peak-motifs dmrl_quinoa

Sequence composition (test sequences)

Nb of peaks: 17
Total seq. size: 12 kb
Min length: 455 bp
Mean length: 686.529 bp
Max length: 701 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: 44776
Total seq. size: 30909 kb
Min length: 201 bp
Mean length: 690.3 bp
Max length: 701 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=0.79; evalue=0.16

arATAAATrw

WYATTTATYT

[ 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: 3
(107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499)
Mean nb of predicted sites per peak: 1.67

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

Motif 2 oligos_6-8nt_m2

k-mer sig=0.61; evalue=0.25

wtCGCTaCyy

RRGTAGCGAW

[ 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 (29.41%)
Max nb of predicted sites per peak: 1
(gene-LOC110794951|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110794951)
Mean nb of predicted sites per peak: 1.00

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

Motif 3 oligos_6-8nt_m3

k-mer sig=0.51; evalue=0.31

gkCAtGCCkr

YMGGCATGMC

[ 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: 5
(107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548)
Mean nb of predicted sites per peak: 2.29

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

Motif 4 oligos_6-8nt_m4

k-mer sig=0.47; evalue=0.34

GrCaSGCCGars

SYTCGGCSTGYC

[ 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 (35.29%)
Max nb of predicted sites per peak: 3
(107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548)
Mean nb of predicted sites per peak: 1.50

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

Motif 5 oligos_6-8nt_m5

k-mer sig=0.51; evalue=0.31

ktaaaGGCATGrk

MYCATGCCTTTAM

[ 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: 2
(AUR62023693.v1.0|Chenopodium_quinoa.PI614886.392.v1.JGI|AUR62023693.v1.0)
Mean nb of predicted sites per peak: 1.36

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

Motif 6 oligos_6-8nt_m6

k-mer sig=0.05; evalue=0.89

hwGtCCTArg

CYTAGGACWD

[ 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 (35.29%)
Max nb of predicted sites per peak: 2
(T459_31204|Capsicum_annuum.ASM51225v2.60|T459_31204)
Mean nb of predicted sites per peak: 1.67

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

Motif 7 dyads_test_vs_ctrl_m1

k-mer sig=4.40; evalue=4e-05

GkGCAKStgmaGrGSCbk

MVGSCYCTKCASMTGCMC

[ 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
(107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548)
Mean nb of predicted sites per peak: 1.67

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

Motif 8 dyads_test_vs_ctrl_m2

k-mer sig=2.24; evalue=0.0058

yRCACTMwmawkCACCC

GGGTGMWTKWKAGTGYR

[ 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 (47.06%)
Max nb of predicted sites per peak: 2
(107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499)
Mean nb of predicted sites per peak: 1.12

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

Motif 9 dyads_test_vs_ctrl_m3

k-mer sig=2.24; evalue=0.0058

GmYGakmtaGaTSGGCky

RMGCCSATCTAKMTCRKC

[ 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 (35.29%)
Max nb of predicted sites per peak: 3
(107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142)
Mean nb of predicted sites per peak: 1.83

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

Motif 10 dyads_test_vs_ctrl_m4

k-mer sig=4.40; evalue=4e-05

srsmsGSmrrrGmkSvSSSswkbbkb

VMVVMWSSSSBSMKCYYYKSCSKSYS

[ 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: 13 (76.47%)
Max nb of predicted sites per peak: 4
(107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548)
Mean nb of predicted sites per peak: 2.15

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

Motif 11 dyads_test_vs_ctrl_m5

k-mer sig=4.40; evalue=4e-05

mrssaKScsgrKmSCvKSSvsckrc

GYMGSBSSMBGSKMYCSGSMTSSYK

[ 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: 4
(107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937)
Mean nb of predicted sites per peak: 2.43

[ 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_quinoa_up2 (29/05/2026 16:26)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results