RSAT - peak-motifs result

Analysis: Promoter_regions_2000 (25/02/2025 15:39)

peak-motifs  -v 1 -title Promoter_regions_2000 -i $RSAT/public_html/tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/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 ArabidopsisPBM tf $RSAT/public_html/motif_databases/ArabidopsisPBM/ArabidopsisPBM_2015-11-06.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/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf

motif discovery
oligos_6nt_mkv1	oligos_6nt_mkv1_m1 assembly: ctcctc (sig=1.87; e-value=0.013) RC: gaggag oligos_6nt_mkv1_m2 assembly: cccgcc (sig=0.83; e-value=0.15) RC: ggcggg oligos_6nt_mkv1_m3 assembly: atatat (sig=0.74; e-value=0.18) RC: atatat oligos_6nt_mkv1_m4 assembly: aggtag (sig=0.57; e-value=0.27) RC: ctacct oligos_6nt_mkv1_m5 assembly: cgccgc (sig=0.51; e-value=0.31) RC: gcggcg	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
positions_6nt	Not a single significant pattern	[positions_6nt]
oligos_7nt_mkv1	oligos_7nt_mkv1_m1 assembly: aaaaaaa (sig=2.11; e-value=0.0078) RC: ttttttt oligos_7nt_mkv1_m2 assembly: cccgccg (sig=1.66; e-value=0.022) RC: cggcggg oligos_7nt_mkv1_m3 assembly: cctcctct (sig=0.98; e-value=0.1) RC: agaggagg oligos_7nt_mkv1_m4 assembly: cgtcgtc (sig=0.98; e-value=0.1) RC: gacgacg oligos_7nt_mkv1_m5 assembly: tagtacta (sig=0.91; e-value=0.12) RC: tagtacta	[ 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_mkv1_m1	k-mer sig=1.87; evalue=0.013 ysCTCCTCkk MMGAGGAGSR	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ysCTCCTCkk 7274_TOE2_ArabidopsisPBM_20140210_ 7274_TOE2_ArabidopsisPBM_20140210_ D 7 0.5385 0.752 0.405 NA NA Total matches= 1		[ 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 (66.67%) Max nb of predicted sites per peak: 3  (TraesCS3B02G448000) Mean nb of predicted sites per peak: 2.00	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 2   oligos_6nt_mkv1_m2	k-mer sig=0.83; evalue=0.15 vcCCCGCCgc GCGGCGGGGB	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor vcCCCGCCgc 7213_DEAR3_ArabidopsisPBM_20140210_ 7213_DEAR3_ArabidopsisPBM_20140210_ D 10 1.0000 0.716 0.716 NA NA 7251_RAP2.6_ArabidopsisPBM_20140210_ 7251_RAP2.6_ArabidopsisPBM_20140210_ D 9 0.8182 0.728 0.596 NA NA 7221_ERF1_ArabidopsisPBM_20140210_ 7221_ERF1_ArabidopsisPBM_20140210_ D 9 0.8182 0.727 0.595 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: 6 (66.67%) Max nb of predicted sites per peak: 5  (TraesCS1A02G333800) Mean nb of predicted sites per peak: 2.50	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 3   oligos_6nt_mkv1_m3	k-mer sig=0.74; evalue=0.18 rtATATATat ATATATATAY	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rtATATATat 7186_AHL20_ArabidopsisPBM_20140210_ 7186_AHL20_ArabidopsisPBM_20140210_ D 10 1.0000 0.767 0.767 NA NA 7185_AHL12_3_ArabidopsisPBM_20140210_ 7185_AHL12_3_ArabidopsisPBM_20140210_ D 9 0.8182 0.707 0.578 NA NA Total matches= 2		[ 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: 3 (33.33%) Max nb of predicted sites per peak: 14  (TraesCS2A02G004600) Mean nb of predicted sites per peak: 7.00	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 4   oligos_6nt_mkv1_m4	k-mer sig=0.57; evalue=0.27 sgAGGTAGwa TWCTACCTCS	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor sgAGGTAGwa 7265_STY1_2_ArabidopsisPBM_20140210_ 7265_STY1_2_ArabidopsisPBM_20140210_ R 9 0.8182 0.707 0.579 NA NA 7237_MYB111_2_ArabidopsisPBM_20140210_ 7237_MYB111_2_ArabidopsisPBM_20140210_ D 8 0.6667 0.790 0.527 NA NA 7236_MYB111_ArabidopsisPBM_20140210_ 7236_MYB111_ArabidopsisPBM_20140210_ D 8 0.6667 0.760 0.507 NA NA Total matches= 5 (2 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: 5 (55.56%) Max nb of predicted sites per peak: 4  (TraesCS6A02G024100) Mean nb of predicted sites per peak: 2.00	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 5   oligos_6nt_mkv1_m5	k-mer sig=0.51; evalue=0.31 scCGCCGCrg CYGCGGCGGS	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor scCGCCGCrg 7251_RAP2.6_ArabidopsisPBM_20140210_ 7251_RAP2.6_ArabidopsisPBM_20140210_ D 10 1.0000 0.904 0.904 NA NA 7248_RAP2.3_ArabidopsisPBM_20140210_ 7248_RAP2.3_ArabidopsisPBM_20140210_ D 10 1.0000 0.884 0.884 NA NA 7256_RRTF1_ArabidopsisPBM_20140210_ 7256_RRTF1_ArabidopsisPBM_20140210_ D 10 1.0000 0.873 0.873 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: 6 (66.67%) Max nb of predicted sites per peak: 6  (TraesCS1A02G333800) Mean nb of predicted sites per peak: 2.83	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 6   oligos_7nt_mkv1_m1	k-mer sig=2.11; evalue=0.0078 raAAAAAAAww WWTTTTTTTTY	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor raAAAAAAAww 7217_DOF5.7_ArabidopsisPBM_20140210_ 7217_DOF5.7_ArabidopsisPBM_20140210_ D 9 0.7500 0.722 0.541 NA NA Total matches= 1		[ 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: 5 (55.56%) Max nb of predicted sites per peak: 5  (TraesCS2B02G538800) Mean nb of predicted sites per peak: 3.20	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 7   oligos_7nt_mkv1_m2	k-mer sig=1.66; evalue=0.022 swCcCGCCGhs SDCGGCGGGWS	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor swCcCGCCGhs 7256_RRTF1_ArabidopsisPBM_20140210_ 7256_RRTF1_ArabidopsisPBM_20140210_ D 9 0.7500 0.770 0.578 NA NA 7251_RAP2.6_ArabidopsisPBM_20140210_ 7251_RAP2.6_ArabidopsisPBM_20140210_ D 9 0.7500 0.765 0.574 NA NA 7221_ERF1_ArabidopsisPBM_20140210_ 7221_ERF1_ArabidopsisPBM_20140210_ D 9 0.7500 0.765 0.574 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: 5 (55.56%) Max nb of predicted sites per peak: 4  (TraesCS1A02G333800) Mean nb of predicted sites per peak: 2.20	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 8   oligos_7nt_mkv1_m3	k-mer sig=0.98; evalue=0.1 ytcCTCCTCkky RMMGAGGAGGAR	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ytcCTCCTCkky Total matches= 0		No match
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 6 (66.67%) Max nb of predicted sites per peak: 4  (TraesCS3A02G230000) Mean nb of predicted sites per peak: 2.17	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 9   oligos_7nt_mkv1_m4	k-mer sig=0.98; evalue=0.1 syCGTCGTCgb VCGACGACGRS	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor syCGTCGTCgb Total matches= 0		No match
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 6 (66.67%) Max nb of predicted sites per peak: 7  (TraesCS2A02G004600) Mean nb of predicted sites per peak: 2.83	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 10   oligos_7nt_mkv1_m5	k-mer sig=0.91; evalue=0.12 wrTAGTAcTAct AGTAGTACTAYW	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
ArabidopsisPBM name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wrTAGTAcTAct Total matches= 0		No match
Predicted sites on test peaks	Distribution of sites Nb of predicted sites per peak Nb peaks with at least one predicted site: 5 (55.56%) Max nb of predicted sites per peak: 10  (TraesCS3A02G230000) Mean nb of predicted sites per peak: 4.00	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]

Command:  peak-motifs  -v 1 -title Promoter_regions_2000 -i $RSAT/public_html/tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/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 ArabidopsisPBM tf $RSAT/public_html/motif_databases/ArabidopsisPBM/ArabidopsisPBM_2015-11-06.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/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf

Warning: Not a single pattern was found in file tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab

Warning: Not a single pattern was found in file tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab