peak-motifs MEsalmon4_Up2

Sequence composition (test sequences)

Nb of peaks: 518
Total seq. size: 657 kb
Min length: 2 bp
Mean length: 1267.77 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: tacata (sig=0.69; e-value=0.2)	RC: tatgta
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

oligos_7nt_test_vs_ctrl_m1	assembly: tatgtaa (sig=0.81; e-value=0.15)	RC: ttacata
oligos_7nt_test_vs_ctrl_m2	assembly: ggcgtca (sig=0.20; e-value=0.63)	RC: tgacgcc
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

Not a single significant pattern

[oligos_8nt_test_vs_ctrl]

dyads_test_vs_ctrl

dyads_test_vs_ctrl_m1	assembly: catnnnnnnnnnnnnnntag (sig=1.09; e-value=0.081)	RC: ctannnnnnnnnnnnnnatg
dyads_test_vs_ctrl_m2	assembly: agtnnnnnnnnnnnnnncta (sig=0.47; e-value=0.34)	RC: tagnnnnnnnnnnnnnnact
dyads_test_vs_ctrl_m3	assembly: gtannnnnnnnnnntta (sig=0.47; e-value=0.34)	RC: taannnnnnnnnnntac
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=0.69; evalue=0.2

gtTACATAww

WWTATGTAAC

[ 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 gtTACATAww

ANAC55:ANAC55_2:ArabidopsisPBM ANAC55/ANAC55_2/ArabidopsisPBM R 10 1.0000 0.707 0.707 NA NA

AT3G49930:UN0355.1:JASPAR AT3G49930/UN0355.1/JASPAR D 10 0.9091 0.734 0.667 NA NA

TRANSCRIPTION:1qn7_B:3D-footprint TRANSCRIPTION/1qn7_B/3D-footprint R 8 0.8000 0.700 0.560 NA NA

Total matches= 21 (18 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: 78 (15.06%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr13g0302751)
Mean nb of predicted sites per peak: 1.12

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

Motif 2 oligos_7nt_test_vs_ctrl_m1

k-mer sig=0.81; evalue=0.15

mmTAtGTAAsk

MSTTACATAKK

[ 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 mmTAtGTAAsk

ANAC55:ANAC55_2:ArabidopsisPBM ANAC55/ANAC55_2/ArabidopsisPBM R 10 0.9091 0.756 0.687 NA NA

e_gw1.327.11.1:M1415_1.02:CISBP e_gw1.327.11.1/M1415_1.02/CISBP D 10 0.9091 0.753 0.685 NA NA

NAC083:MA1043.1:JASPAR NAC083/MA1043.1/JASPAR D 10 0.9091 0.707 0.642 NA NA

Total matches= 31 (28 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: 144 (27.80%)
Max nb of predicted sites per peak: 4
(gene-Lalb_Chr12g0207721)
Mean nb of predicted sites per peak: 1.28

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

Motif 3 oligos_7nt_test_vs_ctrl_m2

k-mer sig=0.20; evalue=0.63

kkGGCGtCamg

CKTGACGCCMM

[ 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 kkGGCGtCamg

TGA7:MA1070.1:JASPAR TGA7/MA1070.1/JASPAR R 10 0.9091 0.794 0.722 NA NA

AT1G77920:M0259_1.02:CISBP AT1G77920/M0259_1.02/CISBP R 10 0.9091 0.793 0.721 NA NA

GRMZM2G087741:M1210_1.02:CISBP GRMZM2G087741/M1210_1.02/CISBP R 10 0.9091 0.780 0.710 NA NA

Total matches= 85 (82 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 (12.36%)
Max nb of predicted sites per peak: 3
(gene-Lalb_Chr17g0335621)
Mean nb of predicted sites per peak: 1.22

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

Motif 4 dyads_test_vs_ctrl_m1

k-mer sig=1.09; evalue=0.081

wwCatrshrtwbwwkktrttaGtg

CACTAAYAMMWWVWAYDSYATGWW

[ 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 wwCatrshrtwbwwkktrttaGtg

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: 54 (10.42%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr07g0188431)
Mean nb of predicted sites per peak: 1.04

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

Motif 5 dyads_test_vs_ctrl_m2

k-mer sig=0.47; evalue=0.34

sdaGtamwGtwytCwwkwtCtagy

RCTAGAWMWWGARWACWKTACTHS

[ 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 sdaGtamwGtwytCwwkwtCtagy

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: 54 (10.42%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr15g0084161)
Mean nb of predicted sites per peak: 1.04

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

Motif 6 dyads_test_vs_ctrl_m3

k-mer sig=0.47; evalue=0.34

dwGTAvwrtwbtmkysttakw

WMTAASRMKAVWAYWBTACWH

[ 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 dwGTAvwrtwbtmkysttakw

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 (9.65%)
Max nb of predicted sites per peak: 2
(gene-Lalb_Chr14g0365631)
Mean nb of predicted sites per peak: 1.10

[ 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_Up2_W1 (26/05/2025 03:59)

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 wwCatrshrtwbwwkktrttaGtg

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor sdaGtamwGtwytCwwkwtCtagy

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor dwGTAvwrtwbtmkysttakw

Total matches= 0

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: MEsalmon4_Up2_W1 (26/05/2025 03:59)

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 wwCatrshrtwbwwkktrttaGtg Total matches= 0

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

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

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor sdaGtamwGtwytCwwkwtCtagy

Total matches= 0

footprintDB-plants

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

columns aligned correlation cor dwGTAvwrtwbtmkysttakw

Total matches= 0