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 

CACGTG
CACGTG
19 MA0281.1 (CBF1),  MA0569.1 (MYC4),  MA0409.1 (TYE7),  MA0004.1 (Arnt),  MA0059.1 (MYC::MAX),  MA0104.3 (Mycn),  MA0561.1 (PIF4),  MA0550.1 (BZR1),  MA0580.1 (DYT1),  MA0357.1 (PHO4)
MGGRAR
CGGGAG
0
CYCCKCCC
CCCCGCCC
5 MA0079.3 (SP1),  MA0599.1 (KLF5),  MA0162.2 (EGR1),  MA0516.1 (SP2),  MA0039.2 (Klf4)
SCGCGTGB
GCGCGTGC
1 MA0557.1 (FHY3)
BCACATG
GCACATG
2 MA0058.2 (MAX),  MA0147.2 (Myc)
CGCCDCCW
CGCCGCCT
1 MA0567.1 (ERF1)
RKAAA
AGAAA
0
RTGASTCA
GTGACTCA
13 MA0477.1 (FOSL1),  MA0491.1 (JUND),  MA0490.1 (JUNB),  MA0478.1 (FOSL2),  MA0303.1 (GCN4),  MA0489.1 (JUN),  MA0476.1 (FOS),  MA0501.1 (NFE2::MAF),  MA0591.1 (Bach1::Mafk),  MA0099.2 (JUN::FOS)
BATTGGCY
GATTGGCC
2 MA0314.1 (HAP3),  MA0502.1 (NFYB)
TGACGTMA
TGACGTCA
2 MA0018.2 (CREB1),  MA0286.1 (CST6)
ASGWGG
AGGAGG
0
CYGGRA
CTGGGA
0
AAVATGGC
AAGATGGC
1 MA0095.2 (YY1)
GCGGCKGC
GCGGCGGC
0
AGRGGGCG
AGGGGGCG
4 MA0443.1 (btd),  MA0139.1 (CTCF),  MA0155.1 (INSM1),  MA0516.1 (SP2)
GCATGCGC
GCATGCGC
2 MA0565.1 (FUS3),  MA0506.1 (NRF1)
RACTACA
GACTACA
0
TTTAAAWR
TTTAAAAA
0
GGGCGTGK
GGGCGTGG
1 MA0039.2 (Klf4)
AGCAGCWG
AGCAGCAG
0
CCTKTAA
CCTTTAA
0
CCWGGA
CCAGGA
0
GSGCGGGA
GGGCGGGA
6 MA0290.1 (DAL81),  MA0470.1 (E2F4),  MA0469.1 (E2F3),  MA0024.2 (E2F1),  MA0471.1 (E2F6),  MA0410.1 (UGA3)
GATTGGTY
GATTGGTC
3 MA0060.2 (NFYA),  MA0502.1 (NFYB),  MA0314.1 (HAP3)
AAATA
AAATA
0
CGCGCTSC
CGCGCTGC
0
CACRCACA
CACACACA
1 MA0538.1 (DAF-12)
RGGAA
GGGAA
0
ATTASTCA
ATTACTCA
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

JASPAR_CORE_2014.meme 593 59

Matches to Query: CACGTG

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Summary 

Alignment 

Name MA0281.1
Alt. Name CBF1
Database JASPAR_CORE_2014.meme
p-value 5.38052e-06
E-value 0.00319065
q-value 0.000878556
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0569.1
Alt. Name MYC4
Database JASPAR_CORE_2014.meme
p-value 5.38052e-06
E-value 0.00319065
q-value 0.000878556
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0409.1
Alt. Name TYE7
Database JASPAR_CORE_2014.meme
p-value 7.54126e-06
E-value 0.00447197
q-value 0.000878556
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0004.1
Alt. Name Arnt
Database JASPAR_CORE_2014.meme
p-value 7.58397e-06
E-value 0.00449729
q-value 0.000878556
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0059.1
Alt. Name MYC::MAX
Database JASPAR_CORE_2014.meme
p-value 1.0761e-05
E-value 0.00638128
q-value 0.000878556
Overlap 6
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0104.3
Alt. Name Mycn
Database JASPAR_CORE_2014.meme
p-value 1.13119e-05
E-value 0.00670793
q-value 0.000878556
Overlap 6
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0561.1
Alt. Name PIF4
Database JASPAR_CORE_2014.meme
p-value 1.13119e-05
E-value 0.00670793
q-value 0.000878556
Overlap 6
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0550.1
Alt. Name BZR1
Database JASPAR_CORE_2014.meme
p-value 1.61415e-05
E-value 0.00957189
q-value 0.000878556
Overlap 6
Offset 4
Orientation Normal
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Summary 

Alignment 

Name MA0580.1
Alt. Name DYT1
Database JASPAR_CORE_2014.meme
p-value 1.61415e-05
E-value 0.00957189
q-value 0.000878556
Overlap 6
Offset 7
Orientation Normal
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Summary 

Alignment 

Name MA0357.1
Alt. Name PHO4
Database JASPAR_CORE_2014.meme
p-value 1.70796e-05
E-value 0.0101282
q-value 0.000878556
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0566.1
Alt. Name MYC2
Database JASPAR_CORE_2014.meme
p-value 1.70796e-05
E-value 0.0101282
q-value 0.000878556
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0551.1
Alt. Name HY5
Database JASPAR_CORE_2014.meme
p-value 1.97284e-05
E-value 0.011699
q-value 0.000930243
Overlap 6
Offset 5
Orientation Normal
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Summary 

Alignment 

Name MA0549.1
Alt. Name BES1
Database JASPAR_CORE_2014.meme
p-value 2.26236e-05
E-value 0.0134158
q-value 0.000984699
Overlap 6
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0552.1
Alt. Name PIL5
Database JASPAR_CORE_2014.meme
p-value 3.39352e-05
E-value 0.0201236
q-value 0.00137154
Overlap 6
Offset 7
Orientation Normal
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Summary 

Alignment 

Name MA0568.1
Alt. Name MYC3
Database JASPAR_CORE_2014.meme
p-value 4.04596e-05
E-value 0.0239925
q-value 0.00152621
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0464.1
Alt. Name Bhlhe40
Database JASPAR_CORE_2014.meme
p-value 4.55029e-05
E-value 0.0269832
q-value 0.00157925
Overlap 6
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0560.1
Alt. Name PIF3
Database JASPAR_CORE_2014.meme
p-value 4.74475e-05
E-value 0.0281364
q-value 0.00157925
Overlap 6
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0562.1
Alt. Name PIF5
Database JASPAR_CORE_2014.meme
p-value 5.97201e-05
E-value 0.035414
q-value 0.0018773
Overlap 6
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0570.1
Alt. Name ABF1
Database JASPAR_CORE_2014.meme
p-value 7.97021e-05
E-value 0.0472634
q-value 0.00237357
Overlap 6
Offset 3
Orientation Normal
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Matches to Query: MGGRAR

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Matches to Query: CYCCKCCC

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Summary 

Alignment 

Name MA0079.3
Alt. Name SP1
Database JASPAR_CORE_2014.meme
p-value 5.85444e-07
E-value 0.000347168
q-value 0.000683705
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0599.1
Alt. Name KLF5
Database JASPAR_CORE_2014.meme
p-value 4.2502e-06
E-value 0.00252037
q-value 0.0018632
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0162.2
Alt. Name EGR1
Database JASPAR_CORE_2014.meme
p-value 4.78627e-06
E-value 0.00283826
q-value 0.0018632
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0516.1
Alt. Name SP2
Database JASPAR_CORE_2014.meme
p-value 1.35837e-05
E-value 0.00805511
q-value 0.00396588
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0039.2
Alt. Name Klf4
Database JASPAR_CORE_2014.meme
p-value 2.67538e-05
E-value 0.015865
q-value 0.00624883
Overlap 8
Offset 1
Orientation Reverse Complement
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Matches to Query: SCGCGTGB

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Summary 

Alignment 

Name MA0557.1
Alt. Name FHY3
Database JASPAR_CORE_2014.meme
p-value 4.61801e-05
E-value 0.0273848
q-value 0.0269327
Overlap 8
Offset 3
Orientation Reverse Complement
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Matches to Query: BCACATG

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Summary 

Alignment 

Name MA0058.2
Alt. Name MAX
Database JASPAR_CORE_2014.meme
p-value 4.40919e-06
E-value 0.00261465
q-value 0.00508959
Overlap 7
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0147.2
Alt. Name Myc
Database JASPAR_CORE_2014.meme
p-value 5.93985e-05
E-value 0.0352233
q-value 0.0342823
Overlap 7
Offset 2
Orientation Reverse Complement
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Matches to Query: CGCCDCCW

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Summary 

Alignment 

Name MA0567.1
Alt. Name ERF1
Database JASPAR_CORE_2014.meme
p-value 1.93396e-05
E-value 0.0114684
q-value 0.0226997
Overlap 8
Offset 0
Orientation Normal
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Matches to Query: RKAAA

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Matches to Query: RTGASTCA

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Summary 

Alignment 

Name MA0477.1
Alt. Name FOSL1
Database JASPAR_CORE_2014.meme
p-value 2.69243e-10
E-value 1.59661e-07
q-value 3.12268e-07
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0491.1
Alt. Name JUND
Database JASPAR_CORE_2014.meme
p-value 2.83309e-09
E-value 1.68002e-06
q-value 1.64291e-06
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0490.1
Alt. Name JUNB
Database JASPAR_CORE_2014.meme
p-value 5.91631e-09
E-value 3.50837e-06
q-value 2.28724e-06
Overlap 8
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0478.1
Alt. Name FOSL2
Database JASPAR_CORE_2014.meme
p-value 2.9442e-08
E-value 1.74591e-05
q-value 8.53669e-06
Overlap 8
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0303.1
Alt. Name GCN4
Database JASPAR_CORE_2014.meme
p-value 1.03047e-07
E-value 6.11068e-05
q-value 2.26287e-05
Overlap 8
Offset 6
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0489.1
Alt. Name JUN
Database JASPAR_CORE_2014.meme
p-value 1.17065e-07
E-value 6.94197e-05
q-value 2.26287e-05
Overlap 8
Offset 5
Orientation Normal
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Summary 

Alignment 

Name MA0476.1
Alt. Name FOS
Database JASPAR_CORE_2014.meme
p-value 7.91103e-07
E-value 0.000469124
q-value 0.00011469
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0501.1
Alt. Name NFE2::MAF
Database JASPAR_CORE_2014.meme
p-value 5.89245e-06
E-value 0.00349422
q-value 0.000552236
Overlap 8
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0591.1
Alt. Name Bach1::Mafk
Database JASPAR_CORE_2014.meme
p-value 5.89245e-06
E-value 0.00349422
q-value 0.000552236
Overlap 8
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0099.2
Alt. Name JUN::FOS
Database JASPAR_CORE_2014.meme
p-value 8.11971e-06
E-value 0.00481499
q-value 0.000672659
Overlap 7
Offset -1
Orientation Normal
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Summary 

Alignment 

Name MA0150.2
Alt. Name Nfe2l2
Database JASPAR_CORE_2014.meme
p-value 1.037e-05
E-value 0.00614941
q-value 0.000801808
Overlap 8
Offset 4
Orientation Normal
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Summary 

Alignment 

Name MA0462.1
Alt. Name BATF::JUN
Database JASPAR_CORE_2014.meme
p-value 3.00677e-05
E-value 0.0178302
q-value 0.0016606
Overlap 8
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0272.1
Alt. Name ARG81
Database JASPAR_CORE_2014.meme
p-value 3.26148e-05
E-value 0.0193406
q-value 0.00171939
Overlap 8
Offset 0
Orientation Normal
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Matches to Query: BATTGGCY

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Summary 

Alignment 

Name MA0314.1
Alt. Name HAP3
Database JASPAR_CORE_2014.meme
p-value 6.35925e-06
E-value 0.00377103
q-value 0.00752883
Overlap 8
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0502.1
Alt. Name NFYB
Database JASPAR_CORE_2014.meme
p-value 2.16176e-05
E-value 0.0128192
q-value 0.0127967
Overlap 8
Offset 2
Orientation Reverse Complement
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Matches to Query: TGACGTMA

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Summary 

Alignment 

Name MA0018.2
Alt. Name CREB1
Database JASPAR_CORE_2014.meme
p-value 1.07549e-06
E-value 0.000637767
q-value 0.000838903
Overlap 8
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0286.1
Alt. Name CST6
Database JASPAR_CORE_2014.meme
p-value 3.1062e-05
E-value 0.0184197
q-value 0.012175
Overlap 8
Offset 1
Orientation Normal
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Matches to Query: ASGWGG

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Matches to Query: CYGGRA

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Matches to Query: AAVATGGC

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Summary 

Alignment 

Name MA0095.2
Alt. Name YY1
Database JASPAR_CORE_2014.meme
p-value 3.75586e-07
E-value 0.000222723
q-value 0.000445445
Overlap 8
Offset 1
Orientation Normal
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Matches to Query: GCGGCKGC

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Matches to Query: AGRGGGCG

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Summary 

Alignment 

Name MA0443.1
Alt. Name btd
Database JASPAR_CORE_2014.meme
p-value 7.90109e-06
E-value 0.00468534
q-value 0.00930661
Overlap 8
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0139.1
Alt. Name CTCF
Database JASPAR_CORE_2014.meme
p-value 2.88762e-05
E-value 0.0171236
q-value 0.0161547
Overlap 8
Offset 8
Orientation Normal
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Summary 

Alignment 

Name MA0155.1
Alt. Name INSM1
Database JASPAR_CORE_2014.meme
p-value 4.11449e-05
E-value 0.0243989
q-value 0.0161547
Overlap 8
Offset 4
Orientation Normal
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Summary 

Alignment 

Name MA0516.1
Alt. Name SP2
Database JASPAR_CORE_2014.meme
p-value 7.62039e-05
E-value 0.0451889
q-value 0.02244
Overlap 8
Offset 3
Orientation Reverse Complement
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Matches to Query: GCATGCGC

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Summary 

Alignment 

Name MA0565.1
Alt. Name FUS3
Database JASPAR_CORE_2014.meme
p-value 4.09044e-06
E-value 0.00242563
q-value 0.0048135
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0506.1
Alt. Name NRF1
Database JASPAR_CORE_2014.meme
p-value 1.85655e-05
E-value 0.0110093
q-value 0.00863558
Overlap 8
Offset 2
Orientation Normal
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Matches to Query: RACTACA

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Matches to Query: TTTAAAWR

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Matches to Query: GGGCGTGK

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Summary 

Alignment 

Name MA0039.2
Alt. Name Klf4
Database JASPAR_CORE_2014.meme
p-value 3.45118e-05
E-value 0.0204655
q-value 0.0396142
Overlap 8
Offset 1
Orientation Normal
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Matches to Query: AGCAGCWG

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Matches to Query: CCTKTAA

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Matches to Query: CCWGGA

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Matches to Query: GSGCGGGA

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Summary 

Alignment 

Name MA0290.1
Alt. Name DAL81
Database JASPAR_CORE_2014.meme
p-value 1.17981e-06
E-value 0.000699625
q-value 0.000608268
Overlap 8
Offset 9
Orientation Normal
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Summary 

Alignment 

Name MA0470.1
Alt. Name E2F4
Database JASPAR_CORE_2014.meme
p-value 1.49047e-06
E-value 0.000883847
q-value 0.000608268
Overlap 8
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0469.1
Alt. Name E2F3
Database JASPAR_CORE_2014.meme
p-value 1.55319e-06
E-value 0.000921042
q-value 0.000608268
Overlap 8
Offset 6
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0024.2
Alt. Name E2F1
Database JASPAR_CORE_2014.meme
p-value 3.57151e-06
E-value 0.0021179
q-value 0.000944789
Overlap 8
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0471.1
Alt. Name E2F6
Database JASPAR_CORE_2014.meme
p-value 4.02081e-06
E-value 0.00238434
q-value 0.000944789
Overlap 8
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0410.1
Alt. Name UGA3
Database JASPAR_CORE_2014.meme
p-value 7.49284e-06
E-value 0.00444325
q-value 0.00146719
Overlap 8
Offset 0
Orientation Normal
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Matches to Query: GATTGGTY

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Summary 

Alignment 

Name MA0060.2
Alt. Name NFYA
Database JASPAR_CORE_2014.meme
p-value 6.65022e-06
E-value 0.00394358
q-value 0.00788669
Overlap 8
Offset 8
Orientation Normal
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Summary 

Alignment 

Name MA0502.1
Alt. Name NFYB
Database JASPAR_CORE_2014.meme
p-value 2.49684e-05
E-value 0.0148063
q-value 0.0148054
Overlap 8
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0314.1
Alt. Name HAP3
Database JASPAR_CORE_2014.meme
p-value 7.72398e-05
E-value 0.0458032
q-value 0.0305336
Overlap 8
Offset 3
Orientation Normal
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Matches to Query: AAATA

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Matches to Query: CGCGCTSC

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Matches to Query: CACRCACA

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Summary 

Alignment 

Name MA0538.1
Alt. Name DAF-12
Database JASPAR_CORE_2014.meme
p-value 5.26666e-05
E-value 0.0312313
q-value 0.0624626
Overlap 8
Offset 4
Orientation Reverse Complement
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Matches to Query: RGGAA

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Matches to Query: ATTASTCA

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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 first motif database):
A: 0.250   C: 0.250   G: 0.250   T: 0.250

Result calculation took 7.151 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.