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
5 MA0036.2 (GATA2),  MA0482.1 (Gata4),  MA0035.3 (Gata1),  MA0140.2 (TAL1::GATA1),  MA0037.2 (GATA3)
CABCTGB
CATCTGC
2 MA0091.1 (TAL1::TCF3),  MA0461.1 (Atoh1)
AGATA
AGATA
0
GATWA
GATTA
1 MA0212.1 (bcd)
CCMCDCCC
CCCCACCC
5 MA0599.1 (KLF5),  MA0039.2 (Klf4),  MA0493.1 (Klf1),  MA0079.3 (SP1),  MA0162.2 (EGR1)
GBCTGK
GCCTGG
0
TGTGKB
TGTGTG
0
TGAGTCAB
TGAGTCAT
13 MA0591.1 (Bach1::Mafk),  MA0491.1 (JUND),  MA0476.1 (FOS),  MA0501.1 (NFE2::MAF),  MA0478.1 (FOSL2),  MA0490.1 (JUNB),  MA0477.1 (FOSL1),  MA0099.2 (JUN::FOS),  MA0150.2 (Nfe2l2),  MA0489.1 (JUN)
CNGCCTCC
CAGCCTCC
0
RDAAACA
AAAAACA
0
STGATA
CTGATA
0
BTTCCY
CTTCCT
3 MA0518.1 (Stat4),  MA0137.3 (STAT1),  MA0080.3 (Spi1)
GCCACYGC
GCCACTGC
0
CAGGCRK
CAGGCAG
0
AAAHAAAA
AAAAAAAA
0
CCTCCCAC
CCTCCCAC
0
RAGGTCA
GAGGTCA
7 MA0512.1 (Rxra),  MA0160.1 (NR4A2),  MA0071.1 (RORA_1),  MA0504.1 (NR2C2),  MA0115.1 (NR1H2::RXRA),  MA0141.2 (Esrrb),  MA0592.1 (ESRRA)
CTGCDGCC
CTGCAGCC
0
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)
AMCATRTG
AACATATG
1 MA0249.1 (twi)
CMCRG
CCCAG
0
GGAAA
GGAAA
0
SAGAAA
GAGAAA
0
AAWGTGCT
AAAGTGCT
0
CTGSCTTC
CTGCCTTC
0
AAAMATAC
AAAAATAC
0
CRCCRCC
CACCACC
0
GAMAGGGA
GACAGGGA
0
GYGACAGA
GTGACAGA
2 MA0513.1 (SMAD2::SMAD3::SMAD4),  MA0207.1 (achi)
GRAACAGA
GGAACAGA
0
TCAAGCGA
TCAAGCGA
0
TCACTGCA
TCACTGCA
0
CCGCAGKG
CCGCAGTG
0
CTYCTGC
CTCCTGC
0
CTCGTTAA
CTCGTTAA
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

JASPAR_CORE_2014.meme 593 58

Matches to Query: HGATAA

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Summary 

Alignment 

Name MA0036.2
Alt. Name GATA2
Database JASPAR_CORE_2014.meme
p-value 2.11032e-06
E-value 0.00125142
q-value 0.00249208
Overlap 6
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0482.1
Alt. Name Gata4
Database JASPAR_CORE_2014.meme
p-value 4.46975e-06
E-value 0.00265056
q-value 0.00263918
Overlap 6
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0035.3
Alt. Name Gata1
Database JASPAR_CORE_2014.meme
p-value 1.52199e-05
E-value 0.0090254
q-value 0.00599108
Overlap 6
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0140.2
Alt. Name TAL1::GATA1
Database JASPAR_CORE_2014.meme
p-value 3.29762e-05
E-value 0.0195549
q-value 0.00973542
Overlap 6
Offset 11
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0037.2
Alt. Name GATA3
Database JASPAR_CORE_2014.meme
p-value 4.30947e-05
E-value 0.0255552
q-value 0.0101781
Overlap 6
Offset 0
Orientation Normal
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Matches to Query: CABCTGB

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Summary 

Alignment 

Name MA0091.1
Alt. Name TAL1::TCF3
Database JASPAR_CORE_2014.meme
p-value 1.89048e-05
E-value 0.0112105
q-value 0.0221727
Overlap 7
Offset 4
Orientation Normal
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Summary 

Alignment 

Name MA0461.1
Alt. Name Atoh1
Database JASPAR_CORE_2014.meme
p-value 7.65636e-05
E-value 0.0454022
q-value 0.0304804
Overlap 6
Offset 2
Orientation Reverse Complement
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Matches to Query: AGATA

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Matches to Query: GATWA

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Summary 

Alignment 

Name MA0212.1
Alt. Name bcd
Database JASPAR_CORE_2014.meme
p-value 2.41034e-05
E-value 0.0142933
q-value 0.027457
Overlap 5
Offset 1
Orientation Reverse Complement
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Matches to Query: CCMCDCCC

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Summary 

Alignment 

Name MA0599.1
Alt. Name KLF5
Database JASPAR_CORE_2014.meme
p-value 6.24146e-08
E-value 3.70119e-05
q-value 7.33293e-05
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 1.52333e-07
E-value 9.03335e-05
q-value 8.94861e-05
Overlap 8
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0493.1
Alt. Name Klf1
Database JASPAR_CORE_2014.meme
p-value 3.32681e-06
E-value 0.0019728
q-value 0.00130286
Overlap 8
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0079.3
Alt. Name SP1
Database JASPAR_CORE_2014.meme
p-value 2.64264e-05
E-value 0.0156709
q-value 0.00776194
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 7.01456e-05
E-value 0.0415963
q-value 0.0164824
Overlap 8
Offset 1
Orientation Normal
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Matches to Query: GBCTGK

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Matches to Query: TGTGKB

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Matches to Query: TGAGTCAB

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Summary 

Alignment 

Name MA0591.1
Alt. Name Bach1::Mafk
Database JASPAR_CORE_2014.meme
p-value 6.24496e-07
E-value 0.000370326
q-value 0.000723035
Overlap 8
Offset 4
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0491.1
Alt. Name JUND
Database JASPAR_CORE_2014.meme
p-value 2.22371e-06
E-value 0.00131866
q-value 0.00101087
Overlap 8
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0476.1
Alt. Name FOS
Database JASPAR_CORE_2014.meme
p-value 3.28915e-06
E-value 0.00195047
q-value 0.00101087
Overlap 8
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0501.1
Alt. Name NFE2::MAF
Database JASPAR_CORE_2014.meme
p-value 5.44517e-06
E-value 0.00322899
q-value 0.00101087
Overlap 8
Offset 7
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0478.1
Alt. Name FOSL2
Database JASPAR_CORE_2014.meme
p-value 5.45622e-06
E-value 0.00323554
q-value 0.00101087
Overlap 8
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0490.1
Alt. Name JUNB
Database JASPAR_CORE_2014.meme
p-value 5.45622e-06
E-value 0.00323554
q-value 0.00101087
Overlap 8
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0477.1
Alt. Name FOSL1
Database JASPAR_CORE_2014.meme
p-value 6.35558e-06
E-value 0.00376886
q-value 0.00101087
Overlap 8
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0099.2
Alt. Name JUN::FOS
Database JASPAR_CORE_2014.meme
p-value 7.59105e-06
E-value 0.00450149
q-value 0.00101087
Overlap 7
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0150.2
Alt. Name Nfe2l2
Database JASPAR_CORE_2014.meme
p-value 7.85795e-06
E-value 0.00465977
q-value 0.00101087
Overlap 8
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0489.1
Alt. Name JUN
Database JASPAR_CORE_2014.meme
p-value 9.54836e-06
E-value 0.00566218
q-value 0.0011055
Overlap 8
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0303.1
Alt. Name GCN4
Database JASPAR_CORE_2014.meme
p-value 2.9617e-05
E-value 0.0175629
q-value 0.00311729
Overlap 8
Offset 7
Orientation Normal
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Summary 

Alignment 

Name MA0272.1
Alt. Name ARG81
Database JASPAR_CORE_2014.meme
p-value 3.25192e-05
E-value 0.0192839
q-value 0.00313753
Overlap 8
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0462.1
Alt. Name BATF::JUN
Database JASPAR_CORE_2014.meme
p-value 6.89259e-05
E-value 0.0408731
q-value 0.00469422
Overlap 8
Offset 0
Orientation Reverse Complement
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Matches to Query: CNGCCTCC

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Matches to Query: RDAAACA

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Matches to Query: STGATA

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Matches to Query: BTTCCY

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Summary 

Alignment 

Name MA0518.1
Alt. Name Stat4
Database JASPAR_CORE_2014.meme
p-value 5.16111e-05
E-value 0.0306054
q-value 0.0266749
Overlap 6
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0137.3
Alt. Name STAT1
Database JASPAR_CORE_2014.meme
p-value 7.40066e-05
E-value 0.0438859
q-value 0.0266749
Overlap 6
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0080.3
Alt. Name Spi1
Database JASPAR_CORE_2014.meme
p-value 7.45394e-05
E-value 0.0442019
q-value 0.0266749
Overlap 6
Offset 3
Orientation Reverse Complement
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Matches to Query: GCCACYGC

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Matches to Query: CAGGCRK

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Matches to Query: AAAHAAAA

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Matches to Query: CCTCCCAC

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Matches to Query: RAGGTCA

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Summary 

Alignment 

Name MA0512.1
Alt. Name Rxra
Database JASPAR_CORE_2014.meme
p-value 3.19131e-06
E-value 0.00189245
q-value 0.00362314
Overlap 7
Offset 2
Orientation Normal
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Summary 

Alignment 

Name MA0160.1
Alt. Name NR4A2
Database JASPAR_CORE_2014.meme
p-value 6.21021e-06
E-value 0.00368266
q-value 0.00362314
Overlap 7
Offset 0
Orientation Normal
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Summary 

Alignment 

Name MA0071.1
Alt. Name RORA_1
Database JASPAR_CORE_2014.meme
p-value 1.74991e-05
E-value 0.0103769
q-value 0.00547294
Overlap 7
Offset 3
Orientation Normal
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Summary 

Alignment 

Name MA0504.1
Alt. Name NR2C2
Database JASPAR_CORE_2014.meme
p-value 1.91881e-05
E-value 0.0113786
q-value 0.00547294
Overlap 7
Offset 8
Orientation Normal
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Summary 

Alignment 

Name MA0115.1
Alt. Name NR1H2::RXRA
Database JASPAR_CORE_2014.meme
p-value 2.34521e-05
E-value 0.0139071
q-value 0.00547294
Overlap 7
Offset 1
Orientation Normal
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Summary 

Alignment 

Name MA0141.2
Alt. Name Esrrb
Database JASPAR_CORE_2014.meme
p-value 4.37641e-05
E-value 0.0259521
q-value 0.00851091
Overlap 7
Offset 5
Orientation Normal
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Summary 

Alignment 

Name MA0592.1
Alt. Name ESRRA
Database JASPAR_CORE_2014.meme
p-value 5.96482e-05
E-value 0.0353714
q-value 0.00994279
Overlap 7
Offset 2
Orientation Normal
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Matches to Query: CTGCDGCC

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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: AMCATRTG

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Summary 

Alignment 

Name MA0249.1
Alt. Name twi
Database JASPAR_CORE_2014.meme
p-value 3.68231e-05
E-value 0.0218361
q-value 0.043481
Overlap 8
Offset 1
Orientation Reverse Complement
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Matches to Query: CMCRG

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Matches to Query: GGAAA

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Matches to Query: SAGAAA

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Matches to Query: AAWGTGCT

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Matches to Query: CTGSCTTC

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Matches to Query: AAAMATAC

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Matches to Query: CRCCRCC

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Matches to Query: GAMAGGGA

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Matches to Query: GYGACAGA

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Summary 

Alignment 

Name MA0513.1
Alt. Name SMAD2::SMAD3::SMAD4
Database JASPAR_CORE_2014.meme
p-value 7.127e-05
E-value 0.0422631
q-value 0.0451121
Overlap 8
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name MA0207.1
Alt. Name achi
Database JASPAR_CORE_2014.meme
p-value 7.61434e-05
E-value 0.045153
q-value 0.0451121
Overlap 6
Offset -1
Orientation Normal
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Matches to Query: GRAACAGA

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Matches to Query: TCAAGCGA

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Matches to Query: TCACTGCA

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Matches to Query: CCGCAGKG

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Matches to Query: CTYCTGC

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Matches to Query: CTCGTTAA

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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 8.227 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.