peak-motifs dmrl_medicago

Sequence composition (test sequences)

Nb of peaks: 17
Total seq. size: 28 kb
Min length: 455 bp
Mean length: 1627.71 bp
Max length: 1701 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: 44708
Total seq. size: 64249 kb
Min length: 201 bp
Mean length: 1437.09 bp
Max length: 1701 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=4.56; evalue=2.8e-05

GkCCCGtCCCGTCCCG

CGGGACGGGACGGGMC

[ 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: 5 (29.41%)
Max nb of predicted sites per peak: 27
(107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548)
Mean nb of predicted sites per peak: 7.80

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

Motif 2 oligos_6-8nt_m2

k-mer sig=2.02; evalue=0.0095

rrCrGGCCGmss

SSKCGGCCYGYY

[ 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: 9 (52.94%)
Max nb of predicted sites per peak: 6
(107759548|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107759548)
Mean nb of predicted sites per peak: 2.22

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

Motif 3 oligos_6-8nt_m3

k-mer sig=1.17; evalue=0.068

wwaTATaaTata

TATATTATATWW

[ 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: 11 (64.71%)
Max nb of predicted sites per peak: 12
(107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499)
Mean nb of predicted sites per peak: 2.55

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

Motif 4 oligos_6-8nt_m4

k-mer sig=0.92; evalue=0.12

SbtCTCGATCyv

BRGATCGAGAVS

[ 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: 13 (76.47%)
Max nb of predicted sites per peak: 6
(107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937)
Mean nb of predicted sites per peak: 1.77

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

Motif 5 oligos_6-8nt_m5

k-mer sig=0.40; evalue=0.4

ksaTGGCGrb

VYCGCCATSM

[ 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: 8 (47.06%)
Max nb of predicted sites per peak: 4
(107761937|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107761937)
Mean nb of predicted sites per peak: 1.62

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

Motif 6 oligos_6-8nt_m6

k-mer sig=0.23; evalue=0.59

cbCTCTTArr

YYTAAGAGVG

[ 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: 13 (76.47%)
Max nb of predicted sites per peak: 3
(gene-LSAT_8X33320|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_8X33320)
Mean nb of predicted sites per peak: 1.62

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

Motif 7 oligos_6-8nt_m7

k-mer sig=0.22; evalue=0.6

wraGTaACahk

MDTGTTACTYW

[ 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: 8 (47.06%)
Max nb of predicted sites per peak: 4
(107812499|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107812499)
Mean nb of predicted sites per peak: 2.12

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

Motif 8 oligos_6-8nt_m8

k-mer sig=0.17; evalue=0.68

kkGATTTAyr

YRTAAATCMM

[ 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 (70.59%)
Max nb of predicted sites per peak: 5
(BVRB_4g096340|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_4g096340)
Mean nb of predicted sites per peak: 1.92

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

Motif 9 oligos_6-8nt_m9

k-mer sig=0.12; evalue=0.76

mrGtCCTArg

CYTAGGACYK

[ 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: 8 (47.06%)
Max nb of predicted sites per peak: 3
(107793142|Nicotiana_tabacum_GCF_000715075.1_ASM71507v2|LOC107793142)
Mean nb of predicted sites per peak: 1.88

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

Motif 10 oligos_6-8nt_m10

k-mer sig=0.09; evalue=0.81

gmaACTTATdt

AHATAAGTTKC

[ 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: 9 (52.94%)
Max nb of predicted sites per peak: 7
(gene25542|Medicago_truncatula.MtrunA17r50ANR.60|gene25542)
Mean nb of predicted sites per peak: 2.11

[ 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: dmrl_medicago_up1 (29/05/2026 16:48)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results