peak-motifs df

Sequence composition (test sequences)

Nb of peaks: 17
Total seq. size: 26 kb
Min length: 459 bp
Mean length: 1522.76 bp
Max length: 1701 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_6-8nt_m1

k-mer sig=4.89; evalue=1.3e-05

mttCaCCaaCCCCvy

RBGGGGTTGGTGAAK

[ 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: 10 (58.82%)
Max nb of predicted sites per peak: 5
(CYP73A5)
Mean nb of predicted sites per peak: 2.30

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

Motif 2 oligos_6-8nt_m2

k-mer sig=1.56; evalue=0.028

wrTACATAmc

GKTATGTAYW

[ 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: 11 (64.71%)
Max nb of predicted sites per peak: 4
(OMT1)
Mean nb of predicted sites per peak: 1.64

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

Motif 3 oligos_6-8nt_m3

k-mer sig=1.52; evalue=0.03

ywaaCGGCGtyk

MRACGCCGTTWR

[ 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: 7 (41.18%)
Max nb of predicted sites per peak: 8
(CYP73A5)
Mean nb of predicted sites per peak: 2.14

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

Motif 4 oligos_6-8nt_m4

k-mer sig=1.38; evalue=0.042

sySatGCatGCaybw

WVRTGCATGCATSRS

[ 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: 9 (52.94%)
Max nb of predicted sites per peak: 8
(CYP82C4)
Mean nb of predicted sites per peak: 3.67

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

Motif 5 oligos_6-8nt_m5

k-mer sig=1.27; evalue=0.054

arGAAaaCaara

TYTTGTTTTCYT

[ 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: 12 (70.59%)
Max nb of predicted sites per peak: 5
(ABCG37)
Mean nb of predicted sites per peak: 1.75

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

Motif 6 dyads_m1

k-mer sig=3.78; evalue=0.00017

ytcACCaACCCCcc

GGGGGGTTGGTGAR

[ 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: 10 (58.82%)
Max nb of predicted sites per peak: 8
(4CL1)
Mean nb of predicted sites per peak: 2.50

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

Motif 7 dyads_m2

k-mer sig=1.49; evalue=0.032

srACCAAAmc

GKTTTGGTYS

[ 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: 12 (70.59%)
Max nb of predicted sites per peak: 3
(AT3G61930)
Mean nb of predicted sites per peak: 1.67

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

Motif 8 dyads_m3

k-mer sig=1.34; evalue=0.046

wrTACATAmc

GKTATGTAYW

[ 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: 11 (64.71%)
Max nb of predicted sites per peak: 4
(OMT1)
Mean nb of predicted sites per peak: 1.64

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

Motif 9 dyads_m4

k-mer sig=1.20; evalue=0.063

bGCATGCayg

CRTGCATGCV

[ 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: 10 (58.82%)
Max nb of predicted sites per peak: 7
(CYP82C4)
Mean nb of predicted sites per peak: 2.80

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

Motif 10 dyads_m5

k-mer sig=0.84; evalue=0.14

aaGAAarCAArr

YYTTGYTTTCTT

[ 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: 14 (82.35%)
Max nb of predicted sites per peak: 4
(AT5G20950)
Mean nb of predicted sites per peak: 2.21

[ 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) ]

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: df (26/02/2026 16:12)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results