peak-motifs RRTF1

Sequence composition (test sequences)

Nb of peaks: 791
Total seq. size: 749 kb
Min length: 1 bp
Mean length: 947.364 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: 17911
Total seq. size: 16456 kb
Min length: 1 bp
Mean length: 918.776 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) ]

Reference motif(s)

Reference motif(s)
[transfac format]
[tab format]

Motif discovery

Motif 1 oligos_6nt_test_vs_ctrl_m1

k-mer sig=5.33; evalue=4.7e-06

ssaGCCGCGCCGss

SSCGGCGCGGCTSS

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ssaGCCGCGCCGss

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 328 (41.47%)
Max nb of predicted sites per peak: 14
(SETIT_014037mg)
Mean nb of predicted sites per peak: 2.16

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

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=5.33; evalue=4.7e-06

ssmGCCGCGCrCGCGCCGss

SSCGGCGCGYGCGCGGCKSS

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ssmGCCGCGCrCGCGCCGss

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 339 (42.86%)
Max nb of predicted sites per peak: 25
(SETIT_030430mg)
Mean nb of predicted sites per peak: 3.05

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

Motif 3 oligos_6nt_test_vs_ctrl_m3

k-mer sig=3.72; evalue=0.00019

ssCCGCCCCGGtss

SSACCGGGGCGGSS

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ssCCGCCCCGGtss

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 264 (33.38%)
Max nb of predicted sites per peak: 10
(SETIT_0221572mg)
Mean nb of predicted sites per peak: 1.78

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

Motif 4 oligos_6nt_test_vs_ctrl_m4

k-mer sig=3.04; evalue=0.00091

kcGATCGAks

SMTCGATCGM

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor kcGATCGAks

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 291 (36.79%)
Max nb of predicted sites per peak: 9
(SETIT_036502mg)
Mean nb of predicted sites per peak: 1.77

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

Motif 5 oligos_6nt_test_vs_ctrl_m5

k-mer sig=2.67; evalue=0.0021

rvTAAAGCGrr

YYCGCTTTABY

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor rvTAAAGCGrr

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 52 (6.57%)
Max nb of predicted sites per peak: 2
(SETIT_035510mg)
Mean nb of predicted sites per peak: 1.04

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

Motif 6 oligos_7nt_test_vs_ctrl_m1

k-mer sig=2.77; evalue=0.0017

ssCCGGCCGGss

SSCCGGCCGGSS

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ssCCGGCCGGss

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 231 (29.20%)
Max nb of predicted sites per peak: 14
(SETIT_025974mg)
Mean nb of predicted sites per peak: 2.87

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

Motif 7 oligos_7nt_test_vs_ctrl_m2

k-mer sig=2.09; evalue=0.0081

svAACCGGGvs

SBCCCGGTTBS

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor svAACCGGGvs

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 70 (8.85%)
Max nb of predicted sites per peak: 14
(SETIT_023964mg)
Mean nb of predicted sites per peak: 1.43

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

Motif 8 oligos_7nt_test_vs_ctrl_m3

k-mer sig=1.44; evalue=0.036

waCTCCAAGha

TDCTTGGAGTW

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor waCTCCAAGha

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 134 (16.94%)
Max nb of predicted sites per peak: 3
(SETIT_036928mg)
Mean nb of predicted sites per peak: 1.13

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

Motif 9 oligos_7nt_test_vs_ctrl_m4

k-mer sig=1.36; evalue=0.044

vkCGATCGATCGrk

MYCGATCGATCGMB

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor vkCGATCGATCGrk

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 123 (15.55%)
Max nb of predicted sites per peak: 10
(SETIT_036502mg)
Mean nb of predicted sites per peak: 3.07

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

Motif 10 oligos_7nt_test_vs_ctrl_m5

k-mer sig=1.29; evalue=0.051

gsAGGCGTGsg

CSCACGCCTSC

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor gsAGGCGTGsg

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 167 (21.11%)
Max nb of predicted sites per peak: 4
(SETIT_000233mg)
Mean nb of predicted sites per peak: 1.22

[ 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) ]
Discovered motifs versus reference motif(s)
Motifs versus reference motif(s)		[ Reference motif(s): matrix ] [ table: html txt ] [ alignments (logo): html text ] [ 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: RRTF1_Scan (25/03/2025 06:38)

Command

Sequence composition

Reference motifs

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ssaGCCGCGCCGss

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ssmGCCGCGCrCGCGCCGss

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ssCCGCCCCGGtss

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor kcGATCGAks

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor rvTAAAGCGrr

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ssCCGGCCGGss

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor svAACCGGGvs

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor waCTCCAAGha

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor vkCGATCGATCGrk

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor gsAGGCGTGsg

Total matches= 0

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: RRTF1_Scan (25/03/2025 06:38)

Command

Sequence composition

Reference motifs

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Reference motifs name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor ssaGCCGCGCCGss Total matches= 0

Reference motifs name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor ssmGCCGCGCrCGCGCCGss Total matches= 0

Reference motifs name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor ssCCGCCCCGGtss Total matches= 0

Reference motifs name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor kcGATCGAks Total matches= 0

Reference motifs name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor rvTAAAGCGrr Total matches= 0

Reference motifs name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor ssCCGGCCGGss Total matches= 0

Reference motifs name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor svAACCGGGvs Total matches= 0

Reference motifs name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor waCTCCAAGha Total matches= 0

Reference motifs name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor vkCGATCGATCGrk Total matches= 0

Reference motifs name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor gsAGGCGTGsg Total matches= 0

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ssaGCCGCGCCGss

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ssmGCCGCGCrCGCGCCGss

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ssCCGCCCCGGtss

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor kcGATCGAks

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor rvTAAAGCGrr

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor ssCCGGCCGGss

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor svAACCGGGvs

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor waCTCCAAGha

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor vkCGATCGATCGrk

Total matches= 0

Reference motifs

name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match

columns aligned correlation cor gsAGGCGTGsg

Total matches= 0