peak-motifs W7/regulonW7.rm.fna

Sequence composition (test sequences)

Nb of peaks: 314
Total seq. size: 203 kb
Min length: 201 bp
Mean length: 646.873 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=6.13; evalue=7.4e-07

mmsGGTCAAACGyr

YRCGTTTGACCSKK

[ 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 mmsGGTCAAACGyr

WRKY1:UP00582A_2:UniPROBE WRKY1/UP00582A_2/UniPROBE R 13 0.9286 0.752 0.698 NA NA

0700010421:M1703_1.02:CISBP 0700010421/M1703_1.02/CISBP D 13 0.9286 0.733 0.681 NA NA

WRKY20:MA1295.1:JASPAR WRKY20/MA1295.1/JASPAR R 13 0.9286 0.725 0.673 NA NA

Total matches= 75 (72 more)

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

Motif 2 oligos_5-7nt_m2oligos_5-7nt_m2

k-mer sig=3.60; evalue=0.00025

waTAAAAGgak

MTCCTTTTATW

[ 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 waTAAAAGgak

PBF:M00355:TRANSFAC PBF/M00355/TRANSFAC D 11 1.0000 0.799 0.799 NA NA

Dof:M01136:TRANSFAC Dof/M01136/TRANSFAC D 11 1.0000 0.779 0.779 NA NA

Dof2:M00353:TRANSFAC Dof2/M00353/TRANSFAC D 11 1.0000 0.778 0.778 NA NA

Total matches= 92 (89 more)

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

Motif 3 oligos_5-7nt_m3oligos_5-7nt_m3

k-mer sig=2.04; evalue=0.0091

grrGCACGTGGAss

SSTCCACGTGCYYC

[ 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 grrGCACGTGGAss

BZR1:M07162:TRANSFAC BZR1/M07162/TRANSFAC R 14 1.0000 0.759 0.759 NA NA

ABZ1:M01065:TRANSFAC ABZ1/M01065/TRANSFAC D 14 1.0000 0.727 0.727 NA NA

HBI1:M08128:TRANSFAC HBI1/M08128/TRANSFAC D 12 0.8571 0.839 0.719 NA NA

Total matches= 145 (142 more)

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

Motif 4 oligos_5-7nt_m4oligos_5-7nt_m4

k-mer sig=1.90; evalue=0.013

rrCGGAAGGrr

YYCCTTCCGYY

[ 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 rrCGGAAGGrr

FLORICAULALEAFY_HOMOLOG_1:4bhk_A:3D-footprint FLORICAULALEAFY_HOMOLOG_1/4bhk_A/3D-footprint D 7 0.6364 0.709 0.451 NA NA

ARF3:MA1009.1:JASPAR ARF3/MA1009.1/JASPAR D 7 0.5833 0.755 0.441 NA NA

ATERF10:M05168:TRANSFAC ATERF10/M05168/TRANSFAC R 8 0.6154 0.711 0.437 NA NA

Total matches= 5 (2 more)

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

Motif 5 oligos_5-7nt_m5oligos_5-7nt_m5

k-mer sig=1.38; evalue=0.042

kcCGCAGCCgs

SCGGCTGCGGM

[ 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 kcCGCAGCCgs

ERF1:ERF1:ArabidopsisPBM ERF1/ERF1/ArabidopsisPBM D 10 0.9091 0.766 0.696 NA NA

RAP2.6:RAP2.6:ArabidopsisPBM RAP2.6/RAP2.6/ArabidopsisPBM D 10 0.9091 0.762 0.693 NA NA

RAP2-6:M07520:TRANSFAC RAP2-6/M07520/TRANSFAC D 10 0.9091 0.759 0.690 NA NA

Total matches= 124 (121 more)

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

Motif 6 dyads_test_vs_ctrl_m1dyads_test_vs_ctrl_m1

k-mer sig=2.84; evalue=0.0014

ytGGTCAAAsw

WSTTTGACCAR

[ 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 ytGGTCAAAsw

WRKY60:M08171:TRANSFAC WRKY60/M08171/TRANSFAC D 11 1.0000 0.890 0.890 NA NA

WRKY60:M1684_1.02:CISBP WRKY60/M1684_1.02/CISBP D 11 1.0000 0.888 0.888 NA NA

WRKY18:M1694_1.02:CISBP WRKY18/M1694_1.02/CISBP D 10 0.9091 0.871 0.792 NA NA

Total matches= 110 (107 more)

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

Motif 7 dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2

k-mer sig=2.84; evalue=0.0014

gdCGTykrmsrrgmykkmwasGGACrg

CYGTCCSTWKMMRKCYYSKYMRACGHC

[ 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 gdCGTykrmsrrgmykkmwasGGACrg

Total matches= 0

No match

Motif 8 dyads_test_vs_ctrl_m3dyads_test_vs_ctrl_m3

k-mer sig=2.84; evalue=0.0014

vrAAAbryrrmkkwydkwvdbkACGkr

YMCGTMVHBWMHRWMMKYYRYVTTTYB

[ 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 vrAAAbryrrmkkwydkwvdbkACGkr

OBP3.ampDAP:M0274:AthalianaCistrome OBP3.ampDAP/M0274/AthalianaCistrome R 18 0.6429 0.709 0.455 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=2.84; evalue=0.0014

raGTCwwwrwsvgrkgkwmdykwCGAcw

WGTCGWMRHKWMCMYCBSWYWWWGACTY

[ 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 raGTCwwwrwsvgrkgkwmdykwCGAcw

Total matches= 0

No match

Motif 10 dyads_test_vs_ctrl_m5dyads_test_vs_ctrl_m5

k-mer sig=2.84; evalue=0.0014

abTCCdktrrrrdargkwmwhktAAAwt

AWTTTAMDWKWMCYTHYYYYAMHGGAVT

[ 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 abTCCdktrrrrdargkwmwhktAAAwt

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: W7/regulonW7.rm.fna (18/02/2021 12:34)

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 gdCGTykrmsrrgmykkmwasGGACrg

Total matches= 0

footDB

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

columns aligned correlation cor vrAAAbryrrmkkwydkwvdbkACGkr

OBP3.ampDAP:M0274:AthalianaCistrome OBP3.ampDAP/M0274/AthalianaCistrome R 18 0.6429 0.709 0.455 NA NA

Total matches= 1

footDB

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

columns aligned correlation cor raGTCwwwrwsvgrkgkwmdykwCGAcw

Total matches= 0

footDB

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

columns aligned correlation cor abTCCdktrrrrdargkwmwhktAAAwt

Total matches= 0

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: W7/regulonW7.rm.fna (18/02/2021 12:34)

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 gdCGTykrmsrrgmykkmwasGGACrg Total matches= 0

footDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor vrAAAbryrrmkkwydkwvdbkACGkr OBP3.ampDAP:M0274:AthalianaCistrome OBP3.ampDAP/M0274/AthalianaCistrome R 18 0.6429 0.709 0.455 NA NA Total matches= 1

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

footDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor abTCCdktrrrrdargkwmwhktAAAwt 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 gdCGTykrmsrrgmykkmwasGGACrg

Total matches= 0

footDB

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

columns aligned correlation cor vrAAAbryrrmkkwydkwvdbkACGkr

OBP3.ampDAP:M0274:AthalianaCistrome OBP3.ampDAP/M0274/AthalianaCistrome R 18 0.6429 0.709 0.455 NA NA

Total matches= 1

footDB

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

columns aligned correlation cor raGTCwwwrwsvgrkgkwmdykwCGAcw

Total matches= 0

footDB

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

columns aligned correlation cor abTCCdktrrrrdargkwmwhktAAAwt

Total matches= 0