peak-motifs D6/regulonD6.rm.fna

Sequence composition (test sequences)

Nb of peaks: 95
Total seq. size: 62 kb
Min length: 201 bp
Mean length: 654.147 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=1.30; evalue=0.05

wrCACACAvs

SBTGTGTGYW

[ 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 wrCACACAvs

CONS_ARATH:CONS2:EEADannot CONS_ARATH/CONS2/EEADannot R 8 0.6667 0.726 0.484 NA NA

CONS_ARATH:CONS1:EEADannot CONS_ARATH/CONS1/EEADannot R 6 0.4615 0.992 0.458 NA NA

Transcription_factor_MYC2:5gnj_I:3D-footprint Transcription_factor_MYC2/5gnj_I/3D-footprint D 5 0.5000 0.877 0.439 NA NA

Total matches= 4 (1 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

tdCTACTAsw

WSTAGTAGHA

[ 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 tdCTACTAsw

At3g60580:M09157:TRANSFAC At3g60580/M09157/TRANSFAC R 8 0.8000 0.887 0.709 NA NA

At3g60580.DAP:M0307:AthalianaCistrome At3g60580.DAP/M0307/AthalianaCistrome R 8 0.8000 0.885 0.708 NA NA

AtMYB116_II:AtMYB116_II:AthaMYB AtMYB116_II/AtMYB116_II/AthaMYB R 7 0.6364 0.844 0.537 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=0.90; evalue=0.13

vwTCACGTGAwk

MWTCACGTGAWB

[ 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 vwTCACGTGAwk

ABF4:M09561:TRANSFAC ABF4/M09561/TRANSFAC R 12 1.0000 0.783 0.783 NA NA

fgenesh1_pg.scaffold_37000071:M0251_1.02:CISBP fgenesh1_pg.scaffold_37000071/M0251_1.02/CISBP D 10 0.8333 0.916 0.764 NA NA

LOC_Os02g49560:M0327_1.02:CISBP LOC_Os02g49560/M0327_1.02/CISBP R 11 0.9167 0.833 0.763 NA NA

Total matches= 151 (148 more)

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

Motif 4 oligos_5-7nt_m4oligos_5-7nt_m4

k-mer sig=0.79; evalue=0.16

amTCACGAGmh

DKCTCGTGAKT

[ 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 amTCACGAGmh

BIM1:M0163_1.02:CISBP BIM1/M0163_1.02/CISBP R 10 0.9091 0.775 0.705 NA NA

BIM1:M08080:TRANSFAC BIM1/M08080/TRANSFAC R 10 0.9091 0.773 0.703 NA NA

fgenesh1_pg.scaffold_37000071:M0251_1.02:CISBP fgenesh1_pg.scaffold_37000071/M0251_1.02/CISBP D 10 0.9091 0.732 0.665 NA NA

Total matches= 45 (42 more)

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

Motif 5 oligos_5-7nt_m5oligos_5-7nt_m5

k-mer sig=1.09; evalue=0.081

twcTACTACArs

SYTGTAGTAGWA

[ 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 twcTACTACArs

At3g60580:M09157:TRANSFAC At3g60580/M09157/TRANSFAC R 8 0.6667 0.858 0.572 NA NA

At3g60580.DAP:M0307:AthalianaCistrome At3g60580.DAP/M0307/AthalianaCistrome R 8 0.6667 0.857 0.571 NA NA

AZF2:M05153:TRANSFAC AZF2/M05153/TRANSFAC R 10 0.7143 0.735 0.525 NA NA

Total matches= 11 (8 more)

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

Motif 6 dyads_test_vs_ctrl_m1dyads_test_vs_ctrl_m1

k-mer sig=2.62; evalue=0.0024

wsCACAmawCACwh

DWGTGWTKTGTGSW

[ 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 wsCACAmawCACwh

CONS_ARATH:CONS1:EEADannot CONS_ARATH/CONS1/EEADannot R 9 0.6429 0.858 0.551 NA NA

CONS_ARATH:NF_CO:EEADannot CONS_ARATH/NF_CO/EEADannot D 8 0.5714 0.787 0.450 NA NA

STZ.ampDAP:M0304:AthalianaCistrome STZ.ampDAP/M0304/AthalianaCistrome D 8 0.5714 0.756 0.432 NA NA

Total matches= 5 (2 more)

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

Motif 7 dyads_test_vs_ctrl_m2dyads_test_vs_ctrl_m2

k-mer sig=2.23; evalue=0.0059

mcACGTkrtaCACgw

WCGTGTAYMACGTGK

[ 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 mcACGTkrtaCACgw

bHLH18:M09504:TRANSFAC bHLH18/M09504/TRANSFAC R 15 0.8824 0.819 0.723 NA NA

bHLH18:MA1361.1:JASPAR bHLH18/MA1361.1/JASPAR R 15 0.8824 0.819 0.722 NA NA

BZIP17:M0263_1.02:CISBP BZIP17/M0263_1.02/CISBP R 10 0.6667 0.860 0.573 NA NA

Total matches= 128 (125 more)

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

Motif 8 dyads_test_vs_ctrl_m3dyads_test_vs_ctrl_m3

k-mer sig=2.62; evalue=0.0024

swACGarmtkysmmykwysAATtw

WAATTSRWMRKKSRMAKYTCGTWS

[ 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 swACGarmtkysmmykwysAATtw

Total matches= 0

No match

Motif 9 dyads_test_vs_ctrl_m4dyads_test_vs_ctrl_m4

k-mer sig=2.62; evalue=0.0024

twCAYRTGwCAbRTGKktktrYkktk

MAMMRYAMAMMCAYVTGWCAYRTGWA

[ 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 twCAYRTGwCAbRTGKktktrYkktk

Total matches= 0

No match

Motif 10 dyads_test_vs_ctrl_m5dyads_test_vs_ctrl_m5

k-mer sig=2.62; evalue=0.0024

waTgCryGgwbyryrygkdtwtAaaw

WTTTAWAHMCRYRYRVWCCRYGCATW

[ 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 waTgCryGgwbyryrygkdtwtAaaw

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: D6/regulonD6.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 swACGarmtkysmmykwysAATtw

Total matches= 0

footDB

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

columns aligned correlation cor twCAYRTGwCAbRTGKktktrYkktk

Total matches= 0

footDB

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

columns aligned correlation cor waTgCryGgwbyryrygkdtwtAaaw

Total matches= 0

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: D6/regulonD6.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 swACGarmtkysmmykwysAATtw Total matches= 0

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

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

Total matches= 0

footDB

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

columns aligned correlation cor twCAYRTGwCAbRTGKktktrYkktk

Total matches= 0

footDB

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

columns aligned correlation cor waTgCryGgwbyryrygkdtwtAaaw

Total matches= 0