peak-motifs origins

Sequence composition (test sequences)

Nb of peaks: 1691
Total seq. size: 8455 kb
Min length: 5000 bp
Mean length: 5000 bp
Max length: 5000 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: 2437
Total seq. size: 12183 kb
Min length: 4999 bp
Mean length: 4999 bp
Max length: 4999 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=74.20; evalue=6.3e-75

ssgCCCaGgCCCtGCCCCtCCCcs

SGGGGAGGGGCAGGGCCTGGGCSS

[ 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: 1275 (75.40%)
Max nb of predicted sites per peak: 165
(::chr12:132595100-132600101)
Mean nb of predicted sites per peak: 8.29

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

Motif 2 oligos_6-8nt_m2

k-mer sig=59.89; evalue=1.3e-60

ssCaGGagGGGCaGGGaGGCcCrs

SYGGGCCTCCCTGCCCCTCCTGSS

[ 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: 1436 (84.92%)
Max nb of predicted sites per peak: 89
(::chr12:132595100-132600101)
Mean nb of predicted sites per peak: 5.76

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

Motif 3 oligos_6-8nt_m3

k-mer sig=59.89; evalue=1.3e-60

ssggggCtCCCtGCCCCtCCCCss

SSGGGGAGGGGCAGGGAGCCCCSS

[ 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: 1334 (78.89%)
Max nb of predicted sites per peak: 232
(::chr12:132595100-132600101)
Mean nb of predicted sites per peak: 8.40

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

Motif 4 oligos_6-8nt_m4

k-mer sig=74.20; evalue=6.3e-75

grGsCCAGGCaGGGaGGgGCaGgs

SCCTGCCCCTCCCTGCCTGGSCYC

[ 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: 1499 (88.65%)
Max nb of predicted sites per peak: 107
(::chr12:132595100-132600101)
Mean nb of predicted sites per peak: 6.30

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

Motif 5 oligos_6-8nt_m5

k-mer sig=74.20; evalue=6.3e-75

ssGGGGaGGGGCaGGGCCtGGcss

SSGCCAGGCCCTGCCCCTCCCCSS

[ 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: 1274 (75.34%)
Max nb of predicted sites per peak: 160
(::chr12:132595100-132600101)
Mean nb of predicted sites per peak: 8.73

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

Motif 6 oligos_6-8nt_m6

k-mer sig=59.89; evalue=1.3e-60

bsCaGaGgCCCtGCCCCtCCCCcs

SGGGGGAGGGGCAGGGCCTCTGSV

[ 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: 1328 (78.53%)
Max nb of predicted sites per peak: 112
(::chr12:132595100-132600101)
Mean nb of predicted sites per peak: 6.67

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

Motif 7 oligos_6-8nt_m7

k-mer sig=59.89; evalue=1.3e-60

ccmgCCCCtCCCtGCCCCaCCCcs

SGGGGTGGGGCAGGGAGGGGCKGG

[ 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: 1344 (79.48%)
Max nb of predicted sites per peak: 275
(::chr12:132595100-132600101)
Mean nb of predicted sites per peak: 8.16

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

Motif 8 oligos_6-8nt_m8

k-mer sig=74.20; evalue=6.3e-75

ssCCCCaGgCCCtGCCCCtCCCcs

SGGGGAGGGGCAGGGCCTGGGGSS

[ 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: 1296 (76.64%)
Max nb of predicted sites per peak: 247
(::chr12:132595100-132600101)
Mean nb of predicted sites per peak: 9.00

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

Motif 9 oligos_6-8nt_m9

k-mer sig=74.20; evalue=6.3e-75

ssCtCCaGGCCCtGCCCCtCCCcs

SGGGGAGGGGCAGGGCCTGGAGSS

[ 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: 1346 (79.60%)
Max nb of predicted sites per peak: 214
(::chr12:132595100-132600101)
Mean nb of predicted sites per peak: 7.49

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

Motif 10 oligos_6-8nt_m10

k-mer sig=74.20; evalue=6.3e-75

gaGmCCAGCCTGGGCArsrwGGyg

CRCCWYSYTGCCCAGGCTGGKCTC

[ 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: 1526 (90.24%)
Max nb of predicted sites per peak: 56
(::chr7:156938150-156943151)
Mean nb of predicted sites per peak: 6.22

[ 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: origins_rerun (13/11/2025 15:19)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results