peak-motifs CDS

Sequence composition (test sequences)

Nb of peaks: 2309
Total seq. size: 120 kb
Min length: 52 bp
Mean length: 52 bp
Max length: 52 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=7.74; evalue=1.8e-08

csGCGGCGgcg

CGCCGCCGCSG

[ 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: 106 (4.59%)
Max nb of predicted sites per peak: 6
(M28550:6;-;30281664)
Mean nb of predicted sites per peak: 1.60

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

Motif 2 oligos_6nt_mkv3_m2

k-mer sig=7.74; evalue=1.8e-08

cgCCGCCGCcg

CGGCGGCGGCG

[ 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: 112 (4.85%)
Max nb of predicted sites per peak: 6
(M32622:8;-;2170970)
Mean nb of predicted sites per peak: 1.68

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

Motif 3 oligos_6nt_mkv3_m3

k-mer sig=3.78; evalue=0.00017

wtTTGCAGgww

WWCCTGCAAAW

[ 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: 51 (2.21%)
Max nb of predicted sites per peak: 1
(M8826:11;-;26512637)
Mean nb of predicted sites per peak: 1.00

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

Motif 4 oligos_6nt_mkv3_m4

k-mer sig=3.47; evalue=0.00034

ysGCCATGGCsr

YSGCCATGGCSR

[ 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: 31 (1.34%)
Max nb of predicted sites per peak: 2
(M12509:2;+;29285099)
Mean nb of predicted sites per peak: 1.03

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

Motif 5 oligos_6nt_mkv3_m5

k-mer sig=2.91; evalue=0.0012

wtTTACAGdw

WHCTGTAAAW

[ 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: 41 (1.78%)
Max nb of predicted sites per peak: 1
(M8708:11;-;21480948)
Mean nb of predicted sites per peak: 1.00

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

Motif 6 oligos_6nt_mkv3_m6

k-mer sig=2.90; evalue=0.0013

twTTTCAGsw

WSCTGAAAWA

[ 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: 50 (2.17%)
Max nb of predicted sites per peak: 1
(M9224:12;+;5762801)
Mean nb of predicted sites per peak: 1.00

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

Motif 7 oligos_6nt_mkv3_m7

k-mer sig=2.02; evalue=0.0095

gvCGGTGGmg

CKCCACCGBC

[ 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: 57 (2.47%)
Max nb of predicted sites per peak: 2
(M2413:1;+;41713552)
Mean nb of predicted sites per peak: 1.05

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

Motif 8 oligos_6nt_mkv3_m8

k-mer sig=1.40; evalue=0.04

gaCGACGAsg

CSTCGTCGTC

[ 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: 55 (2.38%)
Max nb of predicted sites per peak: 4
(M8903:11;-;28960312)
Mean nb of predicted sites per peak: 1.31

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

Motif 9 oligos_6nt_mkv3_m9

k-mer sig=1.40; evalue=0.04

csTCGTCGtc

GACGACGASG

[ 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: 69 (2.99%)
Max nb of predicted sites per peak: 3
(M22370:4;-;29466731)
Mean nb of predicted sites per peak: 1.16

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

Motif 10 oligos_6nt_mkv3_m10

k-mer sig=7.74; evalue=1.8e-08

cgGCGGCGrcg

CGYCGCCGCCG

[ 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: 119 (5.15%)
Max nb of predicted sites per peak: 6
(M28550:6;-;30281664)
Mean nb of predicted sites per peak: 1.61

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

Motif 11 positions_6nt_m1

k-mer sig=3.04; evalue=0.00091

cgCCGCCGCCgc

GCGGCGGCGGCG

[ 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: 103 (4.46%)
Max nb of predicted sites per peak: 6
(M32622:8;-;2170970)
Mean nb of predicted sites per peak: 1.83

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

Motif 12 positions_6nt_m2

k-mer sig=3.04; evalue=0.00091

cgsCGGCGGCGgc

GCCGCCGCCGSCG

[ 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 (6.11%)
Max nb of predicted sites per peak: 6
(M4594:1;-;37529003)
Mean nb of predicted sites per peak: 1.79

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

Motif 13 positions_6nt_m3

k-mer sig=1.10; evalue=0.079

sgTGTACAcs

SGTGTACACS

[ 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: 35 (1.52%)
Max nb of predicted sites per peak: 1
(M9405:12;+;13105264)
Mean nb of predicted sites per peak: 1.00

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

Motif 14 positions_6nt_m4

k-mer sig=3.04; evalue=0.00091

cgGCGGCGGCggcg

CGCCGCCGCCGCCG

[ 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: 86 (3.72%)
Max nb of predicted sites per peak: 8
(M4594:1;-;37529003)
Mean nb of predicted sites per peak: 1.79

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

Motif 15 positions_6nt_m5

k-mer sig=0.25; evalue=0.56

rwTAATcTwh

DWAGATTAWY

[ 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: 16 (0.69%)
Max nb of predicted sites per peak: 1
(M8737:11;-;22519034)
Mean nb of predicted sites per peak: 1.00

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

Motif 16 positions_6nt_m6

k-mer sig=0.22; evalue=0.6

wrTWcTATrt

AYATAGWAYW

[ 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: 34 (1.47%)
Max nb of predicted sites per peak: 2
(M6029:10;+;23115813)
Mean nb of predicted sites per peak: 1.03

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

Motif 17 positions_6nt_m7

k-mer sig=0.17; evalue=0.68

kyTGTGCAsv

BSTGCACARM

[ 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: 42 (1.82%)
Max nb of predicted sites per peak: 1
(M9060:12;+;2605024)
Mean nb of predicted sites per peak: 1.00

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

Motif 18 positions_6nt_m8

k-mer sig=0.04; evalue=0.91

wwTTTATTww

WWAATAAAWW

[ 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: 32 (1.39%)
Max nb of predicted sites per peak: 2
(M6842:10;-;21441210)
Mean nb of predicted sites per peak: 1.09

[ 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: CDS_NUE (09/04/2026 08:58)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results