peak-motifs COLI_HNS

Sequence composition (test sequences)

Nb of peaks: 420
Total seq. size: 342 kb
Min length: 142 bp
Mean length: 813.964 bp
Max length: 1000 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: 9265
Total seq. size: 4642 kb
Min length: 388 bp
Mean length: 500.988 bp
Max length: 501 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=248.63; evalue=2.3e-249

rmtAtaAATAaAaatataataaht

ADTTATTATATTTTTATTTATAKY

[ 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: 94 (22.38%)
Max nb of predicted sites per peak: 4
(COLI_HNSHA_merge_peak_430)
Mean nb of predicted sites per peak: 1.31

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

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=248.63; evalue=2.3e-249

yraaaAAtaTaAtaAaTAatttkh

DMAAATTATTTATTATATTTTTYR

[ 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: 84 (20.00%)
Max nb of predicted sites per peak: 3
(COLI_HNSHA_merge_peak_333)
Mean nb of predicted sites per peak: 1.24

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

Motif 3 oligos_6nt_test_vs_ctrl_m3

k-mer sig=248.63; evalue=2.3e-249

wwtaaAttaAataAATgaataadk

MHTTATTCATTTATTTAATTTAWW

[ 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: 91 (21.67%)
Max nb of predicted sites per peak: 6
(COLI_HNSHA_merge_peak_67)
Mean nb of predicted sites per peak: 1.44

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

Motif 4 oligos_6nt_test_vs_ctrl_m4

k-mer sig=248.63; evalue=2.3e-249

atttataTtATTtattAAataawm

KWTTATTTAATAAATAATATAAAT

[ 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: 70 (16.67%)
Max nb of predicted sites per peak: 4
(COLI_HNSHA_merge_peak_261)
Mean nb of predicted sites per peak: 1.43

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

Motif 5 oligos_6nt_test_vs_ctrl_m5

k-mer sig=248.63; evalue=2.3e-249

wraAAttaaAaATAAatataaawa

TWTTTATATTTATTTTTAATTTYW

[ 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: 81 (19.29%)
Max nb of predicted sites per peak: 4
(COLI_HNSHA_merge_peak_201)
Mean nb of predicted sites per peak: 1.36

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

Motif 6 oligos_7nt_test_vs_ctrl_m1

k-mer sig=105.32; evalue=4.8e-106

mrtaataaATAAaAatAataAtgw

WCATTATTATTTTTATTTATTAYK

[ 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: 94 (22.38%)
Max nb of predicted sites per peak: 5
(COLI_HNSHA_merge_peak_295)
Mean nb of predicted sites per peak: 1.38

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

Motif 7 oligos_7nt_test_vs_ctrl_m2

k-mer sig=105.32; evalue=4.8e-106

dwtatattTAttTttATtatttyy

RRAAATAATAAAAATAAATATAWH

[ 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: 93 (22.14%)
Max nb of predicted sites per peak: 3
(COLI_HNSHA_merge_peak_295)
Mean nb of predicted sites per peak: 1.27

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

Motif 8 oligos_7nt_test_vs_ctrl_m3

k-mer sig=105.32; evalue=4.8e-106

whtAaaaTaAAaatAtaAataAwt

AWTTATTTATATTTTTATTTTADW

[ 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: 95 (22.62%)
Max nb of predicted sites per peak: 4
(COLI_HNSHA_merge_peak_201)
Mean nb of predicted sites per peak: 1.27

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

Motif 9 oligos_7nt_test_vs_ctrl_m4

k-mer sig=96.16; evalue=6.9e-97

yyTTttTaTTttTaattaaaaawy

RWTTTTTAATTAAAAATAAAAARR

[ 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 (18.57%)
Max nb of predicted sites per peak: 4
(COLI_HNSHA_merge_peak_261)
Mean nb of predicted sites per peak: 1.28

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

Motif 10 oligos_7nt_test_vs_ctrl_m5

k-mer sig=105.32; evalue=4.8e-106

rraaTAaTaAaTAaaAatAattwy

RWAATTATTTTTATTTATTATTYY

[ 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: 89 (21.19%)
Max nb of predicted sites per peak: 3
(COLI_HNSHA_merge_peak_374)
Mean nb of predicted sites per peak: 1.26

[ 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: COLI_HNS_df2 (14/04/2025 15:11)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results