peak-motifs Peakmotifstreatdmsomerged

Sequence composition (test sequences)

Nb of peaks: 2109
Total seq. size: 395 kb
Min length: 17 bp
Mean length: 187.446 bp
Max length: 1000 bp [ view peaks in genome browser : ]
[ coordinates: UCSC BED track ]
[ 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=72.43; evalue=3.7e-73

sgCCCCGCCCCgcc

GGCGGGGCGGGGCS

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 425 (20.15%)
Max nb of predicted sites per peak: 8
(chromosome_GRCh38_19_1_58617616_1:29811581-29811879())
Mean nb of predicted sites per peak: 1.73

[ 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=46.14; evalue=7.2e-47

mvhcycAgCCAATcAgmr

YKCTGATTGGCTGRGDBK

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 222 (10.53%)
Max nb of predicted sites per peak: 5
(chromosome_GRCh38_20_1_64444167_1:46788897-46789082())
Mean nb of predicted sites per peak: 1.26

[ 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=46.14; evalue=7.2e-47

whAACCAATcAkmr

YKMTGATTGGTTDW

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 236 (11.19%)
Max nb of predicted sites per peak: 5
(chromosome_GRCh38_20_1_64444167_1:46788897-46789082())
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 4 oligos_6nt_mkv3_m4

k-mer sig=22.28; evalue=5.2e-23

sgAATgGAATsr

YSATTCCATTCS

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 100 (4.74%)
Max nb of predicted sites per peak: 79
(chromosome_GRCh38_16_1_90338345_1:46397350-46398512())
Mean nb of predicted sites per peak: 12.84

[ 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=18.59; evalue=2.6e-19

gcgcgTGCGCAcgcgc

GCGCGTGCGCACGCGC

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 141 (6.69%)
Max nb of predicted sites per peak: 12
(chromosome_GRCh38_3_1_198295559_1:129893649-129893816())
Mean nb of predicted sites per peak: 3.06

[ view in genome browser :

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

Motif 6 oligos_7nt_mkv4_m1

k-mer sig=50.22; evalue=6e-51

ccggCCCCGCCccctccccss

SSGGGGAGGGGGCGGGGCCGG

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 523 (24.80%)
Max nb of predicted sites per peak: 13
(chromosome_GRCh38_19_1_58617616_1:29811581-29811879())
Mean nb of predicted sites per peak: 2.08

[ view in genome browser :

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

Motif 7 oligos_7nt_mkv4_m2

k-mer sig=38.70; evalue=2e-39

rkAATsgAATgGAATsrW

WYSATTCCATTCSATTMY

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 89 (4.22%)
Max nb of predicted sites per peak: 110
(chromosome_GRCh38_16_1_90338345_1:46397350-46398512())
Mean nb of predicted sites per peak: 19.03

[ view in genome browser :

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

Motif 8 oligos_7nt_mkv4_m3

k-mer sig=20.96; evalue=1.1e-21

mtcAGCCAATcrgar

YTCYGATTGGCTGAK

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 258 (12.23%)
Max nb of predicted sites per peak: 5
(chromosome_GRCh38_17_1_83257441_1:82022912-82023296())
Mean nb of predicted sites per peak: 1.34

[ view in genome browser :

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

Motif 9 oligos_7nt_mkv4_m4

k-mer sig=13.18; evalue=6.6e-14

gggGCGGAGCcgaggs

SCCTCGGCTCCGCCCC

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 312 (14.79%)
Max nb of predicted sites per peak: 7
(chromosome_GRCh38_2_1_242193529_1:112054529-112054780())
Mean nb of predicted sites per peak: 1.47

[ view in genome browser :

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

Motif 10 oligos_7nt_mkv4_m5

k-mer sig=10.06; evalue=8.7e-11

cscCCCCACCCccrc

GYGGGGGTGGGGGSG

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 280 (13.28%)
Max nb of predicted sites per peak: 5
(chromosome_GRCh38_19_1_58617616_1:1249404-1249893())
Mean nb of predicted sites per peak: 1.33

[ view in genome browser :

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

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: Peakmotifstreatdmsomerged (19/12/2025 09:10)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results