peak-motifs dd

Sequence composition (test sequences)

Nb of peaks: 48
Total seq. size: 31 kb
Min length: 201 bp
Mean length: 637.208 bp
Max length: 701 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) ]

Sequence composition (ctrl sequences)

Nb of peaks: 29600
Total seq. size: 16966 kb
Min length: 201 bp
Mean length: 573.17 bp
Max length: 701 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=2.48; evalue=0.0033

bsaaAaGTCtaawg

CWTTAGACTTTTSV

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 18 (37.50%)
Max nb of predicted sites per peak: 2
(RABA1E)
Mean nb of predicted sites per peak: 1.17

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

Motif 2 oligos_6-8nt_m2

k-mer sig=1.32; evalue=0.048

wrAATATTbk

MVAATATTYW

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 0 (0.00%)
Max nb of predicted sites per peak:
Mean nb of predicted sites per peak: 0.00

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

Motif 3 oligos_6-8nt_m3

k-mer sig=1.11; evalue=0.078

kmTAAATAkw

WMTATTTAKM

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 14 (29.17%)
Max nb of predicted sites per peak: 2
(CYP71A12)
Mean nb of predicted sites per peak: 1.07

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

Motif 4 oligos_6-8nt_m4

k-mer sig=1.04; evalue=0.091

wamACAAAAcs

SGTTTTGTKTW

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 8 (16.67%)
Max nb of predicted sites per peak: 2
(FOX2)
Mean nb of predicted sites per peak: 1.25

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

Motif 5 oligos_6-8nt_m5

k-mer sig=0.83; evalue=0.15

vbCTATAAww

WWTTATAGVB

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 22 (45.83%)
Max nb of predicted sites per peak: 4
(AT1G51890)
Mean nb of predicted sites per peak: 1.36

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

Motif 6 dyads_test_vs_ctrl_m1

k-mer sig=2.30; evalue=0.005

myaaGtCTark

MYTAGACTTRK

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 19 (39.58%)
Max nb of predicted sites per peak: 2
(RABA1E)
Mean nb of predicted sites per peak: 1.21

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

Motif 7 dyads_test_vs_ctrl_m2

k-mer sig=2.30; evalue=0.005

hwatTrGRbytmaaaCaww

WWTGTTTKARVYCYAATWD

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 13 (27.08%)
Max nb of predicted sites per peak: 1
(UGT72E2)
Mean nb of predicted sites per peak: 1.00

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

Motif 8 dyads_test_vs_ctrl_m3

k-mer sig=2.30; evalue=0.005

rwGaCwrRyCywaaGwtamwttakd

HMTAAWKTAWCTTWRGRYYWGTCWY

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 10 (20.83%)
Max nb of predicted sites per peak: 5
(AT2G28960)
Mean nb of predicted sites per peak: 1.70

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

Motif 9 dyads_test_vs_ctrl_m4

k-mer sig=2.30; evalue=0.005

myatakRCytatrtwtwmwtrbaaawr

YWTTTVYAWKWAWAYATARGYMTATRK

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 13 (27.08%)
Max nb of predicted sites per peak: 3
(SAL4)
Mean nb of predicted sites per peak: 1.38

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

Motif 10 dyads_test_vs_ctrl_m5

k-mer sig=2.30; evalue=0.005

rbaaTrrGCytatrtwmwwktwyaCasr

YSTGTRWAMWWKWAYATARGCYYATTVY

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 17 (35.42%)
Max nb of predicted sites per peak: 2
(WRKY31)
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) ]

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: dd (22/07/2026 13:26)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results