peak-motifs navajowhite2

Motif discovery

Motif 1 oligos_6nt_test_vs_ctrl_m1

k-mer sig=2.28; evalue=0.0052

rrAAAGTGrr

YYCACTTTYY

[ 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 rrAAAGTGrr

cdf3:M0651_1.02:CISBP cdf3/M0651_1.02/CISBP D 9 0.9000 0.896 0.806 NA NA

CDF3:MA0974.1:JASPAR CDF3/MA0974.1/JASPAR D 9 0.9000 0.895 0.805 NA NA

C3H67:UN0851.1:JASPAR C3H67/UN0851.1/JASPAR D 10 1.0000 0.800 0.800 NA NA

Total matches= 108 (105 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 (31.47%)
Max nb of predicted sites per peak: 5
(gene-Lalb_Chr12g0197021)
Mean nb of predicted sites per peak: 1.38

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

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=1.50; evalue=0.032

ayACaGTArw

WYTACTGTRT

[ 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 ayACaGTArw

ALOG:EEAD0170:EEADannot ALOG/EEAD0170/EEADannot R 10 0.9091 0.864 0.786 NA NA

AtMYB104_I:AtMYB104_I:AthaMYB AtMYB104_I/AtMYB104_I/AthaMYB R 8 0.8000 0.838 0.671 NA NA

At5g28300:At5g28300:ArabidopsisPBM At5g28300/At5g28300/ArabidopsisPBM D 9 0.8182 0.751 0.615 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: 83 (17.89%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr25g0285141)
Mean nb of predicted sites per peak: 1.12

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

Motif 3 oligos_6nt_test_vs_ctrl_m3

k-mer sig=1.42; evalue=0.038

ygaAACGGtgr

YCACCGTTTCR

[ 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 ygaAACGGtgr

MYB70:MA1393.2:JASPAR MYB70/MA1393.2/JASPAR R 10 0.8333 0.885 0.737 NA NA

MYB44.ampDAP:M0554:AthalianaCistrome MYB44.ampDAP/M0554/AthalianaCistrome D 11 1.0000 0.735 0.735 NA NA

MYB3R1:MA1178.2:JASPAR MYB3R1/MA1178.2/JASPAR D 11 0.8462 0.858 0.726 NA NA

Total matches= 70 (67 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: 58 (12.50%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr24g0396451)
Mean nb of predicted sites per peak: 1.14

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

Motif 4 oligos_6nt_test_vs_ctrl_m4

k-mer sig=1.38; evalue=0.042

vvaAACGGCrm

KYGCCGTTTBB

[ 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 vvaAACGGCrm

DOF4.2:MA1273.2:JASPAR DOF4.2/MA1273.2/JASPAR D 10 0.8333 0.749 0.624 NA NA

PC-MYB1:MA2352.1:JASPAR PC-MYB1/MA2352.1/JASPAR R 9 0.8182 0.749 0.613 NA NA

MYB3R3:EEAD0045:EEADannot MYB3R3/EEAD0045/EEADannot R 11 0.7857 0.750 0.589 NA NA

Total matches= 52 (49 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: 58 (12.50%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr18g0054911)
Mean nb of predicted sites per peak: 1.17

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

Motif 5 oligos_6nt_test_vs_ctrl_m5

k-mer sig=1.26; evalue=0.055

rdaGaGGGrr

YYCCCTCTHY

[ 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 rdaGaGGGrr

CURE3UTR1:EEAD0076:EEADannot CURE3UTR1/EEAD0076/EEADannot R 9 0.8182 0.711 0.582 NA NA

Lysine-specific:6jnl_A:3D-footprint Lysine-specific/6jnl_A/3D-footprint D 6 0.6000 0.845 0.507 NA NA

Lysine-specific:6a57_A:3D-footprint Lysine-specific/6a57_A/3D-footprint D 6 0.6000 0.792 0.475 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: 107 (23.06%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr25g0285141)
Mean nb of predicted sites per peak: 1.17

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

Motif 6 oligos_6nt_test_vs_ctrl_m6

k-mer sig=1.10; evalue=0.079

grGCGGGArv

BYTCCCGCYC

[ 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 grGCGGGArv

E2Fa:E2Fa:Athamap E2Fa/E2Fa/Athamap R 8 0.8000 0.921 0.737 NA NA

E2Fb:E2Fb:Athamap E2Fb/E2Fb/Athamap R 8 0.8000 0.918 0.734 NA NA

E2Fc:E2Fc:Athamap E2Fc/E2Fc/Athamap R 9 0.7500 0.866 0.649 NA NA

Total matches= 12 (9 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: 80 (17.24%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr20g0123591)
Mean nb of predicted sites per peak: 1.19

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

Motif 7 oligos_6nt_test_vs_ctrl_m7

k-mer sig=0.19; evalue=0.65

scAACACTkc

GMAGTGTTGS

[ 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 scAACACTkc

ZAT6:ZAT6:ArabidopsisPBM ZAT6/ZAT6/ArabidopsisPBM D 10 1.0000 0.872 0.872 NA NA

TRB1:MA2032.1:JASPAR TRB1/MA2032.1/JASPAR D 10 0.9091 0.706 0.641 NA NA

TRB1:MA2032.2:JASPAR TRB1/MA2032.2/JASPAR D 9 0.9000 0.705 0.635 NA NA

Total matches= 30 (27 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: 97 (20.91%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr05g0213431)
Mean nb of predicted sites per peak: 1.22

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

Motif 8 oligos_6nt_test_vs_ctrl_m8

k-mer sig=1.42; evalue=0.038

bsaCCGTtasa

TSTAACGGTSV

[ 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 bsaCCGTtasa

MYB44.ampDAP:M0554:AthalianaCistrome MYB44.ampDAP/M0554/AthalianaCistrome R 11 1.0000 0.857 0.857 NA NA

MYB119:MA1176.1:JASPAR MYB119/MA1176.1/JASPAR D 11 1.0000 0.840 0.840 NA NA

MYB3R1:MA1178.2:JASPAR MYB3R1/MA1178.2/JASPAR R 11 0.8462 0.965 0.817 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: 67 (14.44%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr05g0222061)
Mean nb of predicted sites per peak: 1.15

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

Motif 9 oligos_7nt_test_vs_ctrl_m1

k-mer sig=0.95; evalue=0.11

ksAACGGTCmm

KKGACCGTTSM

[ 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 ksAACGGTCmm

MYB73:MA1394.2:JASPAR MYB73/MA1394.2/JASPAR D 11 0.9167 0.938 0.860 NA NA

MYB44:MA2027.1:JASPAR MYB44/MA2027.1/JASPAR D 11 0.9167 0.935 0.858 NA NA

MYB70:MA1393.2:JASPAR MYB70/MA1393.2/JASPAR R 11 1.0000 0.842 0.842 NA NA

Total matches= 107 (104 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 (11.21%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr22g0351091)
Mean nb of predicted sites per peak: 1.10

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

Motif 10 oligos_7nt_test_vs_ctrl_m2

k-mer sig=0.81; evalue=0.15

rdaGtaaaGkr

YMCTTTACTHY

[ 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 rdaGtaaaGkr

ONAC127:UN0430.1:JASPAR ONAC127/UN0430.1/JASPAR D 11 0.9167 0.754 0.691 NA NA

LOC_Os02g01380:M1284_1.02:CISBP LOC_Os02g01380/M1284_1.02/CISBP R 10 0.9091 0.703 0.639 NA NA

GTL1.DAP:M0771:AthalianaCistrome GTL1.DAP/M0771/AthalianaCistrome D 10 0.9091 0.701 0.637 NA NA

Total matches= 62 (59 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: 67 (14.44%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr20g0113441)
Mean nb of predicted sites per peak: 1.04

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

Motif 11 oligos_7nt_test_vs_ctrl_m3

k-mer sig=0.56; evalue=0.28

kkGGaCCCAcb

VGTGGGTCCMM

[ 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 kkGGaCCCAcb

PCF2:PCF2:Athamap PCF2/PCF2/Athamap D 10 0.9091 0.863 0.785 NA NA

At5g08330.ampDAP:M0757:AthalianaCistrome At5g08330.ampDAP/M0757/AthalianaCistrome R 11 0.9167 0.831 0.762 NA NA

TCP20.ampDAP:M0759:AthalianaCistrome TCP20.ampDAP/M0759/AthalianaCistrome D 11 0.9167 0.830 0.761 NA NA

Total matches= 71 (68 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: 45 (9.70%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr14g0372811)
Mean nb of predicted sites per peak: 1.22

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

Motif 12 oligos_8nt_test_vs_ctrl_m1

k-mer sig=1.33; evalue=0.047

tgGGaCCCACsc

GSGTGGGTCCCA

[ 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 tgGGaCCCACsc

At1g72010.ampDAP:M0748:AthalianaCistrome At1g72010.ampDAP/M0748/AthalianaCistrome R 12 0.9231 0.917 0.847 NA NA

At1g72010:MA1288.1:JASPAR At1g72010/MA1288.1/JASPAR R 12 0.9231 0.909 0.839 NA NA

At1g69690.ampDAP:M0756:AthalianaCistrome At1g69690.ampDAP/M0756/AthalianaCistrome R 12 0.9231 0.906 0.837 NA NA

Total matches= 78 (75 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 (13.79%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr14g0372811)
Mean nb of predicted sites per peak: 1.27

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

Motif 13 oligos_8nt_test_vs_ctrl_m2

k-mer sig=0.41; evalue=0.39

mvACACAGtAry

RYTACTGTGTBK

[ 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 mvACACAGtAry

ALOG:EEAD0170:EEADannot ALOG/EEAD0170/EEADannot R 11 0.9167 0.785 0.720 NA NA

REF6:MA1415.1:JASPAR REF6/MA1415.1/JASPAR D 10 0.7692 0.710 0.546 NA NA

Lysine-specific:6jnm_A:3D-footprint Lysine-specific/6jnm_A/3D-footprint R 7 0.5833 0.912 0.532 NA NA

Total matches= 6 (3 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: 22 (4.74%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr10g0101111)
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: navajowhite2 (20/05/2025 09:36)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results