peak-motifs up4

Sequence composition (test sequences)

Nb of peaks: 17
Total seq. size: 3 kb
Min length: 201 bp
Mean length: 201 bp
Max length: 201 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_6-7nt_m1

k-mer sig=2.58; evalue=0.0026

smdrACCAAACsM

KSGTTTGGTYHKS

[ 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: 6 (35.29%)
Max nb of predicted sites per peak: 3
(PAL2)
Mean nb of predicted sites per peak: 1.50

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

Motif 2 oligos_6-7nt_m2

k-mer sig=2.54; evalue=0.0029

YrCCACCGtbd

HVACGGTGGYR

[ 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: 7 (41.18%)
Max nb of predicted sites per peak: 2
(PAL1)
Mean nb of predicted sites per peak: 1.29

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

Motif 3 oligos_6-7nt_m3

k-mer sig=1.28; evalue=0.052

srrGAGATCTctbk

MVAGAGATCTCYYS

[ 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: 6 (35.29%)
Max nb of predicted sites per peak: 2
(UGT73B1)
Mean nb of predicted sites per peak: 1.50

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

Motif 4 oligos_6-7nt_m4

k-mer sig=1.10; evalue=0.079

rrCCACGAmww

WWKTCGTGGYY

[ 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: 4 (23.53%)
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 5 oligos_6-7nt_m5

k-mer sig=0.89; evalue=0.13

ryCaGCCACsr

YSGTGGCTGRY

[ 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: 4 (23.53%)
Max nb of predicted sites per peak: 2
(PAL2)
Mean nb of predicted sites per peak: 1.50

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

Motif 6 oligos_6-7nt_m6

k-mer sig=0.44; evalue=0.36

rgGTaGTAAhG

CDTTACTACCY

[ 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 (47.06%)
Max nb of predicted sites per peak: 2
(UGT73B1)
Mean nb of predicted sites per peak: 1.25

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

Motif 7 oligos_6-7nt_m7

k-mer sig=0.43; evalue=0.37

waaCGSCGTTwa

TWAACGSCGTTW

[ 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: 3 (17.65%)
Max nb of predicted sites per peak: 4
(CYP73A5)
Mean nb of predicted sites per peak: 2.33

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

Motif 8 oligos_6-7nt_m8

k-mer sig=2.58; evalue=0.0026

bmtsACCAAaCsc

GSGTTTGGTSAKV

[ 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: 6 (35.29%)
Max nb of predicted sites per peak: 2
(PAL2)
Mean nb of predicted sites per peak: 1.33

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

Motif 9 oligos_6-7nt_m9

k-mer sig=0.07; evalue=0.85

dcSATGGCCcd

HGGGCCATSGH

[ 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: 4 (23.53%)
Max nb of predicted sites per peak: 3
(ATMYB72)
Mean nb of predicted sites per peak: 2.00

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

Motif 10 oligos_6-7nt_m10

k-mer sig=0.02; evalue=0.95

sSCTTTTACmw

WKGTAAAAGSS

[ 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: 6 (35.29%)
Max nb of predicted sites per peak: 2
(CYP73A5)
Mean nb of predicted sites per peak: 1.17

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

Motif 11 dyads_m1

k-mer sig=0.70; evalue=0.2

CsCCrCCGtb

VACGGYGGSG

[ 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: 6 (35.29%)
Max nb of predicted sites per peak: 2
(PAL1)
Mean nb of predicted sites per peak: 1.33

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

Motif 12 dyads_m2

k-mer sig=0.57; evalue=0.27

kyACCwAmCGCvr

YBGCGKTWGGTRM

[ 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: 5 (29.41%)
Max nb of predicted sites per peak: 2
(PAL2)
Mean nb of predicted sites per peak: 1.40

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

Motif 13 dyads_m3

k-mer sig=0.19; evalue=0.65

vmTCAvbmrwkhykkrcryaaACAww

WWTGTTTRYGYMMRDMWYKVBTGAKB

[ 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: 7 (41.18%)
Max nb of predicted sites per peak: 2
(CCoAOMT1)
Mean nb of predicted sites per peak: 1.29

[ 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: up4 (26/02/2026 15:39)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results