peak-motifs CYP82C4

peak-motifs  -v 1 -title CYP82C4_Angler -i $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.142119_2026-03-30.142119_XX18DY/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.142119_2026-03-30.142119_XX18DY/peak-motifscontrol_seq -markov auto -disco oligos,dyads -nmotifs 10 -minol 6 -maxol 8 -merge_lengths -2str -origin end -offset -200 -motif_db footprintDB tf $RSAT/public_html/motif_databases/footprintDB/footprintDB.motif.tf -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/2026/03/30/peak-motifs.2026-03-30.142119_2026-03-30.142119_XX18DY

Sequence composition (test sequences)

Nb of peaks: 14
Total seq. size: 20 kb
Min length: 238 bp
Mean length: 1433.43 bp
Max length: 1701 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: 34262
Total seq. size: 34842 kb
Min length: 201 bp
Mean length: 1016.92 bp
Max length: 1701 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_6-8nt

oligos_6-8nt_m1	assembly: agtagg (sig=0.01; e-value=0.98)	RC: cctact
oligos_6-8nt_m2	: (sig=; e-value=1)	RC:
oligos_6-8nt_m3	: (sig=; e-value=1)	RC:
oligos_6-8nt_m4	: (sig=; e-value=1)	RC:
oligos_6-8nt_m5	: (sig=; e-value=1)	RC:
oligos_6-8nt_m6	: (sig=; e-value=1)	RC:
oligos_6-8nt_m7	: (sig=; e-value=1)	RC:
oligos_6-8nt_m8	: (sig=; e-value=1)	RC:
oligos_6-8nt_m9	: (sig=; e-value=1)	RC:
oligos_6-8nt_m10	: (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: cttnnaaa (sig=0.03; e-value=0.93)	RC: tttnnaag
dyads_test_vs_ctrl_m2	: (sig=; e-value=1)	RC:
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:
dyads_test_vs_ctrl_m6	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m7	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m8	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m9	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m10	: (sig=; e-value=1)	RC:

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

Motif discovery

Motif 1 oligos_6-8nt_m1

k-mer sig=0.01; evalue=0.98

rraGtAGGtm

KACCTACTYY

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

footprintDB

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

columns aligned correlation cor rraGtAGGtm

ZKSCAN1:MA1585.1:JASPAR ZKSCAN1/MA1585.1/JASPAR D 10 1.0000 0.905 0.905 NA NA

ZKSCAN1:MA1585.2:JASPAR ZKSCAN1/MA1585.2/JASPAR D 9 0.9000 0.931 0.838 NA NA

LM111:CN0111.1:JASPAR LM111/CN0111.1/JASPAR R 10 0.8333 0.851 0.709 NA NA

Total matches= 113 (110 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: 10 (71.43%)
Max nb of predicted sites per peak: 4
(BHLH101)
Mean nb of predicted sites per peak: 1.30

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

Motif 2 dyads_test_vs_ctrl_m1

k-mer sig=0.03; evalue=0.93

kbCTTkrAAAmk

MKTTTYMAAGVM

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

footprintDB

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

columns aligned correlation cor kbCTTkrAAAmk

HOXA13:HOXA13_full_2:HumanTF HOXA13/HOXA13_full_2/HumanTF D 11 0.9167 0.705 0.646 NA NA

ZFP91:UN0313.1:JASPAR ZFP91/UN0313.1/JASPAR D 12 0.8571 0.722 0.619 NA NA

die-1:M0382_1.02:CISBP die-1/M0382_1.02/CISBP R 10 0.8333 0.736 0.613 NA NA

Total matches= 100 (97 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: 10 (71.43%)
Max nb of predicted sites per peak: 4
(AtMYB10)
Mean nb of predicted sites per peak: 2.10

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

Predicted sites on test peaks (all motifs)

[tab]
[bed]

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 footprintDB 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: CYP82C4_Angler (30/03/2026 14:54)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results