peak-motifs motifs_DEGs_post-c_20250701

peak-motifs  -v 1 -title motifs_DEGs_post-c_20250701_01 -i $RSAT/public_html/tmp/www-data/2025/07/01/peak-motifs.2025-07-01.152913_2025-07-01.152913_ZlcJuL/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2025/07/01/peak-motifs.2025-07-01.152913_2025-07-01.152913_ZlcJuL/peak-motifscontrol_seq -markov auto -disco oligos,dyads -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -motif_db JASPAR2024_CORE_plants_non-redundant tf $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_plants_non-redundant_pfms_transfac.txt -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,motifs_vs_db,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2025/07/01/peak-motifs.2025-07-01.152913_2025-07-01.152913_ZlcJuL

Sequence composition (test sequences)

Nb of peaks: 226
Total seq. size: 142 kb
Min length: 46 bp
Mean length: 629.836 bp
Max length: 3000 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: 17602
Total seq. size: 9502 kb
Min length: 1 bp
Mean length: 539.814 bp
Max length: 3000 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

oligos_6nt_test_vs_ctrl

oligos_6nt_test_vs_ctrl_m1	assembly: acaacc (sig=0.14; e-value=0.72)	RC: ggttgt
oligos_6nt_test_vs_ctrl_m2	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m3	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m4	: (sig=; e-value=1)	RC:
oligos_6nt_test_vs_ctrl_m5	: (sig=; e-value=1)	RC:

[ discovered words: text ]
[ assembly: text sig matrices ]
[ matrices: tab format transfac format ]

oligos_7nt_test_vs_ctrl

oligos_7nt_test_vs_ctrl_m1	assembly: cgcgacg (sig=0.14; e-value=0.72)	RC: cgtcgcg
oligos_7nt_test_vs_ctrl_m2	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m3	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m4	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m5	: (sig=; e-value=1)	RC:

[ discovered words: text ]
[ assembly: text sig matrices ]
[ matrices: tab format transfac format ]

dyads_test_vs_ctrl

dyads_test_vs_ctrl_m1	assembly: taannnnnnnnnnncga (sig=1.35; e-value=0.045)	RC: tcgnnnnnnnnnnntta
dyads_test_vs_ctrl_m2	assembly: gggnnnnnnnnnnnnnnnnnntta (sig=1.35; e-value=0.045)	RC: taannnnnnnnnnnnnnnnnnccc
dyads_test_vs_ctrl_m3	assembly: cccnnnnnnnnnnnnnncga (sig=1.35; e-value=0.045)	RC: tcgnnnnnnnnnnnnnnggg
dyads_test_vs_ctrl_m4	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m5	: (sig=; e-value=1)	RC:

[ discovered words: text ]
[ assembly: text sig matrices ]
[ matrices: tab format transfac format ]

Motif discovery

Motif 1 oligos_6nt_test_vs_ctrl_m1

k-mer sig=0.14; evalue=0.72

vsACAACCbm

KVGGTTGTSB

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor vsACAACCbm

AT1G76870 MA1367.2 D 8 0.8000 0.719 0.575 NA NA

Gam1 MA0034.2 D 7 0.6364 0.847 0.539 NA NA

MYB65 MA1177.2 D 7 0.6364 0.709 0.451 NA NA

Total matches= 9 (6 more)

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 58 (25.66%)
Max nb of predicted sites per peak: 5
(CHLRE_06g258600v5)
Mean nb of predicted sites per peak: 1.52

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 2 oligos_7nt_test_vs_ctrl_m1

k-mer sig=0.14; evalue=0.72

syCGCGAcGdm

KHCGTCGCGRS

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor syCGCGAcGdm

MYB124 MA1426.2 D 7 0.6364 0.700 0.446 NA NA

Total matches= 1

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 28 (12.39%)
Max nb of predicted sites per peak: 4
(CHLRE_06g259000v5)
Mean nb of predicted sites per peak: 1.43

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 3 dyads_test_vs_ctrl_m1

k-mer sig=1.35; evalue=0.045

kmTAAvttdcwkrdrtCGAsd

HSTCGAYHYMWGHAABTTAKM

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor kmTAAvttdcwkrdrtCGAsd

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 30 (13.27%)
Max nb of predicted sites per peak: 3
(CHLRE_12g549000v5)
Mean nb of predicted sites per peak: 1.20

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 4 dyads_test_vs_ctrl_m2

k-mer sig=1.35; evalue=0.045

hkgggTmratkkkrkrdkkykAmTTAhw

WDTAAKTMRMMHYMYMMMATYKACCCMD

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor hkgggTmratkkkrkrdkkykAmTTAhw

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 32 (14.16%)
Max nb of predicted sites per peak: 4
(CHLRE_01g048150v5)
Mean nb of predicted sites per peak: 1.31

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 5 dyads_test_vs_ctrl_m3

k-mer sig=1.35; evalue=0.045

awcccTAAkmywmhdmrmsCGAck

MGTCGSKYKHDKWRKMTTAGGGWT

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor awcccTAAkmywmhdmrmsCGAck

Total matches= 0

No match

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 25 (11.06%)
Max nb of predicted sites per peak: 5
(CHLRE_09g396100v5)
Mean nb of predicted sites per peak: 1.56

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

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 JASPAR2024_CORE_plants_non-redundant 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]

RSAT - peak-motifs result

Analysis: motifs_DEGs_post-c_20250701_01 (01/07/2025 15:34)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor syCGCGAcGdm

MYB124 MA1426.2 D 7 0.6364 0.700 0.446 NA NA

Total matches= 1

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor kmTAAvttdcwkrdrtCGAsd

Total matches= 0

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor hkgggTmratkkkrkrdkkykAmTTAhw

Total matches= 0

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor awcccTAAkmywmhdmrmsCGAck

Total matches= 0

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

RSAT - peak-motifs result

Analysis: motifs_DEGs_post-c_20250701_01 (01/07/2025 15:34)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor syCGCGAcGdm MYB124 MA1426.2 D 7 0.6364 0.700 0.446 NA NA Total matches= 1

JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor kmTAAvttdcwkrdrtCGAsd Total matches= 0

JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor hkgggTmratkkkrkrdkkykAmTTAhw Total matches= 0

JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match columns aligned correlation cor awcccTAAkmywmhdmrmsCGAck Total matches= 0

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor syCGCGAcGdm

MYB124 MA1426.2 D 7 0.6364 0.700 0.446 NA NA

Total matches= 1

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor kmTAAvttdcwkrdrtCGAsd

Total matches= 0

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor hkgggTmratkkkrkrdkkykAmTTAhw

Total matches= 0

JASPAR2024_CORE_plants_non-redundant

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

columns aligned correlation cor awcccTAAkmywmhdmrmsCGAck

Total matches= 0