peak-motifs m8

Sequence composition (test sequences)

Nb of peaks: 115
Total seq. size: 36 kb
Min length: 46 bp
Mean length: 312.313 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=2.38; evalue=0.0042

kcCCCATGCAAwm

KWTTGCATGGGGM

[ 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 kcCCCATGCAAwm

LEC2:MA0581.1:JASPAR LEC2/MA0581.1/JASPAR D 11 0.8462 0.778 0.658 NA NA

FUS3.DAP:M0003:AthalianaCistrome FUS3.DAP/M0003/AthalianaCistrome D 13 0.8667 0.732 0.634 NA NA

AtLEC2:AtLEC2:Athamap AtLEC2/AtLEC2/Athamap D 10 0.7692 0.821 0.632 NA NA

Total matches= 22 (19 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: 25 (21.74%)
Max nb of predicted sites per peak: 2
(CHLRE_18g750047v5)
Mean nb of predicted sites per peak: 1.24

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

Motif 2 oligos_6-8nt_m2

k-mer sig=0.33; evalue=0.47

hmAACCTGCCry

RYGGCAGGTTKD

[ 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 hmAACCTGCCry

AtMYB122_II:AtMYB122_II:AthaMYB AtMYB122_II/AtMYB122_II/AthaMYB R 8 0.6667 0.872 0.582 NA NA

AtMYB78_II:AtMYB78_II:AthaMYB AtMYB78_II/AtMYB78_II/AthaMYB R 8 0.6667 0.746 0.498 NA NA

MYB55:MA1041.1:JASPAR MYB55/MA1041.1/JASPAR D 8 0.6667 0.730 0.487 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: 15 (13.04%)
Max nb of predicted sites per peak: 2
(CHLRE_12g546100v5)
Mean nb of predicted sites per peak: 1.13

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

Motif 3 oligos_6-8nt_m3

k-mer sig=2.38; evalue=0.0042

ysCCCATGCAmwbac

GTVWKTGCATGGGSR

[ 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 ysCCCATGCAmwbac

FUS3.DAP:M0003:AthalianaCistrome FUS3.DAP/M0003/AthalianaCistrome D 14 0.8750 0.747 0.653 NA NA

LEC2:MA0581.1:JASPAR LEC2/MA0581.1/JASPAR D 11 0.7333 0.838 0.615 NA NA

AtLEC2:AtLEC2:Athamap AtLEC2/AtLEC2/Athamap D 10 0.6667 0.832 0.555 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: 21 (18.26%)
Max nb of predicted sites per peak: 3
(CHLRE_01g002300v5)
Mean nb of predicted sites per peak: 1.14

[ 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: m8 (19/06/2025 09:29)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results