peak-motifs gg

Sequence composition (test sequences)

Nb of peaks: 49
Total seq. size: 31 kb
Min length: 201 bp
Mean length: 629.388 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: 34262
Total seq. size: 19694 kb
Min length: 201 bp
Mean length: 574.793 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_6-7nt_m1

k-mer sig=2.77; evalue=0.0017

bsaaaaGTCtavw

WBTAGACTTTTSV

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor bsaaaaGTCtavw

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 18 (36.73%)
Max nb of predicted sites per peak: 2
(WRKY31)
Mean nb of predicted sites per peak: 1.28

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

Motif 2 oligos_6-7nt_m2

k-mer sig=1.42; evalue=0.038

wrAATATTbk

MVAATATTYW

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor wrAATATTbk

7233_KAN4_ArabidopsisPBM_20140210_ 7233_KAN4_ArabidopsisPBM_20140210_ D 10 1.0000 0.787 0.787 NA NA

7183_AHL12_ArabidopsisPBM_20140210_ 7183_AHL12_ArabidopsisPBM_20140210_ D 10 1.0000 0.755 0.755 NA NA

7209_CCA1_ArabidopsisPBM_20140210_ 7209_CCA1_ArabidopsisPBM_20140210_ D 10 1.0000 0.727 0.727 NA NA

Total matches= 7 (4 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 0 (0.00%)
Max nb of predicted sites per peak:
Mean nb of predicted sites per peak: 0.00

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

Motif 3 oligos_6-7nt_m3

k-mer sig=1.37; evalue=0.043

kmTAAATAka

TMTATTTAKM

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor kmTAAATAka

7187_AHL20_2_ArabidopsisPBM_20140210_ 7187_AHL20_2_ArabidopsisPBM_20140210_ D 8 0.6667 0.816 0.544 NA NA

7183_AHL12_ArabidopsisPBM_20140210_ 7183_AHL12_ArabidopsisPBM_20140210_ D 8 0.6667 0.750 0.500 NA NA

7209_CCA1_ArabidopsisPBM_20140210_ 7209_CCA1_ArabidopsisPBM_20140210_ D 8 0.6667 0.747 0.498 NA NA

Total matches= 9 (6 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 13 (26.53%)
Max nb of predicted sites per peak: 2
(CYP71A12)
Mean nb of predicted sites per peak: 1.08

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

Motif 4 oligos_6-7nt_m4

k-mer sig=1.09; evalue=0.081

waACAAAAcva

TBGTTTTGTTW

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor waACAAAAcva

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 17 (34.69%)
Max nb of predicted sites per peak: 3
(FOX2)
Mean nb of predicted sites per peak: 1.41

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

Motif 5 oligos_6-7nt_m5

k-mer sig=0.51; evalue=0.31

ckTATTCAvs

SBTGAATAMG

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ckTATTCAvs

7234_KAN4_2_ArabidopsisPBM_20140210_ 7234_KAN4_2_ArabidopsisPBM_20140210_ D 9 0.8182 0.758 0.621 NA NA

7232_KAN1_ArabidopsisPBM_20140210_ 7232_KAN1_ArabidopsisPBM_20140210_ D 8 0.6667 0.777 0.518 NA NA

7233_KAN4_ArabidopsisPBM_20140210_ 7233_KAN4_ArabidopsisPBM_20140210_ D 8 0.6667 0.763 0.508 NA NA

Total matches= 3

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 17 (34.69%)
Max nb of predicted sites per peak: 4
(PER37)
Mean nb of predicted sites per peak: 1.24

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

Motif 6 dyads_test_vs_ctrl_m1

k-mer sig=1.95; evalue=0.011

saaAaGTCtavw

WBTAGACTTTTS

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor saaAaGTCtavw

7211_DAG2_ArabidopsisPBM_20140210_ 7211_DAG2_ArabidopsisPBM_20140210_ D 9 0.6923 0.708 0.490 NA NA

Total matches= 1

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 13 (26.53%)
Max nb of predicted sites per peak: 3
(VSR7)
Mean nb of predicted sites per peak: 1.31

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

Motif 7 dyads_test_vs_ctrl_m2

k-mer sig=1.95; evalue=0.011

hwatTrGRbywmaaaCaak

MTTGTTTKWRVYCYAATWD

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor hwatTrGRbywmaaaCaak

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 11 (22.45%)
Max nb of predicted sites per peak: 2
(RABA1E)
Mean nb of predicted sites per peak: 1.18

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

Motif 8 dyads_test_vs_ctrl_m3

k-mer sig=1.95; evalue=0.011

amGaCwrRtYytawrwtwmwttakd

HMTAAWKWAWYWTARRAYYWGTCKT

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor amGaCwrRtYytawrwtwmwttakd

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 13 (26.53%)
Max nb of predicted sites per peak: 4
(AT2G28960)
Mean nb of predicted sites per peak: 1.69

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

Motif 9 dyads_test_vs_ctrl_m4

k-mer sig=1.95; evalue=0.011

avttTrRRCYyaaaybaaaky

RMTTTVRTTTRRGYYYAAABT

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor avttTrRRCYyaaaybaaaky

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 14 (28.57%)
Max nb of predicted sites per peak: 4
(AT3G07720)
Mean nb of predicted sites per peak: 1.21

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

Motif 10 dyads_test_vs_ctrl_m5

k-mer sig=1.95; evalue=0.011

vmaTagRcytatattwamatwaaaawa

TWTTTTWATKTWAATATARGYCTATKB

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor vmaTagRcytatattwamatwaaaawa

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 8 (16.33%)
Max nb of predicted sites per peak: 2
(WRKY31)
Mean nb of predicted sites per peak: 1.38

[ 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) ]
Discovered motifs versus transcription factor databases
Motifs versus ArabidopsisPBM database		[ table: html txt ] [ alignments (logo): html text ] [ 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: gg (07/11/2025 16:25)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor bsaaaaGTCtavw

Total matches= 0

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor waACAAAAcva

Total matches= 0

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor saaAaGTCtavw

7211_DAG2_ArabidopsisPBM_20140210_ 7211_DAG2_ArabidopsisPBM_20140210_ D 9 0.6923 0.708 0.490 NA NA

Total matches= 1

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor hwatTrGRbywmaaaCaak

Total matches= 0

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor amGaCwrRtYytawrwtwmwttakd

Total matches= 0

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor avttTrRRCYyaaaybaaaky

Total matches= 0

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor vmaTagRcytatattwamatwaaaawa

Total matches= 0

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: gg (07/11/2025 16:25)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor bsaaaaGTCtavw Total matches= 0

ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor waACAAAAcva Total matches= 0

ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor saaAaGTCtavw 7211_DAG2_ArabidopsisPBM_20140210_ 7211_DAG2_ArabidopsisPBM_20140210_ D 9 0.6923 0.708 0.490 NA NA Total matches= 1

ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor hwatTrGRbywmaaaCaak Total matches= 0

ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor amGaCwrRtYytawrwtwmwttakd Total matches= 0

ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor avttTrRRCYyaaaybaaaky Total matches= 0

ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor vmaTagRcytatattwamatwaaaawa Total matches= 0

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor bsaaaaGTCtavw

Total matches= 0

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor waACAAAAcva

Total matches= 0

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor saaAaGTCtavw

7211_DAG2_ArabidopsisPBM_20140210_ 7211_DAG2_ArabidopsisPBM_20140210_ D 9 0.6923 0.708 0.490 NA NA

Total matches= 1

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor hwatTrGRbywmaaaCaak

Total matches= 0

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor amGaCwrRtYytawrwtwmwttakd

Total matches= 0

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor avttTrRRCYyaaaybaaaky

Total matches= 0

ArabidopsisPBM

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor vmaTagRcytatattwamatwaaaawa

Total matches= 0