peak-motifs nhr-148_motif

Sequence composition (test sequences)

Nb of peaks: 240
Total seq. size: 240 kb
Min length: 999 bp
Mean length: 999 bp
Max length: 999 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=5.30; evalue=5e-06

attCTGAAAatCyg

CRGATTTTCAGAAT

[ 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 (21.25%)
Max nb of predicted sites per peak: 10
(caenorhabditis_elegans_prjna13758|WBGene00007703)
Mean nb of predicted sites per peak: 3.22

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

Motif 2 oligos_6nt_mkv3_m2

k-mer sig=5.12; evalue=7.6e-06

rrAAATTGmv

BKCAATTTYY

[ 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: 23 (9.58%)
Max nb of predicted sites per peak: 5
(caenorhabditis_elegans_prjna13758|WBGene00004751)
Mean nb of predicted sites per peak: 2.52

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

Motif 3 oligos_6nt_mkv3_m3

k-mer sig=4.75; evalue=1.8e-05

rytACtGtAgy

RCTACAGTARY

[ 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: 45 (18.75%)
Max nb of predicted sites per peak: 12
(caenorhabditis_elegans_prjna13758|WBGene00022059)
Mean nb of predicted sites per peak: 5.73

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

Motif 4 oligos_6nt_mkv3_m4

k-mer sig=3.54; evalue=0.00029

scCCCSCCCmcm

KGKGGGSGGGGS

[ 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: 43 (17.92%)
Max nb of predicted sites per peak: 22
(caenorhabditis_elegans_prjna13758|WBGene00013052)
Mean nb of predicted sites per peak: 5.81

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

Motif 5 oligos_6nt_mkv3_m5

k-mer sig=3.09; evalue=0.00081

grCGAGACCcss

SSGGGTCTCGYC

[ 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: 43 (17.92%)
Max nb of predicted sites per peak: 7
(caenorhabditis_elegans_prjna13758|WBGene00022059)
Mean nb of predicted sites per peak: 2.72

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

Motif 6 positions_6nt_m1

k-mer sig=1.63; evalue=0.023

hkrGAAATAtd

HATATTTCYMD

[ 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: 47 (19.58%)
Max nb of predicted sites per peak: 6
(caenorhabditis_elegans_prjna13758|WBGene00013052)
Mean nb of predicted sites per peak: 3.02

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

Motif 7 oligos_7nt_mkv4_m1

k-mer sig=11.41; evalue=3.9e-12

rrcTACaGTAgy

RCTACTGTAGYY

[ 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: 48 (20.00%)
Max nb of predicted sites per peak: 12
(caenorhabditis_elegans_prjna13758|WBGene00022059)
Mean nb of predicted sites per peak: 5.73

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

Motif 8 oligos_7nt_mkv4_m2

k-mer sig=5.18; evalue=6.6e-06

krCGaGACCCvk

MBGGGTCTCGYM

[ 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 (17.08%)
Max nb of predicted sites per peak: 7
(caenorhabditis_elegans_prjna13758|WBGene00022059)
Mean nb of predicted sites per peak: 3.05

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

Motif 9 oligos_7nt_mkv4_m3

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

rrsTACCGTAry

RYTACGGTASYY

[ 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: 45 (18.75%)
Max nb of predicted sites per peak: 12
(caenorhabditis_elegans_prjna13758|WBGene00022059)
Mean nb of predicted sites per peak: 5.91

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

Motif 10 oligos_7nt_mkv4_m4

k-mer sig=2.43; evalue=0.0037

mrAAAATTGar

YTCAATTTTYK

[ 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: 61 (25.42%)
Max nb of predicted sites per peak: 18
(caenorhabditis_elegans_prjna13758|WBGene00007820)
Mean nb of predicted sites per peak: 3.92

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

Motif 11 oligos_7nt_mkv4_m5

k-mer sig=2.08; evalue=0.0083

mrAAAAATCrr

YYGATTTTTYK

[ 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 (21.25%)
Max nb of predicted sites per peak: 18
(caenorhabditis_elegans_prjna13758|WBGene00007820)
Mean nb of predicted sites per peak: 4.25

[ 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: nhr-148_motif_search (09/04/2026 16:37)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results