peak-motifs m7

Sequence composition (test sequences)

Nb of peaks: 123
Total seq. size: 35 kb
Min length: 46 bp
Mean length: 287.87 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=1.18; evalue=0.066

hsCGTGCCwy

RWGGCACGSD

[ 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 hsCGTGCCwy

ABF3:MA0930.2:JASPAR ABF3/MA0930.2/JASPAR D 10 1.0000 0.765 0.765 NA NA

GLYMA-08G357600:UN0420.1:JASPAR GLYMA-08G357600/UN0420.1/JASPAR D 10 1.0000 0.753 0.753 NA NA

MYC3:M0165_1.02:CISBP MYC3/M0165_1.02/CISBP D 10 1.0000 0.709 0.709 NA NA

Total matches= 98 (95 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: 22 (17.89%)
Max nb of predicted sites per peak: 3
(CHLRE_09g393950v5)
Mean nb of predicted sites per peak: 1.41

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

Motif 2 oligos_6-8nt_m2

k-mer sig=1.03; evalue=0.093

cvCCCATGCArg

CYTGCATGGGBG

[ 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 cvCCCATGCArg

AtLEC2:AtLEC2:Athamap AtLEC2/AtLEC2/Athamap D 10 0.8333 0.815 0.679 NA NA

LEC2:MA0581.1:JASPAR LEC2/MA0581.1/JASPAR D 10 0.7692 0.835 0.642 NA NA

FUS3:MA0565.2:JASPAR FUS3/MA0565.2/JASPAR D 10 0.8333 0.755 0.629 NA NA

Total matches= 21 (18 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: 14 (11.38%)
Max nb of predicted sites per peak: 2
(CHLRE_01g034550v5)
Mean nb of predicted sites per peak: 1.07

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

Motif 3 oligos_6-8nt_m3

k-mer sig=0.61; evalue=0.25

ksCCACGGcw

WGCCGTGGSM

[ 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 ksCCACGGcw

GBF1:M0268_1.02:CISBP GBF1/M0268_1.02/CISBP R 10 1.0000 0.709 0.709 NA NA

GBF3:M0264_1.02:CISBP GBF3/M0264_1.02/CISBP R 10 1.0000 0.708 0.708 NA NA

BZIP68:MA0968.3:JASPAR BZIP68/MA0968.3/JASPAR D 10 1.0000 0.701 0.701 NA NA

Total matches= 73 (70 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: 20 (16.26%)
Max nb of predicted sites per peak: 4
(CHLRE_15g635350v5)
Mean nb of predicted sites per peak: 1.75

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

Motif 4 oligos_6-8nt_m4

k-mer sig=0.42; evalue=0.38

cyCCTCCCCCyc

GRGGGGGAGGRG

[ 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 cyCCTCCCCCyc

ERF003:UN0363.1:JASPAR ERF003/UN0363.1/JASPAR D 12 0.9231 0.734 0.678 NA NA

ERF057:MA1753.2:JASPAR ERF057/MA1753.2/JASPAR D 12 0.8571 0.701 0.601 NA NA

ABI4:ABI4:Athamap ABI4/ABI4/Athamap D 10 0.8333 0.702 0.585 NA NA

Total matches= 14 (11 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: 16 (13.01%)
Max nb of predicted sites per peak: 9
(CHLRE_19g750597v5)
Mean nb of predicted sites per peak: 2.38

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

Motif 5 oligos_6-8nt_m5

k-mer sig=0.16; evalue=0.69

ysCCCATCCCmr

YKGGGATGGGSR

[ 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 ysCCCATCCCmr

ODO1motif1B:EEAD0088:EEADannot ODO1motif1B/EEAD0088/EEADannot D 9 0.7500 0.700 0.525 NA NA

Nuclear:6r2v_A:3D-footprint Nuclear/6r2v_A/3D-footprint D 7 0.5833 0.703 0.410 NA NA

TCP8:MA1428.2:JASPAR TCP8/MA1428.2/JASPAR D 7 0.5385 0.745 0.401 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: 16 (13.01%)
Max nb of predicted sites per peak: 2
(CHLRE_15g635350v5)
Mean nb of predicted sites per peak: 1.12

[ 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: m7 (19/06/2025 09:28)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results