peak-motifs Oct4_Chen2008_sites_from

Sequence composition (test sequences)

Nb of peaks: 1000
Total seq. size: 409 kb
Min length: 150 bp
Mean length: 409.09 bp
Max length: 839 bp [ seq: converted purged ]
[ lengths: list distrib graph ]

Nucleotide composition profiles

Transition frequencies
Position profiles

[ 1nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Dinucleotide composition profiles

Transition frequencies
Position profiles

[ 2nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Motif discovery

Motif 1 oligos_6nt_mkv3_m1

k-mer sig=48.15; evalue=7.1e-49

yryattTGCATATGCAaatryr

YRYATTTGCATATGCAAATRYR

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

JASPAR2024_CORE_vertebrates_non-redundant

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor yryattTGCATATGCAaatryr

POU2F2 MA0507.3 R 13 0.5909 0.861 0.509 NA NA

Pou5f1::Sox2 MA0142.1 R 15 0.6818 0.715 0.488 NA NA

POU1F1 MA0784.3 R 14 0.6364 0.717 0.457 NA NA

Total matches= 5 (2 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 268 (26.80%)
Max nb of predicted sites per peak: 14
(mm9_chr7_57241511_57241780_+)
Mean nb of predicted sites per peak: 2.71

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 2 oligos_6nt_mkv3_m2

k-mer sig=23.87; evalue=1.3e-24

ccCCCCaCCCCcc

GGGGGGTGGGGGG

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

JASPAR2024_CORE_vertebrates_non-redundant

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ccCCCCaCCCCcc

PATZ1 MA1961.2 R 11 0.8462 0.918 0.777 NA NA

KLF5 MA0599.1 D 10 0.7692 0.917 0.705 NA NA

ZNF281 MA1630.3 R 10 0.7692 0.883 0.679 NA NA

Total matches= 32 (29 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 253 (25.30%)
Max nb of predicted sites per peak: 25
(mm9_chr11_6289161_6289580_+)
Mean nb of predicted sites per peak: 2.42

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 3 oligos_6nt_mkv3_m3

k-mer sig=48.15; evalue=7.1e-49

yhcaTTTGCATaacAAwgsmm

KKSCWTTGTTATGCAAATGDR

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

JASPAR2024_CORE_vertebrates_non-redundant

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor yhcaTTTGCATaacAAwgsmm

POU2F1::SOX2 MA1962.1 D 17 0.8095 0.932 0.755 NA NA

Pou5f1::Sox2 MA0142.1 R 15 0.7143 0.988 0.705 NA NA

POU2F2 MA0507.3 R 13 0.6190 0.915 0.566 NA NA

Total matches= 11 (8 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 723 (72.30%)
Max nb of predicted sites per peak: 5
(mm9_chr16_97067031_97067600_+)
Mean nb of predicted sites per peak: 1.22

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 4 oligos_6nt_mkv3_m4

k-mer sig=12.94; evalue=1.1e-13

atTTACATAws

SWTATGTAAAT

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

JASPAR2024_CORE_vertebrates_non-redundant

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor atTTACATAws

POU3F1 MA0786.2 R 10 0.9091 0.826 0.751 NA NA

TEF MA0843.2 D 10 0.9091 0.789 0.717 NA NA

NFIL3 MA0025.3 R 9 0.8182 0.871 0.713 NA NA

Total matches= 42 (39 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 240 (24.00%)
Max nb of predicted sites per peak: 4
(mm9_chr8_15844801_15845180_+)
Mean nb of predicted sites per peak: 1.18

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 5 oligos_6nt_mkv3_m5

k-mer sig=14.70; evalue=2e-15

rmaAAACAAAGcma

TKGCTTTGTTTTKY

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

JASPAR2024_CORE_vertebrates_non-redundant

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor rmaAAACAAAGcma

Sox6 MA0515.1 R 10 0.7143 0.822 0.587 NA NA

SOX4 MA0867.3 D 8 0.5714 0.939 0.536 NA NA

FOXD3 MA0041.3 D 12 0.7500 0.702 0.526 NA NA

Total matches= 32 (29 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 202 (20.20%)
Max nb of predicted sites per peak: 10
(mm9_chr10_28355921_28356220_+)
Mean nb of predicted sites per peak: 1.45

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Predicted sites on test peaks (all motifs)

[tab]
[bed]

Word significance table
Word comparisons		[tab] [html] [heatmap]
Comparisons between discovered motifs
Discovered motifs versus discovered motifs		[ Discovered motif(s): tf ] [ table: html txt ] [ alignments (logo): html text ] [ clustering: html ] [ graph: gml (for CytoScape) ]
Discovered motifs versus transcription factor databases
Motifs versus JASPAR2024_CORE_vertebrates_non-redundant database		[ table: html txt ] [ alignments (logo): html text ] [ graph: gml (for CytoScape) ]

Log files
Parameters and files		[txt] [html]
Time log		[time table] [time log] [html]

Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J. (2012). RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res 40(4): e31.
Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J. (2012). A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat Protoc 7(8): 1551-1568.

RSAT - peak-motifs result

Analysis: Oct4_Chen2008_sites_from_Jaspar (04/03/2026 11:02)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results