peak-motifs MEsalmon4_Up4

Sequence composition (test sequences)

Nb of peaks: 518
Total seq. size: 243 kb
Min length: 2 bp
Mean length: 469.882 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) ]

Sequence composition (ctrl sequences)

Nb of peaks: 41359
Total seq. size: 18852 kb
Min length: 1 bp
Mean length: 455.805 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=1.32; evalue=0.048

ssatGaGCsr

YSGCTCATSS

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

footprintDB-plants

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

columns aligned correlation cor ssatGaGCsr

HB-1:M0841_1.02:CISBP HB-1/M0841_1.02/CISBP R 8 0.8000 0.707 0.565 NA NA

OsLUX1:EEAD0074:EEADannot OsLUX1/EEAD0074/EEADannot R 7 0.5385 0.858 0.462 NA NA

MBD2:MA2370.1:JASPAR MBD2/MA2370.1/JASPAR D 5 0.5000 0.829 0.415 NA NA

Total matches= 4 (1 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 62 (11.97%)
Max nb of predicted sites per peak: 4
(gene-Lalb_Chr18g0057561)
Mean nb of predicted sites per peak: 1.15

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

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=0.08; evalue=0.83

gdatGGGCyk

MRGCCCATHC

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

footprintDB-plants

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

columns aligned correlation cor gdatGGGCyk

ASR1:MA1812.2:JASPAR ASR1/MA1812.2/JASPAR R 9 0.9000 0.867 0.780 NA NA

TZP2:EEAD0062:EEADannot TZP2/EEAD0062/EEADannot D 10 0.6667 0.963 0.642 NA NA

ASR1:MA1812.1:JASPAR ASR1/MA1812.1/JASPAR R 10 0.6667 0.867 0.578 NA NA

Total matches= 3

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 75 (14.48%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr25g0283681)
Mean nb of predicted sites per peak: 1.32

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

Motif 3 oligos_8nt_test_vs_ctrl_m1

k-mer sig=0.56; evalue=0.28

rrGaTGaatAkr

YMTATTCATCYY

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

footprintDB-plants

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

columns aligned correlation cor rrGaTGaatAkr

AT5G18090.DAP:M0009:AthalianaCistrome AT5G18090.DAP/M0009/AthalianaCistrome D 12 0.8000 0.867 0.694 NA NA

REM21:UN0408.1:JASPAR REM21/UN0408.1/JASPAR R 12 0.8000 0.867 0.694 NA NA

KAN2:MA1383.2:JASPAR KAN2/MA1383.2/JASPAR R 10 0.8333 0.739 0.616 NA NA

Total matches= 33 (30 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 24 (4.63%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr16g0378451)
Mean nb of predicted sites per peak: 1.04

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

Motif 4 oligos_8nt_test_vs_ctrl_m2

k-mer sig=0.41; evalue=0.39

mdaGttataagk

MCTTATAACTHK

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

footprintDB-plants

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

columns aligned correlation cor mdaGttataagk

TRANSCRIPTION:1qnb_B:3D-footprint TRANSCRIPTION/1qnb_B/3D-footprint R 7 0.5833 0.913 0.532 NA NA

TATA-box-binding:6njq_A:3D-footprint TATA-box-binding/6njq_A/3D-footprint R 7 0.5833 0.901 0.526 NA NA

AtMYB63_I:AtMYB63_I:AthaMYB AtMYB63_I/AtMYB63_I/AthaMYB D 7 0.5385 0.963 0.519 NA NA

Total matches= 94 (91 more)

[ match table: html text ]
[ alignments (logos): html text ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 28 (5.41%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr19g0129031)
Mean nb of predicted sites per peak: 1.07

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

Motif 5 dyads_test_vs_ctrl_m1

k-mer sig=1.07; evalue=0.085

tmAaTSmkCatsgstmsmmgatkatGsm

KSCATMATCKKSKASCSATGMKSATTKA

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

footprintDB-plants

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

columns aligned correlation cor tmAaTSmkCatsgstmsmmgatkatGsm

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: 20 (3.86%)
Max nb of predicted sites per peak: 1
(gene-Lalb_Chr24g0402661)
Mean nb of predicted sites per peak: 1.00

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

Motif 6 dyads_test_vs_ctrl_m2

k-mer sig=0.48; evalue=0.33

wwaGGmtSakCcmdymmhbmvtatmg

CKATABKVDKKRHKGGMTSAKCCTWW

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

footprintDB-plants

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

columns aligned correlation cor wwaGGmtSakCcmdymmhbmvtatmg

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: 25 (4.83%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr10g0091331)
Mean nb of predicted sites per peak: 1.04

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

Motif 7 dyads_test_vs_ctrl_m3

k-mer sig=0.48; evalue=0.33

dmatabswSMtsayysyvcamsYttayt

ARTAARSKTGBRSRRTSAKSWSVTATKH

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

footprintDB-plants

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

columns aligned correlation cor dmatabswSMtsayysyvcamsYttayt

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: 20 (3.86%)
Max nb of predicted sites per peak: 1
(gene-Lalb_Chr24g0394221)
Mean nb of predicted sites per peak: 1.00

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

Motif 8 dyads_test_vs_ctrl_m4

k-mer sig=0.48; evalue=0.33

dgarabswSmthvbyhbtsaMktymtwgtk

MACWAKRAMKTSAVDRVBDAKSWSVTYTCH

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

footprintDB-plants

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

columns aligned correlation cor dgarabswSmthvbyhbtsaMktymtwgtk

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: 20 (3.86%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr20g0108201)
Mean nb of predicted sites per peak: 1.15

[ 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 transcription factor databases
Motifs versus footprintDB-plants database		[ 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: MEsalmon4_Up4_W1 (26/05/2025 03:35)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

footprintDB-plants

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

columns aligned correlation cor tmAaTSmkCatsgstmsmmgatkatGsm

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor wwaGGmtSakCcmdymmhbmvtatmg

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor dmatabswSMtsayysyvcamsYttayt

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor dgarabswSmthvbyhbtsaMktymtwgtk

Total matches= 0

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: MEsalmon4_Up4_W1 (26/05/2025 03:35)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor tmAaTSmkCatsgstmsmmgatkatGsm Total matches= 0

footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor wwaGGmtSakCcmdymmhbmvtatmg Total matches= 0

footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor dmatabswSMtsayysyvcamsYttayt Total matches= 0

footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor dgarabswSmthvbyhbtsaMktymtwgtk Total matches= 0

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

footprintDB-plants

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

columns aligned correlation cor tmAaTSmkCatsgstmsmmgatkatGsm

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor wwaGGmtSakCcmdymmhbmvtatmg

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor dmatabswSMtsayysyvcamsYttayt

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor dgarabswSmthvbyhbtsaMktymtwgtk

Total matches= 0