peak-motifs MEsalmon4

motif discovery

oligos_6nt_test_vs_ctrl

oligos_6nt_test_vs_ctrl_m1	assembly: aagccc (sig=1.06; e-value=0.087)	RC: gggctt
oligos_6nt_test_vs_ctrl_m2	assembly: tacata (sig=0.38; e-value=0.42)	RC: tatgta
oligos_6nt_test_vs_ctrl_m3	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m4	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m5	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m6	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m7	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m8	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m9	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m10	: (sig=; e-value=1)	RC:

[ discovered words: text ]
[ assembly: text sig matrices ]
[ matrices: tab format transfac format ]

oligos_7nt_test_vs_ctrl

oligos_7nt_test_vs_ctrl_m1	assembly: cccaata (sig=0.07; e-value=0.85)	RC: tattggg
oligos_7nt_test_vs_ctrl_m2	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m3	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m4	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m5	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m6	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m7	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m8	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m9	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m10	: (sig=; e-value=1)	RC:

[ discovered words: text ]
[ assembly: text sig matrices ]
[ matrices: tab format transfac format ]

oligos_8nt_test_vs_ctrl

oligos_8nt_test_vs_ctrl_m1	assembly: cccgtgga (sig=0.49; e-value=0.32)	RC: tccacggg
oligos_8nt_test_vs_ctrl_m2	: (sig=; e-value=1)	RC:
oligos_8nt_test_vs_ctrl_m3	: (sig=; e-value=1)	RC:
oligos_8nt_test_vs_ctrl_m4	: (sig=; e-value=1)	RC:
oligos_8nt_test_vs_ctrl_m5	: (sig=; e-value=1)	RC:
oligos_8nt_test_vs_ctrl_m6	: (sig=; e-value=1)	RC:
oligos_8nt_test_vs_ctrl_m7	: (sig=; e-value=1)	RC:
oligos_8nt_test_vs_ctrl_m8	: (sig=; e-value=1)	RC:
oligos_8nt_test_vs_ctrl_m9	: (sig=; e-value=1)	RC:
oligos_8nt_test_vs_ctrl_m10	: (sig=; e-value=1)	RC:

[ discovered words: text ]
[ assembly: text sig matrices ]
[ matrices: tab format transfac format ]

dyads_test_vs_ctrl

dyads_test_vs_ctrl_m1	assembly: cgtnnnnnnnnnnnnata (sig=1.23; e-value=0.059)	RC: tatnnnnnnnnnnnnacg
dyads_test_vs_ctrl_m2	assembly: aatnnnnnnnnnntac (sig=1.08; e-value=0.083)	RC: gtannnnnnnnnnatt
dyads_test_vs_ctrl_m3	assembly: catnnnnnnnnnnnnnntag (sig=1.08; e-value=0.083)	RC: ctannnnnnnnnnnnnnatg
dyads_test_vs_ctrl_m4	assembly: acgnnnnnnnnnnnnnngtg (sig=1.08; e-value=0.083)	RC: cacnnnnnnnnnnnnnncgt
dyads_test_vs_ctrl_m5	assembly: ctannnnnnnnnnnnnntta (sig=1.08; e-value=0.083)	RC: taannnnnnnnnnnnnntag
dyads_test_vs_ctrl_m6	assembly: cacnnnnnnnnnnnnnnnnnnnntta (sig=1.23; e-value=0.059)	RC: taannnnnnnnnnnnnnnnnnnngtg
dyads_test_vs_ctrl_m7	assembly: aatnnnnnnnnnnnnnnnnnata (sig=1.23; e-value=0.059)	RC: tatnnnnnnnnnnnnnnnnnatt
dyads_test_vs_ctrl_m8	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m9	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m10	: (sig=; e-value=1)	RC:

[ discovered words: text ]
[ assembly: text sig matrices ]
[ matrices: tab format transfac format ]

Motif discovery

Motif 1 oligos_6nt_test_vs_ctrl_m1

k-mer sig=1.06; evalue=0.087

skaaGCCCrh

DYGGGCTTMS

[ 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 skaaGCCCrh

ASR1:MA1812.2:JASPAR ASR1/MA1812.2/JASPAR D 8 0.7273 0.793 0.577 NA NA

TRP5:MA1802.1:JASPAR TRP5/MA1802.1/JASPAR D 9 0.8182 0.700 0.573 NA NA

TZP2:EEAD0062:EEADannot TZP2/EEAD0062/EEADannot R 10 0.6667 0.850 0.567 NA NA

Total matches= 15 (12 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: 121 (22.92%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr13g0300891)
Mean nb of predicted sites per peak: 1.21

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

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=0.38; evalue=0.42

awTACATAww

WWTATGTAWT

[ 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 awTACATAww

ANAC55:ANAC55_2:ArabidopsisPBM ANAC55/ANAC55_2/ArabidopsisPBM R 10 1.0000 0.708 0.708 NA NA

AT3G49930:UN0355.1:JASPAR AT3G49930/UN0355.1/JASPAR D 10 0.9091 0.736 0.669 NA NA

TRANSCRIPTION:1qn7_B:3D-footprint TRANSCRIPTION/1qn7_B/3D-footprint R 8 0.8000 0.704 0.563 NA NA

Total matches= 20 (17 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: 189 (35.80%)
Max nb of predicted sites per peak: 4
(gene-Lalb_Chr24g0397801)
Mean nb of predicted sites per peak: 1.36

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

Motif 3 oligos_7nt_test_vs_ctrl_m1

k-mer sig=0.07; evalue=0.85

rrCCCAatata

TATATTGGGYY

[ 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 rrCCCAatata

ASR1:MA1812.1:JASPAR ASR1/MA1812.1/JASPAR D 11 0.7333 0.767 0.562 NA NA

Nuclear:6r2v_A:3D-footprint Nuclear/6r2v_A/3D-footprint D 7 0.6364 0.836 0.532 NA NA

TZP2:EEAD0062:EEADannot TZP2/EEAD0062/EEADannot R 11 0.7333 0.720 0.528 NA NA

Total matches= 36 (33 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: 85 (16.10%)
Max nb of predicted sites per peak: 5
(gene-Lalb_Chr20g0108271)
Mean nb of predicted sites per peak: 1.21

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

Motif 4 oligos_8nt_test_vs_ctrl_m1

k-mer sig=0.49; evalue=0.32

svCCCGtGGabg

CVTCCACGGGBS

[ 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 svCCCGtGGabg

Zm00001d034298:MA1834.1:JASPAR Zm00001d034298/MA1834.1/JASPAR R 11 0.9167 0.826 0.757 NA NA

LOC_Os02g49560:M0327_1.02:CISBP LOC_Os02g49560/M0327_1.02/CISBP R 11 0.9167 0.794 0.728 NA NA

BES1:MA0549.1:JASPAR BES1/MA0549.1/JASPAR D 11 0.9167 0.738 0.677 NA NA

Total matches= 155 (152 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: 99 (18.75%)
Max nb of predicted sites per peak: 4
(gene-Lalb_Chr22g0354521)
Mean nb of predicted sites per peak: 1.34

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

Motif 5 dyads_test_vs_ctrl_m1

k-mer sig=1.23; evalue=0.059

mwCGtdrwCyhttaktGatakt

AMTATCAMTAADRGWYHACGWK

[ 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 mwCGtdrwCyhttaktGatakt

WRKY24.ampDAP:M0803:AthalianaCistrome WRKY24.ampDAP/M0803/AthalianaCistrome D 13 0.5909 0.708 0.418 NA NA

Total matches= 1

[ 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: 43 (8.14%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr07g0179411)
Mean nb of predicted sites per peak: 1.02

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

Motif 6 dyads_test_vs_ctrl_m2

k-mer sig=1.08; evalue=0.083

rwaaTrrdyymttavtaCww

WWGTABTAAKRRHYYATTWY

[ 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 rwaaTrrdyymttavtaCww

ATHB13:MA1212.1:JASPAR ATHB13/MA1212.1/JASPAR D 11 0.5500 0.802 0.441 NA NA

HAT5.DAP:M0442:AthalianaCistrome HAT5.DAP/M0442/AthalianaCistrome D 11 0.5500 0.797 0.438 NA NA

ATHB20:MA1209.1:JASPAR ATHB20/MA1209.1/JASPAR D 11 0.5500 0.790 0.435 NA NA

Total matches= 10 (7 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: 48 (9.09%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr21g0318011)
Mean nb of predicted sites per peak: 1.17

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

Motif 7 dyads_test_vs_ctrl_m3

k-mer sig=1.08; evalue=0.083

ytCatvrwCywttayywmCtaGdy

RHCTAGKWRRTAAWRGWYBATGAR

[ 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 ytCatvrwCywttayywmCtaGdy

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: 50 (9.47%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr22g0351071)
Mean nb of predicted sites per peak: 1.06

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

Motif 8 dyads_test_vs_ctrl_m4

k-mer sig=1.08; evalue=0.083

gmaCGrrkyyhtktkgtGaGtGtg

CACACTCACMAMADRRMYYCGTKC

[ 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 gmaCGrrkyyhtktkgtGaGtGtg

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: 46 (8.71%)
Max nb of predicted sites per peak: 1
(gene-Lalb_Chr25g0278611)
Mean nb of predicted sites per peak: 1.00

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

Motif 9 dyads_test_vs_ctrl_m5

k-mer sig=1.08; evalue=0.083

raCtarwsCwttrtcwytattays

SRTAATARWGAYAAWGSWYTAGTY

[ 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 raCtarwsCwttrtcwytattays

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: 40 (7.58%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr14g0372461)
Mean nb of predicted sites per peak: 1.05

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

Motif 10 dyads_test_vs_ctrl_m6

k-mer sig=1.23; evalue=0.059

syCaCkydCywyktbswwgmwmGrGttasr

YSTAACYCKWKCWWSVAMRWRGHRMGTGRS

[ 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 syCaCkydCywyktbswwgmwmGrGttasr

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: 59 (11.17%)
Max nb of predicted sites per peak: 4
(gene-Lalb_Chr06g0161821)
Mean nb of predicted sites per peak: 1.12

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

Motif 11 dyads_test_vs_ctrl_m7

k-mer sig=1.23; evalue=0.059

rkaatvgwyymktactahsamkakwmy

RKWMTMKTSDTAGTAMKRRWCBATTMY

[ 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 rkaatvgwyymktactahsamkakwmy

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: 40 (7.58%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr08g0243901)
Mean nb of predicted sites per peak: 1.05

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

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]

RSAT - peak-motifs result

Analysis: MEsalmon4_Up1 (25/05/2025 14:18)

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 mwCGtdrwCyhttaktGatakt

WRKY24.ampDAP:M0803:AthalianaCistrome WRKY24.ampDAP/M0803/AthalianaCistrome D 13 0.5909 0.708 0.418 NA NA

Total matches= 1

footprintDB-plants

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

columns aligned correlation cor ytCatvrwCywttayywmCtaGdy

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor gmaCGrrkyyhtktkgtGaGtGtg

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor raCtarwsCwttrtcwytattays

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor syCaCkydCywyktbswwgmwmGrGttasr

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor rkaatvgwyymktactahsamkakwmy

Total matches= 0

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: MEsalmon4_Up1 (25/05/2025 14:18)

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 mwCGtdrwCyhttaktGatakt WRKY24.ampDAP:M0803:AthalianaCistrome WRKY24.ampDAP/M0803/AthalianaCistrome D 13 0.5909 0.708 0.418 NA NA Total matches= 1

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

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

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

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

footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor rkaatvgwyymktactahsamkakwmy 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 mwCGtdrwCyhttaktGatakt

WRKY24.ampDAP:M0803:AthalianaCistrome WRKY24.ampDAP/M0803/AthalianaCistrome D 13 0.5909 0.708 0.418 NA NA

Total matches= 1

footprintDB-plants

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

columns aligned correlation cor ytCatvrwCywttayywmCtaGdy

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor gmaCGrrkyyhtktkgtGaGtGtg

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor raCtarwsCwttrtcwytattays

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor syCaCkydCywyktbswwgmwmGrGttasr

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor rkaatvgwyymktactahsamkakwmy

Total matches= 0