peak-motifs MEgreen

Motif discovery

Motif 1 oligos_6nt_test_vs_ctrl_m1

k-mer sig=4.34; evalue=4.6e-05

kgaaaaaGtCaACgr

YCGTTGACTTTTTCM

[ 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 kgaaaaaGtCaACgr

WRKY43.ampDAP:M0828:AthalianaCistrome WRKY43.ampDAP/M0828/AthalianaCistrome D 15 1.0000 0.931 0.931 NA NA

WRKY24:MA1315.1:JASPAR WRKY24/MA1315.1/JASPAR R 14 0.9333 0.932 0.870 NA NA

WRKY45:MA1087.2:JASPAR WRKY45/MA1087.2/JASPAR D 14 0.8750 0.969 0.848 NA NA

Total matches= 247 (244 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: 64 (9.52%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr22g0351621)
Mean nb of predicted sites per peak: 1.06

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

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=3.16; evalue=0.00069

rvATATTAgkv

BMCTAATATBY

[ 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 rvATATTAgkv

ATHB22:M0844_1.02:CISBP ATHB22/M0844_1.02/CISBP R 11 0.8462 0.862 0.730 NA NA

LHY1.ampDAP:M0592:AthalianaCistrome LHY1.ampDAP/M0592/AthalianaCistrome D 11 1.0000 0.722 0.722 NA NA

At3g09600.ampDAP:M0586:AthalianaCistrome At3g09600.ampDAP/M0586/AthalianaCistrome D 11 1.0000 0.709 0.709 NA NA

Total matches= 50 (47 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: 52 (7.74%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr23g0266081)
Mean nb of predicted sites per peak: 1.04

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

Motif 3 oligos_6nt_test_vs_ctrl_m3

k-mer sig=2.62; evalue=0.0024

msaCGtCays

SRTGACGTSK

[ 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 msaCGtCays

TGA6:MA1069.1:JASPAR TGA6/MA1069.1/JASPAR R 10 1.0000 0.930 0.930 NA NA

TGA6:M0265_1.02:CISBP TGA6/M0265_1.02/CISBP R 10 1.0000 0.930 0.930 NA NA

TGA2:M0269_1.02:CISBP TGA2/M0269_1.02/CISBP R 10 1.0000 0.915 0.915 NA NA

Total matches= 227 (224 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: 82 (12.20%)
Max nb of predicted sites per peak: 4
(gene-Lalb_Chr04g0256321)
Mean nb of predicted sites per peak: 1.23

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

Motif 4 oligos_6nt_test_vs_ctrl_m4

k-mer sig=1.58; evalue=0.026

syGaGACacr

YGTGTCTCRS

[ 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 syGaGACacr

ARF2:MA1206.1:JASPAR ARF2/MA1206.1/JASPAR D 10 1.0000 0.753 0.753 NA NA

ARF1:ARF1:Athamap ARF1/ARF1/Athamap R 10 0.9091 0.747 0.679 NA NA

LEC1-A:UN0424.1:JASPAR LEC1-A/UN0424.1/JASPAR R 10 0.9091 0.704 0.640 NA NA

Total matches= 25 (22 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: 167 (24.85%)
Max nb of predicted sites per peak: 4
(gene-Lalb_Chr20g0119161)
Mean nb of predicted sites per peak: 1.24

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

Motif 5 oligos_6nt_test_vs_ctrl_m5

k-mer sig=1.44; evalue=0.036

dvATGAATgrr

YYCATTCATBH

[ 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 dvATGAATgrr

EIL3:MA1751.1:JASPAR EIL3/MA1751.1/JASPAR R 11 1.0000 0.748 0.748 NA NA

EIL3:M0680_1.02:CISBP EIL3/M0680_1.02/CISBP D 11 1.0000 0.747 0.747 NA NA

HAT2:MA1198.1:JASPAR HAT2/MA1198.1/JASPAR R 11 1.0000 0.720 0.720 NA NA

Total matches= 50 (47 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: 146 (21.73%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr05g0215361)
Mean nb of predicted sites per peak: 1.12

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

Motif 6 oligos_7nt_test_vs_ctrl_m1

k-mer sig=4.23; evalue=5.9e-05

smaaaaGTCAACtmy

RKAGTTGACTTTTKS

[ 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 smaaaaGTCAACtmy

WRKY45:MA1087.2:JASPAR WRKY45/MA1087.2/JASPAR D 15 1.0000 0.941 0.941 NA NA

WRKY8.DAP:M0792:AthalianaCistrome WRKY8.DAP/M0792/AthalianaCistrome D 15 1.0000 0.923 0.923 NA NA

WRKY40.DAP:M0812:AthalianaCistrome WRKY40.DAP/M0812/AthalianaCistrome R 15 1.0000 0.897 0.897 NA NA

Total matches= 233 (230 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: 59 (8.78%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr14g0371271)
Mean nb of predicted sites per peak: 1.10

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

Motif 7 oligos_7nt_test_vs_ctrl_m2

k-mer sig=0.93; evalue=0.12

rrtGaGaCAkr

YMTGTCTCAYY

[ 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 rrtGaGaCAkr

ARF2:MA1206.1:JASPAR ARF2/MA1206.1/JASPAR D 10 0.9091 0.716 0.651 NA NA

SGR5:MA1159.2:JASPAR SGR5/MA1159.2/JASPAR D 11 0.8462 0.717 0.607 NA NA

SGR5.ampDAP:M0303:AthalianaCistrome SGR5.ampDAP/M0303/AthalianaCistrome R 11 0.7333 0.748 0.549 NA NA

Total matches= 14 (11 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: 86 (12.80%)
Max nb of predicted sites per peak: 4
(gene-Lalb_Chr18g0057891)
Mean nb of predicted sites per peak: 1.14

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

Motif 8 oligos_7nt_test_vs_ctrl_m3

k-mer sig=0.83; evalue=0.15

rkAACaaaGya

TRCTTTGTTMY

[ 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 rkAACaaaGya

REF6:MA1415.1:JASPAR REF6/MA1415.1/JASPAR D 11 1.0000 0.781 0.781 NA NA

REF6:MA1415.2:JASPAR REF6/MA1415.2/JASPAR D 9 0.8182 0.786 0.643 NA NA

Lysine-specific:6jnm_A:3D-footprint Lysine-specific/6jnm_A/3D-footprint R 7 0.6364 0.876 0.558 NA NA

Total matches= 41 (38 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: 130 (19.35%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr25g0282811)
Mean nb of predicted sites per peak: 1.11

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

Motif 9 oligos_7nt_test_vs_ctrl_m4

k-mer sig=0.67; evalue=0.21

ybACGtCAtva

TBATGACGTVR

[ 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 ybACGtCAtva

TGA1:MA0588.1:JASPAR TGA1/MA0588.1/JASPAR R 11 1.0000 0.890 0.890 NA NA

TGA9.ampDAP:M0184:AthalianaCistrome TGA9.ampDAP/M0184/AthalianaCistrome R 11 1.0000 0.881 0.881 NA NA

TGA4:MA1335.1:JASPAR TGA4/MA1335.1/JASPAR D 11 1.0000 0.847 0.847 NA NA

Total matches= 189 (186 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: 39 (5.80%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr09g0333491)
Mean nb of predicted sites per peak: 1.15

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

Motif 10 oligos_8nt_test_vs_ctrl_m1

k-mer sig=8.37; evalue=4.3e-09

amAAAGTCAAagr

YCTTTGACTTTKT

[ 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 amAAAGTCAAagr

WRKY17.ampDAP:M0837:AthalianaCistrome WRKY17.ampDAP/M0837/AthalianaCistrome D 13 1.0000 0.883 0.883 NA NA

WRKY45.DAP:M0805:AthalianaCistrome WRKY45.DAP/M0805/AthalianaCistrome R 12 0.9231 0.949 0.876 NA NA

WRKY59:MA1304.1:JASPAR WRKY59/MA1304.1/JASPAR D 12 0.9231 0.923 0.852 NA NA

Total matches= 252 (249 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: 75 (11.16%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr13g0295111)
Mean nb of predicted sites per peak: 1.03

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

Motif 11 oligos_8nt_test_vs_ctrl_m2

k-mer sig=0.82; evalue=0.15

mcaCGtGtCGkk

MMCGACACGTGK

[ 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 mcaCGtGtCGkk

ATAREB1:M0256_1.02:CISBP ATAREB1/M0256_1.02/CISBP R 12 0.9231 0.871 0.804 NA NA

ABF2:MA0941.1:JASPAR ABF2/MA0941.1/JASPAR R 12 0.9231 0.871 0.804 NA NA

ABF1:MA0570.2:JASPAR ABF1/MA0570.2/JASPAR D 12 1.0000 0.796 0.796 NA NA

Total matches= 313 (310 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: 96 (14.29%)
Max nb of predicted sites per peak: 5
(gene-Lalb_Chr17g0341231)
Mean nb of predicted sites per peak: 1.39

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

Motif 12 oligos_8nt_test_vs_ctrl_m3

k-mer sig=0.40; evalue=0.4

mraGtCaaCGtbk

MVACGTTGACTYK

[ 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 mraGtCaaCGtbk

VOZ2:UP00581A_2:UniPROBE VOZ2/UP00581A_2/UniPROBE D 13 1.0000 0.950 0.950 NA NA

AT3G42860:UN0354.1:JASPAR AT3G42860/UN0354.1/JASPAR D 12 0.9231 0.978 0.903 NA NA

WRKY55:MA1305.1:JASPAR WRKY55/MA1305.1/JASPAR R 12 0.9231 0.970 0.895 NA NA

Total matches= 174 (171 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: 83 (12.35%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr22g0360751)
Mean nb of predicted sites per peak: 1.10

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

Motif 13 dyads_test_vs_ctrl_m1

k-mer sig=3.67; evalue=0.00021

vkaaAsgsrvyradtGACrw

WYGTCAHTYRBYSCSTTTMB

[ 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 vkaaAsgsrvyradtGACrw

At3g45610.ampDAP:M0254:AthalianaCistrome At3g45610.ampDAP/M0254/AthalianaCistrome R 14 0.6667 0.784 0.523 NA NA

COG1.ampDAP:M0276:AthalianaCistrome COG1.ampDAP/M0276/AthalianaCistrome R 14 0.6667 0.758 0.505 NA NA

dof24.DAP:M0252:AthalianaCistrome dof24.DAP/M0252/AthalianaCistrome R 14 0.6667 0.755 0.503 NA NA

Total matches= 13 (10 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: 65 (9.67%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr22g0360751)
Mean nb of predicted sites per peak: 1.03

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

Motif 14 dyads_test_vs_ctrl_m2

k-mer sig=3.54; evalue=0.00029

rkATAgksgsyTAAkw

WMTTARSCSMCTATMY

[ 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 rkATAgksgsyTAAkw

HMGB9:UN0401.1:JASPAR HMGB9/UN0401.1/JASPAR D 11 0.6875 0.744 0.511 NA NA

At1g76110.DAP:M0146:AthalianaCistrome At1g76110.DAP/M0146/AthalianaCistrome D 11 0.6875 0.744 0.511 NA NA

WOX11:UN0413.1:JASPAR WOX11/UN0413.1/JASPAR R 11 0.6875 0.704 0.484 NA NA

Total matches= 13 (10 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: 64 (9.52%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr22g0361171)
Mean nb of predicted sites per peak: 1.08

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

Motif 15 dyads_test_vs_ctrl_m3

k-mer sig=3.67; evalue=0.00021

ttaatsgvsgcmtwatykKactttakk

MMTAAAGTMMRATWAKGCSBCSATTAA

[ 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 ttaatsgvsgcmtwatykKactttakk

ATHB23:MA1327.1:JASPAR ATHB23/MA1327.1/JASPAR D 18 0.5806 0.702 0.407 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: 26 (3.87%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr09g0335031)
Mean nb of predicted sites per peak: 1.04

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

Motif 16 dyads_test_vs_ctrl_m4

k-mer sig=3.67; evalue=0.00021

ggaatsgssgcmwwwttkKahtGaGdk

MHCTCADTMMAAWWWKGCSSCSATTCC

[ 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 ggaatsgssgcmwwwttkKahtGaGdk

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: 33 (4.91%)
Max nb of predicted sites per peak: 1
(gene-Lalb_Chr25g0285571)
Mean nb of predicted sites per peak: 1.00

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

Motif 17 dyads_test_vs_ctrl_m5

k-mer sig=3.67; evalue=0.00021

akaaasssrsyrawdRwyktwwttGakk

MMTCAAWWAMRWYHWTYRSYSSSTTTMT

[ 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 akaaasssrsyrawdRwyktwwttGakk

OBP3.ampDAP:M0274:AthalianaCistrome OBP3.ampDAP/M0274/AthalianaCistrome R 18 0.6207 0.701 0.435 NA NA

DOF3.4:MA1278.2:JASPAR DOF3.4/MA1278.2/JASPAR R 17 0.6071 0.710 0.431 NA NA

Total matches= 2

[ 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: 51 (7.59%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr22g0351621)
Mean nb of predicted sites per peak: 1.02

[ 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: MEgreen (21/05/2025 03:24)

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 ttaatsgvsgcmtwatykKactttakk

ATHB23:MA1327.1:JASPAR ATHB23/MA1327.1/JASPAR D 18 0.5806 0.702 0.407 NA NA

Total matches= 1

footprintDB-plants

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

columns aligned correlation cor ggaatsgssgcmwwwttkKahtGaGdk

Total matches= 0

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: MEgreen (21/05/2025 03:24)

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 ttaatsgvsgcmtwatykKactttakk ATHB23:MA1327.1:JASPAR ATHB23/MA1327.1/JASPAR D 18 0.5806 0.702 0.407 NA NA Total matches= 1

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

ATHB23:MA1327.1:JASPAR ATHB23/MA1327.1/JASPAR D 18 0.5806 0.702 0.407 NA NA

Total matches= 1

footprintDB-plants

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

columns aligned correlation cor ggaatsgssgcmwwwttkKahtGaGdk

Total matches= 0