peak-motifs Oct4_Chen2008_sites_from

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

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ 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

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ 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

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ 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

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ 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

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 6 dyads_m1

k-mer sig=138.70; evalue=2e-139

ttGCATgamAATGCAaAtghv

BDCATTTGCATTKTCATGCAA

[ 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 ttGCATgamAATGCAaAtghv

Pou5f1::Sox2 MA0142.1 D 15 0.7143 0.737 0.526 NA NA

POU1F1 MA0784.3 R 14 0.6667 0.753 0.502 NA NA

POU2F2 MA0507.3 D 13 0.6190 0.789 0.488 NA NA

Total matches= 6 (3 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: 342 (34.20%)
Max nb of predicted sites per peak: 5
(mm9_chr19_37543741_37544020_+)
Mean nb of predicted sites per peak: 1.35

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 7 dyads_m2

k-mer sig=138.70; evalue=2e-139

yrcaTtTGCATATGCAaAtgyr

YRCATTTGCATATGCAAATGYR

[ 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 yrcaTtTGCATATGCAaAtgyr

POU2F2 MA0507.3 D 13 0.5909 0.874 0.517 NA NA

Pou5f1::Sox2 MA0142.1 D 15 0.6818 0.719 0.490 NA NA

POU1F1 MA0784.3 R 14 0.6364 0.741 0.472 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: 213 (21.30%)
Max nb of predicted sites per peak: 16
(mm9_chr2_105210341_105210690_+)
Mean nb of predicted sites per peak: 2.90

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 8 dyads_m3

k-mer sig=73.26; evalue=5.5e-74

ccCCCCCCmCCCCcc

GGGGGGKGGGGGGGG

[ 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 ccCCCCCCmCCCCcc

PATZ1 MA1961.2 R 11 0.7333 0.920 0.674 NA NA

ZNF740 MA0753.3 D 10 0.6667 0.944 0.629 NA NA

ZNF281 MA1630.3 R 10 0.6667 0.911 0.607 NA NA

Total matches= 26 (23 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: 237 (23.70%)
Max nb of predicted sites per peak: 51
(mm9_chr11_6289161_6289580_+)
Mean nb of predicted sites per peak: 4.39

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 9 dyads_m4

k-mer sig=67.73; evalue=1.9e-68

aaAAAAACAAAGGmm

KKCCTTTGTTTTTTT

[ 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 aaAAAAACAAAGGmm

TCF7L1 MA1421.1 D 12 0.8000 0.738 0.590 NA NA

Sox6 MA0515.1 R 10 0.6667 0.828 0.552 NA NA

Sox17 MA0078.3 D 10 0.6667 0.763 0.509 NA NA

Total matches= 16 (13 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: 229 (22.90%)
Max nb of predicted sites per peak: 24
(mm9_chr6_39395781_39396231_+)
Mean nb of predicted sites per peak: 2.16

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 10 dyads_m5

k-mer sig=138.70; evalue=2e-139

bhcATTTGCATaaCAAwGsaaabc

GVTTTSCWTTGTTATGCAAATGDV

[ 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 bhcATTTGCATaaCAAwGsaaabc

POU2F1::SOX2 MA1962.1 D 17 0.7083 0.937 0.664 NA NA

Pou5f1::Sox2 MA0142.1 R 15 0.6250 0.974 0.609 NA NA

POU2F2 MA0507.3 R 13 0.5417 0.921 0.499 NA NA

Total matches= 7 (4 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: 594 (59.40%)
Max nb of predicted sites per peak: 5
(mm9_chr16_97067031_97067600_+)
Mean nb of predicted sites per peak: 1.17

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

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]

RSAT - peak-motifs result

Analysis: Oct4_Chen2008_sites_from_Jaspar (11/04/2026 09:25)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results