peak-motifs MEnavajowhite2_Up4

motif discovery

oligos_6nt_test_vs_ctrl

oligos_6nt_test_vs_ctrl_m1	assembly: aacggc (sig=0.82; e-value=0.15)	RC: gccgtt
oligos_6nt_test_vs_ctrl_m2	assembly: acagta (sig=0.04; e-value=0.91)	RC: tactgt
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: ataatac (sig=0.41; e-value=0.39)	RC: gtattat
oligos_7nt_test_vs_ctrl_m2	assembly: ggaccca (sig=0.23; e-value=0.59)	RC: tgggtcc
oligos_7nt_test_vs_ctrl_m3	assembly: ccgacag (sig=0.11; e-value=0.78)	RC: ctgtcgg
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: ggacccac (sig=0.54; e-value=0.29)	RC: gtgggtcc
oligos_8nt_test_vs_ctrl_m2	assembly: gttcttaa (sig=0.07; e-value=0.85)	RC: ttaagaac
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: gggnnncac (sig=0.92; e-value=0.12)	RC: gtgnnnccc
dyads_test_vs_ctrl_m2	assembly: cgtnnnnnnnnnnnnnnnnnttc (sig=0.92; e-value=0.12)	RC: gaannnnnnnnnnnnnnnnnacg
dyads_test_vs_ctrl_m3	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m4	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m5	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m6	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m7	: (sig=; e-value=1)	RC:
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=0.82; evalue=0.15

smaaCGGCgm

KCGCCGTTKS

[ 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 smaaCGGCgm

PC-MYB1:MA2352.1:JASPAR PC-MYB1/MA2352.1/JASPAR R 9 0.9000 0.896 0.806 NA NA

MYB56:MA1174.2:JASPAR MYB56/MA1174.2/JASPAR D 10 1.0000 0.781 0.781 NA NA

MYB70:MA1393.2:JASPAR MYB70/MA1393.2/JASPAR R 10 0.9091 0.817 0.743 NA NA

Total matches= 87 (84 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: 32 (7.21%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr09g0330761)
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=0.04; evalue=0.91

ayACAGTArm

KYTACTGTRT

[ 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 ayACAGTArm

ALOG:EEAD0170:EEADannot ALOG/EEAD0170/EEADannot R 10 0.9091 0.879 0.799 NA NA

AtMYB104_I:AtMYB104_I:AthaMYB AtMYB104_I/AtMYB104_I/AthaMYB R 8 0.8000 0.840 0.672 NA NA

SPL11.DAP:M0741:AthalianaCistrome SPL11.DAP/M0741/AthalianaCistrome D 10 0.9091 0.705 0.641 NA NA

Total matches= 23 (20 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: 47 (10.59%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr13g0296891)
Mean nb of predicted sites per peak: 1.13

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

Motif 3 oligos_7nt_test_vs_ctrl_m1

k-mer sig=0.41; evalue=0.39

taATAaTACgv

BCGTATTATTA

[ 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 taATAaTACgv

ATHB22:M0844_1.02:CISBP ATHB22/M0844_1.02/CISBP D 11 0.8462 0.759 0.642 NA NA

Zm00001d005692:MA1824.2:JASPAR Zm00001d005692/MA1824.2/JASPAR D 8 0.7273 0.820 0.597 NA NA

Zm00001d005692:MA1824.1:JASPAR Zm00001d005692/MA1824.1/JASPAR D 10 0.7692 0.745 0.573 NA NA

Total matches= 26 (23 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: 49 (11.04%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr19g0123931)
Mean nb of predicted sites per peak: 1.06

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

Motif 4 oligos_7nt_test_vs_ctrl_m2

k-mer sig=0.23; evalue=0.59

kgGGaCCCacb

VGTGGGTCCCM

[ 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 kgGGaCCCacb

PCF2:PCF2:Athamap PCF2/PCF2/Athamap D 10 0.9091 0.879 0.799 NA NA

At5g08330.ampDAP:M0757:AthalianaCistrome At5g08330.ampDAP/M0757/AthalianaCistrome R 11 0.9167 0.855 0.784 NA NA

TCP20.ampDAP:M0759:AthalianaCistrome TCP20.ampDAP/M0759/AthalianaCistrome D 11 0.9167 0.855 0.784 NA NA

Total matches= 74 (71 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 (8.78%)
Max nb of predicted sites per peak: 4
(gene-Lalb_Chr14g0372811)
Mean nb of predicted sites per peak: 1.41

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

Motif 5 oligos_7nt_test_vs_ctrl_m3

k-mer sig=0.11; evalue=0.78

kmCCGACaGcr

YGCTGTCGGKM

[ 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 kmCCGACaGcr

RAP2-10:MA0980.2:JASPAR RAP2-10/MA0980.2/JASPAR D 11 0.9167 0.853 0.782 NA NA

ARF2:MA1206.1:JASPAR ARF2/MA1206.1/JASPAR D 10 0.9091 0.823 0.748 NA NA

MP.DAP:M0140:AthalianaCistrome MP.DAP/M0140/AthalianaCistrome D 10 0.9091 0.815 0.741 NA NA

Total matches= 161 (158 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 (6.31%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr07g0194361)
Mean nb of predicted sites per peak: 1.11

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

Motif 6 oligos_8nt_test_vs_ctrl_m1

k-mer sig=0.54; evalue=0.29

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 0.933 0.861 NA NA

At1g72010:MA1288.1:JASPAR At1g72010/MA1288.1/JASPAR R 12 0.9231 0.926 0.855 NA NA

At1g69690.ampDAP:M0756:AthalianaCistrome At1g69690.ampDAP/M0756/AthalianaCistrome R 12 0.9231 0.925 0.854 NA NA

Total matches= 80 (77 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 (11.71%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr14g0372811)
Mean nb of predicted sites per peak: 1.35

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

Motif 7 oligos_8nt_test_vs_ctrl_m2

k-mer sig=0.07; evalue=0.85

kkGTTCTTAayy

RRTTAAGAACMM

[ 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 kkGTTCTTAayy

PEND:MA0127.1:JASPAR PEND/MA0127.1/JASPAR D 10 0.8333 0.724 0.603 NA NA

HB-1:M0841_1.02:CISBP HB-1/M0841_1.02/CISBP D 8 0.6667 0.825 0.550 NA NA

ONAC127:UN0430.2:JASPAR ONAC127/UN0430.2/JASPAR R 8 0.6667 0.740 0.493 NA NA

Total matches= 11 (8 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: 20 (4.50%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr18g0057731)
Mean nb of predicted sites per peak: 1.05

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

Motif 8 dyads_test_vs_ctrl_m1

k-mer sig=0.92; evalue=0.12

gkGGGyssCaCsy

RSGTGSSRCCCMC

[ 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 gkGGGyssCaCsy

At1g72010:MA1288.1:JASPAR At1g72010/MA1288.1/JASPAR R 13 1.0000 0.827 0.827 NA NA

At1g72010.ampDAP:M0748:AthalianaCistrome At1g72010.ampDAP/M0748/AthalianaCistrome R 13 1.0000 0.822 0.822 NA NA

At1g69690.ampDAP:M0756:AthalianaCistrome At1g69690.ampDAP/M0756/AthalianaCistrome R 13 1.0000 0.804 0.804 NA NA

Total matches= 95 (92 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 (10.14%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr11g0066101)
Mean nb of predicted sites per peak: 1.20

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

Motif 9 dyads_test_vs_ctrl_m2

k-mer sig=0.92; evalue=0.12

ymSGTGGSsCCCaCrygkbyyyytbss

SSVARRRRVMCRYGTGGGSSCCACSKR

[ 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 ymSGTGGSsCCCaCrygkbyyyytbss

TCP20.DAP:M0752:AthalianaCistrome TCP20.DAP/M0752/AthalianaCistrome R 21 0.7778 0.912 0.709 NA NA

At2g45680:MA1285.1:JASPAR At2g45680/MA1285.1/JASPAR R 21 0.7778 0.858 0.667 NA NA

TCP14:MA1283.1:JASPAR TCP14/MA1283.1/JASPAR R 20 0.7407 0.897 0.664 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: 35 (7.88%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr14g0373551)
Mean nb of predicted sites per peak: 1.60

[ 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: MEnavajowhite2_Up4_W1 (26/05/2025 03:11)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results