peak-motifs m10

Sequence composition (test sequences)

Nb of peaks: 92
Total seq. size: 24 kb
Min length: 46 bp
Mean length: 262.163 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=1.05; evalue=0.089

wbGAAGGAACky

RMGTTCCTTCVW

[ 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 wbGAAGGAACky

NTL8:MA1678.2:JASPAR NTL8/MA1678.2/JASPAR D 12 0.9231 0.802 0.741 NA NA

NAC045:UN0375.1:JASPAR NAC045/UN0375.1/JASPAR D 12 0.9231 0.776 0.716 NA NA

NTL8:UP00577A_2:UniPROBE NTL8/UP00577A_2/UniPROBE D 12 0.9231 0.752 0.694 NA NA

Total matches= 10 (7 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: 17 (18.48%)
Max nb of predicted sites per peak: 2
(CHLRE_08g362050v5)
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=0.67; evalue=0.21

gtAGTACGtr

YACGTACTAC

[ 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 gtAGTACGtr

fgenesh1_pg.scaffold_194000034:M1570_1.02:CISBP fgenesh1_pg.scaffold_194000034/M1570_1.02/CISBP D 10 1.0000 0.823 0.823 NA NA

AT1G76580:M1564_1.02:CISBP AT1G76580/M1564_1.02/CISBP D 10 1.0000 0.803 0.803 NA NA

SPL5:MA1059.1:JASPAR SPL5/MA1059.1/JASPAR D 9 0.9000 0.857 0.771 NA NA

Total matches= 71 (68 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: 12 (13.04%)
Max nb of predicted sites per peak: 7
(CHLRE_08g362050v5)
Mean nb of predicted sites per peak: 1.75

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

Motif 3 oligos_6-8nt_m3

k-mer sig=0.51; evalue=0.31

gsACCGACccy

RGGGTCGGTSC

[ 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 gsACCGACccy

DEAR5.ampDAP:M0135:AthalianaCistrome DEAR5.ampDAP/M0135/AthalianaCistrome R 11 1.0000 0.840 0.840 NA NA

estExt_gwp_gw1.C_550163:M0073_1.02:CISBP estExt_gwp_gw1.C_550163/M0073_1.02/CISBP R 10 0.9091 0.902 0.820 NA NA

PHYPADRAFT_182268:MA1008.1:JASPAR PHYPADRAFT_182268/MA1008.1/JASPAR R 10 0.9091 0.901 0.819 NA NA

Total matches= 208 (205 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 (6.52%)
Max nb of predicted sites per peak: 3
(CHLRE_16g676421v5)
Mean nb of predicted sites per peak: 1.33

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

Motif 4 oligos_6-8nt_m4

k-mer sig=0.44; evalue=0.36

syCCCGCCdc

GHGGCGGGRS

[ 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 syCCCGCCdc

ERF1:M0025_1.02:CISBP ERF1/M0025_1.02/CISBP D 10 1.0000 0.766 0.766 NA NA

AT5G23930:UN0357.1:JASPAR AT5G23930/UN0357.1/JASPAR D 10 1.0000 0.759 0.759 NA NA

ERF105:MA1000.3:JASPAR ERF105/MA1000.3/JASPAR R 10 1.0000 0.746 0.746 NA NA

Total matches= 152 (149 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 (23.91%)
Max nb of predicted sites per peak: 3
(CHLRE_09g412450v5)
Mean nb of predicted sites per peak: 1.45

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

Motif 5 oligos_6-8nt_m5

k-mer sig=0.33; evalue=0.47

scATGCAGct

AGCTGCATGS

[ 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 scATGCAGct

LEC2:MA0581.1:JASPAR LEC2/MA0581.1/JASPAR D 10 0.9091 0.776 0.705 NA NA

LEC2:M0146_1.02:CISBP LEC2/M0146_1.02/CISBP R 8 0.8000 0.821 0.657 NA NA

AtLEC2:AtLEC2:Athamap AtLEC2/AtLEC2/Athamap D 9 0.8182 0.777 0.636 NA NA

Total matches= 28 (25 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 (22.83%)
Max nb of predicted sites per peak: 5
(CHLRE_03g179550v5)
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 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: m10 (19/06/2025 09:36)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results