RSAT - peak-motifs result

Analysis: H3Kup (08/04/2025 09:11)

peak-motifs  -v 1 -title H3Kup -i $RSAT/public_html/tmp/www-data/2025/04/08/peak-motifs.2025-04-08.090621_2025-04-08.090621_zBE3cb/peak-motifspeak_seq -max_seq_len 2000 -min_markov -3 -max_markov -3 -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 -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.2025-04-08.090621_2025-04-08.090621_zBE3cb

motif discovery
oligos_6nt_mkv3	oligos_6nt_mkv3_m1 assembly: gccaccaccgt (sig=67.98; e-value=1e-68) RC: acggtggtggc oligos_6nt_mkv3_m2 assembly: gccgccgc (sig=61.13; e-value=7.4e-62) RC: gcggcggc oligos_6nt_mkv3_m3 assembly: aacagaga (sig=56.44; e-value=3.6e-57) RC: tctctgtt oligos_6nt_mkv3_m4 assembly: aaaccctaaa (sig=51.34; e-value=4.6e-52) RC: tttagggttt oligos_6nt_mkv3_m5 assembly: agattcat (sig=40.33; e-value=4.7e-41) RC: atgaatct	[ 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_mkv4	oligos_7nt_mkv4_m1 assembly: ctaaaccctaa (sig=41.63; e-value=2.3e-42) RC: ttagggtttag oligos_7nt_mkv4_m2 assembly: gaaacagagc (sig=30.02; e-value=9.5e-31) RC: gctctgtttc oligos_7nt_mkv4_m3 assembly: caagaaca (sig=26.05; e-value=8.9e-27) RC: tgttcttg oligos_7nt_mkv4_m4 assembly: tcaaatcc (sig=18.01; e-value=9.8e-19) RC: ggatttga oligos_7nt_mkv4_m5 assembly: tcttcctc (sig=15.26; e-value=5.5e-16) RC: gaggaaga	[ 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_mkv3_m1	k-mer sig=67.98; evalue=1e-68 ccgCCaCCaCCGycg CGRCGGTGGTGGCGG	[ 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 ccgCCaCCaCCGycg ERF014 MA1222.1 D 15 1.0000 0.865 0.865 NA NA DREB2D MA1250.2 D 14 0.9333 0.895 0.836 NA NA ERF057 MA1753.2 D 14 0.9333 0.848 0.792 NA NA Total matches= 57 (54 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: 718 (43.36%) Max nb of predicted sites per peak: 26  (2:18145600-18147599(.)) Mean nb of predicted sites per peak: 2.94	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 2   oligos_6nt_mkv3_m2	k-mer sig=61.13; evalue=7.4e-62 ccgCCGCCGCcg CGGCGGCGGCGG	[ 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 ccgCCGCCGCcg LOB MA2022.2 D 12 0.9231 0.956 0.883 NA NA ERF115 MA2013.2 D 11 0.9167 0.950 0.871 NA NA ERF073 MA1754.2 D 11 0.9167 0.949 0.870 NA NA Total matches= 68 (65 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: 655 (39.55%) Max nb of predicted sites per peak: 22  (2:14857000-14857999(.)) Mean nb of predicted sites per peak: 3.16	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 3   oligos_6nt_mkv3_m3	k-mer sig=56.44; evalue=3.6e-57 raAACAGAGarr YYTCTCTGTTTY	[ 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 raAACAGAGarr REF6 MA1415.2 D 9 0.7500 0.983 0.737 NA NA AT3G10030 MA1662.2 D 8 0.6667 0.834 0.556 NA NA TEM1 MA1800.1 D 8 0.6667 0.718 0.478 NA NA Total matches= 3		[ 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: 410 (24.76%) Max nb of predicted sites per peak: 8  (3:9302000-9303599(.)) Mean nb of predicted sites per peak: 1.48	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 4   oligos_6nt_mkv3_m4	k-mer sig=51.34; evalue=4.6e-52 mmAAACCCtAaamm KKTTTAGGGTTTKK	[ 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 mmAAACCCtAaamm AT1G72740 MA1353.2 R 11 0.7857 0.969 0.761 NA NA TRB2 MA1355.2 D 11 0.7857 0.890 0.700 NA NA TRB1 MA2032.2 D 9 0.6429 0.972 0.625 NA NA Total matches= 13 (10 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: 513 (30.98%) Max nb of predicted sites per peak: 5  (5:506200-507199(.)) Mean nb of predicted sites per peak: 1.31	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 5   oligos_6nt_mkv3_m5	k-mer sig=40.33; evalue=4.7e-41 avAGATTCATsw WSATGAATCTBT	[ 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 avAGATTCATsw HHO5 MA1164.2 D 8 0.6667 0.954 0.636 NA NA EIL3 MA1751.2 D 8 0.6667 0.889 0.592 NA NA HHO3 MA1386.3 D 8 0.6667 0.875 0.583 NA NA Total matches= 17 (14 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: 150 (9.06%) Max nb of predicted sites per peak: 2  (5:8221400-8221999(.)) Mean nb of predicted sites per peak: 1.09	[ sites: text ] [ 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	[ sites: text ] [ 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	[ sites: text ] [ 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	[ sites: text ] [ 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	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 10   oligos_7nt_mkv4_m1	k-mer sig=41.63; evalue=2.3e-42 myctaAACCCtAamy RKTTAGGGTTTAGRK	[ 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 myctaAACCCtAamy AT1G72740 MA1353.2 R 11 0.7333 0.983 0.721 NA NA TRB2 MA1355.2 D 11 0.7333 0.911 0.668 NA NA TRP2 MA1356.1 D 15 0.7143 0.880 0.629 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: 491 (29.65%) Max nb of predicted sites per peak: 5  (5:21735200-21736799(.)) Mean nb of predicted sites per peak: 1.32	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 11   oligos_7nt_mkv4_m2	k-mer sig=30.02; evalue=9.5e-31 mrGAAACAGAGcar YTGCTCTGTTTCYK	[ 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 mrGAAACAGAGcar REF6 MA1415.2 D 9 0.6429 0.957 0.615 NA NA NTL8 MA1678.3 D 7 0.4667 0.886 0.413 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: 509 (30.74%) Max nb of predicted sites per peak: 7  (3:9302000-9303599(.)) Mean nb of predicted sites per peak: 1.48	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 12   oligos_7nt_mkv4_m3	k-mer sig=26.05; evalue=8.9e-27 aaCAAGAACAav BTTGTTCTTGTT	[ 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 aaCAAGAACAav SBP6 MA2420.1 D 8 0.6667 0.755 0.504 NA NA NAC053 MA2049.2 D 7 0.5833 0.823 0.480 NA NA NAC078 MA1677.2 D 7 0.5833 0.822 0.480 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: 401 (24.21%) Max nb of predicted sites per peak: 6  (5:1239000-1240199(.)) Mean nb of predicted sites per peak: 1.41	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 13   oligos_7nt_mkv4_m4	k-mer sig=18.01; evalue=9.8e-19 chTCAAATCCwh DWGGATTTGADG	[ 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 chTCAAATCCwh TCX3 MA1682.2 D 10 0.7143 0.734 0.525 NA NA PK25870.1 MA2089.1 D 7 0.5833 0.769 0.449 NA NA WRKY57 MA1089.2 D 6 0.5000 0.843 0.422 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: 199 (12.02%) Max nb of predicted sites per peak: 3  (3:21737800-21739399(.)) Mean nb of predicted sites per peak: 1.11	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 14   oligos_7nt_mkv4_m5	k-mer sig=15.26; evalue=5.5e-16 yyTCTTCCTCyt ARGAGGAAGARR	[ 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 yyTCTTCCTCyt NTL8 MA1678.3 R 7 0.5385 0.842 0.453 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: 745 (44.99%) Max nb of predicted sites per peak: 9  (5:26041000-26042599(.)) Mean nb of predicted sites per peak: 2.08	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]

Command:  peak-motifs  -v 1 -title H3Kup -i $RSAT/public_html/tmp/www-data/2025/04/08/peak-motifs.2025-04-08.090621_2025-04-08.090621_zBE3cb/peak-motifspeak_seq -max_seq_len 2000 -min_markov -3 -max_markov -3 -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 -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.2025-04-08.090621_2025-04-08.090621_zBE3cb

Warning: Not a single pattern was found in file tmp/www-data/2025/04/08/peak-motifs.2025-04-08.090621_2025-04-08.090621_zBE3cb/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab