peak-motifs m2

Sequence composition (test sequences)

Nb of peaks: 721
Total seq. size: 337 kb
Min length: 201 bp
Mean length: 467.639 bp
Max length: 1000 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=5.05; evalue=8.9e-06

ccCCCTCCCcycc

GGRGGGGAGGGGG

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

footprintDB-plants

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

columns aligned correlation cor ccCCCTCCCcycc

ODO1motif1B:EEAD0088:EEADannot ODO1motif1B/EEAD0088/EEADannot D 9 0.6923 0.703 0.487 NA NA

TB1:MA1430.1:JASPAR TB1/MA1430.1/JASPAR D 9 0.6429 0.706 0.454 NA NA

TB1:MA1430.2:JASPAR TB1/MA1430.2/JASPAR D 8 0.5714 0.738 0.422 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: 132 (18.31%)
Max nb of predicted sites per peak: 23
(CHLRE_12g541300v5)
Mean nb of predicted sites per peak: 3.20

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

Motif 2 oligos_6-8nt_m2

k-mer sig=4.39; evalue=4.1e-05

wwTACAGTAtww

WWATACTGTAWW

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

footprintDB-plants

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

columns aligned correlation cor wwTACAGTAtww

ALOG:EEAD0170:EEADannot ALOG/EEAD0170/EEADannot R 11 0.9167 0.732 0.671 NA NA

AtMYB104_I:AtMYB104_I:AthaMYB AtMYB104_I/AtMYB104_I/AthaMYB R 8 0.6667 0.739 0.493 NA NA

SPL14:M1561_1.02:CISBP SPL14/M1561_1.02/CISBP R 8 0.6154 0.730 0.449 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: 111 (15.40%)
Max nb of predicted sites per peak: 4
(CHLRE_13g607950v5)
Mean nb of predicted sites per peak: 1.36

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

Motif 3 oligos_6-8nt_m3

k-mer sig=4.35; evalue=4.5e-05

ssCCCATGCAgv

BCTGCATGGGSS

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

footprintDB-plants

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

columns aligned correlation cor ssCCCATGCAgv

AtLEC2:AtLEC2:Athamap AtLEC2/AtLEC2/Athamap D 10 0.8333 0.811 0.676 NA NA

LEC2:MA0581.1:JASPAR LEC2/MA0581.1/JASPAR D 10 0.7692 0.840 0.646 NA NA

FUS3:MA0565.2:JASPAR FUS3/MA0565.2/JASPAR D 10 0.8333 0.751 0.626 NA NA

Total matches= 20 (17 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: 87 (12.07%)
Max nb of predicted sites per peak: 2
(CHLRE_13g586916v5)
Mean nb of predicted sites per peak: 1.05

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

Motif 4 oligos_6-8nt_m4

k-mer sig=4.24; evalue=5.8e-05

waTAcATAyw

WRTATGTATW

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

footprintDB-plants

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

columns aligned correlation cor waTAcATAyw

AT3G49930:UN0355.1:JASPAR AT3G49930/UN0355.1/JASPAR D 10 0.9091 0.747 0.679 NA NA

MYB3:M1319_1.02:CISBP MYB3/M1319_1.02/CISBP R 10 0.9091 0.702 0.638 NA NA

MYB3:MA1038.1:JASPAR MYB3/MA1038.1/JASPAR R 10 0.9091 0.702 0.638 NA NA

Total matches= 29 (26 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: 150 (20.80%)
Max nb of predicted sites per peak: 8
(CHLRE_16g656500v5)
Mean nb of predicted sites per peak: 1.39

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

Motif 5 oligos_6-8nt_m5

k-mer sig=3.85; evalue=0.00014

rhCAAAATGdw

WHCATTTTGDY

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

footprintDB-plants

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

columns aligned correlation cor rhCAAAATGdw

DOF2.2:MA1272.2:JASPAR DOF2.2/MA1272.2/JASPAR D 10 0.9091 0.702 0.639 NA NA

AT2G31460:UN0390.2:JASPAR AT2G31460/UN0390.2/JASPAR D 8 0.7273 0.732 0.532 NA NA

C3H36:UN0844.1:JASPAR C3H36/UN0844.1/JASPAR D 8 0.6667 0.708 0.472 NA NA

Total matches= 11 (8 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: 83 (11.51%)
Max nb of predicted sites per peak: 2
(CHLRE_08g365900v5)
Mean nb of predicted sites per peak: 1.04

[ 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 footprintDB-plants 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: m2 (19/06/2025 08:56)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results