peak-motifs W12/regulonW12.rm.fna

Sequence composition (test sequences)

Nb of peaks: 51
Total seq. size: 34 kb
Min length: 201 bp
Mean length: 661.078 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=3.07; evalue=0.00085

tmTAAATATTTAka

TMTAAATATTTAKA

[ 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 tmTAAATATTTAka

RVE1:M09349:TRANSFAC RVE1/M09349/TRANSFAC D 13 0.8667 0.702 0.608 NA NA

RVE1:MA1184.1:JASPAR RVE1/MA1184.1/JASPAR D 13 0.8667 0.701 0.608 NA NA

LCL1.ampDAP:M0611:AthalianaCistrome LCL1.ampDAP/M0611/AthalianaCistrome R 11 0.7857 0.757 0.595 NA NA

Total matches= 39 (36 more)

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

Motif 2 oligos_5-7nt_m2oligos_5-7nt_m2

k-mer sig=1.09; evalue=0.081

amTATCCATrg

CYATGGATAKT

[ 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 amTATCCATrg

AT1G19000:M1318_1.02:CISBP AT1G19000/M1318_1.02/CISBP R 10 0.9091 0.773 0.703 NA NA

AT3G16350:M09552:TRANSFAC AT3G16350/M09552/TRANSFAC D 10 0.9091 0.767 0.697 NA NA

PK00738.1:M1302_1.02:CISBP PK00738.1/M1302_1.02/CISBP R 10 0.9091 0.761 0.692 NA NA

Total matches= 51 (48 more)

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

Motif 3 oligos_5-7nt_m3oligos_5-7nt_m3

k-mer sig=3.07; evalue=0.00085

akCAATATTTAtr

YATAAATATTGMT

[ 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 akCAATATTTAtr

HAT5.ampDAP:M0441:AthalianaCistrome HAT5.ampDAP/M0441/AthalianaCistrome D 13 0.9286 0.710 0.659 NA NA

ATHB53:M09225:TRANSFAC ATHB53/M09225/TRANSFAC D 11 0.8462 0.708 0.599 NA NA

ATHB20:M09243:TRANSFAC ATHB20/M09243/TRANSFAC D 11 0.8462 0.707 0.599 NA NA

Total matches= 26 (23 more)

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

Motif 4 oligos_5-7nt_m4oligos_5-7nt_m4

k-mer sig=3.07; evalue=0.00085

krTAAATAcKwa

TWMGTATTTAYM

[ 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 krTAAATAcKwa

At4g04450:M05157:TRANSFAC At4g04450/M05157/TRANSFAC R 8 0.6154 0.846 0.521 NA NA

LOC_Os02g01380:M1284_1.02:CISBP LOC_Os02g01380/M1284_1.02/CISBP R 9 0.6923 0.713 0.493 NA NA

TRANSCRIPTION_INITIATION_FACTOR_TFIID-1:1qnb_B:3D-footprint TRANSCRIPTION_INITIATION_FACTOR_TFIID-1/1qnb_B/3D-footprint D 8 0.6667 0.740 0.493 NA NA

Total matches= 24 (21 more)

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

Motif 5 oligos_5-7nt_m5oligos_5-7nt_m5

k-mer sig=0.24; evalue=0.58

msATGACGAmg

CKTCGTCATSK

[ 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 msATGACGAmg

TGA1:M07200:TRANSFAC TGA1/M07200/TRANSFAC D 11 1.0000 0.721 0.721 NA NA

TGA1:TGA1:Athamap TGA1/TGA1/Athamap D 11 0.9167 0.772 0.708 NA NA

TGA1:M0273_1.02:CISBP TGA1/M0273_1.02/CISBP D 10 0.9091 0.771 0.701 NA NA

Total matches= 26 (23 more)

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

Motif 6 dyads_test_vs_ctrl_m1dyads_test_vs_ctrl_m1

k-mer sig=2.67; evalue=0.0021

gmRATAKSgATrAATATAtg

CATATATTYATCSMTATYKC

[ 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 gmRATAKSgATrAATATAtg

At5g65330:M05264:TRANSFAC At5g65330/M05264/TRANSFAC D 11 0.5500 0.744 0.409 NA NA

RVE1:RVE1_2:ArabidopsisPBM RVE1/RVE1_2/ArabidopsisPBM D 10 0.5000 0.817 0.409 NA NA

EPR1.ampDAP:M0582:AthalianaCistrome EPR1.ampDAP/M0582/AthalianaCistrome D 11 0.5500 0.740 0.407 NA NA

Total matches= 8 (5 more)

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

Motif 7 dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2

k-mer sig=1.42; evalue=0.038

TyCGTAksCATAsys

SRSTATGSMTACGRA

[ 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 TyCGTAksCATAsys

Total matches= 0

No match

Motif 8 dyads_test_vs_ctrl_m3dyads_test_vs_ctrl_m3

k-mer sig=2.67; evalue=0.0021

rkATATydATwwAwAwTadww

WWHTAWTWTWWATHRATATMY

[ 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 rkATATydATwwAwAwTadww

ATHB22:M0844_1.02:CISBP ATHB22/M0844_1.02/CISBP R 13 0.6190 0.719 0.445 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=2.67; evalue=0.0021

tyTATatwTwwATataakATAwk

MWTATMTTATATWWAWATATARA

[ 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 tyTATatwTwwATataakATAwk

At1g76110.ampDAP:M0145:AthalianaCistrome At1g76110.ampDAP/M0145/AthalianaCistrome R 15 0.6522 0.702 0.458 NA NA

Total matches= 1

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

Motif 10 dyads_test_vs_ctrl_m5dyads_test_vs_ctrl_m5

k-mer sig=2.67; evalue=0.0021

tkTATmwAtrwATrtrwdATAtkkATrrr

YYYATMMATATHWYAYATWYATWKATAMA

[ 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 tkTATmwAtrwATrtrwdATAtkkATrrr

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: W12/regulonW12.rm.fna (18/02/2021 13:54)

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 TyCGTAksCATAsys

Total matches= 0

footDB

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

columns aligned correlation cor rkATATydATwwAwAwTadww

ATHB22:M0844_1.02:CISBP ATHB22/M0844_1.02/CISBP R 13 0.6190 0.719 0.445 NA NA

Total matches= 1

footDB

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

columns aligned correlation cor tyTATatwTwwATataakATAwk

At1g76110.ampDAP:M0145:AthalianaCistrome At1g76110.ampDAP/M0145/AthalianaCistrome R 15 0.6522 0.702 0.458 NA NA

Total matches= 1

footDB

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

columns aligned correlation cor tkTATmwAtrwATrtrwdATAtkkATrrr

Total matches= 0

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: W12/regulonW12.rm.fna (18/02/2021 13:54)

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 TyCGTAksCATAsys Total matches= 0

footDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor rkATATydATwwAwAwTadww ATHB22:M0844_1.02:CISBP ATHB22/M0844_1.02/CISBP R 13 0.6190 0.719 0.445 NA NA Total matches= 1

footDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor tyTATatwTwwATataakATAwk At1g76110.ampDAP:M0145:AthalianaCistrome At1g76110.ampDAP/M0145/AthalianaCistrome R 15 0.6522 0.702 0.458 NA NA Total matches= 1

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

Total matches= 0

footDB

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

columns aligned correlation cor rkATATydATwwAwAwTadww

ATHB22:M0844_1.02:CISBP ATHB22/M0844_1.02/CISBP R 13 0.6190 0.719 0.445 NA NA

Total matches= 1

footDB

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

columns aligned correlation cor tyTATatwTwwATataakATAwk

At1g76110.ampDAP:M0145:AthalianaCistrome At1g76110.ampDAP/M0145/AthalianaCistrome R 15 0.6522 0.702 0.458 NA NA

Total matches= 1

footDB

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

columns aligned correlation cor tkTATmwAtrwATrtrwdATAtkkATrrr

Total matches= 0