peak-motifs origins

Sequence composition (test sequences)

Nb of peaks: 2437
Total seq. size: 12183 kb
Min length: 4999 bp
Mean length: 4999 bp
Max length: 4999 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: 1691
Total seq. size: 8455 kb
Min length: 5000 bp
Mean length: 5000 bp
Max length: 5000 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_6-8nt_m1

k-mer sig=230.94; evalue=1.1e-231

wmwAyTAAAAATAmAAwwATtwry

RYWAATWWTTKTATTTTTARTWKW

[ 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: 2319 (95.16%)
Max nb of predicted sites per peak: 783
(::chr2:64840401-64845401)
Mean nb of predicted sites per peak: 30.72

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

Motif 2 oligos_6-8nt_m2

k-mer sig=230.94; evalue=1.1e-231

wawAwAtAwAwwwAwAwATAwAwa

TWTWTATWTWTWWWTWTATWTWTW

[ 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: 2281 (93.60%)
Max nb of predicted sites per peak: 1467
(::chr8:120919251-120924251)
Mean nb of predicted sites per peak: 41.11

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

Motif 3 oligos_6-8nt_m3

k-mer sig=230.94; evalue=1.1e-231

wawAaAwwwAwAwATAwAtAwAwa

TWTWTATWTATWTWTWWWTTTWTW

[ 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: 2282 (93.64%)
Max nb of predicted sites per peak: 1435
(::chr8:120919251-120924251)
Mean nb of predicted sites per peak: 41.30

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

Motif 4 oligos_6-8nt_m4

k-mer sig=230.94; evalue=1.1e-231

wwAAwwAAAAAAwAAAAwwAwwwa

TWWWTWWTTTTWTTTTTTWWTTWW

[ 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: 2312 (94.87%)
Max nb of predicted sites per peak: 1129
(::chr2:64840401-64845401)
Mean nb of predicted sites per peak: 50.27

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

Motif 5 oligos_6-8nt_m5

k-mer sig=230.94; evalue=1.1e-231

watwtATAtAwAwATAwATAtAta

TATATATWTATWTWTATATAWATW

[ 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: 2126 (87.24%)
Max nb of predicted sites per peak: 1467
(::chr8:120919251-120924251)
Mean nb of predicted sites per peak: 28.10

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

Motif 6 oligos_6-8nt_m6

k-mer sig=230.94; evalue=1.1e-231

aamAAAAAAAAAAAaAAAAAAaaa

TTTTTTTTTTTTTTTTTTTTTKTT

[ 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: 2265 (92.94%)
Max nb of predicted sites per peak: 329
(::chr10:102660150-102665150)
Mean nb of predicted sites per peak: 49.20

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

Motif 7 oligos_6-8nt_m7

k-mer sig=230.94; evalue=1.1e-231

wwTTwwTkTATTTTTArTAkArwy

RWYTMTAYTAAAAATAMAWWAAWW

[ 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: 2333 (95.73%)
Max nb of predicted sites per peak: 723
(::chr2:64840401-64845401)
Mean nb of predicted sites per peak: 26.54

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

Motif 8 oligos_6-8nt_m8

k-mer sig=230.94; evalue=1.1e-231

twTaTwTwTwTaTwTawtTwTwtw

WAWAWAAWTAWATAWAWAWATAWA

[ 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: 2278 (93.48%)
Max nb of predicted sites per peak: 1445
(::chr8:120919251-120924251)
Mean nb of predicted sites per peak: 40.66

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

Motif 9 oligos_6-8nt_m9

k-mer sig=230.94; evalue=1.1e-231

wwTTtTaTTTTTAAAAAtAaAaww

WWTTTTATTTTTAAAAATAAAAWW

[ 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: 2073 (85.06%)
Max nb of predicted sites per peak: 1057
(::chr2:64840401-64845401)
Mean nb of predicted sites per peak: 24.81

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

Motif 10 oligos_6-8nt_m10

k-mer sig=230.94; evalue=1.1e-231

waAaAAAAwAAAAAwwAAAAwraa

TTYWTTTTWWTTTTTWTTTTTTTW

[ 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: 2300 (94.38%)
Max nb of predicted sites per peak: 483
(::chr3:16534551-16539551)
Mean nb of predicted sites per peak: 48.51

[ 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: origins_reverse (13/11/2025 19:48)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results