peak-motifs motifs_DEGs_post-c_20250701

peak-motifs  -v 1 -title motifs_DEGs_post-c_20250701_02 -i $RSAT/public_html/tmp/www-data/2025/07/02/peak-motifs.2025-07-02.105518_2025-07-02.105518_TSbjs4/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2025/07/02/peak-motifs.2025-07-02.105518_2025-07-02.105518_TSbjs4/peak-motifscontrol_seq -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2025/07/02/peak-motifs.2025-07-02.105518_2025-07-02.105518_TSbjs4

Sequence composition (test sequences)

Nb of peaks: 226
Total seq. size: 181 kb
Min length: 800 bp
Mean length: 800 bp
Max length: 800 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: agcgcc (sig=2.42; e-value=0.0038)	RC: ggcgct
oligos_6nt_test_vs_ctrl_m2	assembly: gaaggc (sig=1.48; e-value=0.033)	RC: gccttc
oligos_6nt_test_vs_ctrl_m3	assembly: gcagctgc (sig=0.59; e-value=0.26)	RC: gcagctgc
oligos_6nt_test_vs_ctrl_m4	assembly: aagaag (sig=0.43; e-value=0.37)	RC: cttctt
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

Not a single significant pattern

[oligos_7nt_test_vs_ctrl]

Motif discovery

Motif 1 oligos_6nt_test_vs_ctrl_m1

k-mer sig=2.42; evalue=0.0038

vmAGCGCCwg

CWGGCGCTKB

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 102 (45.13%)
Max nb of predicted sites per peak: 4
(CHLRE_11g467779v5)
Mean nb of predicted sites per peak: 1.36

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

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=1.48; evalue=0.033

rwGAAGGCrr

YYGCCTTCWY

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 116 (51.33%)
Max nb of predicted sites per peak: 4
(CHLRE_01g004651v5)
Mean nb of predicted sites per peak: 1.37

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

Motif 3 oligos_6nt_test_vs_ctrl_m3

k-mer sig=0.59; evalue=0.26

cwGCAGCTGChg

CDGCAGCTGCWG

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 29 (12.83%)
Max nb of predicted sites per peak: 8
(CHLRE_12g541800v5)
Mean nb of predicted sites per peak: 2.28

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

Motif 4 oligos_6nt_test_vs_ctrl_m4

k-mer sig=0.43; evalue=0.37

rkAAGAAGdw

WHCTTCTTMY

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

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 59 (26.11%)
Max nb of predicted sites per peak: 7
(CHLRE_16g687500v5)
Mean nb of predicted sites per peak: 1.41

[ 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) ]

Log files
Parameters and files		[txt] [html]
Time log		[time table] [time log] [html]

RSAT - peak-motifs result

Analysis: motifs_DEGs_post-c_20250701_02 (02/07/2025 10:59)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results