peak-motifs random1

peak-motifs  -v 1 -title random1 -i $RSAT/public_html/tmp/www-data/2025/06/05/peak-motifs.2025-06-05.162109_2025-06-05.162109_q1zl2w/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2025/06/05/peak-motifs.2025-06-05.162109_2025-06-05.162109_q1zl2w/peak-motifscontrol_seq -markov auto -disco oligos,dyads -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/2025/06/05/peak-motifs.2025-06-05.162109_2025-06-05.162109_q1zl2w

Sequence composition (test sequences)

Nb of peaks: 88
Total seq. size: 47 kb
Min length: 247 bp
Mean length: 537.591 bp
Max length: 1201 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: 17743
Total seq. size: 9629 kb
Min length: 201 bp
Mean length: 542.692 bp
Max length: 1201 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: gtccca (sig=0.63; e-value=0.23)	RC: tgggac
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: tgggaca (sig=0.87; e-value=0.13)	RC: tgtccca
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: cccnnnnnnnnnnnnnntac (sig=1.39; e-value=0.041)	RC: gtannnnnnnnnnnnnnggg
dyads_test_vs_ctrl_m2	assembly: gccnnnnnnnnnnnnacc (sig=0.21; e-value=0.62)	RC: ggtnnnnnnnnnnnnggc
dyads_test_vs_ctrl_m3	: (sig=; e-value=1)	RC:
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=0.63; evalue=0.23

ctGTCCCAkc

GMTGGGACAG

[ 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: 24 (27.27%)
Max nb of predicted sites per peak: 3
(CHLRE_02g115650v5)
Mean nb of predicted sites per peak: 1.33

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

Motif 2 oligos_7nt_test_vs_ctrl_m1

k-mer sig=0.87; evalue=0.13

gwTGGGACArg

CYTGTCCCAWC

[ 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: 18 (20.45%)
Max nb of predicted sites per peak: 3
(CHLRE_02g115650v5)
Mean nb of predicted sites per peak: 1.22

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

Motif 3 dyads_test_vs_ctrl_m1

k-mer sig=1.39; evalue=0.041

vyCCCwhmmcyabwhsdmtTACkk

MMGTAAKHSDWVTRGKKDWGGGRB

[ 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: 25 (28.41%)
Max nb of predicted sites per peak: 3
(CHLRE_10g420550v5)
Mean nb of predicted sites per peak: 1.56

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

Motif 4 dyads_test_vs_ctrl_m2

k-mer sig=0.21; evalue=0.62

ckGCCacwysyvcmsccACCcm

KGGGTGGSKGBRSRWGTGGCMG

[ 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: 27 (30.68%)
Max nb of predicted sites per peak: 5
(CHLRE_12g537226v5)
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: random1 (05/06/2025 16:25)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results