0.00020361
q-value 5.69754e-05
Overlap 9
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name CETS1P54_01_M00032_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.11902e-08
E-value 0.000266367
q-value 6.08094e-05
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ELK1_02_M00025_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.56522e-08
E-value 0.0002794
q-value 6.08094e-05
Overlap 10
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ETV4_13_H
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.07292e-07
E-value 0.000313401
q-value 6.13884e-05
Overlap 7
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GABP_B_M00341_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.50542e-07
E-value 0.000439733
q-value 7.21402e-05
Overlap 10
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elk3_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.52976e-07
E-value 0.000446842
q-value 7.21402e-05
Overlap 10
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elf4_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.63909e-07
E-value 0.000478778
q-value 7.21402e-05
Overlap 10
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elk4_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.47139e-07
E-value 0.00101399
q-value 0.000141871
Overlap 10
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name SAP1A_01_M01167_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.87407e-07
E-value 0.00113162
q-value 0.000147773
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Etv6_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.71729e-07
E-value 0.00137792
q-value 0.000168691
Overlap 10
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Erg_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.78279e-07
E-value 0.00168915
q-value 0.000194629
Overlap 10
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Eip74EF_MA0026.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.07356e-07
E-value 0.00206619
q-value 0.000224845
Overlap 7
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elk1_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.74849e-07
E-value 0.00226333
q-value 0.000230933
Overlap 10
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Etv1_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.0685e-07
E-value 0.00264891
q-value 0.000230933
Overlap 10
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gabpa_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.0685e-07
E-value 0.00264891
q-value 0.000230933
Overlap 10
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ELK4_MA0076.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.18851e-07
E-value 0.00268397
q-value 0.000230933
Overlap 9
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Etv4_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.28314e-07
E-value 0.0027116
q-value 0.000230933
Overlap 10
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gabpa_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.05734e-06
E-value 0.0030885
q-value 0.000241912
Overlap 10
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ERG_01_M01752_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.07361e-06
E-value 0.00313603
q-value 0.000241912
Overlap 9
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name EHF_01_M01751_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.09929e-06
E-value 0.00321103
q-value 0.000241912
Overlap 9
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elf3_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.22839e-06
E-value 0.00358814
q-value 0.000260311
Overlap 10
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name CETS1P54_03_M01078_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.44314e-06
E-value 0.00421542
q-value 0.000294896
Overlap 10
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Fli1_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.90761e-06
E-value 0.00557211
q-value 0.000367272
Overlap 10
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ETS_class_MF0001.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.92571e-06
E-value 0.005625
q-value 0.000367272
Overlap 8
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gm5454_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.49525e-06
E-value 0.00728861
q-value 0.000460543
Overlap 10
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ELK1_04_M01165_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.61616e-06
E-value 0.00764181
q-value 0.000467771
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Ets1_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.83277e-06
E-value 0.00827451
q-value 0.000478465
Overlap 10
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Etv3_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.84322e-06
E-value 0.00830506
q-value 0.000478465
Overlap 10
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GABPA_MA0062.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.50207e-06
E-value 0.0102295
q-value 0.000556596
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name NRF2_01_M00108_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.50207e-06
E-value 0.0102295
q-value 0.000556596
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ELK1_03_M01163_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 3.7655e-06
E-value 0.010999
q-value 0.000582289
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Etv5_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 5.28017e-06
E-value 0.0154234
q-value 0.000795029
Overlap 10
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gm4881_EMBO10_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.67767e-06
E-value 0.0195055
q-value 0.000979667
Overlap 10
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name FLI1_Q6_M01208_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.43742e-06
E-value 0.0217247
q-value 0.00106385
Overlap 9
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name ELK1_MA0028.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.51263e-06
E-value 0.0277864
q-value 0.0013275
Overlap 8
Offset -2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name CETS168_Q6_M00743_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.04304e-05
E-value 0.0304673
q-value 0.00142093
Overlap 8
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Elf3_primary_SCI09_U
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.2372e-05
E-value 0.0361386
q-value 0.00164623
Overlap 10
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: 18_e_k4me3_280_0.542

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Matches to Query: 19_h_k36me3_21_0.533

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Matches to Query: 20_h_k36me3_11_0.522

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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 55.359 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.