peak-motifs Exc_L5_or_6_NP_control_MDD

peak-motifs  -v 1 -title Exc_L5_or_6_NP_control_MDD_down -i $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.174416_2025-05-16.174416_Ix0OVW/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -motif_db JASPAR2024_CORE_vertebrates_non-redundant tf $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -scan_markov 2 -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/2025/05/16/peak-motifs.2025-05-16.174416_2025-05-16.174416_Ix0OVW

Sequence composition (test sequences)

Nb of peaks: 23
Total seq. size: 14 kb
Min length: 253 bp
Mean length: 628.217 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) ]

Trinucleotide composition profiles

Transition frequencies
Position profiles

[ 3nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

motif discovery

oligos_6nt_mkv2

oligos_6nt_mkv2_m1	assembly: cctcagc (sig=0.80; e-value=0.16)	RC: gctgagg
oligos_6nt_mkv2_m2	assembly: cagatgg (sig=0.50; e-value=0.32)	RC: ccatctg
oligos_6nt_mkv2_m3	: (sig=; e-value=1)	RC:
oligos_6nt_mkv2_m4	: (sig=; e-value=1)	RC:
oligos_6nt_mkv2_m5	: (sig=; e-value=1)	RC:

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

oligos_7nt_mkv2

oligos_7nt_mkv2_m1	assembly: ctgaggc (sig=0.66; e-value=0.22)	RC: gcctcag
oligos_7nt_mkv2_m2	: (sig=; e-value=1)	RC:
oligos_7nt_mkv2_m3	: (sig=; e-value=1)	RC:
oligos_7nt_mkv2_m4	: (sig=; e-value=1)	RC:
oligos_7nt_mkv2_m5	: (sig=; e-value=1)	RC:

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

Motif discovery

Motif 1 oligos_6nt_mkv2_m1

k-mer sig=0.80; evalue=0.16

srCCTCAGCcb

VGGCTGAGGYS

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

JASPAR2024_CORE_vertebrates_non-redundant

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

columns aligned correlation cor srCCTCAGCcb

TFAP2C MA0814.3 R 9 0.8182 0.779 0.637 NA NA

TFAP2A MA0003.5 D 9 0.8182 0.777 0.636 NA NA

FEZF2 MA2341.1 D 8 0.7273 0.764 0.556 NA NA

Total matches= 18 (15 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: 8 (34.78%)
Max nb of predicted sites per peak: 2
(chr18:50522707-50524647)
Mean nb of predicted sites per peak: 1.25

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

Motif 2 oligos_6nt_mkv2_m2

k-mer sig=0.50; evalue=0.32

gvCAGATGGkd

HMCCATCTGBC

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

JASPAR2024_CORE_vertebrates_non-redundant

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

columns aligned correlation cor gvCAGATGGkd

TAL1::TCF3 MA0091.2 R 10 0.9091 0.840 0.764 NA NA

Msgn1 MA1524.3 D 10 0.9091 0.800 0.727 NA NA

NEUROD1 MA1109.2 D 8 0.7273 0.973 0.708 NA NA

Total matches= 32 (29 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: 6 (26.09%)
Max nb of predicted sites per peak: 2
(chr5:6858525-6859371)
Mean nb of predicted sites per peak: 1.67

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

Motif 3 oligos_7nt_mkv2_m1

k-mer sig=0.66; evalue=0.22

gsCTGAGGCmr

YKGCCTCAGSC

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

JASPAR2024_CORE_vertebrates_non-redundant

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

columns aligned correlation cor gsCTGAGGCmr

TFAP2C MA0814.3 D 9 0.8182 0.917 0.750 NA NA

TFAP2A MA0003.5 R 9 0.8182 0.904 0.739 NA NA

TFAP2B MA0812.2 R 9 0.8182 0.823 0.673 NA NA

Total matches= 12 (9 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: 12 (52.17%)
Max nb of predicted sites per peak: 2
(chr5:6858525-6859371)
Mean nb of predicted sites per peak: 1.25

[ 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_vertebrates_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: Exc_L5_or_6_NP_control_MDD_down (16/05/2025 17:45)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results