peak-motifs COLI_Lsr2

Sequence composition (test sequences)

Nb of peaks: 673
Total seq. size: 473 kb
Min length: 151 bp
Mean length: 703.474 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=254.36; evalue=4.4e-255

wmataataAATAatttAtTtaatk

MATTAAATAAATTATTTATTATKW

[ 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 (15.01%)
Max nb of predicted sites per peak: 5
(COLI_Lsr2AHA_merge_peak_170)
Mean nb of predicted sites per peak: 1.34

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

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=254.36; evalue=4.4e-255

wttAtaaAAATAAatataatttwa

TWAAATTATATTTATTTTTATAAW

[ 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: 105 (15.60%)
Max nb of predicted sites per peak: 4
(COLI_Lsr2AHA_merge_peak_327)
Mean nb of predicted sites per peak: 1.43

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

Motif 3 oligos_6nt_test_vs_ctrl_m3

k-mer sig=254.36; evalue=4.4e-255

wwtaAAttAAaTaAATgaataart

AYTTATTCATTTATTTAATTTAWW

[ 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: 131 (19.47%)
Max nb of predicted sites per peak: 6
(COLI_Lsr2AHA_merge_peak_88)
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=254.36; evalue=4.4e-255

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: 123 (18.28%)
Max nb of predicted sites per peak: 4
(COLI_Lsr2AHA_merge_peak_98)
Mean nb of predicted sites per peak: 1.41

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

Motif 5 oligos_6nt_test_vs_ctrl_m5

k-mer sig=254.36; evalue=4.4e-255

wtaaatTATTtattAAATaaATww

WWATTTATTTAATAAATAATTTAW

[ 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: 117 (17.38%)
Max nb of predicted sites per peak: 7
(COLI_Lsr2AHA_merge_peak_521)
Mean nb of predicted sites per peak: 1.59

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

Motif 6 oligos_7nt_test_vs_ctrl_m1

k-mer sig=100.25; evalue=5.6e-101

adattAATaAatAaaaaTaattmt

AKAATTATTTTTATTTATTAATHT

[ 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 (18.72%)
Max nb of predicted sites per peak: 3
(COLI_Lsr2AHA_merge_peak_661)
Mean nb of predicted sites per peak: 1.31

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

Motif 7 oligos_7nt_test_vs_ctrl_m2

k-mer sig=100.25; evalue=5.6e-101

wtaTaTTtAtttttATtaatttwa

TWAAATTAATAAAAATAAATATAW

[ 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: 134 (19.91%)
Max nb of predicted sites per peak: 4
(COLI_Lsr2AHA_merge_peak_299)
Mean nb of predicted sites per peak: 1.28

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

Motif 8 oligos_7nt_test_vs_ctrl_m3

k-mer sig=98.76; evalue=1.7e-99

wtataAAttAAAaATaAaAAatww

WWATTTTTTATTTTTAATTTATAW

[ 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: 120 (17.83%)
Max nb of predicted sites per peak: 6
(COLI_Lsr2AHA_merge_peak_369)
Mean nb of predicted sites per peak: 1.35

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

Motif 9 oligos_7nt_test_vs_ctrl_m4

k-mer sig=100.25; evalue=5.6e-101

wtaatTAttttTATTtATAtttmy

RKAAATATAAATAAAAATAATTAW

[ 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: 109 (16.20%)
Max nb of predicted sites per peak: 5
(COLI_Lsr2AHA_merge_peak_319)
Mean nb of predicted sites per peak: 1.34

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

Motif 10 oligos_7nt_test_vs_ctrl_m5

k-mer sig=100.25; evalue=5.6e-101

wrttaATaaaTAAaaatAAtaAwk

MWTTATTATTTTTATTTATTAAYW

[ 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: 132 (19.61%)
Max nb of predicted sites per peak: 4
(COLI_Lsr2AHA_merge_peak_452)
Mean nb of predicted sites per peak: 1.34

[ 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_Lsr2_df1 (14/04/2025 15:09)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results