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 

HGATAA
AGATAA
9 MA0035.2 (Gata1),  UP00100_1 (Gata6_primary),  MA0140.1 (Tal1::Gata1),  UP00032_1 (Gata3_primary),  MA0307.1 (GLN3),  MA0029.1 (Evi1),  MA0300.1 (GAT1),  MA0309.1 (GZF3),  UP00080_1 (Gata5_primary)
CAGMYG
CAGCTG
5 MA0091.1 (TAL1::TCF3),  MA0048.1 (NHLH1),  UP00099_1 (Ascl2_primary),  UP00046_2 (Tcfe2a_secondary),  MA0055.1 (Myf)
TATCW
TATCT
6 MA0035.2 (Gata1),  MA0140.1 (Tal1::Gata1),  UP00100_1 (Gata6_primary),  UP00032_1 (Gata3_primary),  MA0037.1 (GATA3),  UP00080_2 (Gata5_secondary)
VAGGAAR
CAGGAAG
10 MA0156.1 (FEV),  MA0080.2 (SPI1),  MA0136.1 (ELF5),  MA0144.1 (Stat3),  UP00407_1 (Elf3_primary),  MA0026.1 (Eip74EF),  MA0081.1 (SPIB),  UP00085_1 (Sfpi1_primary),  MA0098.1 (ETS1),  MA0305.1 (GCR2)
CMCRCCC
CCCACCC
15 MA0039.2 (Klf4),  UP00093_1 (Klf7_primary),  UP00096_2 (Sox13_secondary),  UP00099_2 (Ascl2_secondary),  MA0270.1 (AFT2),  UP00002_1 (Sp4_primary),  MA0450.1 (hkb),  MA0079.1 (SP1),  UP00043_2 (Bcl6b_secondary),  MA0079.2 (SP1)
TAATCW
TAATCT
0
CACAGC
CACAGC
5 UP00006_2 (Zic3_secondary),  UP00102_2 (Zic1_secondary),  MA0332.1 (MET28),  UP00057_2 (Zic2_secondary),  MA0335.1 (MET4)
CAGGWGGC
CAGGAGGC
7 MA0086.1 (sna),  MA0139.1 (CTCF),  MA0155.1 (INSM1),  MA0104.2 (Mycn),  MA0373.1 (RPN4),  MA0147.1 (Myc),  MA0103.1 (ZEB1)
ACGTGA
ACGTGA
7 MA0409.1 (TYE7),  MA0281.1 (CBF1),  UP00050_1 (Bhlhb2_primary),  MA0058.1 (MAX),  MA0093.1 (USF1),  MA0004.1 (Arnt),  MA0104.1 (Mycn)

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

JASPAR_CORE_2009.meme 476 41
uniprobe_mouse.meme 386 19

Matches to Query: HGATAA

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Summary 

Alignment 

Name MA0035.2
Alt. Name Gata1
Database JASPAR_CORE_2009.meme
p-value 1.33175e-06
E-value 0.00114797
q-value 0.00165588
Overlap 6
Offset 2
Orientation Normal
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Summary 

Alignment 

Name UP00100_1
Alt. Name Gata6_primary
Database uniprobe_mouse.meme
p-value 2.66351e-06
E-value 0.00229594
q-value 0.00165588
Overlap 6
Offset 5
Orientation Normal
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Summary 

Alignment 

Name MA0140.1
Alt. Name Tal1::Gata1
Database JASPAR_CORE_2009.meme
p-value 2.88546e-06
E-value 0.00248727
q-value 0.00165588
Overlap 6
Offset 11
Orientation Normal
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Summary 

Alignment 

Name UP00032_1
Alt. Name Gata3_primary
Database uniprobe_mouse.meme
p-value 2.87525e-05
E-value 0.0247847
q-value 0.0123751
Overlap 6
Offset 7
Orientation Normal
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Summary 

Alignment 

Name MA0307.1
Alt. Name GLN3
Database JASPAR_CORE_2009.meme
p-value 0.000208735
E-value 0.17993
q-value 0.071872
Overlap 5
Offset -1
Orientation Normal
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Summary 

Alignment 

Name MA0029.1
Alt. Name Evi1
Database JASPAR_CORE_2009.meme
p-value 0.000250723
E-value 0.216123
q-value 0.071941
Overlap 6
Offset 6
Orientation Normal
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Summary 

Alignment 

Name MA0300.1
Alt. Name GAT1
Database JASPAR_CORE_2009.meme
p-value 0.000445728
E-value 0.384218
q-value 0.0959211
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0309.1
Alt. Name GZF3
Database JASPAR_CORE_2009.meme
p-value 0.000445728
E-value 0.384218
q-value 0.0959211
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name UP00080_1
Alt. Name Gata5_primary
Database uniprobe_mouse.meme
p-value 0.000938631
E-value 0.8091
q-value 0.179551
Overlap 6
Offset 5
Orientation Normal
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Matches to Query: CAGMYG

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Summary 

Alignment 

Name MA0091.1
Alt. Name TAL1::TCF3
Database JASPAR_CORE_2009.meme
p-value 3.71739e-05
E-value 0.0320439
q-value 0.0417231
Overlap 6
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0048.1
Alt. Name NHLH1
Database JASPAR_CORE_2009.meme
p-value 5.80636e-05
E-value 0.0500509
q-value 0.0417231
Overlap 6
Offset 3
Orientation Normal
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Summary 

Alignment 

Name UP00099_1
Alt. Name Ascl2_primary
Database uniprobe_mouse.meme
p-value 9.95356e-05
E-value 0.0857997
q-value 0.0427153
Overlap 6
Offset 6
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00046_2
Alt. Name Tcfe2a_secondary
Database uniprobe_mouse.meme
p-value 0.000347354
E-value 0.299419
q-value 0.0993769
Overlap 6
Offset 5
Orientation Normal
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Summary 

Alignment 

Name MA0055.1
Alt. Name Myf
Database JASPAR_CORE_2009.meme
p-value 0.00109551
E-value 0.94433
q-value 0.252986
Overlap 6
Offset 3
Orientation Reverse Complement
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Matches to Query: TATCW

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Summary 

Alignment 

Name MA0035.2
Alt. Name Gata1
Database JASPAR_CORE_2009.meme
p-value 1.3257e-06
E-value 0.00114275
q-value 0.00227701
Overlap 5
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0140.1
Alt. Name Tal1::Gata1
Database JASPAR_CORE_2009.meme
p-value 1.29552e-05
E-value 0.0111673
q-value 0.0111258
Overlap 5
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00100_1
Alt. Name Gata6_primary
Database uniprobe_mouse.meme
p-value 3.22355e-05
E-value 0.027787
q-value 0.0184558
Overlap 5
Offset 7
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00032_1
Alt. Name Gata3_primary
Database uniprobe_mouse.meme
p-value 0.000342027
E-value 0.294828
q-value 0.14438
Overlap 5
Offset 10
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0037.1
Alt. Name GATA3
Database JASPAR_CORE_2009.meme
p-value 0.000420298
E-value 0.362297
q-value 0.14438
Overlap 5
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00080_2
Alt. Name Gata5_secondary
Database uniprobe_mouse.meme
p-value 0.000832993
E-value 0.71804
q-value 0.238456
Overlap 5
Offset 8
Orientation Normal
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Matches to Query: VAGGAAR

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Summary 

Alignment 

Name MA0156.1
Alt. Name FEV
Database JASPAR_CORE_2009.meme
p-value 1.90986e-06
E-value 0.0016463
q-value 0.00327459
Overlap 7
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0080.2
Alt. Name SPI1
Database JASPAR_CORE_2009.meme
p-value 1.92332e-05
E-value 0.016579
q-value 0.012691
Overlap 6
Offset -1
Orientation Normal
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Summary 

Alignment 

Name MA0136.1
Alt. Name ELF5
Database JASPAR_CORE_2009.meme
p-value 2.59094e-05
E-value 0.0223339
q-value 0.012691
Overlap 7
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0144.1
Alt. Name Stat3
Database JASPAR_CORE_2009.meme
p-value 2.96075e-05
E-value 0.0255216
q-value 0.012691
Overlap 7
Offset 3
Orientation Normal
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Summary 

Alignment 

Name UP00407_1
Alt. Name Elf3_primary
Database uniprobe_mouse.meme
p-value 4.43229e-05
E-value 0.0382064
q-value 0.015199
Overlap 7
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0026.1
Alt. Name Eip74EF
Database JASPAR_CORE_2009.meme
p-value 0.000211773
E-value 0.182548
q-value 0.0518714
Overlap 7
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0081.1
Alt. Name SPIB
Database JASPAR_CORE_2009.meme
p-value 0.000211773
E-value 0.182548
q-value 0.0518714
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name UP00085_1
Alt. Name Sfpi1_primary
Database uniprobe_mouse.meme
p-value 0.000465449
E-value 0.401217
q-value 0.0980884
Overlap 7
Offset 4
Orientation Normal
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Summary 

Alignment 

Name MA0098.1
Alt. Name ETS1
Database JASPAR_CORE_2009.meme
p-value 0.000514878
E-value 0.443825
q-value 0.0980884
Overlap 6
Offset -1
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0305.1
Alt. Name GCR2
Database JASPAR_CORE_2009.meme
p-value 0.000624146
E-value 0.538014
q-value 0.107014
Overlap 6
Offset -1
Orientation Reverse Complement
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Matches to Query: CMCRCCC

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Summary 

Alignment 

Name MA0039.2
Alt. Name Klf4
Database JASPAR_CORE_2009.meme
p-value 1.44832e-09
E-value 1.24845e-06
q-value 2.46141e-06
Overlap 7
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00093_1
Alt. Name Klf7_primary
Database uniprobe_mouse.meme
p-value 5.02464e-06
E-value 0.00433124
q-value 0.00426968
Overlap 7
Offset 5
Orientation Normal
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Summary 

Alignment 

Name UP00096_2
Alt. Name Sox13_secondary
Database uniprobe_mouse.meme
p-value 1.02977e-05
E-value 0.0088766
q-value 0.00583362
Overlap 7
Offset 5
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00099_2
Alt. Name Ascl2_secondary
Database uniprobe_mouse.meme
p-value 5.32162e-05
E-value 0.0458724
q-value 0.0214907
Overlap 7
Offset 5
Orientation Normal
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Summary 

Alignment 

Name MA0270.1
Alt. Name AFT2
Database JASPAR_CORE_2009.meme
p-value 6.32266e-05
E-value 0.0545013
q-value 0.0214907
Overlap 7
Offset 0
Orientation Normal
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Summary 

Alignment 

Name UP00002_1
Alt. Name Sp4_primary
Database uniprobe_mouse.meme
p-value 0.000154094
E-value 0.132829
q-value 0.0374409
Overlap 7
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0450.1
Alt. Name hkb
Database JASPAR_CORE_2009.meme
p-value 0.000168023
E-value 0.144836
q-value 0.0374409
Overlap 7
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0079.1
Alt. Name SP1
Database JASPAR_CORE_2009.meme
p-value 0.000176244
E-value 0.151923
q-value 0.0374409
Overlap 7
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00043_2
Alt. Name Bcl6b_secondary
Database uniprobe_mouse.meme
p-value 0.000222943
E-value 0.192177
q-value 0.042099
Overlap 7
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0079.2
Alt. Name SP1
Database JASPAR_CORE_2009.meme
p-value 0.000261875
E-value 0.225736
q-value 0.0445055
Overlap 7
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0290.1
Alt. Name DAL81
Database JASPAR_CORE_2009.meme
p-value 0.000289816
E-value 0.249821
q-value 0.0447765
Overlap 7
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0443.1
Alt. Name btd
Database JASPAR_CORE_2009.meme
p-value 0.000443224
E-value 0.382059
q-value 0.0627715
Overlap 7
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name UP00007_1
Alt. Name Egr1_primary
Database uniprobe_mouse.meme
p-value 0.000658222
E-value 0.567388
q-value 0.0860498
Overlap 7
Offset 0
Orientation Normal
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Summary 

Alignment 

Name UP00021_1
Alt. Name Zfp281_primary
Database uniprobe_mouse.meme
p-value 0.000859453
E-value 0.740849
q-value 0.104331
Overlap 7
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0162.1
Alt. Name Egr1
Database JASPAR_CORE_2009.meme
p-value 0.00112624
E-value 0.970815
q-value 0.127602
Overlap 6
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: TAATCW

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Matches to Query: CACAGC

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Summary 

Alignment 

Name UP00006_2
Alt. Name Zic3_secondary
Database uniprobe_mouse.meme
p-value 8.62559e-05
E-value 0.0743526
q-value 0.148672
Overlap 6
Offset 3
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name UP00102_2
Alt. Name Zic1_secondary
Database uniprobe_mouse.meme
p-value 0.000173757
E-value 0.149779
q-value 0.149745
Overlap 6
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0332.1
Alt. Name MET28
Database JASPAR_CORE_2009.meme
p-value 0.000413798
E-value 0.356694
q-value 0.205572
Overlap 5
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name UP00057_2
Alt. Name Zic2_secondary
Database uniprobe_mouse.meme
p-value 0.000515411
E-value 0.444284
q-value 0.205572
Overlap 6
Offset 3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0335.1
Alt. Name MET4
Database JASPAR_CORE_2009.meme
p-value 0.00059634
E-value 0.514045
q-value 0.205572
Overlap 6
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: CAGGWGGC

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Summary 

Alignment 

Name MA0086.1
Alt. Name sna
Database JASPAR_CORE_2009.meme
p-value 0.000176543
E-value 0.15218
q-value 0.18594
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0139.1
Alt. Name CTCF
Database JASPAR_CORE_2009.meme
p-value 0.00021739
E-value 0.18739
q-value 0.18594
Overlap 8
Offset 7
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0155.1
Alt. Name INSM1
Database JASPAR_CORE_2009.meme
p-value 0.000531586
E-value 0.458227
q-value 0.247256
Overlap 8
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0104.2
Alt. Name Mycn
Database JASPAR_CORE_2009.meme
p-value 0.000583905
E-value 0.503326
q-value 0.247256
Overlap 8
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0373.1
Alt. Name RPN4
Database JASPAR_CORE_2009.meme
p-value 0.00075382
E-value 0.649793
q-value 0.247256
Overlap 6
Offset -2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0147.1
Alt. Name Myc
Database JASPAR_CORE_2009.meme
p-value 0.000952796
E-value 0.82131
q-value 0.247256
Overlap 8
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0103.1
Alt. Name ZEB1
Database JASPAR_CORE_2009.meme
p-value 0.00101177
E-value 0.872145
q-value 0.247256
Overlap 6
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: ACGTGA

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Summary 

Alignment 

Name MA0409.1
Alt. Name TYE7
Database JASPAR_CORE_2009.meme
p-value 4.83951e-06
E-value 0.00417166
q-value 0.00815874
Overlap 6
Offset 1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name MA0281.1
Alt. Name CBF1
Database JASPAR_CORE_2009.meme
p-value 9.77548e-06
E-value 0.00842646
q-value 0.00824004
Overlap 6
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name UP00050_1
Alt. Name Bhlhb2_primary
Database uniprobe_mouse.meme
p-value 7.02354e-05
E-value 0.060543
q-value 0.0296018
Overlap 6
Offset 9
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0058.1
Alt. Name MAX
Database JASPAR_CORE_2009.meme
p-value 0.000237579
E-value 0.204793
q-value 0.0639856
Overlap 6
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0093.1
Alt. Name USF1
Database JASPAR_CORE_2009.meme
p-value 0.000257957
E-value 0.222359
q-value 0.0639856
Overlap 6
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0004.1
Alt. Name Arnt
Database JASPAR_CORE_2009.meme
p-value 0.000341589
E-value 0.294449
q-value 0.0639856
Overlap 5
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name MA0104.1
Alt. Name Mycn
Database JASPAR_CORE_2009.meme
p-value 0.000341589
E-value 0.294449
q-value 0.0639856
Overlap 5
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]
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TOMTOM version
4.9.0 (Release date: Wed Oct 3 11:07:26 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 ./background):
A: 0.236   C: 0.264   G: 0.264   T: 0.236

Result calculation took 3.740 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.