peak-motifs STR-all

Sequence composition (test sequences)

Nb of peaks: 2642
Total seq. size: 4672 kb
Min length: 500 bp
Mean length: 1768.42 bp
Max length: 20602 bp [ view peaks in genome browser : ]
[ coordinates: UCSC BED track ]
[ 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: 2643
Total seq. size: 4674 kb
Min length: 500 bp
Mean length: 1768.6 bp
Max length: 20602 bp [ view peaks in genome browser : ]
[ coordinates: UCSC BED track ]
[ 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=56.98; evalue=1e-57

ggrKGGGGGGGGGGGGGGGKGGg

CCCMCCCCCCCCCCCCCCCMYCC

[ 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: 453 (17.15%)
Max nb of predicted sites per peak: 39
(chr_026:857213-859473)
Mean nb of predicted sites per peak: 7.96

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=55.58; evalue=2.6e-56

grSaaGGaaGrrGrGGGGGGkrrs

SYYMCCCCCCYCYYCTTCCTTSYC

[ 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: 846 (32.02%)
Max nb of predicted sites per peak: 37
(chr_066:637-8375)
Mean nb of predicted sites per peak: 3.77

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 3 oligos_6nt_test_vs_ctrl_m3

k-mer sig=30.79; evalue=1.6e-31

asCtGaaGCtCCaGsd

HSCTGGAGCTTCAGST

[ 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: 808 (30.58%)
Max nb of predicted sites per peak: 33
(chr_179:2044785-2047697)
Mean nb of predicted sites per peak: 2.11

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 4 oligos_6nt_test_vs_ctrl_m4

k-mer sig=55.58; evalue=2.6e-56

ggaaaGGGGGGtass

SSTACCCCCCTTTCC

[ 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: 823 (31.15%)
Max nb of predicted sites per peak: 27
(chr_026:857213-859473)
Mean nb of predicted sites per peak: 2.92

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 5 oligos_6nt_test_vs_ctrl_m5

k-mer sig=29.06; evalue=8.7e-30

ssaCCtGGtaCtbs

SVAGTACCAGGTSS

[ 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: 633 (23.96%)
Max nb of predicted sites per peak: 14
(chr_135:1858366-1865482)
Mean nb of predicted sites per peak: 1.78

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 6 oligos_7nt_test_vs_ctrl_m1

k-mer sig=33.55; evalue=2.8e-34

cCcMMCCCCCCCCCCCCYYyycy

RGRRRRGGGGGGGGGGGGKKGGG

[ 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: 414 (15.67%)
Max nb of predicted sites per peak: 36
(chr_026:857213-859473)
Mean nb of predicted sites per peak: 8.09

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 7 oligos_7nt_test_vs_ctrl_m2

k-mer sig=33.55; evalue=2.8e-34

cCCMCCCCCCCCCCCCCCYYyyyy

RRRRRRGGGGGGGGGGGGGGKGGG

[ 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: 341 (12.91%)
Max nb of predicted sites per peak: 36
(chr_026:857213-859473)
Mean nb of predicted sites per peak: 9.11

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 8 oligos_7nt_test_vs_ctrl_m3

k-mer sig=24.75; evalue=1.8e-25

bstGCttCttCttSyk

MRSAAGAAGAAGCASV

[ 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: 913 (34.56%)
Max nb of predicted sites per peak: 31
(chr_066:637-8375)
Mean nb of predicted sites per peak: 2.17

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 9 oligos_7nt_test_vs_ctrl_m4

k-mer sig=21.84; evalue=1.4e-22

saGGaGGaGGags

SCTCCTCCTCCTS

[ 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: 993 (37.59%)
Max nb of predicted sites per peak: 28
(chr_066:637-8375)
Mean nb of predicted sites per peak: 2.77

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 10 oligos_7nt_test_vs_ctrl_m5

k-mer sig=32.60; evalue=2.5e-33

sstaaCCCCCCttttyc

GRAAAAGGGGGGTTASS

[ 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: 679 (25.70%)
Max nb of predicted sites per peak: 12
(chr_052:334860-337719)
Mean nb of predicted sites per peak: 1.87

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 11 dyads_test_vs_ctrl_m1

k-mer sig=76.38; evalue=4.2e-77

CCMCCCCCCYCCyyCc

GGRRGGRGGGGGGKGG

[ 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: 758 (28.69%)
Max nb of predicted sites per peak: 42
(chr_004:494406-496811)
Mean nb of predicted sites per peak: 5.45

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 12 dyads_test_vs_ctrl_m2

k-mer sig=76.38; evalue=4.2e-77

csaaGssSsbssCsMwGssGscGaaGss

SSCTTCGSCSSCWKSGSSVSSSSCTTSG

[ 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: 1060 (40.12%)
Max nb of predicted sites per peak: 40
(chr_179:2044785-2047697)
Mean nb of predicted sites per peak: 3.39

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 13 dyads_test_vs_ctrl_m3

k-mer sig=76.38; evalue=4.2e-77

ssaGCssssssSGsssScsSsGGaGCss

SSGCTCCSSSGSSSSCSSSSSSSGCTSS

[ 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: 1075 (40.69%)
Max nb of predicted sites per peak: 74
(chr_023:18150-21170)
Mean nb of predicted sites per peak: 5.69

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 14 dyads_test_vs_ctrl_m4

k-mer sig=76.38; evalue=4.2e-77

ssCCtsSsssbsStGCwsSkSskkmaGss

SSCTKMMSSMSSWGCASSVSSSSSAGGSS

[ 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: 1060 (40.12%)
Max nb of predicted sites per peak: 55
(chr_179:2878018-2883821)
Mean nb of predicted sites per peak: 4.37

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 15 dyads_test_vs_ctrl_m5

k-mer sig=76.38; evalue=4.2e-77

ssaaGssSsbssCsaaGssGscGaaGCtss

SSAGCTTCGSCSSCTTSGSSVSSSSCTTSS

[ 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: 1076 (40.73%)
Max nb of predicted sites per peak: 31
(chr_179:2044785-2047697)
Mean nb of predicted sites per peak: 3.27

[ view in genome browser :

]
[ sites: text BED (UCSC track) ]
[ 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: STR-all (09/04/2026 05:37)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results