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.

Query Motifs | Target Databases | Matches | Program information | Explanation

Query Motifs

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Name	Alt. Name	Preview	Matches	List
RAGGTCR	2.6e-2321	AAGGTCA	10	Rara_primary, MA0141.1 (Esrrb) , Nr2f2_primary, MA0115.1 (NR1H2::RXRA) , MA0065.1 (PPARG::RXRA) , Esrra_primary, MA0160.1 (NR4A2) , MA0071.1 (RORA_1) , MA0065.2 (PPARG::RXRA) , MA0017.1 (NR2F1)
AAGGRCR	2.5e-270	AAGGGCA	0
AAGGTKA	4.2e-148	AAGGTGA	0
CMCRCCC	5.3e-061	CCCACCC	4	MA0039.2 (Klf4) , Sox13_secondary, Klf7_primary, Ascl2_secondary
RGGTCAY	1.1e-057	GGGTCAC	8	MA0066.1 (PPARG) , Rxra_primary, Nr2f2_secondary, MA0258.1 (ESR2) , MA0112.1 (ESR1) , MA0074.1 (RXRA::VDR) , Esrra_secondary, MA0159.1 (RXR::RAR_DR5)
ACAAWGV	1.4e-023	ACAAAGG	5	Sox11_primary, Sox4_primary, MA0442.1 (SOX10) , Sox12_secondary, MA0143.1 (Sox2)
CTGCRG	6.7e-021	CTGCAG	0
GGSAGGR	2.0e-020	GGGAGGG	0
AAWGTCA	1.6e-019	AAAGTCA	0
TAHAYA	6.1e-019	TACACA	0
AGGWCA	3.0e-017	AGGACA	0
CVGGAA	1.8e-016	CAGGAA	3	MA0156.1 (FEV) , MA0144.1 (Stat3) , MA0080.2 (SPI1)
CAAGGYC	6.2e-016	CAAGGCC	2	MA0141.1 (Esrrb) , Esrra_primary
ATGBWAA	3.0e-012	ATGCAAA	3	Pou2f3_3986.2, MA0142.1 (Pou5f1) , Pou2f2_3748.1
CACGTG	3.6e-010	CACGTG	10	MA0093.1 (USF1) , MA0058.1 (MAX) , MA0104.1 (Mycn) , MA0059.1 (MYC::MAX) , Max_primary, Bhlhb2_primary, Bhlhb2_secondary, MA0004.1 (Arnt) , MA0147.1 (Myc) , MA0104.2 (Mycn)
AGGGTYA	8.3e-008	AGGGTCA	1	MA0074.1 (RXRA::VDR)
CACMGC	3.1e-007	CACAGC	1	Zic3_secondary
CAGCRKC	2.9e-006	CAGCAGC	0
CWTTATM	4.0e-005	CTTTATC	0
AACAAWA	9.2e-005	AACAAAA	0
CGCCGCC	1.1e-004	CGCCGCC	0
AGGAHGC	5.8e-004	AGGAAGC	0
CGCSCTC	2.4e-003	CGCCCTC	0
CTRTAGC	5.1e-003	CTGTAGC	0
CTGCATA	6.4e-003	CTGCATA	0
ACACACA	9.8e-003	ACACACA	0
AGRAAGG	1.4e-002	AGAAAGG	1	MA0149.1 (EWSR1-FLI1)
CTRGGAA	1.1e-002	CTGGGAA	0

Target Databases

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Database	Number of Motifs	Motifs Matched
jaspar_vertebrates.meme	146	27
uniprobe_mouse.meme	386	18

Matches to Query: RAGGTCR (2.6e-2321)

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Summary

Alignment

Name	Rara_primary
Database	uniprobe_mouse.meme
p-value	1.4361e-07
E-value	7.64006e-05
q-value	0.000110636
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0141.1
Alt. Name	Esrrb
Database	jaspar_vertebrates.meme
p-value	2.11292e-07
E-value	0.000112407
q-value	0.000110636
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	Nr2f2_primary
Database	uniprobe_mouse.meme
p-value	5.34353e-07
E-value	0.000284276
q-value	0.000149891
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0115.1
Alt. Name	NR1H2::RXRA
Database	jaspar_vertebrates.meme
p-value	5.72521e-07
E-value	0.000304581
q-value	0.000149891
Overlap	7
Offset	1
Orientation	Normal

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Summary

Alignment

Name	MA0065.1
Alt. Name	PPARG::RXRA
Database	jaspar_vertebrates.meme
p-value	1.30721e-06
E-value	0.000695435
q-value	0.000273791
Overlap	7
Offset	10
Orientation	Normal

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Summary

Alignment

Name	Esrra_primary
Database	uniprobe_mouse.meme
p-value	1.81886e-06
E-value	0.000967634
q-value	0.000282983
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	MA0160.1
Alt. Name	NR4A2
Database	jaspar_vertebrates.meme
p-value	1.89153e-06
E-value	0.00100629
q-value	0.000282983
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0071.1
Alt. Name	RORA_1
Database	jaspar_vertebrates.meme
p-value	9.08091e-06
E-value	0.00483105
q-value	0.00118873
Overlap	7
Offset	3
Orientation	Normal

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Summary

Alignment

Name	MA0065.2
Alt. Name	PPARG::RXRA
Database	jaspar_vertebrates.meme
p-value	4.06009e-05
E-value	0.0215997
q-value	0.00472431
Overlap	7
Offset	8
Orientation	Normal

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Summary

Alignment

Name	MA0017.1
Alt. Name	NR2F1
Database	jaspar_vertebrates.meme
p-value	5.28563e-05
E-value	0.0281196
q-value	0.00553531
Overlap	7
Offset	7
Orientation	Reverse Complement

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Matches to Query: AAGGRCR (2.5e-270)

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Matches to Query: AAGGTKA (4.2e-148)

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Matches to Query: CMCRCCC (5.3e-061)

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Summary

Alignment

Name	MA0039.2
Alt. Name	Klf4
Database	jaspar_vertebrates.meme
p-value	5.75868e-09
E-value	3.06362e-06
q-value	6.03648e-06
Overlap	7
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	Sox13_secondary
Database	uniprobe_mouse.meme
p-value	5.23106e-06
E-value	0.00278292
q-value	0.0027417
Overlap	7
Offset	5
Orientation	Reverse Complement

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Summary

Alignment

Name	Klf7_primary
Database	uniprobe_mouse.meme
p-value	1.0118e-05
E-value	0.00538278
q-value	0.00353537
Overlap	7
Offset	5
Orientation	Normal

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Summary

Alignment

Name	Ascl2_secondary
Database	uniprobe_mouse.meme
p-value	3.8098e-05
E-value	0.0202681
q-value	0.00998398
Overlap	7
Offset	5
Orientation	Normal

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Matches to Query: RGGTCAY (1.1e-057)

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Summary

Alignment

Name	MA0066.1
Alt. Name	PPARG
Database	jaspar_vertebrates.meme
p-value	5.17149e-06
E-value	0.00275123
q-value	0.00432293
Overlap	7
Offset	3
Orientation	Reverse Complement

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Summary

Alignment

Name	Rxra_primary
Database	uniprobe_mouse.meme
p-value	8.32781e-06
E-value	0.00443039
q-value	0.00432293
Overlap	7
Offset	6
Orientation	Reverse Complement

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Summary

Alignment

Name	Nr2f2_secondary
Database	uniprobe_mouse.meme
p-value	1.47747e-05
E-value	0.00786013
q-value	0.00511298
Overlap	7
Offset	6
Orientation	Normal

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Summary

Alignment

Name	MA0258.1
Alt. Name	ESR2
Database	jaspar_vertebrates.meme
p-value	2.89602e-05
E-value	0.0154068
q-value	0.00610657
Overlap	7
Offset	2
Orientation	Normal

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Summary

Alignment

Name	MA0112.1
Alt. Name	ESR1
Database	jaspar_vertebrates.meme
p-value	4.27318e-05
E-value	0.0227333
q-value	0.00739396
Overlap	7
Offset	1
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0074.1
Alt. Name	RXRA::VDR
Database	jaspar_vertebrates.meme
p-value	4.98958e-05
E-value	0.0265446
q-value	0.0074002
Overlap	7
Offset	0
Orientation	Normal

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Summary

Alignment

Name	Esrra_secondary
Database	uniprobe_mouse.meme
p-value	6.84661e-05
E-value	0.0364239
q-value	0.00859758
Overlap	7
Offset	6
Orientation	Normal

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Summary

Alignment

Name	MA0159.1
Alt. Name	RXR::RAR_DR5
Database	jaspar_vertebrates.meme
p-value	7.45318e-05
E-value	0.0396509
q-value	0.00859758
Overlap	7
Offset	0
Orientation	Normal

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Matches to Query: ACAAWGV (1.4e-023)

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Summary

Alignment

Name	Sox11_primary
Database	uniprobe_mouse.meme
p-value	1.15072e-06
E-value	0.000612183
q-value	0.00118396
Overlap	7
Offset	6
Orientation	Normal

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Summary

Alignment

Name	Sox4_primary
Database	uniprobe_mouse.meme
p-value	2.62884e-06
E-value	0.00139854
q-value	0.00118396
Overlap	7
Offset	6
Orientation	Normal

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Summary

Alignment

Name	MA0442.1
Alt. Name	SOX10
Database	jaspar_vertebrates.meme
p-value	3.38516e-06
E-value	0.00180091
q-value	0.00118396
Overlap	6
Offset	0
Orientation	Reverse Complement

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Summary

Alignment

Name	Sox12_secondary
Database	uniprobe_mouse.meme
p-value	7.89189e-06
E-value	0.00419848
q-value	0.00207013
Overlap	7
Offset	6
Orientation	Normal

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Summary

Alignment

Name	MA0143.1
Alt. Name	Sox2
Database	jaspar_vertebrates.meme
p-value	1.31651e-05
E-value	0.00700383
q-value	0.00276268
Overlap	7
Offset	8
Orientation	Reverse Complement

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Matches to Query: CTGCRG (6.7e-021)

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Matches to Query: GGSAGGR (2.0e-020)

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Matches to Query: AAWGTCA (1.6e-019)

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Matches to Query: TAHAYA (6.1e-019)

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Matches to Query: AGGWCA (3.0e-017)

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Matches to Query: CVGGAA (1.8e-016)

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Summary

Alignment

Name	MA0156.1
Alt. Name	FEV
Database	jaspar_vertebrates.meme
p-value	3.48738e-06
E-value	0.00185529
q-value	0.00366263
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0144.1
Alt. Name	Stat3
Database	jaspar_vertebrates.meme
p-value	1.55009e-05
E-value	0.00824646
q-value	0.00557292
Overlap	6
Offset	3
Orientation	Normal

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Summary

Alignment

Name	MA0080.2
Alt. Name	SPI1
Database	jaspar_vertebrates.meme
p-value	1.59188e-05
E-value	0.00846881
q-value	0.00557292
Overlap	5
Offset	-1
Orientation	Normal

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Matches to Query: CAAGGYC (6.2e-016)

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Summary

Alignment

Name	MA0141.1
Alt. Name	Esrrb
Database	jaspar_vertebrates.meme
p-value	6.21491e-05
E-value	0.0330633
q-value	0.0495163
Overlap	7
Offset	4
Orientation	Normal

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Summary

Alignment

Name	Esrra_primary
Database	uniprobe_mouse.meme
p-value	9.32237e-05
E-value	0.049595
q-value	0.0495163
Overlap	7
Offset	4
Orientation	Normal

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Matches to Query: ATGBWAA (3.0e-012)

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Summary

Alignment

Name	Pou2f3_3986.2
Database	uniprobe_mouse.meme
p-value	1.2081e-05
E-value	0.00642711
q-value	0.0052438
Overlap	7
Offset	4
Orientation	Normal

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Summary

Alignment

Name	MA0142.1
Alt. Name	Pou5f1
Database	jaspar_vertebrates.meme
p-value	1.37291e-05
E-value	0.00730387
q-value	0.0052438
Overlap	7
Offset	7
Orientation	Normal

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Summary

Alignment

Name	Pou2f2_3748.1
Database	uniprobe_mouse.meme
p-value	1.47852e-05
E-value	0.0078657
q-value	0.0052438
Overlap	7
Offset	4
Orientation	Normal

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Matches to Query: CACGTG (3.6e-010)

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Summary

Alignment

Name	MA0093.1
Alt. Name	USF1
Database	jaspar_vertebrates.meme
p-value	3.89986e-07
E-value	0.000207473
q-value	0.00010171
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0058.1
Alt. Name	MAX
Database	jaspar_vertebrates.meme
p-value	6.82476e-07
E-value	0.000363077
q-value	0.00010171
Overlap	6
Offset	3
Orientation	Normal

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Summary

Alignment

Name	MA0104.1
Alt. Name	Mycn
Database	jaspar_vertebrates.meme
p-value	7.75444e-07
E-value	0.000412536
q-value	0.00010171
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0059.1
Alt. Name	MYC::MAX
Database	jaspar_vertebrates.meme
p-value	7.79972e-07
E-value	0.000414945
q-value	0.00010171
Overlap	6
Offset	3
Orientation	Normal

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Summary

Alignment

Name	Max_primary
Database	uniprobe_mouse.meme
p-value	1.26745e-06
E-value	0.000674286
q-value	0.000129866
Overlap	6
Offset	4
Orientation	Normal

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Summary

Alignment

Name	Bhlhb2_primary
Database	uniprobe_mouse.meme
p-value	1.85243e-06
E-value	0.000985495
q-value	0.000129866
Overlap	6
Offset	8
Orientation	Normal

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Summary

Alignment

Name	Bhlhb2_secondary
Database	uniprobe_mouse.meme
p-value	1.94993e-06
E-value	0.00103736
q-value	0.000129866
Overlap	6
Offset	8
Orientation	Normal

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Summary

Alignment

Name	MA0004.1
Alt. Name	Arnt
Database	jaspar_vertebrates.meme
p-value	1.99178e-06
E-value	0.00105963
q-value	0.000129866
Overlap	6
Offset	0
Orientation	Normal

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Summary

Alignment

Name	MA0147.1
Alt. Name	Myc
Database	jaspar_vertebrates.meme
p-value	4.64749e-06
E-value	0.00247247
q-value	0.000269352
Overlap	6
Offset	2
Orientation	Reverse Complement

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Summary

Alignment

Name	MA0104.2
Alt. Name	Mycn
Database	jaspar_vertebrates.meme
p-value	7.83326e-06
E-value	0.00416729
q-value	0.000408589
Overlap	6
Offset	2
Orientation	Reverse Complement

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Matches to Query: AGGGTYA (8.3e-008)

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Summary

Alignment

Name	MA0074.1
Alt. Name	RXRA::VDR
Database	jaspar_vertebrates.meme
p-value	4.11705e-05
E-value	0.0219027
q-value	0.0432394
Overlap	6
Offset	-1
Orientation	Normal

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Matches to Query: CACMGC (3.1e-007)

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Summary

Alignment

Name	Zic3_secondary
Database	uniprobe_mouse.meme
p-value	5.99251e-05
E-value	0.0318802
q-value	0.0637194
Overlap	6
Offset	3
Orientation	Normal

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Matches to Query: CAGCRKC (2.9e-006)

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Matches to Query: CWTTATM (4.0e-005)

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Matches to Query: AACAAWA (9.2e-005)

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Matches to Query: CGCCGCC (1.1e-004)

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Matches to Query: AGGAHGC (5.8e-004)

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Matches to Query: CGCSCTC (2.4e-003)

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Matches to Query: CTRTAGC (5.1e-003)

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Matches to Query: CTGCATA (6.4e-003)

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Matches to Query: ACACACA (9.8e-003)

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Matches to Query: AGRAAGG (1.4e-002)

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Summary

Alignment

Name	MA0149.1
Alt. Name	EWSR1-FLI1
Database	jaspar_vertebrates.meme
p-value	2.65885e-05
E-value	0.0141451
q-value	0.0282901
Overlap	7
Offset	3
Orientation	Normal

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Matches to Query: CTRGGAA (1.1e-002)

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TOMTOM version

4.5.0 (Release date: Wed Oct 20 15:18:53 EST 2010)

Reference

Shobhit Gupta, John A. Stamatoyannopoulos, Timothy L. Bailey and William Stafford Noble, "Quantifying similarity between motifs",
Genome Biology, 8:R24, 2007

Command line summary

tomtom -oc CHEN_RESULTS.13.10.10/Esrrb.tomtom -min-overlap 5 -dist pearson -evalue -thresh 0.05 -no-ssc CHEN_RESULTS.13.10.10/Esrrb.dreme motif_databases/jaspar_vertebrates.meme motif_databases/uniprobe_mouse.meme

Background letter frequencies (from first motif database):

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

Result calculation took 12.976 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                  = tlb-kamikaze-lt.imb.uq.edu.au
when                  = Fri Nov 19 15:48:43 2010

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

Alt. Name

Preview

Matches

List

Target Databases

Database

Number of Motifs

Motifs Matched

Matches to Query: RAGGTCR (2.6e-2321)

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: AAGGRCR (2.5e-270)

Matches to Query: AAGGTKA (4.2e-148)

Matches to Query: CMCRCCC (5.3e-061)

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: RGGTCAY (1.1e-057)

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: ACAAWGV (1.4e-023)

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Summary

Alignment

Matches to Query: CTGCRG (6.7e-021)

Matches to Query: GGSAGGR (2.0e-020)

Matches to Query: AAWGTCA (1.6e-019)

Matches to Query: TAHAYA (6.1e-019)

Matches to Query: AGGWCA (3.0e-017)

Matches to Query: CVGGAA (1.8e-016)

Summary

Alignment

Summary

Alignment