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
TKDYGCAA	TTGTGCAA	2	MA0466.1 (CEBPB), MA0102.3 (CEBPA)
AGGCWGGA	AGGCTGGA	0
CAGTGAGC	CAGTGAGC	0
TTGDGWAA	TTGTGAAA	0
CVRCCTCC	CAGCCTCC	0
RTGASTCA	ATGACTCA	13	MA0303.1 (GCN4), MA0490.1 (JUNB), MA0478.1 (FOSL2), MA0489.1 (JUN), MA0491.1 (JUND), MA0477.1 (FOSL1), MA0476.1 (FOS), MA0591.1 (Bach1::Mafk), MA0501.1 (NFE2::MAF), MA0462.1 (BATF::JUN)
TTGCYYAA	TTGCTCAA	0
CTGYCDCC	CTGTCTCC	0
RTAAAYA	GTAAACA	7	MA0297.1 (FKH2), MA0047.2 (Foxa2), MA0030.1 (FOXF2), MA0458.1 (slp1), MA0593.1 (FOXP2), MA0031.1 (FOXD1), MA0148.3 (FOXA1)
AAWAMAAA	AAAAAAAA	0
CYRTCTC	CTGTCTC	0
CCCRGS	CCCAGC	0
TKAYGWAA	TGATGAAA	0
AYTACAGG	ATTACAGG	0
AGYGARAC	AGTGAGAC	0
ATCRCTTG	ATCACTTG	0
CCMCRCCC	CCCCACCC	6	MA0039.2 (Klf4), MA0599.1 (KLF5), MA0493.1 (Klf1), MA0079.3 (SP1), MA0162.2 (EGR1), MA0472.1 (EGR2)
AAATA	AAATA	0
RCATTCCW	ACATTCCA	2	MA0090.1 (TEAD1), MA0406.1 (TEC1)
AGCAAGAC	AGCAAGAC	0
GGGMGGR	GGGAGGG	1	MA0079.3 (SP1)
CWGGAR	CTGGAG	0
GGSCAACA	GGGCAACA	0
TGWGGHAA	TGAGGCAA	0
ATTGCTTS	ATTGCTTG	0
AGCYGAGA	AGCTGAGA	0
AGGYTGCA	AGGCTGCA	0
AACCDGTT	AACCAGTT	0
GCCACCRY	GCCACCAC	0
AGATAAV	AGATAAA	5	MA0037.2 (GATA3), MA0035.3 (Gata1), MA0029.1 (Mecom), MA0482.1 (Gata4), MA0036.2 (GATA2)
ACACACMC	ACACACAC	1	MA0538.1 (DAF-12)
DGCAAACA	AGCAAACA	2	MA0446.1 (fkh), MA0546.1 (PHA-4)
AGGAAR	AGGAAA	2	MA0156.1 (FEV), MA0474.1 (Erg)
CCTCRGSC	CCTCAGGC	0
TGKYGAAA	TGTTGAAA	0
ATTAGYCA	ATTAGTCA	0
AGAKGGCR	AGAGGGCA	0
CCWCCCAS	CCACCCAC	1	MA0472.1 (EGR2)
CAYCACCA	CACCACCA	0
ATGAWTCA	ATGAATCA	0
TCTGRGWA	TCTGAGAA	0
ABGTCAC	AGGTCAC	1	MA0160.1 (NR4A2)
AGCCARGA	AGCCAAGA	0
TTTWAAAW	TTTAAAAA	0
TGKCGTAA	TGTCGTAA	0
CMGCCTC	CAGCCTC	0
CGTGAVCC	CGTGAGCC	0
GAATRTAC	GAATGTAC	0
GTCTCRAA	GTCTCAAA	0
AGRSAGA	AGGGAGA	0
CCGGAAGY	CCGGAAGT	4	MA0062.2 (GABPA), MA0076.2 (ELK4), MA0026.1 (Eip74EF), MA0028.1 (ELK1)
CTGCACTC	CTGCACTC	0
ATGASTAA	ATGAGTAA	0
GGGTGACA	GGGTGACA	0
TCACSTGA	TCACCTGA	2	MA0086.1 (sna), MA0583.1 (RAV1)
TKTTGTAA	TTTTGTAA	0
GCCTGGCY	GCCTGGCC	0
CCTCCCAA	CCTCCCAA	0
TACAGTMA	TACAGTCA	0
AGTAGCTR	AGTAGCTG	0
CTCCACCC	CTCCACCC	0
ATAMCATC	ATAACATC	0
AAACAGR	AAACAGA	0
AGGKGGCG	AGGGGGCG	5	MA0373.1 (RPN4), MA0139.1 (CTCF), MA0443.1 (btd), MA0531.1 (CTCF), MA0155.1 (INSM1)
CCCTKCCC	CCCTGCCC	0
TTACAGAR	TTACAGAA	0
CATTTCY	CATTTCT	0
TTACYTAA	TTACTTAA	0
AAATTCCT	AAATTCCT	0
CGGGTTCA	CGGGTTCA	0
TGTCAACA	TGTCAACA	0
AAACAAAC	AAACAAAC	1	MA0041.1 (Foxd3)
AARTGTAC	AAGTGTAC	0
TTGCYAAA	TTGCCAAA	0
CSGCGGC	CGGCGGC	2	MA0290.1 (DAL81), MA0412.1 (UME6)
ATGACCTC	ATGACCTC	0
ACASAGCC	ACACAGCC	0
RAAAGAAA	AAAAGAAA	1	MA0277.1 (AZF1)
CTGAGTCA	CTGAGTCA	7	MA0591.1 (Bach1::Mafk), MA0501.1 (NFE2::MAF), MA0150.2 (Nfe2l2), MA0099.2 (JUN::FOS), MA0478.1 (FOSL2), MA0490.1 (JUNB), MA0477.1 (FOSL1)
AGGCGKG	AGGCGGG	0
CCACTAGR	CCACTAGA	0
CACGTGWC	CACGTGTC	12	MA0552.1 (PIL5), MA0580.1 (DYT1), MA0004.1 (Arnt), MA0310.1 (HAC1), MA0570.1 (ABF1), MA0464.1 (Bhlhe40), MA0550.1 (BZR1), MA0409.1 (TYE7), MA0093.2 (USF1), MA0551.1 (HY5)

Target Databases

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Database	Number of Motifs	Motifs Matched
JASPAR_CORE_2014.meme	593	68

Matches to Query: TKDYGCAA

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Summary

Alignment

Name	MA0466.1
Alt. Name	CEBPB
Database	JASPAR_CORE_2014.meme
p-value	2.30438e-08
E-value	1.3665e-05
q-value	2.7282e-05
Overlap	8
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0102.3
Alt. Name	CEBPA
Database	JASPAR_CORE_2014.meme
p-value	1.46021e-07
E-value	8.65905e-05
q-value	8.64386e-05
Overlap	8
Offset	2
Orientation	Reverse Complement

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Matches to Query: AGGCWGGA

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Matches to Query: CAGTGAGC

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Matches to Query: TTGDGWAA

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Matches to Query: CVRCCTCC

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Matches to Query: RTGASTCA

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Summary

Alignment

Name	MA0303.1
Alt. Name	GCN4
Database	JASPAR_CORE_2014.meme
p-value	9.04724e-11
E-value	5.36502e-08
q-value	1.04077e-07
Overlap	8
Offset	6
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0490.1
Alt. Name	JUNB
Database	JASPAR_CORE_2014.meme
p-value	1.79319e-10
E-value	1.06336e-07
q-value	1.04077e-07
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	6.55383e-10
E-value	3.88642e-07
q-value	1.90193e-07
Overlap	8
Offset	2
Orientation	Normal

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Summary

Alignment

Name	MA0489.1
Alt. Name	JUN
Database	JASPAR_CORE_2014.meme
p-value	1.14692e-09
E-value	6.80124e-07
q-value	2.6627e-07
Overlap	8
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0491.1
Alt. Name	JUND
Database	JASPAR_CORE_2014.meme
p-value	3.78511e-09
E-value	2.24457e-06
q-value	7.32296e-07
Overlap	8
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0477.1
Alt. Name	FOSL1
Database	JASPAR_CORE_2014.meme
p-value	2.07764e-08
E-value	1.23204e-05
q-value	3.44533e-06
Overlap	8
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0476.1
Alt. Name	FOS
Database	JASPAR_CORE_2014.meme
p-value	4.83517e-08
E-value	2.86726e-05
q-value	7.01586e-06
Overlap	8
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0591.1
Alt. Name	Bach1::Mafk
Database	JASPAR_CORE_2014.meme
p-value	3.63251e-07
E-value	0.000215408
q-value	3.83331e-05
Overlap	8
Offset	3
Orientation	Normal

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Summary

Alignment

Name	MA0501.1
Alt. Name	NFE2::MAF
Database	JASPAR_CORE_2014.meme
p-value	6.26974e-07
E-value	0.000371796
q-value	5.16704e-05
Overlap	8
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0462.1
Alt. Name	BATF::JUN
Database	JASPAR_CORE_2014.meme
p-value	6.6769e-07
E-value	0.00039594
q-value	5.16704e-05
Overlap	8
Offset	3
Orientation	Normal

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Summary

Alignment

Name	MA0150.2
Alt. Name	Nfe2l2
Database	JASPAR_CORE_2014.meme
p-value	8.09336e-07
E-value	0.000479936
q-value	5.83774e-05
Overlap	8
Offset	4
Orientation	Normal

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Summary

Alignment

Name	MA0099.2
Alt. Name	JUN::FOS
Database	JASPAR_CORE_2014.meme
p-value	1.54135e-05
E-value	0.00914023
q-value	0.000894605
Overlap	7
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	MA0272.1
Alt. Name	ARG81
Database	JASPAR_CORE_2014.meme
p-value	6.39312e-05
E-value	0.0379112
q-value	0.00337325
Overlap	8
Offset	0
Orientation	Normal

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Matches to Query: TTGCYYAA

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Matches to Query: CTGYCDCC

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Matches to Query: RTAAAYA

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Summary

Alignment

Name	MA0297.1
Alt. Name	FKH2
Database	JASPAR_CORE_2014.meme
p-value	3.24911e-05
E-value	0.0192672
q-value	0.0120214
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0047.2
Alt. Name	Foxa2
Database	JASPAR_CORE_2014.meme
p-value	3.9599e-05
E-value	0.0234822
q-value	0.0120214
Overlap	7
Offset	5
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0030.1
Alt. Name	FOXF2
Database	JASPAR_CORE_2014.meme
p-value	4.35563e-05
E-value	0.0258289
q-value	0.0120214
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0458.1
Alt. Name	slp1
Database	JASPAR_CORE_2014.meme
p-value	6.78377e-05
E-value	0.0402277
q-value	0.0120214
Overlap	7
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0593.1
Alt. Name	FOXP2
Database	JASPAR_CORE_2014.meme
p-value	6.78377e-05
E-value	0.0402277
q-value	0.0120214
Overlap	7
Offset	2
Orientation	Normal

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Summary

Alignment

Name	MA0031.1
Alt. Name	FOXD1
Database	JASPAR_CORE_2014.meme
p-value	7.15148e-05
E-value	0.0424083
q-value	0.0120214
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0148.3
Alt. Name	FOXA1
Database	JASPAR_CORE_2014.meme
p-value	7.17471e-05
E-value	0.042546
q-value	0.0120214
Overlap	7
Offset	4
Orientation	Reverse Complement

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Matches to Query: AAWAMAAA

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Matches to Query: CYRTCTC

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Matches to Query: CCCRGS

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Matches to Query: TKAYGWAA

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Matches to Query: AYTACAGG

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Matches to Query: AGYGARAC

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Matches to Query: ATCRCTTG

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Matches to Query: CCMCRCCC

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Summary

Alignment

Name	MA0039.2
Alt. Name	Klf4
Database	JASPAR_CORE_2014.meme
p-value	2.29009e-09
E-value	1.35802e-06
q-value	2.68136e-06
Overlap	8
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0599.1
Alt. Name	KLF5
Database	JASPAR_CORE_2014.meme
p-value	9.46833e-08
E-value	5.61472e-05
q-value	5.54302e-05
Overlap	8
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0493.1
Alt. Name	Klf1
Database	JASPAR_CORE_2014.meme
p-value	3.09638e-06
E-value	0.00183615
q-value	0.00120847
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	2.40593e-05
E-value	0.0142672
q-value	0.00704249
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	3.15598e-05
E-value	0.0187149
q-value	0.00739038
Overlap	8
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0472.1
Alt. Name	EGR2
Database	JASPAR_CORE_2014.meme
p-value	4.37607e-05
E-value	0.0259501
q-value	0.00853956
Overlap	8
Offset	1
Orientation	Normal

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Matches to Query: AAATA

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Matches to Query: RCATTCCW

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Summary

Alignment

Name	MA0090.1
Alt. Name	TEAD1
Database	JASPAR_CORE_2014.meme
p-value	7.2521e-08
E-value	4.3005e-05
q-value	8.601e-05
Overlap	8
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0406.1
Alt. Name	TEC1
Database	JASPAR_CORE_2014.meme
p-value	3.80436e-05
E-value	0.0225599
q-value	0.0225599
Overlap	8
Offset	0
Orientation	Normal

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Matches to Query: AGCAAGAC

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Matches to Query: GGGMGGR

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Summary

Alignment

Name	MA0079.3
Alt. Name	SP1
Database	JASPAR_CORE_2014.meme
p-value	8.14476e-05
E-value	0.0482984
q-value	0.0960181
Overlap	7
Offset	2
Orientation	Reverse Complement

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Matches to Query: CWGGAR

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Matches to Query: GGSCAACA

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Matches to Query: TGWGGHAA

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Matches to Query: ATTGCTTS

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Matches to Query: AGCYGAGA

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Matches to Query: AGGYTGCA

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Matches to Query: AACCDGTT

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Matches to Query: GCCACCRY

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Matches to Query: AGATAAV

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Summary

Alignment

Name	MA0037.2
Alt. Name	GATA3
Database	JASPAR_CORE_2014.meme
p-value	5.54794e-06
E-value	0.00328993
q-value	0.00654601
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0035.3
Alt. Name	Gata1
Database	JASPAR_CORE_2014.meme
p-value	4.49388e-05
E-value	0.0266487
q-value	0.0155259
Overlap	7
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0029.1
Alt. Name	Mecom
Database	JASPAR_CORE_2014.meme
p-value	5.11212e-05
E-value	0.0303149
q-value	0.0155259
Overlap	7
Offset	6
Orientation	Normal

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Summary

Alignment

Name	MA0482.1
Alt. Name	Gata4
Database	JASPAR_CORE_2014.meme
p-value	5.26347e-05
E-value	0.0312124
q-value	0.0155259
Overlap	7
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0036.2
Alt. Name	GATA2
Database	JASPAR_CORE_2014.meme
p-value	8.42142e-05
E-value	0.049939
q-value	0.0198729
Overlap	7
Offset	2
Orientation	Reverse Complement

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Matches to Query: ACACACMC

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Summary

Alignment

Name	MA0538.1
Alt. Name	DAF-12
Database	JASPAR_CORE_2014.meme
p-value	7.23174e-05
E-value	0.0428842
q-value	0.0857685
Overlap	8
Offset	5
Orientation	Reverse Complement

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Matches to Query: DGCAAACA

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Summary

Alignment

Name	MA0446.1
Alt. Name	fkh
Database	JASPAR_CORE_2014.meme
p-value	5.45738e-05
E-value	0.0323623
q-value	0.0468902
Overlap	8
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0546.1
Alt. Name	PHA-4
Database	JASPAR_CORE_2014.meme
p-value	7.96174e-05
E-value	0.0472131
q-value	0.0468902
Overlap	8
Offset	2
Orientation	Normal

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Matches to Query: AGGAAR

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Summary

Alignment

Name	MA0156.1
Alt. Name	FEV
Database	JASPAR_CORE_2014.meme
p-value	1.12563e-05
E-value	0.00667496
q-value	0.0132134
Overlap	6
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0474.1
Alt. Name	Erg
Database	JASPAR_CORE_2014.meme
p-value	8.01297e-05
E-value	0.0475169
q-value	0.0452122
Overlap	6
Offset	2
Orientation	Normal

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Matches to Query: CCTCRGSC

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Matches to Query: TGKYGAAA

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Matches to Query: ATTAGYCA

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Matches to Query: AGAKGGCR

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Matches to Query: CCWCCCAS

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Summary

Alignment

Name	MA0472.1
Alt. Name	EGR2
Database	JASPAR_CORE_2014.meme
p-value	8.17125e-05
E-value	0.0484555
q-value	0.0966589
Overlap	8
Offset	3
Orientation	Normal

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Matches to Query: CAYCACCA

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Matches to Query: ATGAWTCA

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Matches to Query: TCTGRGWA

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Matches to Query: ABGTCAC

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Summary

Alignment

Name	MA0160.1
Alt. Name	NR4A2
Database	JASPAR_CORE_2014.meme
p-value	5.36133e-05
E-value	0.0317927
q-value	0.0627113
Overlap	7
Offset	1
Orientation	Normal

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Matches to Query: AGCCARGA

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Matches to Query: TTTWAAAW

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Matches to Query: TGKCGTAA

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Matches to Query: CMGCCTC

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Matches to Query: CGTGAVCC

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Matches to Query: GAATRTAC

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Matches to Query: GTCTCRAA

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Matches to Query: AGRSAGA

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Matches to Query: CCGGAAGY

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Summary

Alignment

Name	MA0062.2
Alt. Name	GABPA
Database	JASPAR_CORE_2014.meme
p-value	2.6731e-07
E-value	0.000158515
q-value	0.000155684
Overlap	8
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0076.2
Alt. Name	ELK4
Database	JASPAR_CORE_2014.meme
p-value	2.6731e-07
E-value	0.000158515
q-value	0.000155684
Overlap	8
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0026.1
Alt. Name	Eip74EF
Database	JASPAR_CORE_2014.meme
p-value	6.28262e-06
E-value	0.0037256
q-value	0.00243938
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0028.1
Alt. Name	ELK1
Database	JASPAR_CORE_2014.meme
p-value	7.71963e-05
E-value	0.0457774
q-value	0.0212823
Overlap	7
Offset	3
Orientation	Normal

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Matches to Query: CTGCACTC

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Matches to Query: ATGASTAA

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Matches to Query: GGGTGACA

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Matches to Query: TCACSTGA

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Summary

Alignment

Name	MA0086.1
Alt. Name	sna
Database	JASPAR_CORE_2014.meme
p-value	2.0244e-06
E-value	0.00120047
q-value	0.00237638
Overlap	6
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0583.1
Alt. Name	RAV1
Database	JASPAR_CORE_2014.meme
p-value	5.98091e-05
E-value	0.0354668
q-value	0.035104
Overlap	8
Offset	1
Orientation	Normal

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Matches to Query: TKTTGTAA

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Matches to Query: GCCTGGCY

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Matches to Query: CCTCCCAA

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Matches to Query: TACAGTMA

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Matches to Query: AGTAGCTR

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Matches to Query: CTCCACCC

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Matches to Query: ATAMCATC

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Matches to Query: AAACAGR

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Matches to Query: AGGKGGCG

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Summary

Alignment

Name	MA0373.1
Alt. Name	RPN4
Database	JASPAR_CORE_2014.meme
p-value	5.33956e-06
E-value	0.00316636
q-value	0.00627868
Overlap	7
Offset	-1
Orientation	Normal

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Summary

Alignment

Name	MA0139.1
Alt. Name	CTCF
Database	JASPAR_CORE_2014.meme
p-value	1.6496e-05
E-value	0.0097821
q-value	0.00969863
Overlap	8
Offset	8
Orientation	Normal

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Summary

Alignment

Name	MA0443.1
Alt. Name	btd
Database	JASPAR_CORE_2014.meme
p-value	2.94262e-05
E-value	0.0174497
q-value	0.0115339
Overlap	8
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0531.1
Alt. Name	CTCF
Database	JASPAR_CORE_2014.meme
p-value	4.29371e-05
E-value	0.0254617
q-value	0.0126222
Overlap	8
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0155.1
Alt. Name	INSM1
Database	JASPAR_CORE_2014.meme
p-value	8.38725e-05
E-value	0.0497364
q-value	0.0197248
Overlap	8
Offset	4
Orientation	Normal

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Matches to Query: CCCTKCCC

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Matches to Query: TTACAGAR

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Matches to Query: CATTTCY

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Matches to Query: TTACYTAA

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Matches to Query: AAATTCCT

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Matches to Query: CGGGTTCA

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Matches to Query: TGTCAACA

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Matches to Query: AAACAAAC

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Summary

Alignment

Name	MA0041.1
Alt. Name	Foxd3
Database	JASPAR_CORE_2014.meme
p-value	5.1073e-05
E-value	0.0302863
q-value	0.0603637
Overlap	8
Offset	0
Orientation	Reverse Complement

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Matches to Query: AARTGTAC

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Matches to Query: TTGCYAAA

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Matches to Query: CSGCGGC

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Summary

Alignment

Name	MA0290.1
Alt. Name	DAL81
Database	JASPAR_CORE_2014.meme
p-value	6.55701e-05
E-value	0.0388831
q-value	0.0451728
Overlap	7
Offset	8
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0412.1
Alt. Name	UME6
Database	JASPAR_CORE_2014.meme
p-value	7.67667e-05
E-value	0.0455227
q-value	0.0451728
Overlap	7
Offset	1
Orientation	Normal

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Matches to Query: ATGACCTC

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Matches to Query: ACASAGCC

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Matches to Query: RAAAGAAA

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Summary

Alignment

Name	MA0277.1
Alt. Name	AZF1
Database	JASPAR_CORE_2014.meme
p-value	6.07414e-06
E-value	0.00360197
q-value	0.00718519
Overlap	8
Offset	1
Orientation	Normal

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Matches to Query: CTGAGTCA

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Summary

Alignment

Name	MA0591.1
Alt. Name	Bach1::Mafk
Database	JASPAR_CORE_2014.meme
p-value	6.75257e-07
E-value	0.000400427
q-value	0.000784519
Overlap	8
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0501.1
Alt. Name	NFE2::MAF
Database	JASPAR_CORE_2014.meme
p-value	1.72412e-06
E-value	0.0010224
q-value	0.00100155
Overlap	8
Offset	6
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0150.2
Alt. Name	Nfe2l2
Database	JASPAR_CORE_2014.meme
p-value	3.06811e-06
E-value	0.00181939
q-value	0.00118819
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	1.93161e-05
E-value	0.0114545
q-value	0.00561042
Overlap	7
Offset	-1
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0478.1
Alt. Name	FOSL2
Database	JASPAR_CORE_2014.meme
p-value	3.65679e-05
E-value	0.0216848
q-value	0.00849698
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0490.1
Alt. Name	JUNB
Database	JASPAR_CORE_2014.meme
p-value	4.54788e-05
E-value	0.0269689
q-value	0.00880629
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0477.1
Alt. Name	FOSL1
Database	JASPAR_CORE_2014.meme
p-value	7.2515e-05
E-value	0.0430014
q-value	0.0120355
Overlap	8
Offset	1
Orientation	Reverse Complement

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Matches to Query: AGGCGKG

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Matches to Query: CCACTAGR

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Matches to Query: CACGTGWC

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Summary

Alignment

Name	MA0552.1
Alt. Name	PIL5
Database	JASPAR_CORE_2014.meme
p-value	1.41328e-06
E-value	0.000838073
q-value	0.00160457
Overlap	8
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0580.1
Alt. Name	DYT1
Database	JASPAR_CORE_2014.meme
p-value	3.12348e-06
E-value	0.00185223
q-value	0.00169285
Overlap	8
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0004.1
Alt. Name	Arnt
Database	JASPAR_CORE_2014.meme
p-value	5.96415e-06
E-value	0.00353674
q-value	0.00169285
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0310.1
Alt. Name	HAC1
Database	JASPAR_CORE_2014.meme
p-value	1.25847e-05
E-value	0.0074627
q-value	0.00285761
Overlap	8
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0570.1
Alt. Name	ABF1
Database	JASPAR_CORE_2014.meme
p-value	1.98291e-05
E-value	0.0117587
q-value	0.0037427
Overlap	8
Offset	10
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0464.1
Alt. Name	Bhlhe40
Database	JASPAR_CORE_2014.meme
p-value	2.58179e-05
E-value	0.01531
q-value	0.0037427
Overlap	8
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0550.1
Alt. Name	BZR1
Database	JASPAR_CORE_2014.meme
p-value	3.07676e-05
E-value	0.0182452
q-value	0.0037427
Overlap	8
Offset	4
Orientation	Normal

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Summary

Alignment

Name	MA0409.1
Alt. Name	TYE7
Database	JASPAR_CORE_2014.meme
p-value	3.61364e-05
E-value	0.0214289
q-value	0.0037427
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0093.2
Alt. Name	USF1
Database	JASPAR_CORE_2014.meme
p-value	3.65322e-05
E-value	0.0216636
q-value	0.0037427
Overlap	8
Offset	2
Orientation	Normal

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Summary

Alignment

Name	MA0551.1
Alt. Name	HY5
Database	JASPAR_CORE_2014.meme
p-value	3.95581e-05
E-value	0.023458
q-value	0.0037427
Overlap	8
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0561.1
Alt. Name	PIF4
Database	JASPAR_CORE_2014.meme
p-value	5.0252e-05
E-value	0.0297994
q-value	0.00428651
Overlap	8
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0549.1
Alt. Name	BES1
Database	JASPAR_CORE_2014.meme
p-value	7.86652e-05
E-value	0.0466485
q-value	0.00595419
Overlap	8
Offset	2
Orientation	Normal

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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

tomtom -eps -verbosity 1 -min-overlap 5 -dist pearson -evalue -thresh 0.05 -oc /home/cicek/chipSeq/data/PEAKS/tmp_out/tomtom_out /home/cicek/chipSeq/data/PEAKS/tmp_out/dreme_out/dreme.xml /home/cicek/chipSeq/JASPAR_CORE_2014.meme

Background letter frequencies (from first motif database):

A: 0.250 C: 0.250 G: 0.250 T: 0.250

Result calculation took 22.386 seconds

show model parameters...

Model parameters

distance_measure      = value: "pearson"
threshold             = type: "evalue"
background            = from: "first_target", A: "0.25", C: "0.25", G: "0.25", T: "0.25"
host                  = compute-1-35.local
when                  = Fri Dec 12 03:02:00 2014

Explanation of TOMTOM Results

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The TOMTOM results consist of

The query motifs with links to further information on matches. [View]
The target databases with information on the number of matches. [View]
The matches between query motifs and target motifs. [View]
- The summary of match information.
- An alignment of the two motifs.
The program details including:
1. The version of TOMTOM and the date it was released. [View]
2. The reference to cite if you use TOMTOM in your research. [View]
3. The command line summary detailing the parameters with which you ran TOMTOM. [View]
This explanation of how to interpret TOMTOM results.

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.

Query Motifs

Name

Preview

Matches

List

Target Databases

Database

Number of Motifs

Motifs Matched

Matches to Query: TKDYGCAA

Summary

Alignment

Summary

Alignment

Matches to Query: AGGCWGGA

Matches to Query: CAGTGAGC

Matches to Query: TTGDGWAA

Matches to Query: CVRCCTCC

Matches to Query: RTGASTCA

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: TTGCYYAA

Matches to Query: CTGYCDCC

Matches to Query: RTAAAYA

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: AAWAMAAA

Matches to Query: CYRTCTC

Matches to Query: CCCRGS

Matches to Query: TKAYGWAA

Matches to Query: AYTACAGG

Matches to Query: AGYGARAC

Matches to Query: ATCRCTTG

Matches to Query: CCMCRCCC

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment