peak-motifs NG

Sequence composition (test sequences)

Nb of peaks: 513
Total seq. size: 139 kb
Min length: 164 bp
Mean length: 270.094 bp
Max length: 1000 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_mkv3_m1

k-mer sig=21.11; evalue=7.8e-22

ktYGatTCCaTTCGatKmYry

RYRKMATCGAATGGAATCRAM

[ 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: 75 (14.62%)
Max nb of predicted sites per peak: 103
(chromosome_GRCh38_4_1_190214555_1:49149160-49149819())
Mean nb of predicted sites per peak: 32.53

[ view in genome browser :

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

Motif 2 oligos_6nt_mkv3_m2

k-mer sig=6.08; evalue=8.3e-07

mtrTACaTAta

TATATGTAYAK

[ 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: 87 (16.96%)
Max nb of predicted sites per peak: 32
(chromosome_GRCh38_5_1_181538259_1:129550062-129550484())
Mean nb of predicted sites per peak: 6.82

[ view in genome browser :

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

Motif 3 oligos_6nt_mkv3_m3

k-mer sig=4.43; evalue=3.7e-05

kataGATAGAtag

CTATCTATCTATM

[ 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: 42 (8.19%)
Max nb of predicted sites per peak: 114
(chromosome_GRCh38_8_1_145138636_1:68906138-68907030())
Mean nb of predicted sites per peak: 13.36

[ view in genome browser :

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

Motif 4 oligos_6nt_mkv3_m4

k-mer sig=4.21; evalue=6.2e-05

arAAATAAhm

KDTTATTTYT

[ 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: 0 (0.00%)
Max nb of predicted sites per peak:
Mean nb of predicted sites per peak: 0.00

[ view in genome browser :

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

Motif 5 oligos_6nt_mkv3_m5

k-mer sig=5.10; evalue=7.9e-06

ktyGATGATkC

GMATCATCRAM

[ 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: 76 (14.81%)
Max nb of predicted sites per peak: 34
(chromosome_GRCh38_16_1_90338345_1:46399223-46401167())
Mean nb of predicted sites per peak: 10.29

[ view in genome browser :

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

Motif 6 positions_6nt_m1

k-mer sig=2.47; evalue=0.0034

awttaaaaataaaww

WWTTTATTTTTAAWT

[ 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: 22 (4.29%)
Max nb of predicted sites per peak: 2
(chromosome_GRCh38_21_1_46709983_1:16361181-16361381())
Mean nb of predicted sites per peak: 1.05

[ view in genome browser :

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

Motif 7 positions_6nt_m2

k-mer sig=2.47; evalue=0.0034

wtttaaaaaataaawa

TWTTTATTTTTTAAAW

[ 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: 30 (5.85%)
Max nb of predicted sites per peak: 3
(chromosome_GRCh38_5_1_181538259_1:23297943-23298283())
Mean nb of predicted sites per peak: 1.10

[ view in genome browser :

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

Motif 8 positions_6nt_m3

k-mer sig=2.47; evalue=0.0034

wktTaaaaattww

WWAATTTTTAAMW

[ 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: 12 (2.34%)
Max nb of predicted sites per peak: 1
(chromosome_GRCh38_8_1_145138636_1:92877111-92877310())
Mean nb of predicted sites per peak: 1.00

[ view in genome browser :

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

Motif 9 positions_6nt_m4

k-mer sig=0.06; evalue=0.87

rrAAGAAArv

BYTTTCTTYY

[ 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: 28 (5.46%)
Max nb of predicted sites per peak: 9
(chromosome_GRCh38_21_1_46709983_1:8219790-8220183())
Mean nb of predicted sites per peak: 1.32

[ view in genome browser :

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

Motif 10 oligos_7nt_mkv4_m1

k-mer sig=20.64; evalue=2.3e-21

mktYSatTCCaTTCSatkM

KMATSGAATGGAATSRAMK

[ 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: 77 (15.01%)
Max nb of predicted sites per peak: 114
(chromosome_GRCh38_4_1_190214555_1:49149160-49149819())
Mean nb of predicted sites per peak: 37.23

[ view in genome browser :

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

Motif 11 oligos_7nt_mkv4_m2

k-mer sig=20.64; evalue=2.3e-21

KmatCGaAtGGAatCrwM

KWYGATTCCATTCGATKM

[ 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 (15.20%)
Max nb of predicted sites per peak: 105
(chromosome_GRCh38_4_1_190214555_1:49149160-49149819())
Mean nb of predicted sites per peak: 32.28

[ view in genome browser :

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

Motif 12 oligos_7nt_mkv4_m3

k-mer sig=3.25; evalue=0.00056

ctatCTatCta

TAGATAGATAG

[ 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: 29 (5.65%)
Max nb of predicted sites per peak: 83
(chromosome_GRCh38_8_1_145138636_1:68906138-68907030())
Mean nb of predicted sites per peak: 12.69

[ view in genome browser :

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

Motif 13 oligos_7nt_mkv4_m4

k-mer sig=1.62; evalue=0.024

vwGTaGaatayr

YRTATTCTACWB

[ 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: 24 (4.68%)
Max nb of predicted sites per peak: 18
(chromosome_GRCh38_16_1_90338345_1:67340788-67341061())
Mean nb of predicted sites per peak: 3.46

[ view in genome browser :

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

Motif 14 oligos_7nt_mkv4_m5

k-mer sig=1.37; evalue=0.043

atGGaMtCGAatG

CATTCGAKTCCAT

[ 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: 77 (15.01%)
Max nb of predicted sites per peak: 92
(chromosome_GRCh38_4_1_190214555_1:49149160-49149819())
Mean nb of predicted sites per peak: 14.19

[ 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: NG_0.01 (18/12/2025 17:16)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results