RSAT - peak-motifs result

Analysis: MEyellowgreen (21/05/2025 03:41)

peak-motifs  -v 1 -title MEyellowgreen -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/peak-motifspeak_seq -markov auto -disco oligos,dyads,positions -nmotifs 5 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -offset 200 -motif_db footprintDB-plants tf $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2

motif discovery
oligos_6nt_mkv2	oligos_6nt_mkv2_m1 assembly: gggacaga (sig=2.45; e-value=0.0035) RC: tctgtccc oligos_6nt_mkv2_m2 assembly: tagtaa (sig=0.53; e-value=0.3) RC: ttacta oligos_6nt_mkv2_m3 assembly: agatag (sig=0.42; e-value=0.38) RC: ctatct 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 ]
positions_6nt	Not a single significant pattern	[positions_6nt]
oligos_7nt_mkv2	oligos_7nt_mkv2_m1 assembly: cctcttc (sig=0.28; e-value=0.52) RC: gaagagg oligos_7nt_mkv2_m2 assembly: ccttttc (sig=0.04; e-value=0.91) RC: gaaaagg 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 ]
positions_7nt	Not a single significant pattern	[positions_7nt]
oligos_8nt_mkv2	oligos_8nt_mkv2_m1 assembly: cttactac (sig=1.55; e-value=0.028) RC: gtagtaag oligos_8nt_mkv2_m2 assembly: gaaaaggc (sig=0.89; e-value=0.13) RC: gccttttc oligos_8nt_mkv2_m3 assembly: ggaggaga (sig=0.43; e-value=0.37) RC: tctcctcc oligos_8nt_mkv2_m4 assembly: gtgacaga (sig=0.23; e-value=0.59) RC: tctgtcac oligos_8nt_mkv2_m5 assembly: gtggagga (sig=0.14; e-value=0.72) RC: tcctccac	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
positions_8nt	Not a single significant pattern	[positions_8nt]
dyads	dyads_m1 assembly: aatgatt (sig=1.83; e-value=0.015) RC: aatcatt dyads_m2 assembly: ggagagaagg (sig=1.72; e-value=0.019) RC: ccttctctcc dyads_m3 assembly: cttnnnnnnnnttc (sig=1.27; e-value=0.054) RC: gaannnnnnnnaag dyads_m4 assembly: accaaa (sig=1.15; e-value=0.071) RC: tttggt dyads_m5 assembly: cgannaca (sig=1.08; e-value=0.083) RC: tgtnntcg	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]

Motif discovery
Motif 1   oligos_6nt_mkv2_m1	k-mer sig=2.45; evalue=0.0035 wrGGGACaGara TYTCTGTCCCYW	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wrGGGACaGara KNAT3:M0855_1.02:CISBP KNAT3/M0855_1.02/CISBP R 10 0.8333 0.709 0.591 NA NA ARF13:EEAD0027:EEADannot ARF13/EEAD0027/EEADannot D 10 0.8333 0.701 0.584 NA NA ARF14:EEAD0028:EEADannot ARF14/EEAD0028/EEADannot D 8 0.6667 0.854 0.569 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: 16 (18.18%) Max nb of predicted sites per peak: 2  (gene-Lalb_Chr13g0303091) Mean nb of predicted sites per peak: 1.06	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 2   oligos_6nt_mkv2_m2	k-mer sig=0.53; evalue=0.3 rgTAGTAAgd HCTTACTACY	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rgTAGTAAgd ZAT9:UN0417.1:JASPAR ZAT9/UN0417.1/JASPAR R 8 0.8000 0.865 0.692 NA NA At3g60580.DAP:M0307:AthalianaCistrome At3g60580.DAP/M0307/AthalianaCistrome D 8 0.8000 0.865 0.692 NA NA ChFLCrsat:EEAD0164:EEADannot ChFLCrsat/EEAD0164/EEADannot D 10 0.8333 0.736 0.614 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: 26 (29.55%) Max nb of predicted sites per peak: 3  (gene-Lalb_Chr21g0307691) Mean nb of predicted sites per peak: 1.27	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 3   oligos_6nt_mkv2_m3	k-mer sig=0.42; evalue=0.38 krAGATaGrg CYCTATCTYM	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor krAGATaGrg PK29550.1:M1314_1.02:CISBP PK29550.1/M1314_1.02/CISBP D 10 1.0000 0.728 0.728 NA NA LOC_Os08g06110:M1365_1.02:CISBP LOC_Os08g06110/M1365_1.02/CISBP D 9 0.9000 0.769 0.692 NA NA AT5G08520:M1339_1.02:CISBP AT5G08520/M1339_1.02/CISBP D 9 0.9000 0.748 0.673 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: 30 (34.09%) Max nb of predicted sites per peak: 3  (gene-Lalb_Chr22g0361641) Mean nb of predicted sites per peak: 1.27	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 4   oligos_7nt_mkv2_m1	k-mer sig=0.28; evalue=0.52 yyCCTCtTChy RDGAAGAGGRR	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor yyCCTCtTChy TGA5_2:EEAD0137:EEADannot TGA5_2/EEAD0137/EEADannot R 11 0.7333 0.768 0.563 NA NA ONAC127:UN0429.2:JASPAR ONAC127/UN0429.2/JASPAR R 7 0.6364 0.864 0.550 NA NA ONAC127:UN0430.1:JASPAR ONAC127/UN0430.1/JASPAR R 10 0.7692 0.705 0.542 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: 17 (19.32%) Max nb of predicted sites per peak: 2  (gene-Lalb_Chr05g0214501) Mean nb of predicted sites per peak: 1.06	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 5   oligos_7nt_mkv2_m2	k-mer sig=0.04; evalue=0.91 wkCCttttCty RAGAAAAGGMW	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wkCCttttCty Zm00001d044785:MA1827.1:JASPAR Zm00001d044785/MA1827.1/JASPAR D 11 1.0000 0.783 0.783 NA NA Zm00001d044409:MA1825.1:JASPAR Zm00001d044409/MA1825.1/JASPAR D 11 1.0000 0.731 0.731 NA NA YAB4:MA1186.2:JASPAR YAB4/MA1186.2/JASPAR D 11 1.0000 0.708 0.708 NA NA Total matches= 69 (66 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: 21 (23.86%) Max nb of predicted sites per peak: 6  (gene-Lalb_Chr07g0178161) Mean nb of predicted sites per peak: 1.38	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 6   oligos_8nt_mkv2_m1	k-mer sig=1.55; evalue=0.028 wyCTTaCTACww WWGTAGTAAGRW	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wyCTTaCTACww ChFLCrsat:EEAD0164:EEADannot ChFLCrsat/EEAD0164/EEADannot R 12 1.0000 0.704 0.704 NA NA At3g60580.DAP:M0307:AthalianaCistrome At3g60580.DAP/M0307/AthalianaCistrome R 8 0.6667 0.832 0.555 NA NA ZAT9:UN0417.1:JASPAR ZAT9/UN0417.1/JASPAR D 8 0.6667 0.832 0.555 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: 16 (18.18%) Max nb of predicted sites per peak: 4  (gene-Lalb_Chr21g0307691) Mean nb of predicted sites per peak: 1.25	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 7   oligos_8nt_mkv2_m2	k-mer sig=0.89; evalue=0.13 rkGAaAaGGCaw WTGCCTTTTCMY	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rkGAaAaGGCaw Zm00001d044785:MA1827.1:JASPAR Zm00001d044785/MA1827.1/JASPAR R 11 0.9167 0.730 0.669 NA NA DOF4.2:MA1273.2:JASPAR DOF4.2/MA1273.2/JASPAR D 10 0.7692 0.828 0.637 NA NA NAC69:MA2018.1:JASPAR NAC69/MA2018.1/JASPAR D 11 0.8462 0.730 0.618 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: 21 (23.86%) Max nb of predicted sites per peak: 6  (gene-Lalb_Chr07g0178161) Mean nb of predicted sites per peak: 1.48	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 8   oligos_8nt_mkv2_m3	k-mer sig=0.43; evalue=0.37 GwGGaGGaGarr YYTCTCCTCCWC	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor GwGGaGGaGarr NAC:EEAD0003:EEADannot NAC/EEAD0003/EEADannot R 10 0.7692 0.758 0.583 NA NA Zm00001d013777:UN0434.2:JASPAR Zm00001d013777/UN0434.2/JASPAR R 9 0.7500 0.704 0.528 NA NA ChCUC1-chipseq:EEAD0152:EEADannot ChCUC1-chipseq/EEAD0152/EEADannot R 8 0.6667 0.778 0.519 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: 20 (22.73%) Max nb of predicted sites per peak: 12  (gene-Lalb_Chr21g0307691) Mean nb of predicted sites per peak: 2.05	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 9   oligos_8nt_mkv2_m4	k-mer sig=0.23; evalue=0.59 awGtGaCaGAkr YMTCTGTCACWT	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor awGtGaCaGAkr GLYMA-07G038400:MA1809.1:JASPAR GLYMA-07G038400/MA1809.1/JASPAR R 11 0.9167 0.791 0.725 NA NA GRF6:MA2016.1:JASPAR GRF6/MA2016.1/JASPAR R 10 0.8333 0.741 0.618 NA NA KNAT3:M0855_1.02:CISBP KNAT3/M0855_1.02/CISBP R 10 0.8333 0.716 0.596 NA NA Total matches= 19 (16 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: 16 (18.18%) Max nb of predicted sites per peak: 3  (gene-Lalb_Chr13g0302971) Mean nb of predicted sites per peak: 1.56	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 10   oligos_8nt_mkv2_m5	k-mer sig=0.14; evalue=0.72 dvGtGGaGGArr YYTCCTCCACBH	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor dvGtGGaGGArr ChCUC1-chipseq:EEAD0152:EEADannot ChCUC1-chipseq/EEAD0152/EEADannot R 8 0.6667 0.827 0.551 NA NA TF3A.DAP:M0328:AthalianaCistrome TF3A.DAP/M0328/AthalianaCistrome R 12 0.6316 0.781 0.493 NA NA AT3G57600:MA1242.1:JASPAR AT3G57600/MA1242.1/JASPAR R 9 0.6429 0.708 0.455 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: 21 (23.86%) Max nb of predicted sites per peak: 10  (gene-Lalb_Chr21g0307691) Mean nb of predicted sites per peak: 1.71	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 11   dyads_m1	k-mer sig=1.83; evalue=0.015 mbAATGATkry RYMATCATTVK	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor mbAATGATkry HAT1.ampDAP:M0445:AthalianaCistrome HAT1.ampDAP/M0445/AthalianaCistrome D 11 1.0000 0.927 0.927 NA NA HAT2.ampDAP:M0432:AthalianaCistrome HAT2.ampDAP/M0432/AthalianaCistrome R 11 1.0000 0.918 0.918 NA NA ATHB18.ampDAP:M0433:AthalianaCistrome ATHB18.ampDAP/M0433/AthalianaCistrome D 11 1.0000 0.895 0.895 NA NA Total matches= 112 (109 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: 22 (25.00%) Max nb of predicted sites per peak: 3  (gene-Lalb_Chr01g0001801) Mean nb of predicted sites per peak: 1.14	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 12   dyads_m2	k-mer sig=1.72; evalue=0.019 rrGGaGaGaaGGrk MYCCTTCTCTCCYY	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rrGGaGaGaaGGrk ARF1:ARF1:Athamap ARF1/ARF1/Athamap R 11 0.7857 0.736 0.579 NA NA Zm00001d044785:MA1827.1:JASPAR Zm00001d044785/MA1827.1/JASPAR R 11 0.7857 0.731 0.574 NA NA Zm00001d044409:MA1825.1:JASPAR Zm00001d044409/MA1825.1/JASPAR R 11 0.7857 0.700 0.550 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: 35 (39.77%) Max nb of predicted sites per peak: 5  (gene-Lalb_Chr00c24g0406831) Mean nb of predicted sites per peak: 1.29	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 13   dyads_m3	k-mer sig=1.27; evalue=0.054 mmCTTcywyycmyTTCmb VKGAARKGRRWRGAAGKK	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor mmCTTcywyycmyTTCmb DOF3.2:MA1270.2:JASPAR DOF3.2/MA1270.2/JASPAR D 15 0.7895 0.741 0.585 NA NA dof24.ampDAP:M0269:AthalianaCistrome dof24.ampDAP/M0269/AthalianaCistrome R 14 0.7368 0.737 0.543 NA NA CDF3.DAP:M0268:AthalianaCistrome CDF3.DAP/M0268/AthalianaCistrome R 15 0.6818 0.755 0.515 NA NA Total matches= 26 (23 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: 29 (32.95%) Max nb of predicted sites per peak: 3  (gene-Lalb_Chr07g0178161) Mean nb of predicted sites per peak: 1.07	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 14   dyads_m4	k-mer sig=1.15; evalue=0.071 ssACCAAArh DYTTTGGTSS	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ssACCAAArh MYB59:MYB59:ArabidopsisPBM MYB59/MYB59/ArabidopsisPBM R 10 1.0000 0.749 0.749 NA NA MYB41:MA1771.2:JASPAR MYB41/MA1771.2/JASPAR D 10 1.0000 0.720 0.720 NA NA MYB93:MA2025.2:JASPAR MYB93/MA2025.2/JASPAR D 8 0.8000 0.884 0.708 NA NA Total matches= 98 (95 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: 19 (21.59%) Max nb of predicted sites per peak: 3  (gene-Lalb_Chr21g0305331) Mean nb of predicted sites per peak: 1.16	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 15   dyads_m5	k-mer sig=1.08; evalue=0.083 rsCGambaCacv BGTGTVKTCGSY	[ k-mers: statistics assemblies ] [ matrix: tab_format transfac_format ]
footprintDB-plants name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rsCGambaCacv HMG-1:MA0044.1:JASPAR HMG-1/MA0044.1/JASPAR R 9 0.7500 0.768 0.576 NA NA EDF3:M0080_1.02:CISBP EDF3/M0080_1.02/CISBP D 8 0.6667 0.703 0.469 NA NA REM1:UN0407.2:JASPAR REM1/UN0407.2/JASPAR R 7 0.5833 0.739 0.431 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: 14 (15.91%) Max nb of predicted sites per peak: 3  (gene-Lalb_Chr24g0398961) Mean nb of predicted sites per peak: 1.36	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]

Command:  peak-motifs  -v 1 -title MEyellowgreen -i $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/peak-motifspeak_seq -markov auto -disco oligos,dyads,positions -nmotifs 5 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -offset 200 -motif_db footprintDB-plants tf $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2

Warning: Not a single pattern was found in file tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab

Warning: Not a single pattern was found in file tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab

Warning: Not a single pattern was found in file tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/positions_8nt/peak-motifs_positions-2str-noov_8nt_ci50.tab