peak-motifs up3

Sequence composition (test sequences)

Nb of peaks: 17
Total seq. size: 8 kb
Min length: 29 bp
Mean length: 459 bp
Max length: 501 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=1.94; evalue=0.011

kyaCCaACCCCsb

VSGGGGTTGGTRM

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

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor kyaCCaACCCCsb

RAX3 MA0576.2 R 12 0.9231 0.817 0.754 NA NA

MYB63 MA2024.2 D 11 0.8462 0.810 0.686 NA NA

MYB13 MA2041.2 D 10 0.7692 0.860 0.661 NA NA

Total matches= 40 (37 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: 8 (47.06%)
Max nb of predicted sites per peak: 2
(HST)
Mean nb of predicted sites per peak: 1.12

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

Motif 2 oligos_6-8nt_m2

k-mer sig=0.47; evalue=0.34

rrATATCAAwk

MWTTGATATYY

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

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor rrATATCAAwk

CCA1 MA0972.1 D 8 0.7273 0.750 0.546 NA NA

PK02532.1 MA2353.1 D 8 0.7273 0.745 0.542 NA NA

RVE7L MA1191.2 D 8 0.6667 0.806 0.538 NA NA

Total matches= 12 (9 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: 10 (58.82%)
Max nb of predicted sites per peak: 2
(SYP122)
Mean nb of predicted sites per peak: 1.10

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

Motif 3 oligos_6-8nt_m3

k-mer sig=0.30; evalue=0.5

tcACCaCaaAwm

KWTTTGTGGTGA

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

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor tcACCaCaaAwm

MGP MA1158.2 D 12 0.9231 0.758 0.700 NA NA

IDD11 MA2104.1 D 11 0.8462 0.774 0.655 NA NA

IDD1 MA2396.1 R 11 0.8462 0.769 0.651 NA NA

Total matches= 16 (13 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: 7 (41.18%)
Max nb of predicted sites per peak: 2
(HST)
Mean nb of predicted sites per peak: 1.57

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

Motif 4 oligos_6-8nt_m4

k-mer sig=0.29; evalue=0.51

rwAGAGAArk

MYTTCTCTWY

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

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor rwAGAGAArk

Zm00001d027846 MA1823.2 D 8 0.8000 0.711 0.569 NA NA

SGR5 MA1159.2 D 10 0.7692 0.703 0.541 NA NA

AT2G38300 MA1735.2 R 8 0.6667 0.745 0.497 NA NA

Total matches= 4 (1 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: 9 (52.94%)
Max nb of predicted sites per peak: 2
(F6'H1)
Mean nb of predicted sites per peak: 1.22

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

Motif 5 oligos_6-8nt_m5

k-mer sig=0.19; evalue=0.65

yvCaTGCATaas

STTATGCATGBR

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

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor yvCaTGCATaas

GLYMA-08G357600 MA1810.2 R 9 0.7500 0.913 0.685 NA NA

FUS3 MA0565.3 D 7 0.5833 0.927 0.541 NA NA

LEC2 MA0581.2 D 6 0.5000 0.949 0.474 NA NA

Total matches= 4 (1 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: 8 (47.06%)
Max nb of predicted sites per peak: 2
(PAL1)
Mean nb of predicted sites per peak: 1.25

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

Motif 6 oligos_6-8nt_m6

k-mer sig=0.12; evalue=0.76

ymTGACGTaAkk

MMTTACGTCAKR

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

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor ymTGACGTaAkk

TGA3 MA1336.2 D 11 0.9167 0.815 0.747 NA NA

TGA9 MA1348.1 R 11 0.9167 0.801 0.734 NA NA

TGA7 MA1070.3 D 10 0.8333 0.848 0.706 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: 6 (35.29%)
Max nb of predicted sites per peak: 3
(AT5G20950)
Mean nb of predicted sites per peak: 1.33

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

Motif 7 oligos_6-8nt_m7

k-mer sig=0.07; evalue=0.85

sdAGTCGCCkv

BMGGCGACTHS

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

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor sdAGTCGCCkv

ERF15 MA1231.3 D 8 0.7273 0.706 0.513 NA NA

WIN1 MA1804.2 D 6 0.5455 0.845 0.461 NA NA

DEAR3 MA1376.2 D 6 0.5000 0.858 0.429 NA NA

Total matches= 5 (2 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: 5 (29.41%)
Max nb of predicted sites per peak: 2
(CCoAOMT1)
Mean nb of predicted sites per peak: 1.20

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

Motif 8 oligos_6-8nt_m8

k-mer sig=0.01; evalue=0.98

vcCCACCAaha

TDTTGGTGGGB

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

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor vcCCACCAaha

MYB58 MA2042.2 D 9 0.8182 0.838 0.686 NA NA

MYB40 MA1770.2 D 10 0.9091 0.708 0.643 NA NA

MYB83 MA1779.2 D 8 0.7273 0.877 0.638 NA NA

Total matches= 26 (23 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: 6 (35.29%)
Max nb of predicted sites per peak: 2
(CYP98A3)
Mean nb of predicted sites per peak: 1.17

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

Motif 9 dyads_m1

k-mer sig=1.22; evalue=0.06

wyaCCyaCCsm

KSGGTRGGTRW

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

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor wyaCCyaCCsm

MYB63 MA2024.2 D 11 1.0000 0.907 0.907 NA NA

MYB10 MA1762.2 D 10 0.9091 0.911 0.828 NA NA

MYB43 MA1772.2 D 11 0.9167 0.876 0.803 NA NA

Total matches= 50 (47 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: 7 (41.18%)
Max nb of predicted sites per peak: 2
(HST)
Mean nb of predicted sites per peak: 1.43

[ 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 JASPAR2024_CORE_plants_non-redundant 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: up3 (26/02/2026 15:50)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results