peak-motifs dmrl_arabidopsis_up1_w

Sequence composition (test sequences)

Nb of peaks: 13
Total seq. size: 21 kb
Min length: 455 bp
Mean length: 1605.15 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) ]

Sequence composition (ctrl sequences)

Nb of peaks: 34262
Total seq. size: 34842 kb
Min length: 201 bp
Mean length: 1016.92 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=12.82; evalue=1.5e-13

awTAaaaAaaTaa

TTATTTTTTTAWT

[ 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: 4 (30.77%)
Max nb of predicted sites per peak: 2
(gene25542|Medicago_truncatula.MtrunA17r50ANR.60|gene25542)
Mean nb of predicted sites per peak: 1.50

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

Motif 2 oligos_6-8nt_m2

k-mer sig=12.82; evalue=1.5e-13

rrTaAAaAaAymm

KKRTTTTTTTAYY

[ 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: 3 (23.08%)
Max nb of predicted sites per peak: 5
(gene25542|Medicago_truncatula.MtrunA17r50ANR.60|gene25542)
Mean nb of predicted sites per peak: 3.00

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

Motif 3 oligos_6-8nt_m3

k-mer sig=12.82; evalue=1.5e-13

wkTAAAaaAaaTrw

WYATTTTTTTTAMW

[ 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: 5 (38.46%)
Max nb of predicted sites per peak: 5
(gene25542|Medicago_truncatula.MtrunA17r50ANR.60|gene25542)
Mean nb of predicted sites per peak: 2.40

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

Motif 4 oligos_6-8nt_m4

k-mer sig=0.04; evalue=0.91

yvCaTACATakw

WMTATGTATGBR

[ 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 (53.85%)
Max nb of predicted sites per peak: 4
(gene25542|Medicago_truncatula.MtrunA17r50ANR.60|gene25542)
Mean nb of predicted sites per peak: 2.14

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

Motif 5 dyads_test_vs_ctrl_m1

k-mer sig=2.46; evalue=0.0035

rdRCAtGRvvcwRGCCwd

HWGGCYWGBBYCATGYHY

[ 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 (76.92%)
Max nb of predicted sites per peak: 2
(MELO3C011439.2|Cucumis_melo.Melonv4.60|MELO3C011439.2)
Mean nb of predicted sites per peak: 1.30

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

Motif 6 dyads_test_vs_ctrl_m2

k-mer sig=2.46; evalue=0.0035

mvaCtGcmgsmkSmcccSCCkabs

SVTMGGSGGGKSMKSCKGCAGTBK

[ 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: 6 (46.15%)
Max nb of predicted sites per peak: 3
(HanXRQr2_Chr13g0574181|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574181)
Mean nb of predicted sites per peak: 2.00

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

Motif 7 dyads_test_vs_ctrl_m3

k-mer sig=2.46; evalue=0.0035

smmcAsSsCmstvkCvksCCtCms

SKGAGGSMBGMBASKGSSSTGKKS

[ 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: 8 (61.54%)
Max nb of predicted sites per peak: 3
(HanXRQr2_Chr13g0574171|Helianthus_annuus.HanXRQr2.0-SUNRISE.60|HanXRQr2_Chr13g0574171)
Mean nb of predicted sites per peak: 1.88

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

Motif 8 dyads_test_vs_ctrl_m4

k-mer sig=2.46; evalue=0.0035

smmhaSSmMryrvGCvKSMvtcCaasm

KSTTGGABKSMBGCBYRYKKSSTDKKS

[ 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 (53.85%)
Max nb of predicted sites per peak: 5
(AUR62023693.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62023693.v1.0)
Mean nb of predicted sites per peak: 2.29

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

Motif 9 dyads_test_vs_ctrl_m5

k-mer sig=2.46; evalue=0.0035

vcrGtGSmtYgwcdSvKSCarbcrayGk

MCRTYGVYTGSMBSHGWCRAKSCACYGB

[ 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 (76.92%)
Max nb of predicted sites per peak: 5
(T459_03445|Capsicum_annuum.ASM51225v2.60|T459_03445)
Mean nb of predicted sites per peak: 2.30

[ 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: dmrl_arabidopsis_up1_w_nicotinana (29/05/2026 11:15)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results