peak-motifs D2/regulonD2.rm.fna

Sequence composition (test sequences)

Nb of peaks: 750
Total seq. size: 472 kb
Min length: 201 bp
Mean length: 629.172 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=5.31; evalue=4.9e-06

yaTgtGTGGATAAgATATgt

ACATATCTTATCCACACATR

[ 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 yaTgtGTGGATAAgATATgt

AT5G56840.ampDAP:M0583:AthalianaCistrome AT5G56840.ampDAP/M0583/AthalianaCistrome R 16 0.8000 0.760 0.608 NA NA

At5g47390:MA1398.1:JASPAR At5g47390/MA1398.1/JASPAR R 15 0.7500 0.777 0.583 NA NA

At5g47390:M09343:TRANSFAC At5g47390/M09343/TRANSFAC R 15 0.7500 0.775 0.582 NA NA

Total matches= 31 (28 more)

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

Motif 2 oligos_5-7nt_m2oligos_5-7nt_m2

k-mer sig=4.42; evalue=3.8e-05

ykTCTGyGGGCCCrCAGAmr

YKTCTGYGGGCCCRCAGAMR

[ 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 ykTCTGyGGGCCCrCAGAmr

TCP11:M01850:TRANSFAC TCP11/M01850/TRANSFAC D 12 0.6000 0.811 0.487 NA NA

PK14653.1:M1643_1.02:CISBP PK14653.1/M1643_1.02/CISBP D 10 0.5000 0.922 0.461 NA NA

At2g45680:M09587:TRANSFAC At2g45680/M09587/TRANSFAC R 11 0.5500 0.811 0.446 NA NA

Total matches= 21 (18 more)

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

Motif 3 oligos_5-7nt_m3oligos_5-7nt_m3

k-mer sig=4.42; evalue=3.8e-05

skCCTTATCCACACAyr

YRTGTGTGGATAAGGMS

[ 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 skCCTTATCCACACAyr

At1g49010.ampDAP:M0601:AthalianaCistrome At1g49010.ampDAP/M0601/AthalianaCistrome R 15 0.8824 0.704 0.621 NA NA

AT4G00250.DAP:M0403:AthalianaCistrome AT4G00250.DAP/M0403/AthalianaCistrome D 13 0.7647 0.812 0.621 NA NA

AT4G00250:M09219:TRANSFAC AT4G00250/M09219/TRANSFAC D 13 0.7647 0.811 0.620 NA NA

Total matches= 35 (32 more)

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

Motif 4 oligos_5-7nt_m4oligos_5-7nt_m4

k-mer sig=2.94; evalue=0.0011

svsCAGCCACGGCvs

SBGCCGTGGCTGSBS

[ 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 svsCAGCCACGGCvs

WRAF2:M04972:TRANSFAC WRAF2/M04972/TRANSFAC D 10 0.6667 0.758 0.505 NA NA

ERF112:M05000:TRANSFAC ERF112/M05000/TRANSFAC D 10 0.6667 0.752 0.501 NA NA

WRAF1:M04971:TRANSFAC WRAF1/M04971/TRANSFAC D 10 0.6667 0.740 0.493 NA NA

Total matches= 13 (10 more)

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

Motif 5 oligos_5-7nt_m5oligos_5-7nt_m5

k-mer sig=4.42; evalue=3.8e-05

cmrCACCACACAhv

BDTGTGTGGTGYKG

[ 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 cmrCACCACACAhv

CONS_ARATH:NF_CO:EEADannot CONS_ARATH/NF_CO/EEADannot D 8 0.5714 0.773 0.442 NA NA

_LEAFY:2vy2_A:3D-footprint _LEAFY/2vy2_A/3D-footprint R 8 0.5333 0.828 0.442 NA NA

_LEAFY:2vy1_A:3D-footprint _LEAFY/2vy1_A/3D-footprint R 8 0.5333 0.825 0.440 NA NA

Total matches= 6 (3 more)

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

Motif 6 dyads_test_vs_ctrl_m1dyads_test_vs_ctrl_m1

k-mer sig=6.24; evalue=5.8e-07

scCACCaCCCrc

GYGGGTGGTGGS

[ 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 scCACCaCCCrc

ABI4:ABI4:Athamap ABI4/ABI4/Athamap D 10 0.8333 0.837 0.697 NA NA

MYB83:M09319:TRANSFAC MYB83/M09319/TRANSFAC R 11 0.9167 0.756 0.693 NA NA

MYB83.DAP:M0565:AthalianaCistrome MYB83.DAP/M0565/AthalianaCistrome R 11 0.9167 0.755 0.692 NA NA

Total matches= 51 (48 more)

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

Motif 7 dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2

k-mer sig=4.06; evalue=8.7e-05

kyCTCbsscsGCCsc

GSGGCSGSSVGAGRM

[ 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 kyCTCbsscsGCCsc

ERF1:M0025_1.02:CISBP ERF1/M0025_1.02/CISBP D 10 0.6667 0.748 0.498 NA NA

At5g25190:M05067:TRANSFAC At5g25190/M05067/TRANSFAC D 10 0.6667 0.713 0.475 NA NA

At1g68550:M05105:TRANSFAC At1g68550/M05105/TRANSFAC D 10 0.6667 0.708 0.472 NA NA

Total matches= 15 (12 more)

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

Motif 8 dyads_test_vs_ctrl_m3dyads_test_vs_ctrl_m3

k-mer sig=6.24; evalue=5.8e-07

rwAAAbdkrwswskmswAATAwr

YWTATTWSKMSWSWYMHVTTTWY

[ 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 rwAAAbdkrwswskmswAATAwr

Total matches= 0

No match

Motif 9 dyads_test_vs_ctrl_m4dyads_test_vs_ctrl_m4

k-mer sig=6.24; evalue=5.8e-07

waAAAbrsawskskasdrrwdAAAww

WWTTTHWYYHSTMSMSWTSYVTTTTW

[ 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 waAAAbrsawskskasdrrwdAAAww

Total matches= 0

No match

Motif 10 dyads_test_vs_ctrl_m5dyads_test_vs_ctrl_m5

k-mer sig=6.24; evalue=5.8e-07

wrTAAkwvgwsyskavkdrwdTAAdw

WHTTAHWYHMBTMSRSWCBWMTTAYW

[ 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 wrTAAkwvgwsyskavkdrwdTAAdw

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: D2/regulonD2.rm.fna (25/02/2021 19:22)

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 rwAAAbdkrwswskmswAATAwr

Total matches= 0

footDB

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

columns aligned correlation cor waAAAbrsawskskasdrrwdAAAww

Total matches= 0

footDB

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

columns aligned correlation cor wrTAAkwvgwsyskavkdrwdTAAdw

Total matches= 0

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: D2/regulonD2.rm.fna (25/02/2021 19:22)

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 rwAAAbdkrwswskmswAATAwr Total matches= 0

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

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

Total matches= 0

footDB

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

columns aligned correlation cor waAAAbrsawskskasdrrwdAAAww

Total matches= 0

footDB

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

columns aligned correlation cor wrTAAkwvgwsyskavkdrwdTAAdw

Total matches= 0