peak-motifs D3/regulonD3.rm.fna

Sequence composition (test sequences)

Nb of peaks: 627
Total seq. size: 414 kb
Min length: 201 bp
Mean length: 660.15 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=16.53; evalue=3e-17

kkCCAAGTCmAwswyTTGGmA

TKCCAARWSWTKGACTTGGMM

[ 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 kkCCAAGTCmAwswyTTGGmA

Total matches= 0

No match

Motif 2 oligos_5-7nt_m2oligos_5-7nt_m2

k-mer sig=16.53; evalue=3e-17

srCGGGTCRRCGaCTTGGgC

GCCCAAGTCGYYGACCCGYS

[ 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 srCGGGTCRRCGaCTTGGgC

WRKY1:UP00582A_1:UniPROBE WRKY1/UP00582A_1/UniPROBE R 13 0.6500 0.723 0.470 NA NA

WRKY1:UP00582A_2:UniPROBE WRKY1/UP00582A_2/UniPROBE R 13 0.6500 0.717 0.466 NA NA

WRKY12:M07551:TRANSFAC WRKY12/M07551/TRANSFAC R 10 0.5000 0.857 0.428 NA NA

Total matches= 10 (7 more)

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

Motif 3 oligos_5-7nt_m3oligos_5-7nt_m3

k-mer sig=8.59; evalue=2.6e-09

dgdgtAaACGACTTGGks

SMCCAAGTCGTTTACHCH

[ 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 dgdgtAaACGACTTGGks

Myb-8:M05118:TRANSFAC Myb-8/M05118/TRANSFAC D 12 0.6667 0.739 0.493 NA NA

Myb-6:M05002:TRANSFAC Myb-6/M05002/TRANSFAC D 12 0.6667 0.739 0.493 NA NA

Total matches= 2

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

Motif 4 oligos_5-7nt_m4oligos_5-7nt_m4

k-mer sig=4.74; evalue=1.8e-05

dwAGAAAAAtrw

WYATTTTTCTWH

[ 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 dwAGAAAAAtrw

At3g13040:M09212:TRANSFAC At3g13040/M09212/TRANSFAC D 9 0.7500 0.771 0.578 NA NA

At3g13040.DAP:M0399:AthalianaCistrome At3g13040.DAP/M0399/AthalianaCistrome D 9 0.7500 0.771 0.578 NA NA

AT2G28810.ampDAP:M0245:AthalianaCistrome AT2G28810.ampDAP/M0245/AthalianaCistrome R 12 0.8000 0.705 0.564 NA NA

Total matches= 37 (34 more)

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

Motif 5 oligos_5-7nt_m5oligos_5-7nt_m5

k-mer sig=8.59; evalue=2.6e-09

ggsGAGaCGACTTGGmr

YKCCAAGTCGTCTCSCC

[ 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 ggsGAGaCGACTTGGmr

Total matches= 0

No match

Motif 6 dyads_test_vs_ctrl_m1dyads_test_vs_ctrl_m1

k-mer sig=9.40; evalue=4e-10

ckAGTCAACGtCryv

BRYGACGTTGACTMG

[ 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 ckAGTCAACGtCryv

WRKY47:MA1312.1:JASPAR WRKY47/MA1312.1/JASPAR R 14 0.9333 0.870 0.812 NA NA

WRKY47:M09478:TRANSFAC WRKY47/M09478/TRANSFAC R 14 0.9333 0.868 0.810 NA NA

VOZ2:UP00581A_2:UniPROBE VOZ2/UP00581A_2/UniPROBE D 13 0.8667 0.912 0.790 NA NA

Total matches= 166 (163 more)

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

Motif 7 dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2

k-mer sig=8.87; evalue=1.3e-09

gtCGGTCAACgk

MCGTTGACCGAC

[ 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 gtCGGTCAACgk

WRKY60:M08171:TRANSFAC WRKY60/M08171/TRANSFAC D 11 0.9167 0.957 0.877 NA NA

WRKY60:M1684_1.02:CISBP WRKY60/M1684_1.02/CISBP D 11 0.9167 0.957 0.877 NA NA

WRKY1:UP00582A_2:UniPROBE WRKY1/UP00582A_2/UniPROBE R 12 0.9231 0.926 0.855 NA NA

Total matches= 148 (145 more)

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

Motif 8 dyads_test_vs_ctrl_m3dyads_test_vs_ctrl_m3

k-mer sig=6.60; evalue=2.5e-07

khCAAGTCtws

SWAGACTTGDM

[ 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 khCAAGTCtws

bHLH130:M09502:TRANSFAC bHLH130/M09502/TRANSFAC R 11 1.0000 0.702 0.702 NA NA

bHLH130:MA1358.1:JASPAR bHLH130/MA1358.1/JASPAR R 11 1.0000 0.702 0.702 NA NA

bhlh112:M0229_1.02:CISBP bhlh112/M0229_1.02/CISBP R 9 0.8182 0.711 0.582 NA NA

Total matches= 19 (16 more)

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

Motif 9 dyads_test_vs_ctrl_m4dyads_test_vs_ctrl_m4

k-mer sig=3.95; evalue=0.00011

twGTCATTaGTChm

KDGACTAATGACWA

[ 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 twGTCATTaGTChm

ATHB33:M09492:TRANSFAC ATHB33/M09492/TRANSFAC D 11 0.7857 0.731 0.574 NA NA

ATHB33:MA1326.1:JASPAR ATHB33/MA1326.1/JASPAR D 11 0.7857 0.730 0.573 NA NA

HAHB-4:M00820:TRANSFAC HAHB-4/M00820/TRANSFAC R 9 0.6429 0.749 0.481 NA NA

Total matches= 12 (9 more)

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

Motif 10 dyads_test_vs_ctrl_m5dyads_test_vs_ctrl_m5

k-mer sig=3.08; evalue=0.00083

gsCGAGACGACTbg

CVAGTCGTCTCGSC

[ 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 gsCGAGACGACTbg

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: D3/regulonD3.rm.fna (25/02/2021 19:21)

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 kkCCAAGTCmAwswyTTGGmA

Total matches= 0

footDB

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

columns aligned correlation cor ggsGAGaCGACTTGGmr

Total matches= 0

footDB

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

columns aligned correlation cor gsCGAGACGACTbg

Total matches= 0

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: D3/regulonD3.rm.fna (25/02/2021 19:21)

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 kkCCAAGTCmAwswyTTGGmA Total matches= 0

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

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

Total matches= 0

footDB

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

columns aligned correlation cor ggsGAGaCGACTTGGmr

Total matches= 0

footDB

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

columns aligned correlation cor gsCGAGACGACTbg

Total matches= 0