peak-motifs STR

Sequence composition (test sequences)

Nb of peaks: 500
Total seq. size: 1190 kb
Min length: 501 bp
Mean length: 2380.01 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: 500
Total seq. size: 1190 kb
Min length: 501 bp
Mean length: 2380.01 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=38.43; evalue=3.7e-39

ssmymCCCCCCYCCCC

GGGGRGGGGGGKRKSS

[ 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: 182 (36.40%)
Max nb of predicted sites per peak: 33
(chr_120:1036767-1039102)
Mean nb of predicted sites per peak: 6.80

[ 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=10.49; evalue=3.2e-11

gytGCaCCaatykc

GMRATTGGTGCARC

[ 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: 218 (43.60%)
Max nb of predicted sites per peak: 14
(chr_135:162750-168013)
Mean nb of predicted sites per peak: 2.56

[ 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=38.43; evalue=3.7e-39

SCMMCCCCCCYCCCC

GGGGRGGGGGGKKGS

[ 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: 179 (35.80%)
Max nb of predicted sites per peak: 32
(chr_120:1036767-1039102)
Mean nb of predicted sites per peak: 6.63

[ 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=8.17; evalue=6.8e-09

wtatattatatatttw

WAAATATATAATATAW

[ 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: 199 (39.80%)
Max nb of predicted sites per peak: 12
(chr_120:1395824-1416426)
Mean nb of predicted sites per peak: 1.55

[ 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=16.01; evalue=9.8e-17

ysmtaCCCCyCCcs

SGGGRGGGGTAKSR

[ 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: 229 (45.80%)
Max nb of predicted sites per peak: 24
(chr_120:1036767-1039102)
Mean nb of predicted sites per peak: 3.35

[ 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=40.18; evalue=6.6e-41

CCCCCCCCCCCCCCCCCCCCCCcc

GGGGGGGGGGGGGGGGGGGGGGGG

[ 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: 103 (20.60%)
Max nb of predicted sites per peak: 37
(chr_120:1036767-1039102)
Mean nb of predicted sites per peak: 11.87

[ 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=40.18; evalue=6.6e-41

cCCCCCCCCCCCCCCCCCCCcc

GGGGGGGGGGGGGGGGGGGGGG

[ 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: 122 (24.40%)
Max nb of predicted sites per peak: 36
(chr_120:1036767-1039102)
Mean nb of predicted sites per peak: 9.55

[ 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=6.78; evalue=1.7e-07

ysCtGCCaCtss

SSAGTGGCAGSR

[ 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: 162 (32.40%)
Max nb of predicted sites per peak: 8
(chr_179:1680858-1686133)
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 9 oligos_7nt_test_vs_ctrl_m4

k-mer sig=5.81; evalue=1.5e-06

atatataatatat

ATATATTATATAT

[ 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: 174 (34.80%)
Max nb of predicted sites per peak: 5
(chr_166:110592-124034)
Mean nb of predicted sites per peak: 1.38

[ 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=40.18; evalue=6.6e-41

ggGGGGGGGGGGGGGGGGGGGGgg

CCCCCCCCCCCCCCCCCCCCCCCC

[ 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: 121 (24.20%)
Max nb of predicted sites per peak: 37
(chr_120:1036767-1039102)
Mean nb of predicted sites per peak: 10.47

[ 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=50.00; evalue=1e-50

CCCCCCCCCCCCCCCCCC

GGGGGGGGGGGGGGGGGG

[ 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: 126 (25.20%)
Max nb of predicted sites per peak: 35
(chr_120:1036767-1039102)
Mean nb of predicted sites per peak: 8.90

[ 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=50.00; evalue=1e-50

ssmCCCCCCCCCCCCmcc

GGKGGGGGGGGGGGGKSS

[ 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: 185 (37.00%)
Max nb of predicted sites per peak: 40
(chr_135:1858366-1865482)
Mean nb of predicted sites per peak: 7.92

[ 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=50.00; evalue=1e-50

ssCCCSSSSSsSSsSSssSCCCss

SSGGGSSSSSSSSSSSSSSGGGSS

[ 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: 223 (44.60%)
Max nb of predicted sites per peak: 131
(chr_023:18150-21170)
Mean nb of predicted sites per peak: 7.95

[ 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=50.00; evalue=1e-50

ssrkaSSSSSSSSSSSmvmss

SSKBKSSSSSSSSSSSTMYSS

[ 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: 174 (34.80%)
Max nb of predicted sites per peak: 52
(chr_023:18150-21170)
Mean nb of predicted sites per peak: 5.28

[ 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=50.00; evalue=1e-50

ssrbrSSSSSsSSSSSsssmwmtmss

SSKAKWKSSSSSSSSSSSSSSYVYSS

[ 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: 171 (34.20%)
Max nb of predicted sites per peak: 73
(chr_023:18150-21170)
Mean nb of predicted sites per peak: 7.15

[ 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 (09/04/2026 05:10)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results