peak-motifs MYCO_S

peak-motifs  -v 1 -title MYCO_S_df2 -i $RSAT/public_html/tmp/www-data/2025/04/13/peak-motifs.2025-04-13.172640_2025-04-13.172640_Wu3iyl/peak-motifspeak_seq -max_seq_len 1000 -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/2025/04/13/peak-motifs.2025-04-13.172640_2025-04-13.172640_Wu3iyl

Sequence composition (test sequences)

Nb of peaks: 212
Total seq. size: 121 kb
Min length: 189 bp
Mean length: 571.646 bp
Max length: 1000 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_mkv3

oligos_6nt_mkv3_m1	assembly: cggcga (sig=1.29; e-value=0.051)	RC: tcgccg
oligos_6nt_mkv3_m2	assembly: cgatga (sig=0.62; e-value=0.24)	RC: tcatcg
oligos_6nt_mkv3_m3	: (sig=; e-value=1)	RC:
oligos_6nt_mkv3_m4	: (sig=; e-value=1)	RC:
oligos_6nt_mkv3_m5	: (sig=; e-value=1)	RC:

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

positions_6nt

positions_6nt_m1	assembly: aattcc (sig=0.32; e-value=0.48)	RC: ggaatt
positions_6nt_m2	: (sig=; e-value=1)	RC:
positions_6nt_m3	: (sig=; e-value=1)	RC:
positions_6nt_m4	: (sig=; e-value=1)	RC:
positions_6nt_m5	: (sig=; e-value=1)	RC:

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

oligos_7nt_mkv4

oligos_7nt_mkv4_m1	assembly: cacgctc (sig=0.54; e-value=0.29)	RC: gagcgtg
oligos_7nt_mkv4_m2	: (sig=; e-value=1)	RC:
oligos_7nt_mkv4_m3	: (sig=; e-value=1)	RC:
oligos_7nt_mkv4_m4	: (sig=; e-value=1)	RC:
oligos_7nt_mkv4_m5	: (sig=; e-value=1)	RC:

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

positions_7nt

Not a single significant pattern

[positions_7nt]

Motif discovery

Motif 1 oligos_6nt_mkv3_m1

k-mer sig=1.29; evalue=0.051

skCGGCGAym

KRTCGCCGMS

[ 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: 87 (41.04%)
Max nb of predicted sites per peak: 4
(MYCO_S_Lsr2FLAG_merge_peak_79)
Mean nb of predicted sites per peak: 1.39

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

Motif 2 oligos_6nt_mkv3_m2

k-mer sig=0.62; evalue=0.24

stCGATGAgs

SCTCATCGAS

[ 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: 82 (38.68%)
Max nb of predicted sites per peak: 4
(MYCO_S_Lsr2FLAG_merge_peak_74)
Mean nb of predicted sites per peak: 1.43

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

Motif 3 positions_6nt_m1

k-mer sig=0.32; evalue=0.48

ssAATTCCyr

YRGGAATTSS

[ 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: 68 (32.08%)
Max nb of predicted sites per peak: 3
(MYCO_S_Lsr2FLAG_merge_peak_86)
Mean nb of predicted sites per peak: 1.24

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

Motif 4 oligos_7nt_mkv4_m1

k-mer sig=0.54; evalue=0.29

swCACGCTCak

MTGAGCGTGWS

[ 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: 31 (14.62%)
Max nb of predicted sites per peak: 2
(MYCO_S_Lsr2FLAG_merge_peak_259)
Mean nb of predicted sites per peak: 1.10

[ 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: MYCO_S_df2 (13/04/2025 17:27)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results