peak-motifs W8/regulonW8.rm.fna

Sequence composition (test sequences)

Nb of peaks: 245
Total seq. size: 164 kb
Min length: 201 bp
Mean length: 667.927 bp
Max length: 701 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: 34310
Total seq. size: 22214 kb
Min length: 201 bp
Mean length: 647.449 bp
Max length: 701 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

Motif 1 oligos_5-7nt_m1oligos_5-7nt_m1

k-mer sig=4.14; evalue=7.2e-05

sdcTCGCACGGryb

VRYCCGTGCGAGHS

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

footDB

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

columns aligned correlation cor sdcTCGCACGGryb

VND3:UP00579A_1:UniPROBE VND3/UP00579A_1/UniPROBE D 10 0.6250 0.707 0.442 NA NA

At3g54990:M07165:TRANSFAC At3g54990/M07165/TRANSFAC D 8 0.5714 0.725 0.414 NA NA

BZR1:M01156:TRANSFAC BZR1/M01156/TRANSFAC R 6 0.4286 0.959 0.411 NA NA

Total matches= 5 (2 more)

[ match table: html text ]
[ alignments (logos): html text ]

Motif 2 oligos_5-7nt_m2oligos_5-7nt_m2

k-mer sig=4.14; evalue=7.2e-05

yrCTCGCACACGGakr

YMTCCGTGTGCGAGYR

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

footDB

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

columns aligned correlation cor yrCTCGCACACGGakr

CMTA2:M08084:TRANSFAC CMTA2/M08084/TRANSFAC R 9 0.5625 0.819 0.461 NA NA

AT5G64220:M0582_1.02:CISBP AT5G64220/M0582_1.02/CISBP R 9 0.5625 0.819 0.461 NA NA

ANAC55:M07580:TRANSFAC ANAC55/M07580/TRANSFAC D 10 0.6250 0.710 0.444 NA NA

Total matches= 7 (4 more)

[ match table: html text ]
[ alignments (logos): html text ]

Motif 3 oligos_5-7nt_m3oligos_5-7nt_m3

k-mer sig=2.42; evalue=0.0038

scAGGCAGGCAgs

SCTGCCTGCCTGS

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

footDB

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

columns aligned correlation cor scAGGCAGGCAgs

LEC2:M0146_1.02:CISBP LEC2/M0146_1.02/CISBP R 8 0.6154 0.776 0.477 NA NA

FUS3:FUS3:Athamap FUS3/FUS3/Athamap D 8 0.6154 0.734 0.451 NA NA

MADS3:M05222:TRANSFAC MADS3/M05222/TRANSFAC R 13 0.6190 0.704 0.436 NA NA

Total matches= 4 (1 more)

[ match table: html text ]
[ alignments (logos): html text ]

Motif 4 oligos_5-7nt_m4oligos_5-7nt_m4

k-mer sig=2.23; evalue=0.0059

svCTCGCTCGsy

RSCGAGCGAGBS

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

footDB

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

columns aligned correlation cor svCTCGCTCGsy

EDF3:M03186:TRANSFAC EDF3/M03186/TRANSFAC R 10 0.8333 0.707 0.589 NA NA

EDF3:M05120:TRANSFAC EDF3/M05120/TRANSFAC R 9 0.7500 0.743 0.558 NA NA

RAV2:M04996:TRANSFAC RAV2/M04996/TRANSFAC R 9 0.7500 0.727 0.545 NA NA

Total matches= 4 (1 more)

[ match table: html text ]
[ alignments (logos): html text ]

Motif 5 oligos_5-7nt_m5oligos_5-7nt_m5

k-mer sig=2.01; evalue=0.0098

grAACGGArr

YYTCCGTTYC

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

footDB

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

columns aligned correlation cor grAACGGArr

At3g01140:M05083:TRANSFAC At3g01140/M05083/TRANSFAC D 10 0.9091 0.758 0.689 NA NA

MYB119:MA1176.1:JASPAR MYB119/MA1176.1/JASPAR R 10 0.9091 0.747 0.679 NA NA

MYB119:M09285:TRANSFAC MYB119/M09285/TRANSFAC R 10 0.9091 0.747 0.679 NA NA

Total matches= 50 (47 more)

[ match table: html text ]
[ alignments (logos): html text ]

Motif 6 dyads_test_vs_ctrl_m1dyads_test_vs_ctrl_m1

k-mer sig=1.65; evalue=0.022

crCACACGsrs

SYSCGTGTGYG

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

footDB

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

columns aligned correlation cor crCACACGsrs

fgenesh1_pg.C_Chr_14.0001000151:M0253_1.02:CISBP fgenesh1_pg.C_Chr_14.0001000151/M0253_1.02/CISBP R 10 0.9091 0.818 0.743 NA NA

FHY3:M07169:TRANSFAC FHY3/M07169/TRANSFAC D 11 0.9167 0.726 0.666 NA NA

At4g36780:M09110:TRANSFAC At4g36780/M09110/TRANSFAC D 10 0.8333 0.774 0.645 NA NA

Total matches= 96 (93 more)

[ match table: html text ]
[ alignments (logos): html text ]

Motif 7 dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2

k-mer sig=1.63; evalue=0.023

gsAGGCAGgs

SCCTGCCTSC

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

footDB

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

columns aligned correlation cor gsAGGCAGgs

NAC_domain-containing_protein_19:3swm_B:3D-footprint NAC_domain-containing_protein_19/3swm_B/3D-footprint R 6 0.6000 0.745 0.447 NA NA

Total matches= 1

[ match table: html text ]
[ alignments (logos): html text ]

Motif 8 dyads_test_vs_ctrl_m3dyads_test_vs_ctrl_m3

k-mer sig=1.65; evalue=0.022

rrCGTskscsdssbdsbbsCACss

SSGTGSVVSHVSSHSGSMSACGYY

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

footDB

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

columns aligned correlation cor rrCGTskscsdssbdsbbsCACss

ABF1:M07182:TRANSFAC ABF1/M07182/TRANSFAC D 16 0.5926 0.704 0.417 NA NA

Total matches= 1

[ match table: html text ]
[ alignments (logos): html text ]

Motif 9 dyads_test_vs_ctrl_m4dyads_test_vs_ctrl_m4

k-mer sig=1.65; evalue=0.022

krACGksbvkbgrhrskbGcCACgc

GCGTGGCVMSYDYCVMBVSMCGTYM

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

footDB

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

columns aligned correlation cor krACGksbvkbgrhrskbGcCACgc

Total matches= 0

No match

Motif 10 dyads_test_vs_ctrl_m5dyads_test_vs_ctrl_m5

k-mer sig=1.65; evalue=0.022

ccACCkksbgvssgkbsryrcCACAbv

BVTGTGGYRYSVMCSSBCVSMMGGTGG

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

footDB

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

columns aligned correlation cor ccACCkksbgvssgkbsryrcCACAbv

Total matches= 0

No match

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 footDB 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]

Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J. (2012). RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res 40(4): e31.
Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J. (2012). A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat Protoc 7(8): 1551-1568.

RSAT - peak-motifs result

Analysis: W8/regulonW8.rm.fna (18/02/2021 12:56)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

footDB

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

columns aligned correlation cor gsAGGCAGgs

NAC_domain-containing_protein_19:3swm_B:3D-footprint NAC_domain-containing_protein_19/3swm_B/3D-footprint R 6 0.6000 0.745 0.447 NA NA

Total matches= 1

footDB

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

columns aligned correlation cor rrCGTskscsdssbdsbbsCACss

ABF1:M07182:TRANSFAC ABF1/M07182/TRANSFAC D 16 0.5926 0.704 0.417 NA NA

Total matches= 1

footDB

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

columns aligned correlation cor krACGksbvkbgrhrskbGcCACgc

Total matches= 0

footDB

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

columns aligned correlation cor ccACCkksbgvssgkbsryrcCACAbv

Total matches= 0

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: W8/regulonW8.rm.fna (18/02/2021 12:56)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

footDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor gsAGGCAGgs NAC_domain-containing_protein_19:3swm_B:3D-footprint NAC_domain-containing_protein_19/3swm_B/3D-footprint R 6 0.6000 0.745 0.447 NA NA Total matches= 1

footDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor rrCGTskscsdssbdsbbsCACss ABF1:M07182:TRANSFAC ABF1/M07182/TRANSFAC D 16 0.5926 0.704 0.417 NA NA Total matches= 1

footDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor krACGksbvkbgrhrskbGcCACgc Total matches= 0

footDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor ccACCkksbgvssgkbsryrcCACAbv Total matches= 0

Motif comparisons

Logs and parameter files

Publications

Results

footDB

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

columns aligned correlation cor gsAGGCAGgs

NAC_domain-containing_protein_19:3swm_B:3D-footprint NAC_domain-containing_protein_19/3swm_B/3D-footprint R 6 0.6000 0.745 0.447 NA NA

Total matches= 1

footDB

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

columns aligned correlation cor rrCGTskscsdssbdsbbsCACss

ABF1:M07182:TRANSFAC ABF1/M07182/TRANSFAC D 16 0.5926 0.704 0.417 NA NA

Total matches= 1

footDB

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

columns aligned correlation cor krACGksbvkbgrhrskbGcCACgc

Total matches= 0

footDB

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

columns aligned correlation cor ccACCkksbgvssgkbsryrcCACAbv

Total matches= 0