RSAT - peak-motifs result

Analysis: iggonly_ecoli_wenbo_brac_4 (19/03/2026 14:01)

peak-motifs  -v 1 -title iggonly_ecoli_wenbo_brac_4 -i $RSAT/public_html/tmp/www-data/2026/03/19/peak-motifs.2026-03-19.135437_2026-03-19.135437_Ki8YKE/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,positions -nmotifs 10 -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/2026/03/19/peak-motifs.2026-03-19.135437_2026-03-19.135437_Ki8YKE

motif discovery
oligos_6nt_mkv2	oligos_6nt_mkv2_m1 assembly: catgcatg (sig=3.43; e-value=0.00037) RC: catgcatg oligos_6nt_mkv2_m2 assembly: agtaca (sig=1.47; e-value=0.034) RC: tgtact oligos_6nt_mkv2_m3 assembly: actgta (sig=0.96; e-value=0.11) RC: tacagt oligos_6nt_mkv2_m4 assembly: agcgct (sig=0.58; e-value=0.26) RC: agcgct oligos_6nt_mkv2_m5 assembly: ctcctc (sig=0.52; e-value=0.3) RC: gaggag oligos_6nt_mkv2_m6 assembly: aataatt (sig=0.52; e-value=0.3) RC: aattatt oligos_6nt_mkv2_m7 assembly: agataa (sig=0.33; e-value=0.47) RC: ttatct oligos_6nt_mkv2_m8 assembly: cctccct (sig=0.25; e-value=0.56) RC: agggagg oligos_6nt_mkv2_m9 assembly: aatgac (sig=0.14; e-value=0.72) RC: gtcatt oligos_6nt_mkv2_m10 assembly: aattatg (sig=0.10; e-value=0.79) RC: cataatt	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
positions_6nt	positions_6nt_m1 assembly: cactgc (sig=0.51; e-value=0.31) RC: gcagtg positions_6nt_m2 : (sig=; e-value=1) RC: positions_6nt_m3 : (sig=; e-value=1) RC: positions_6nt_m4 : (sig=; e-value=1) RC: positions_6nt_m5 : (sig=; e-value=1) RC: positions_6nt_m6 : (sig=; e-value=1) RC: positions_6nt_m7 : (sig=; e-value=1) RC: positions_6nt_m8 : (sig=; e-value=1) RC: positions_6nt_m9 : (sig=; e-value=1) RC: positions_6nt_m10 : (sig=; e-value=1) RC:	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
oligos_7nt_mkv2	oligos_7nt_mkv2_m1 assembly: actgtac (sig=2.43; e-value=0.0037) RC: gtacagt oligos_7nt_mkv2_m2 assembly: attattat (sig=2.19; e-value=0.0065) RC: ataataat oligos_7nt_mkv2_m3 assembly: tcatgcac (sig=0.87; e-value=0.13) RC: gtgcatga oligos_7nt_mkv2_m4 assembly: tactacta (sig=0.39; e-value=0.41) RC: tagtagta oligos_7nt_mkv2_m5 assembly: tagacta (sig=0.14; e-value=0.72) RC: tagtcta oligos_7nt_mkv2_m6 assembly: agaggag (sig=0.00; e-value=1) RC: ctcctct oligos_7nt_mkv2_m7 : (sig=; e-value=1) RC: oligos_7nt_mkv2_m8 : (sig=; e-value=1) RC: oligos_7nt_mkv2_m9 : (sig=; e-value=1) RC: oligos_7nt_mkv2_m10 : (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]

Motif discovery
Motif 1   oligos_6nt_mkv2_m1	k-mer sig=3.43; evalue=0.00037 dwCATGCATGwh DWCATGCATGWH	[ 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 dwCATGCATGwh Zfp335 MA2002.2 R 7 0.5833 0.735 0.429 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: 11 (3.99%) Max nb of predicted sites per peak: 2  (brac1_R5.macs2_peak_8::scahrs1_100:10004144-10004294(.)) Mean nb of predicted sites per peak: 2.00	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 2   oligos_6nt_mkv2_m2	k-mer sig=1.47; evalue=0.034 cyAGTACAgk MCTGTACTRG	[ 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 cyAGTACAgk NR1I3 MA1534.2 R 8 0.8000 0.722 0.578 NA NA ZBTB32 MA1580.1 D 8 0.6667 0.784 0.523 NA NA Vdr MA0693.4 D 7 0.7000 0.739 0.517 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: 44 (15.94%) Max nb of predicted sites per peak: 3  (brac1_R5.macs2_peak_64::scahrs1_100:132694142-132694292(.)) Mean nb of predicted sites per peak: 1.20	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 3   oligos_6nt_mkv2_m3	k-mer sig=0.96; evalue=0.11 ryACTGTAch DGTACAGTRY	[ 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 ryACTGTAch ZBTB32 MA1580.1 R 10 1.0000 0.941 0.941 NA NA OSR1 MA1542.2 D 7 0.6364 0.765 0.487 NA NA DMRTA2 MA1478.2 R 6 0.6000 0.784 0.471 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: 46 (16.67%) Max nb of predicted sites per peak: 4  (brac1_R5.macs2_peak_64::scahrs1_100:132694142-132694292(.)) Mean nb of predicted sites per peak: 1.26	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 4   oligos_6nt_mkv2_m4	k-mer sig=0.58; evalue=0.26 mcAGCGCTgb VCAGCGCTGK	[ 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 mcAGCGCTgb ZSCAN21 MA2336.1 R 7 0.7000 0.701 0.491 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: 19 (6.88%) Max nb of predicted sites per peak: 4  (brac1_R5.macs2_peak_173::scahrs1_3:54579043-54579193(.)) Mean nb of predicted sites per peak: 2.11	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 5   oligos_6nt_mkv2_m5	k-mer sig=0.52; evalue=0.3 yyCTCCTCyc GRGAGGAGRR	[ 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 yyCTCCTCyc ZNF263 MA0528.3 R 7 0.7000 0.902 0.631 NA NA MAZ MA1522.2 D 8 0.8000 0.765 0.612 NA NA Wt1 MA1627.2 D 9 0.8182 0.719 0.589 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: 29 (10.51%) Max nb of predicted sites per peak: 1  (brac1_R5.macs2_peak_82::scahrs1_100:162945679-162945829(.)) Mean nb of predicted sites per peak: 1.00	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 6   oligos_6nt_mkv2_m6	k-mer sig=0.52; evalue=0.3 wkAATAATTww WWAATTATTMW	[ 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 wkAATAATTww POU4F1 MA0790.2 D 11 0.9167 0.775 0.710 NA NA POU4F3 MA0791.2 D 11 0.9167 0.775 0.710 NA NA HNF1A MA0046.3 D 11 0.8462 0.776 0.656 NA NA Total matches= 106 (103 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: 18 (6.52%) Max nb of predicted sites per peak: 4  (brac1_R5.macs2_peak_118::scahrs1_148:6477735-6477885(.)) Mean nb of predicted sites per peak: 1.44	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 7   oligos_6nt_mkv2_m7	k-mer sig=0.33; evalue=0.47 vgAGATAAwa TWTTATCTCB	[ 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 vgAGATAAwa Gata3 MA0037.5 R 8 0.8000 0.911 0.729 NA NA TRPS1 MA1970.2 R 8 0.8000 0.909 0.728 NA NA GATA6 MA1104.3 R 8 0.8000 0.909 0.727 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: 17 (6.16%) Max nb of predicted sites per peak: 2  (brac1_R5.macs2_peak_231::scahrs1_40:42729036-42729186(.)) Mean nb of predicted sites per peak: 1.06	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 8   oligos_6nt_mkv2_m8	k-mer sig=0.25; evalue=0.56 bkCCTCCCTsy RSAGGGAGGMV	[ 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 bkCCTCCCTsy ZNF148 MA1653.2 D 10 0.9091 0.760 0.691 NA NA MAZ MA1522.2 D 8 0.7273 0.846 0.615 NA NA ZNF263 MA0528.3 R 7 0.6364 0.934 0.595 NA NA Total matches= 21 (18 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: 9 (3.26%) Max nb of predicted sites per peak: 2  (brac1_R5.macs2_peak_224::scahrs1_40:12990473-12990623(.)) Mean nb of predicted sites per peak: 1.11	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 9   oligos_6nt_mkv2_m9	k-mer sig=0.14; evalue=0.72 gmAATGACwk MWGTCATTKC	[ 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 gmAATGACwk NKX6-3 MA1530.2 R 8 0.8000 0.767 0.614 NA NA HOXA5 MA0158.2 D 8 0.8000 0.746 0.597 NA NA HOXD3 MA0912.2 D 8 0.8000 0.717 0.574 NA NA Total matches= 130 (127 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: 37 (13.41%) Max nb of predicted sites per peak: 2  (brac1_R5.macs2_peak_41::scahrs1_100:80765927-80766077(.)) Mean nb of predicted sites per peak: 1.03	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 10   oligos_6nt_mkv2_m10	k-mer sig=0.10; evalue=0.79 akAATTATGwy RWCATAATTMT	[ 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 akAATTATGwy POU4F3 MA0791.2 R 11 0.9167 0.742 0.680 NA NA POU4F1 MA0790.2 R 11 0.9167 0.730 0.669 NA NA LHX5 MA1519.2 D 7 0.6364 0.915 0.582 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 (6.88%) Max nb of predicted sites per peak: 1  (brac1_R5.macs2_peak_99::scahrs1_11:4228347-4228497(.)) Mean nb of predicted sites per peak: 1.00	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 11   positions_6nt_m1	k-mer sig=0.51; evalue=0.31 ygCACTGCmk MKGCAGTGCR	[ 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 ygCACTGCmk ZNF331 MA1726.2 R 9 0.8182 0.704 0.576 NA NA GFI1 MA0038.3 D 9 0.7500 0.748 0.561 NA NA ZSCAN21 MA2336.1 D 6 0.5455 0.832 0.454 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: 25 (9.06%) Max nb of predicted sites per peak: 2  (brac1_R5.macs2_peak_33::scahrs1_100:57048806-57048956(.)) Mean nb of predicted sites per peak: 1.04	[ sites: text ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]

Command:  peak-motifs  -v 1 -title iggonly_ecoli_wenbo_brac_4 -i $RSAT/public_html/tmp/www-data/2026/03/19/peak-motifs.2026-03-19.135437_2026-03-19.135437_Ki8YKE/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,positions -nmotifs 10 -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/2026/03/19/peak-motifs.2026-03-19.135437_2026-03-19.135437_Ki8YKE

Error: Cannot scale matrix with only null values
Error occurred on RSAT site: rsat; host server: rsat; admin: compbio@eead.csic.es

Warning: Matrix file is empty (file size is zero) $RSAT/public_html/tmp/www-data/2026/03/19/peak-motifs.2026-03-19.135437_2026-03-19.135437_Ki8YKE/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_sig_matrices_rescaled.tf

Warning: Input file contained not a single matrix

Error: OpenInputFile: File tmp/www-data/2026/03/19/peak-motifs.2026-03-19.135437_2026-03-19.135437_Ki8YKE/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_sig_sites.ft does not exist.
Error occurred on RSAT site: rsat; host server: rsat; admin: compbio@eead.csic.es

Warning: Matrix file is empty (file size is zero) $RSAT/public_html/tmp/www-data/2026/03/19/peak-motifs.2026-03-19.135437_2026-03-19.135437_Ki8YKE/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices.tf

Warning: Input file contained not a single matrix

Warning: Matrix file is empty (file size is zero) $RSAT/public_html/tmp/www-data/2026/03/19/peak-motifs.2026-03-19.135437_2026-03-19.135437_Ki8YKE/results/oligos_7nt_mkv2/peak-motifs_oligos-2str-noov_7nt_mkv2_pssm_count_matrices.tf

Warning: Input file contained not a single matrix

Warning: Not a single pattern was found in file tmp/www-data/2026/03/19/peak-motifs.2026-03-19.135437_2026-03-19.135437_Ki8YKE/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab