peak-motifs MEnavajowhite2

Sequence composition (test sequences)

Nb of peaks: 464
Total seq. size: 595 kb
Min length: 2 bp
Mean length: 1281.94 bp
Max length: 1501 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: 50495 kb
Min length: 1 bp
Mean length: 1220.9 bp
Max length: 1501 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

oligos_6nt_test_vs_ctrl

oligos_6nt_test_vs_ctrl_m1	assembly: aacggc (sig=0.24; e-value=0.58)	RC: gccgtt
oligos_6nt_test_vs_ctrl_m2	: (sig=; e-value=1)	RC:
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

Not a single significant pattern

[oligos_7nt_test_vs_ctrl]

oligos_8nt_test_vs_ctrl

Not a single significant pattern

[oligos_8nt_test_vs_ctrl]

dyads_test_vs_ctrl

dyads_test_vs_ctrl_m1	assembly: acgntca (sig=0.83; e-value=0.15)	RC: tgancgt
dyads_test_vs_ctrl_m2	assembly: cacnnnnnnnnnnntcg (sig=0.83; e-value=0.15)	RC: cgannnnnnnnnnngtg
dyads_test_vs_ctrl_m3	assembly: cggnnnnnnnnnnnttc (sig=0.83; e-value=0.15)	RC: gaannnnnnnnnnnccg
dyads_test_vs_ctrl_m4	assembly: acannnnnnnnnnnnnnnnnntgt (sig=0.83; e-value=0.15)	RC: acannnnnnnnnnnnnnnnnntgt
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=0.24; evalue=0.58

scAaCGGCgm

KCGCCGTTGS

[ 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 scAaCGGCgm

PC-MYB1:MA2352.1:JASPAR PC-MYB1/MA2352.1/JASPAR R 9 0.9000 0.884 0.795 NA NA

MYB56:MA1174.2:JASPAR MYB56/MA1174.2/JASPAR D 10 1.0000 0.778 0.778 NA NA

MYB3R3:MA2343.1:JASPAR MYB3R3/MA2343.1/JASPAR R 8 0.8000 0.913 0.730 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: 42 (9.05%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr16g0376851)
Mean nb of predicted sites per peak: 1.10

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

Motif 2 dyads_test_vs_ctrl_m1

k-mer sig=0.83; evalue=0.15

scaCGbtCacg

CGTGAVCGTGS

[ 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 scaCGbtCacg

MYB73:MA1394.2:JASPAR MYB73/MA1394.2/JASPAR D 11 0.9167 0.789 0.723 NA NA

MYB44:MA2027.1:JASPAR MYB44/MA2027.1/JASPAR D 11 0.9167 0.788 0.722 NA NA

MYB3R4:MA1180.2:JASPAR MYB3R4/MA1180.2/JASPAR R 11 0.9167 0.722 0.662 NA NA

Total matches= 28 (25 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: 77 (16.59%)
Max nb of predicted sites per peak: 5
(gene-Lalb_Chr16g0379181)
Mean nb of predicted sites per peak: 1.19

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

Motif 3 dyads_test_vs_ctrl_m2

k-mer sig=0.83; evalue=0.15

ssCaCkGwCmGtkssktCGby

RVCGAMSSMACKGWCMGTGSS

[ 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 ssCaCkGwCmGtkssktCGby

SIZF2:MA1405.1:JASPAR SIZF2/MA1405.1/JASPAR R 10 0.4762 0.887 0.422 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: 60 (12.93%)
Max nb of predicted sites per peak: 5
(gene-Lalb_Chr01g0013011)
Mean nb of predicted sites per peak: 1.33

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

Motif 4 dyads_test_vs_ctrl_m3

k-mer sig=0.83; evalue=0.15

swCGGwSrvySwcybtttCsm

KSGAAAVRGWSRBYSWCCGWS

[ 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 swCGGwSrvySwcybtttCsm

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: 41 (8.84%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr15g0083521)
Mean nb of predicted sites per peak: 1.32

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

Motif 5 dyads_test_vs_ctrl_m4

k-mer sig=0.83; evalue=0.15

ssaCaYGrtCrtssysstCgySbyskyb

VRMSRVSRCGASSRSSAYGAYCRTGTSS

[ 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 ssaCaYGrtCrtssysstCgySbyskyb

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: 66 (14.22%)
Max nb of predicted sites per peak: 4
(gene-Lalb_Chr17g0347951)
Mean nb of predicted sites per peak: 1.30

[ 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_Up2 (25/05/2025 13:27)

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 ssCaCkGwCmGtkssktCGby

SIZF2:MA1405.1:JASPAR SIZF2/MA1405.1/JASPAR R 10 0.4762 0.887 0.422 NA NA

Total matches= 1

footprintDB-plants

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

columns aligned correlation cor swCGGwSrvySwcybtttCsm

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor ssaCaYGrtCrtssysstCgySbyskyb

Total matches= 0

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: MEnavajowhite2_Up2 (25/05/2025 13:27)

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 ssCaCkGwCmGtkssktCGby SIZF2:MA1405.1:JASPAR SIZF2/MA1405.1/JASPAR R 10 0.4762 0.887 0.422 NA NA Total matches= 1

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

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

SIZF2:MA1405.1:JASPAR SIZF2/MA1405.1/JASPAR R 10 0.4762 0.887 0.422 NA NA

Total matches= 1

footprintDB-plants

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

columns aligned correlation cor swCGGwSrvySwcybtttCsm

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor ssaCaYGrtCrtssysstCgySbyskyb

Total matches= 0