RSAT - peak-motifs result

Analysis: H3K9ac (08/04/2025 09:13)

peak-motifs  -v 1 -title H3K9ac -i $RSAT/public_html/tmp/www-data/2025/04/08/peak-motifs.2025-04-08.090926_2025-04-08.090926_i19YSh/peak-motifspeak_seq -max_seq_len 2000 -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -motif_db JASPAR2024_CORE_plants_non-redundant tf $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_plants_non-redundant_pfms_transfac.txt -scan_markov 1 -source getfasta -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/2025/04/08/peak-motifs.2025-04-08.090926_2025-04-08.090926_i19YSh

motif discovery
oligos_6nt_mkv4	oligos_6nt_mkv4_m1 assembly: taaaccctaa (sig=10.15; e-value=7.1e-11) RC: ttagggttta oligos_6nt_mkv4_m2 assembly: gaaaaag (sig=10.04; e-value=9.1e-11) RC: ctttttc oligos_6nt_mkv4_m3 assembly: acaaaacagag (sig=7.75; e-value=1.8e-08) RC: ctctgttttgt oligos_6nt_mkv4_m4 assembly: cttagc (sig=7.17; e-value=6.8e-08) RC: gctaag oligos_6nt_mkv4_m5 assembly: taatta (sig=6.06; e-value=8.7e-07) RC: taatta	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
positions_6nt	positions_6nt_m1 assembly: atataaa (sig=3.28; e-value=0.00052) RC: tttatat positions_6nt_m2 assembly: aaaata (sig=0.97; e-value=0.11) RC: tatttt positions_6nt_m3 assembly: aataat (sig=0.81; e-value=0.15) RC: attatt positions_6nt_m4 assembly: cggaga (sig=0.36; e-value=0.44) RC: tctccg positions_6nt_m5 : (sig=; e-value=1) RC:	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
oligos_7nt_mkv5	oligos_7nt_mkv5_m1 assembly: caagaac (sig=13.00; e-value=1e-13) RC: gttcttg oligos_7nt_mkv5_m2 assembly: cttcatc (sig=10.92; e-value=1.2e-11) RC: gatgaag oligos_7nt_mkv5_m3 assembly: catcttc (sig=10.44; e-value=3.6e-11) RC: gaagatg oligos_7nt_mkv5_m4 assembly: ctctgtttc (sig=8.95; e-value=1.1e-09) RC: gaaacagag oligos_7nt_mkv5_m5 assembly: aacccta (sig=8.18; e-value=6.6e-09) RC: tagggtt	[ 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=10.15; evalue=7.1e-11 mmyAAACCCtaamh DKTTAGGGTTTRKK	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor mmyAAACCCtaamh AT1G72740 MA1353.2 R 11 0.7857 0.965 0.758 NA NA TRB2 MA1355.2 D 11 0.7857 0.879 0.691 NA NA TRB1 MA2032.2 D 9 0.6429 0.971 0.624 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: 468 (28.26%) Max nb of predicted sites per peak: 4  (5:506200-507199(.)) Mean nb of predicted sites per peak: 1.28	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 2   oligos_6nt_mkv4_m2	k-mer sig=10.04; evalue=9.1e-11 rrGAAAAAGyw WRCTTTTTCYY	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rrGAAAAAGyw DOF2.5 MA0977.1 D 8 0.7273 0.898 0.653 NA NA DOF1.6 MA1275.2 D 8 0.7273 0.878 0.639 NA NA DOF4.7 MA2380.1 R 8 0.6667 0.957 0.638 NA NA Total matches= 37 (34 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: 369 (22.28%) Max nb of predicted sites per peak: 4  (5:9959600-9961199(.)) Mean nb of predicted sites per peak: 1.22	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 3   oligos_6nt_mkv4_m3	k-mer sig=7.75; evalue=1.8e-08 rracaaAACAGAGaa TTCTCTGTTTTGTYY	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rracaaAACAGAGaa REF6 MA1415.2 D 9 0.6000 0.983 0.590 NA NA Zm00001d027846 MA1823.2 D 8 0.5333 0.784 0.418 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: 465 (28.08%) Max nb of predicted sites per peak: 8  (3:9302000-9303599(.)) Mean nb of predicted sites per peak: 1.41	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 4   oligos_6nt_mkv4_m4	k-mer sig=7.17; evalue=6.8e-08 wvCtTAGCyr YRGCTAAGBW	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wvCtTAGCyr SRM1 MA1681.2 R 9 0.9000 0.709 0.638 NA NA AT5G04760 MA2031.2 D 7 0.7000 0.747 0.523 NA NA NAC062 MA1676.3 R 6 0.5455 0.836 0.456 NA NA Total matches= 6 (3 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: 574 (34.66%) Max nb of predicted sites per peak: 5  (2:12667000-12669599(.)) Mean nb of predicted sites per peak: 1.29	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 5   oligos_6nt_mkv4_m5	k-mer sig=6.06; evalue=8.7e-07 atTAATTAat ATTAATTAAT	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor atTAATTAat ZHD1 MA1329.3 D 9 0.9000 0.931 0.838 NA NA ZHD10 MA1807.2 D 8 0.8000 0.961 0.769 NA NA ZHD5 MA1326.2 R 8 0.8000 0.906 0.724 NA NA Total matches= 29 (26 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: 511 (30.86%) Max nb of predicted sites per peak: 16  (3:4772200-4775199(.)) Mean nb of predicted sites per peak: 3.23	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 6   positions_6nt_m1	k-mer sig=3.28; evalue=0.00052 ataTATAaAya TRTTTATATAT	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ataTATAaAya AHL13 MA2374.1 D 8 0.7273 0.842 0.612 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: 610 (36.84%) Max nb of predicted sites per peak: 20  (5:17978800-17981599(.)) Mean nb of predicted sites per peak: 2.75	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 7   positions_6nt_m2	k-mer sig=0.97; evalue=0.11 asAAAATAwa TWTATTTTST	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor asAAAATAwa KAN2 MA1383.2 R 10 1.0000 0.721 0.721 NA NA RIN MA1814.2 R 9 0.8182 0.815 0.666 NA NA RVE4 MA1187.2 R 8 0.7273 0.849 0.617 NA NA Total matches= 24 (21 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: 470 (28.38%) Max nb of predicted sites per peak: 6  (5:5285000-5286799(.)) Mean nb of predicted sites per peak: 1.40	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 8   positions_6nt_m3	k-mer sig=0.81; evalue=0.15 amAATAATww WWATTATTKT	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor amAATAATww ATHB-53 MA1215.2 D 9 0.9000 0.898 0.808 NA NA Zm00001d005692 MA1824.2 D 8 0.8000 0.964 0.771 NA NA ZHD3 MA1213.3 R 9 0.9000 0.853 0.768 NA NA Total matches= 31 (28 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: 636 (38.41%) Max nb of predicted sites per peak: 8  (5:7812600-7813999(.)) Mean nb of predicted sites per peak: 1.74	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 9   positions_6nt_m4	k-mer sig=0.36; evalue=0.44 gsCGGmGAyg CRTCKCCGSC	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor gsCGGmGAyg Zm00001d031796 MA1831.2 D 10 1.0000 0.730 0.730 NA NA RAP2-11 MA1266.2 R 10 0.9091 0.727 0.661 NA NA LBD18 MA1673.2 D 8 0.8000 0.743 0.594 NA NA Total matches= 38 (35 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: 788 (47.58%) Max nb of predicted sites per peak: 11  (2:15335600-15337799(.)) Mean nb of predicted sites per peak: 2.13	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 10   oligos_7nt_mkv5_m1	k-mer sig=13.00; evalue=1e-13 amCAAGAaCma TKGTTCTTGKT	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor amCAAGAaCma SBP6 MA2420.1 D 8 0.7273 0.710 0.516 NA NA HSFA6B MA1664.3 R 8 0.7273 0.705 0.513 NA NA HSFC1 MA1667.3 D 8 0.7273 0.702 0.511 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: 520 (31.40%) Max nb of predicted sites per peak: 5  (1:2345400-2346799(.)) Mean nb of predicted sites per peak: 1.28	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 11   oligos_7nt_mkv5_m2	k-mer sig=10.92; evalue=1.2e-11 akCtTCaTCry RYGATGAAGMT	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor akCtTCaTCry NAC071 MA1789.1 D 9 0.5294 0.793 0.420 NA NA HSFA1B MA2019.2 D 6 0.4615 0.891 0.411 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: 502 (30.31%) Max nb of predicted sites per peak: 4  (5:817800-818999(.)) Mean nb of predicted sites per peak: 1.27	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 12   oligos_7nt_mkv5_m3	k-mer sig=10.44; evalue=3.6e-11 ayCATCtTCwy RWGAAGATGRT	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ayCATCtTCwy 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: 515 (31.10%) Max nb of predicted sites per peak: 5  (5:24535600-24536999(.)) Mean nb of predicted sites per peak: 1.30	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 13   oligos_7nt_mkv5_m4	k-mer sig=8.95; evalue=1.1e-09 tyCtCTGTTTCyk MRGAAACAGAGRA	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor tyCtCTGTTTCyk REF6 MA1415.2 R 9 0.6923 0.933 0.646 NA NA NTL8 MA1678.3 R 7 0.5000 0.886 0.443 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: 539 (32.55%) Max nb of predicted sites per peak: 9  (3:9302000-9303599(.)) Mean nb of predicted sites per peak: 1.53	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 14   oligos_7nt_mkv5_m5	k-mer sig=8.18; evalue=6.6e-09 maAACCCTAam KTTAGGGTTTK	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
JASPAR2024_CORE_plants_non-redundant name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor maAACCCTAam TRB1 MA2032.2 D 9 0.8182 0.982 0.804 NA NA AT1G72740 MA1353.2 R 10 0.8333 0.956 0.796 NA NA TRB2 MA1355.2 D 10 0.8333 0.889 0.741 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: 369 (22.28%) Max nb of predicted sites per peak: 5  (4:2481000-2482399(.)) Mean nb of predicted sites per peak: 1.24	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]

Predicted sites on test peaks (all motifs)

[tab] [bed]

Command:  peak-motifs  -v 1 -title H3K9ac -i $RSAT/public_html/tmp/www-data/2025/04/08/peak-motifs.2025-04-08.090926_2025-04-08.090926_i19YSh/peak-motifspeak_seq -max_seq_len 2000 -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -motif_db JASPAR2024_CORE_plants_non-redundant tf $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_plants_non-redundant_pfms_transfac.txt -scan_markov 1 -source getfasta -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/2025/04/08/peak-motifs.2025-04-08.090926_2025-04-08.090926_i19YSh

Warning: Not a single pattern was found in file tmp/www-data/2025/04/08/peak-motifs.2025-04-08.090926_2025-04-08.090926_i19YSh/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab