RSAT - peak-motifs result

Analysis: DARs_8C_control_versus_Nr5a2_knockdown (05/01/2026 11:55)

peak-motifs  -v 1 -title DARs_8C_control_versus_Nr5a2_knockdown -i $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.115003_2026-01-05.115003_UARk68/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,positions -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 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/2026/01/05/peak-motifs.2026-01-05.115003_2026-01-05.115003_UARk68

motif discovery
oligos_6nt_mkv4	oligos_6nt_mkv4_m1 assembly: gagttcaaggccag (sig=31.05; e-value=8.9e-32) RC: ctggccttgaactc oligos_6nt_mkv4_m2 assembly: cgagcg (sig=15.20; e-value=6.3e-16) RC: cgctcg oligos_6nt_mkv4_m3 assembly: cggccg (sig=14.84; e-value=1.4e-15) RC: cggccg oligos_6nt_mkv4_m4 assembly: cgcacg (sig=13.16; e-value=6.9e-14) RC: cgtgcg oligos_6nt_mkv4_m5 assembly: gagttcaaggtca (sig=16.43; e-value=3.7e-17) RC: tgaccttgaactc	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
positions_6nt	Not a single significant pattern	[positions_6nt]
oligos_7nt_mkv5	oligos_7nt_mkv5_m1 assembly: ccacaccc (sig=23.22; e-value=6e-24) RC: gggtgtgg oligos_7nt_mkv5_m2 assembly: tggccttgaactca (sig=17.20; e-value=6.3e-18) RC: tgagttcaaggcca oligos_7nt_mkv5_m3 assembly: caaggac (sig=11.11; e-value=7.8e-12) RC: gtccttg oligos_7nt_mkv5_m4 assembly: cggctgc (sig=9.84; e-value=1.4e-10) RC: gcagccg oligos_7nt_mkv5_m5 assembly: attttta (sig=9.33; e-value=4.7e-10) RC: taaaaat	[ 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_mkv4_m1	k-mer sig=31.05; evalue=8.9e-32 sTGAGTTCmAGGmCAGCC GGCTGKCCTKGAACTCAS	[ 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 sTGAGTTCmAGGmCAGCC NR5A1 MA1540.3 D 12 0.6667 0.916 0.611 NA NA NR6A1 MA1541.2 D 14 0.7778 0.723 0.562 NA NA Nr5A2 MA0505.3 R 9 0.5000 0.915 0.457 NA NA Total matches= 8 (5 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: 1762 (26.76%) Max nb of predicted sites per peak: 6  (chr2:91598499-91599075) Mean nb of predicted sites per peak: 1.65	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 2   oligos_6nt_mkv4_m2	k-mer sig=15.20; evalue=6.3e-16 ssCGaGCGss SSCGCTCGSS	[ 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 ssCGaGCGss KLF7 MA1959.2 D 7 0.6364 0.794 0.505 NA NA KLF15 MA1513.2 R 7 0.6364 0.781 0.497 NA NA TCFL5 MA0632.3 R 7 0.6364 0.780 0.496 NA NA Total matches= 9 (6 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: 897 (13.62%) Max nb of predicted sites per peak: 27  (chr6:39206818-39207183) Mean nb of predicted sites per peak: 2.42	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 3   oligos_6nt_mkv4_m3	k-mer sig=14.84; evalue=1.4e-15 ssCGGCCGss SSCGGCCGSS	[ 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 ssCGGCCGss HINFP MA0131.3 R 8 0.8000 0.717 0.574 NA NA KLF7 MA1959.2 D 7 0.6364 0.708 0.451 NA NA KLF15 MA1513.2 D 7 0.6364 0.704 0.448 NA NA Total matches= 4 (1 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: 658 (9.99%) Max nb of predicted sites per peak: 40  (chr14:8213995-8214322) Mean nb of predicted sites per peak: 4.37	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 4   oligos_6nt_mkv4_m4	k-mer sig=13.16; evalue=6.9e-14 srCGCaCGss SSCGTGCGYS	[ 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 srCGCaCGss EPAS1 MA2325.1 D 8 0.7273 0.797 0.580 NA NA EGR1 MA0162.5 D 9 0.8182 0.707 0.579 NA NA TCFL5 MA0632.3 D 8 0.8000 0.702 0.562 NA NA Total matches= 25 (22 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: 873 (13.26%) Max nb of predicted sites per peak: 25  (chr6:39206818-39207183) Mean nb of predicted sites per peak: 2.26	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 5   oligos_6nt_mkv4_m5	k-mer sig=16.43; evalue=3.7e-17 sTGAGTTCmAGGmCAGC GCTGKCCTKGAACTCAS	[ 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 sTGAGTTCmAGGmCAGC NR5A1 MA1540.3 D 12 0.7059 0.934 0.659 NA NA NR6A1 MA1541.2 D 14 0.8235 0.743 0.612 NA NA Nr5A2 MA0505.3 R 9 0.5294 0.941 0.498 NA NA Total matches= 7 (4 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: 1744 (26.49%) Max nb of predicted sites per peak: 6  (chr2:91598499-91599075) Mean nb of predicted sites per peak: 1.63	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 6   oligos_7nt_mkv5_m1	k-mer sig=23.22; evalue=6e-24 srCCACACCcws SWGGGTGTGGYS	[ 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 srCCACACCcws KLF9 MA1107.3 D 11 0.9167 0.902 0.827 NA NA SP3 MA0746.3 D 11 0.9167 0.836 0.766 NA NA KLF16 MA0741.1 D 11 0.9167 0.818 0.750 NA NA Total matches= 34 (31 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: 1350 (20.50%) Max nb of predicted sites per peak: 15  (chr4:151325457-151325918) Mean nb of predicted sites per peak: 1.25	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 7   oligos_7nt_mkv5_m2	k-mer sig=17.20; evalue=6.3e-18 GCTGkCCTkGAACTCAsw WSTGAGTTCMAGGMCAGC	[ 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 GCTGkCCTkGAACTCAsw NR5A1 MA1540.3 R 12 0.6667 0.914 0.610 NA NA NR6A1 MA1541.2 R 14 0.7778 0.729 0.567 NA NA Nr5A2 MA0505.3 D 9 0.5000 0.920 0.460 NA NA Total matches= 7 (4 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: 1693 (25.71%) Max nb of predicted sites per peak: 6  (chr2:91598499-91599075) Mean nb of predicted sites per peak: 1.63	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 8   oligos_7nt_mkv5_m3	k-mer sig=11.11; evalue=7.8e-12 twCAAGGACat ATGTCCTTGWA	[ 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 twCAAGGACat ESRRB MA0141.4 D 10 0.9091 0.779 0.708 NA NA Nr5A2 MA0505.3 R 9 0.8182 0.837 0.685 NA NA ESRRA MA0592.4 D 9 0.8182 0.801 0.655 NA NA Total matches= 11 (8 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: 482 (7.32%) Max nb of predicted sites per peak: 4  (chr8:26760538-26760939) Mean nb of predicted sites per peak: 1.10	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 9   oligos_7nt_mkv5_m4	k-mer sig=9.84; evalue=1.4e-10 bsCGGCTGCsb VSGCAGCCGSV	[ 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 bsCGGCTGCsb NHLH1 MA0048.3 D 9 0.8182 0.739 0.604 NA NA ZNF93 MA1721.2 D 11 0.7857 0.723 0.568 NA NA MYOG MA0500.3 D 8 0.7273 0.733 0.533 NA NA Total matches= 14 (11 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: 826 (12.55%) Max nb of predicted sites per peak: 24  (chr14:8213995-8214322) Mean nb of predicted sites per peak: 2.21	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 10   oligos_7nt_mkv5_m5	k-mer sig=9.33; evalue=4.7e-10 wwATTTTTAww WWTAAAAATWW	[ 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 wwATTTTTAww MEF2A MA0052.5 R 10 0.9091 0.841 0.764 NA NA Hmga1 MA2124.1 D 8 0.7273 0.998 0.726 NA NA MEF2D MA0773.1 R 11 0.9167 0.745 0.683 NA NA Total matches= 47 (44 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: 422 (6.41%) Max nb of predicted sites per peak: 5  (chr11:107111847-107112049) Mean nb of predicted sites per peak: 1.10	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]

Command:  peak-motifs  -v 1 -title DARs_8C_control_versus_Nr5a2_knockdown -i $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.115003_2026-01-05.115003_UARk68/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,positions -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 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/2026/01/05/peak-motifs.2026-01-05.115003_2026-01-05.115003_UARk68

Warning: Not a single pattern was found in file tmp/www-data/2026/01/05/peak-motifs.2026-01-05.115003_2026-01-05.115003_UARk68/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab

Warning: Not a single pattern was found in file tmp/www-data/2026/01/05/peak-motifs.2026-01-05.115003_2026-01-05.115003_UARk68/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab