peak-motifs hsc

Sequence composition (test sequences)

Nb of peaks: 541
Total seq. size: 109 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) ]

Sequence composition (ctrl sequences)

Nb of peaks: 500
Total seq. size: 100 kb
Min length: 200 bp
Mean length: 200 bp
Max length: 200 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_6nt_test_vs_ctrl_m1

k-mer sig=350.00; evalue=0

skCCcCGcCCCggcgCsgCcccss

SSGGGGCSGCGCCGGGGCGGGGMS

[ 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: 78 (14.42%)
Max nb of predicted sites per peak: 6
(chr7:75739096-75739297)
Mean nb of predicted sites per peak: 1.63

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

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=350.00; evalue=0

cbcgcgccgcgCyCcgccccgcvc

GBGCGGGGCGGRGCGCGGCGCGVG

[ 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: 85 (15.71%)
Max nb of predicted sites per peak: 8
(chr1:2204942-2205143)
Mean nb of predicted sites per peak: 1.94

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

Motif 3 oligos_6nt_test_vs_ctrl_m3

k-mer sig=350.00; evalue=0

mcssggCcgCCcCgCcgCGCcgcc

GGCGGCGCGGCGGGGCGGCCSSGK

[ 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: 65 (12.01%)
Max nb of predicted sites per peak: 5
(chr12:43806250-43806451)
Mean nb of predicted sites per peak: 1.49

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

Motif 4 oligos_6nt_test_vs_ctrl_m4

k-mer sig=350.00; evalue=0

syggcsgcgcggCcccGcCcccds

SHGGGGGCGGGGCCGCGCSGCCRS

[ 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: 73 (13.49%)
Max nb of predicted sites per peak: 4
(chr20:58981174-58981375)
Mean nb of predicted sites per peak: 1.49

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

Motif 5 oligos_6nt_test_vs_ctrl_m5

k-mer sig=350.00; evalue=0

mcgcgCccgCcCcgcgccgcggsc

GSCCGCGGCGCGGGGCGGGCGCGK

[ 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: 86 (15.90%)
Max nb of predicted sites per peak: 5
(chr16:70685933-70686134)
Mean nb of predicted sites per peak: 1.60

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

Motif 6 oligos_7nt_test_vs_ctrl_m1

k-mer sig=350.00; evalue=0

csgggccgcgCcCCgcccccgccc

GGGCGGGGGCGGGGCGCGGCCCSG

[ 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: 97 (17.93%)
Max nb of predicted sites per peak: 6
(chr2:25341204-25341405)
Mean nb of predicted sites per peak: 1.69

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

Motif 7 oligos_7nt_test_vs_ctrl_m2

k-mer sig=350.00; evalue=0

gsgcggcGcgGgcgGgGcggrgsg

CSCYCCGCCCCGCCCGCGCCGCSC

[ 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: 101 (18.67%)
Max nb of predicted sites per peak: 8
(chr7:69598241-69598442)
Mean nb of predicted sites per peak: 2.00

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

Motif 8 oligos_7nt_test_vs_ctrl_m3

k-mer sig=156.39; evalue=4.1e-157

scgAGcGgcggcgccgcCgCTcgs

SCGAGCGGCGGCGCCGCCGCTCGS

[ 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: 43 (7.95%)
Max nb of predicted sites per peak: 10
(chr5:180209117-180209318)
Mean nb of predicted sites per peak: 2.88

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

Motif 9 oligos_7nt_test_vs_ctrl_m4

k-mer sig=350.00; evalue=0

gkgmgggGgCGggGccgcgccgrr

YYCGGCGCGGCCCCGCCCCCKCMC

[ 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: 114 (21.07%)
Max nb of predicted sites per peak: 6
(chr1:3772462-3772663)
Mean nb of predicted sites per peak: 1.60

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

Motif 10 oligos_7nt_test_vs_ctrl_m5

k-mer sig=156.02; evalue=9.5e-157

kycggggccgcggagcgygckCkc

GMGMGCRCGCTCCGCGGCCCCGRM

[ 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: 61 (11.28%)
Max nb of predicted sites per peak: 5
(chr8:73746936-73747137)
Mean nb of predicted sites per peak: 1.28

[ 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: hsc (28/07/2026 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