peak-motifs m5

Sequence composition (test sequences)

Nb of peaks: 169
Total seq. size: 98 kb
Min length: 249 bp
Mean length: 578.325 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=2.41; evalue=0.0039

ycgGCACGCCcyw

WRGGGCGTGCCGR

[ 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 ycgGCACGCCcyw

bHLH172:UN0431.1:JASPAR bHLH172/UN0431.1/JASPAR D 10 0.7692 0.892 0.686 NA NA

fgenesh1_pg.C_Chr_14.0001000151:M0253_1.02:CISBP fgenesh1_pg.C_Chr_14.0001000151/M0253_1.02/CISBP R 10 0.7692 0.713 0.549 NA NA

BBM:UN0872.1:JASPAR BBM/UN0872.1/JASPAR D 8 0.6154 0.843 0.519 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: 27 (15.98%)
Max nb of predicted sites per peak: 2
(CHLRE_12g537050v5)
Mean nb of predicted sites per peak: 1.11

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

Motif 2 oligos_6-8nt_m2

k-mer sig=2.32; evalue=0.0048

ssCCCATCGCrc

GYGCGATGGGSS

[ 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 ssCCCATCGCrc

TCP8:MA1428.2:JASPAR TCP8/MA1428.2/JASPAR D 7 0.5385 0.762 0.410 NA NA

Glyma19g26560.1:MA1019.2:JASPAR Glyma19g26560.1/MA1019.2/JASPAR D 7 0.5385 0.751 0.404 NA NA

GLYMA19G26560:MA2390.1:JASPAR GLYMA19G26560/MA2390.1/JASPAR D 7 0.5385 0.751 0.404 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: 24 (14.20%)
Max nb of predicted sites per peak: 2
(CHLRE_13g564250v5)
Mean nb of predicted sites per peak: 1.08

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

Motif 3 oligos_6-8nt_m3

k-mer sig=2.24; evalue=0.0058

ssCCCCGCCCys

SRGGGCGGGGSS

[ 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 ssCCCCGCCCys

ABI4:ABI4:Athamap ABI4/ABI4/Athamap D 10 0.8333 0.839 0.699 NA NA

DEAR3:DEAR3:ArabidopsisPBM DEAR3/DEAR3/ArabidopsisPBM D 10 0.8333 0.750 0.625 NA NA

ERF055:MA1263.2:JASPAR ERF055/MA1263.2/JASPAR R 9 0.7500 0.703 0.527 NA NA

Total matches= 32 (29 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: 33 (19.53%)
Max nb of predicted sites per peak: 12
(CHLRE_17g705700v5)
Mean nb of predicted sites per peak: 2.21

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

Motif 4 oligos_6-8nt_m4

k-mer sig=1.12; evalue=0.076

yaTACcGTAyd

HRTACGGTATR

[ 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 yaTACcGTAyd

RGL2:M0821_1.02:CISBP RGL2/M0821_1.02/CISBP R 9 0.8182 0.768 0.628 NA NA

SPL4:MA1058.1:JASPAR SPL4/MA1058.1/JASPAR R 9 0.8182 0.749 0.613 NA NA

SPL4:M1563_1.02:CISBP SPL4/M1563_1.02/CISBP R 9 0.8182 0.748 0.612 NA NA

Total matches= 58 (55 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 (9.47%)
Max nb of predicted sites per peak: 3
(CHLRE_09g396100v5)
Mean nb of predicted sites per peak: 1.75

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

Motif 5 oligos_6-8nt_m5

k-mer sig=0.86; evalue=0.14

bgcCCCATGCAws

SWTGCATGGGGCV

[ 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 bgcCCCATGCAws

AtLEC2:AtLEC2:Athamap AtLEC2/AtLEC2/Athamap D 10 0.7692 0.795 0.611 NA NA

LEC2:MA0581.1:JASPAR LEC2/MA0581.1/JASPAR D 10 0.7143 0.824 0.588 NA NA

FUS3:MA0565.2:JASPAR FUS3/MA0565.2/JASPAR D 10 0.7692 0.714 0.549 NA NA

Total matches= 17 (14 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: 42 (24.85%)
Max nb of predicted sites per peak: 3
(CHLRE_05g245950v5)
Mean nb of predicted sites per peak: 1.19

[ 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: m5 (19/06/2025 09:20)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results