RSA-tools - peak-motifs result

Analysis: ChIP-seq_FNR_E._coli_tunned_parameters_dyad (05/09/2014 20:54)

peak-motifs  -v 1 -title ChIP-seq_FNR_E._coli_tunned_parameters_dyad -i $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,dyads,positions -nmotifs 5 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -motif_db regulonDB tf $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf -motif_db footprintDB tf $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -scan_markov 1 -source galaxy -task purge,seqlen,composition,disco,merge_words,collect_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/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR

motif discovery
oligos_6nt_mkv3	oligos_6nt_mkv3_m1 asmb: gaagagat (sig=1.01) RC: atctcttc oligos_6nt_mkv3_m2 asmb: atcgac (sig=0.79) RC: gtcgat oligos_6nt_mkv3_m3 asmb: acaaaa (sig=0.71) RC: ttttgt oligos_6nt_mkv3_m4 asmb: gctaaa (sig=0.62) RC: tttagc oligos_6nt_mkv3_m5 asmb: ggtaga (sig=0.49) RC: tctacc	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
positions_6nt	positions_6nt_m1 asmb: atcaaa (sig=3.43) RC: tttgat positions_6nt_m2 asmb: ccctagc (sig=1.54) RC: gctaggg positions_6nt_m3 asmb: aaaatat (sig=0.87) RC: atatttt positions_6nt_m4 asmb: atcgcc (sig=0.46) RC: ggcgat positions_6nt_m5 asmb: atggga (sig=0.24) RC: tcccat	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
oligos_7nt_mkv4	oligos_7nt_mkv4_m1 asmb: gacgtgc (sig=0.53) RC: gcacgtc oligos_7nt_mkv4_m2 asmb: atccaca (sig=0.47) RC: tgtggat oligos_7nt_mkv4_m3 asmb: caaattc (sig=0.19) RC: gaatttg oligos_7nt_mkv4_m4 : (sig=) RC: oligos_7nt_mkv4_m5 : (sig=) RC:	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
positions_7nt	positions_7nt_m1 asmb: aggggcc (sig=5.71) RC: ggcccct positions_7nt_m2 asmb: atataag (sig=3.32) RC: cttatat positions_7nt_m3 asmb: ctcaggc (sig=2.92) RC: gcctgag positions_7nt_m4 asmb: cccctagcca (sig=2.07) RC: tggctagggg positions_7nt_m5 asmb: cactcca (sig=1.51) RC: tggagtg	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
oligos_8nt_mkv5	oligos_8nt_mkv5_m1 asmb: attcgaac (sig=0.44) RC: gttcgaat oligos_8nt_mkv5_m2 asmb: ggattcga (sig=0.32) RC: tcgaatcc oligos_8nt_mkv5_m3 : (sig=) RC: oligos_8nt_mkv5_m4 : (sig=) RC: oligos_8nt_mkv5_m5 : (sig=) RC:	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
positions_8nt	positions_8nt_m1 asmb: caggccgat (sig=8.80) RC: atcggcctg positions_8nt_m2 asmb: tcgttggct (sig=4.63) RC: agccaacga positions_8nt_m3 asmb: tggtaatt (sig=4.63) RC: aattacca positions_8nt_m4 asmb: aagggggaga (sig=4.63) RC: tctccccctt positions_8nt_m5 asmb: aacccgga (sig=4.63) RC: tccgggtt	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]
dyads	dyads_m1 asmb: atcgccagcgt (sig=23.80) RC: acgctggcgat dyads_m2 asmb: cctggcgat (sig=12.03) RC: atcgccagg dyads_m3 asmb: tcctgac (sig=11.17) RC: gtcagga dyads_m4 asmb: tccagac (sig=11.13) RC: gtctgga dyads_m5 asmb: acgctgga (sig=10.16) RC: tccagcgt	[ discovered words: text ] [ assembly: text sig matrices ] [ matrices: tab format transfac format ]

Motif discovery
Motif 1   oligos_6nt_mkv3	ckGAAGAGATCr YGATCTCTTCMG	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ckGAAGAGATCr Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ckGAAGAGATCr 2470_MA0080.1_JASPAR_CORE_2009_ 2470_MA0080.1_JASPAR_CORE_2009_ D 6 0.5000 0.878 0.439 hkGAAG...... sGGAAs 5987_1awc_A_3D-footprint_20130124_ 5987_1awc_A_3D-footprint_20130124_ D 6 0.5000 0.857 0.428 hkGAAG...... cGGAAg 108_MA0062.1_JASPAR_CORE_2009_ 108_MA0062.1_JASPAR_CORE_2009_ D 8 0.5714 0.809 0.462 hkGAAGAG.... ..CGGAAGws Total maches= 10 (7 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 (23.85%) Max nb of predicted sites per peak: 3  (?_gi|49175990|ref|NC_000913.2|_3084066_3085778_+) 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 2   positions_6nt_m1	rkATCAAAsd HSTTTGATMY	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rkATCAAAsd Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rkATCAAAsd 6733_4euw_A_3D-footprint_20130124_ 6733_4euw_A_3D-footprint_20130124_ D 6 0.6000 0.970 0.582 ...TCAAAs. TcAAAg 1939_PB0082.1_JASPAR_CORE_2009_ 1939_PB0082.1_JASPAR_CORE_2009_ D 10 0.5882 0.894 0.526 rkATCAAAsd ...asATCAAAGg.... 3755_UP00058_UniPROBE_20120919_ 3755_UP00058_UniPROBE_20120919_ D 10 0.5882 0.893 0.525 rkATCAAAsd ...wsATCAAAGg.... Total maches= 51 (48 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 (14.68%) Max nb of predicted sites per peak: 2  (?_gi|49175990|ref|NC_000913.2|_2410790_2412114_+) Mean nb of predicted sites per peak: 1.12	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 3   positions_6nt_m2	TCCCCTAGCGC GCGCTAGGGGA	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor TCCCCTAGCGC HipB ECK120026325 D 11 0.5789 0.850 0.492 TCCCCTAGCGC ..TCCbbKWdhGM...... Total maches= 1		[ match table: html text ] [ alignments (logos): html text ]
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor TCCCCTAGCGC 2623_MA0396.1_JASPAR_CORE_2009_ 2623_MA0396.1_JASPAR_CORE_2009_ D 8 0.6667 0.837 0.558 ...CCTAGCGC rcTAGCGc. 3076_HipB_RegulonDB_7.5_ 3076_HipB_RegulonDB_7.5_ D 11 0.5789 0.850 0.492 TCCCCTAGCGC ..TCCbbKWdhGM...... 2588_MA0342.1_JASPAR_CORE_2009_ 2588_MA0342.1_JASPAR_CORE_2009_ R 5 0.4545 0.994 0.452 .CCCCT..... CCCCT Total maches= 16 (13 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: 1 (0.92%) Max nb of predicted sites per peak: 1  (?_gi|49175990|ref|NC_000913.2|_1734954_1736249_+) Mean nb of predicted sites per peak: 1.00	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 4   positions_7nt_m1	vsAGGGGCCGG CCGGCCCCTSB	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor vsAGGGGCCGG Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor vsAGGGGCCGG 2588_MA0342.1_JASPAR_CORE_2009_ 2588_MA0342.1_JASPAR_CORE_2009_ D 5 0.4545 0.994 0.452 ..AGGGG.... AGGGG 2615_MA0381.1_JASPAR_CORE_2009_ 2615_MA0381.1_JASPAR_CORE_2009_ D 6 0.5455 0.926 0.505 .....GGCCgg GGCCrk 2604_MA0366.1_JASPAR_CORE_2009_ 2604_MA0366.1_JASPAR_CORE_2009_ D 5 0.4545 0.990 0.450 ..AGGGG.... AGGGG Total maches= 15 (12 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: 11 (10.09%) Max nb of predicted sites per peak: 3  (?_gi|49175990|ref|NC_000913.2|_2944763_2946198_+) Mean nb of predicted sites per peak: 1.18	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 5   positions_7nt_m2	wwATATAAGkb VMCTTATATWW	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wwATATAAGkb Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wwATATAAGkb 2613_MA0379.1_JASPAR_CORE_2009_ 2613_MA0379.1_JASPAR_CORE_2009_ D 5 0.4545 0.999 0.454 ..ATATA.... ATATA 6327_1tgh_A_3D-footprint_20130124_ 6327_1tgh_A_3D-footprint_20130124_ D 7 0.5833 0.890 0.519 wwATATA.... .AtATATA 6272_1qn7_A_3D-footprint_20130124_ 6272_1qn7_A_3D-footprint_20130124_ R 8 0.7273 0.947 0.689 .wATATAAG.. TATATAAG Total maches= 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: 7 (6.42%) Max nb of predicted sites per peak: 2  (?_gi|49175990|ref|NC_000913.2|_2341114_2343212_+) Mean nb of predicted sites per peak: 1.14	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 6   positions_7nt_m3	sgCTCAGGCgr YCGCCTGAGCS	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor sgCTCAGGCgr Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor sgCTCAGGCgr 5875_TFAP2B_DBD_2_HumanTF_1.0_ 5875_TFAP2B_DBD_2_HumanTF_1.0_ D 10 0.8333 0.785 0.654 sgCTCAGGCg. .GCCysAGGCd 5902_Tcfap2a_DBD_2_HumanTF_1.0_ 5902_Tcfap2a_DBD_2_HumanTF_1.0_ D 10 0.8333 0.785 0.654 sgCTCAGGCg. .GCCysAGGCd 6491_2pe5_C_3D-footprint_20130124_ 6491_2pe5_C_3D-footprint_20130124_ D 5 0.4545 0.951 0.432 .gCTCA..... gcTCA Total maches= 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: 15 (13.76%) Max nb of predicted sites per peak: 2  (?_gi|49175990|ref|NC_000913.2|_4174949_4179737_+) Mean nb of predicted sites per peak: 1.07	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 7   positions_7nt_m4	dymCCCyAGCCAyy RRTGGCTRGGGKRH	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor dymCCCyAGCCAyy Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor dymCCCyAGCCAyy 2547_MA0285.1_JASPAR_CORE_2009_ 2547_MA0285.1_JASPAR_CORE_2009_ D 9 0.6429 0.766 0.492 ....CCyAGCCAy. cwmmGCCmC 2733_PF0046.1_JASPAR_CORE_2009_ 2733_PF0046.1_JASPAR_CORE_2009_ R 8 0.5714 0.753 0.430 ......yAGCCAyy CAGCCAAW Total maches= 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: 20 (18.35%) Max nb of predicted sites per peak: 5  (?_gi|49175990|ref|NC_000913.2|_695647_696755_+) Mean nb of predicted sites per peak: 1.25	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 8   positions_7nt_m5	wkCACTCCASg CSTGGAGTGMW	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wkCACTCCASg Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wkCACTCCASg 2858_PF0171.1_JASPAR_CORE_2009_ 2858_PF0171.1_JASPAR_CORE_2009_ D 7 0.4667 0.926 0.432 ....CTCCAsg CTCCAsG.... 5958_1a0a_B_3D-footprint_20130124_ 5958_1a0a_B_3D-footprint_20130124_ D 5 0.4545 0.924 0.420 ......CCAsg CCAcg 5978_1am9_AB_3D-footprint_20130124_ 5978_1am9_AB_3D-footprint_20130124_ D 10 0.9091 0.772 0.702 wkCACTCCAs. aTCACCCCAC Total maches= 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: 13 (11.93%) Max nb of predicted sites per peak: 1  (?_gi|49175990|ref|NC_000913.2|_876847_878023_+) Mean nb of predicted sites per peak: 1.00	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 9   positions_8nt_m1	akCAGGCCGATsc GSATCGGCCTGMT	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor akCAGGCCGATsc Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor akCAGGCCGATsc 2429_MA0035.1_JASPAR_CORE_2009_ 2429_MA0035.1_JASPAR_CORE_2009_ D 6 0.4615 0.872 0.402 .......CGATvc sGATgs 5095_SigD_2_DBTBS_1.0_ 5095_SigD_2_DBTBS_1.0_ D 8 0.6154 0.860 0.529 .....GCCGATvc GCCGATAT Total maches= 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: 47 (43.12%) Max nb of predicted sites per peak: 3  (?_gi|49175990|ref|NC_000913.2|_2944763_2946198_+) Mean nb of predicted sites per peak: 1.19	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 10   positions_8nt_m2	smTCGTTGGCTgv BCAGCCAACGAKS	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor smTCGTTGGCTgv Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor smTCGTTGGCTgv 7524_NFIA+NFIB+NFIC+NFIX_si_HOCOMOCO_v9_ 7524_NFIA+NFIB+NFIC+NFIX_si_HOCOMOCO_v9_ D 6 0.4615 0.908 0.419 .....TTGGCT.. TTGGCw 7282_WRKY45_ArabidopsisPBM_20140210_ 7282_WRKY45_ArabidopsisPBM_20140210_ D 10 0.7692 0.756 0.582 ..TCGTTGGCTd. dCGTTGACya Total maches= 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: 20 (18.35%) Max nb of predicted sites per peak: 2  (?_gi|49175990|ref|NC_000913.2|_2907250_2908427_+) Mean nb of predicted sites per peak: 1.15	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 11   positions_8nt_m3	dsTGGTAAtTcw WGAATTACCASH	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor dsTGGTAAtTcw Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor dsTGGTAAtTcw 7458_HXD4_f1_HOCOMOCO_v9_ 7458_HXD4_f1_HOCOMOCO_v9_ D 7 0.5833 0.931 0.543 .....TAATTcw TAATTkw 6107_1hdd_C_3D-footprint_20130124_ 6107_1hdd_C_3D-footprint_20130124_ D 7 0.5833 0.895 0.522 ....GTAATTc. GTAAtna 7341_DLX2_f1_HOCOMOCO_v9_ 7341_DLX2_f1_HOCOMOCO_v9_ D 7 0.5833 0.903 0.527 .....TAATTcw TAATTrt Total maches= 86 (83 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 (32.11%) Max nb of predicted sites per peak: 2  (?_gi|49175990|ref|NC_000913.2|_399733_400893_+) Mean nb of predicted sites per peak: 1.11	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 12   positions_8nt_m4	sgAAGGGGGrGAyv BRTCYCCCCCTTCS	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor sgAAGGGGGrGAyv Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor sgAAGGGGGrGAyv 2529_MA0163.1_JASPAR_CORE_2009_ 2529_MA0163.1_JASPAR_CORE_2009_ D 9 0.4737 0.884 0.419 sgAAGGGGG..... .....CcwmGGGGG 2448_MA0057.1_JASPAR_CORE_2009_ 2448_MA0057.1_JASPAR_CORE_2009_ D 10 0.7143 0.783 0.559 .gAAGGGGGrG... bkAKGGGkrr 7511_MZF1_f1_HOCOMOCO_v9_ 7511_MZF1_f1_HOCOMOCO_v9_ D 8 0.5714 0.796 0.455 .....GGGGrGAy. rkGGGGAw Total maches= 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: 20 (18.35%) Max nb of predicted sites per peak: 3  (?_gi|49175990|ref|NC_000913.2|_876847_878023_+) Mean nb of predicted sites per peak: 1.50	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 13   positions_8nt_m5	dtAACCCGGAtg CATCCGGGTTAH	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor dtAACCCGGAtg Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor dtAACCCGGAtg 5241_ELF1_full_HumanTF_1.0_ 5241_ELF1_full_HumanTF_1.0_ D 10 0.7143 0.875 0.625 ..AACCCGGAtg AACCCGGAAG.. 5801_SPDEF_DBD_1_HumanTF_1.0_ 5801_SPDEF_DBD_1_HumanTF_1.0_ D 9 0.6429 0.896 0.576 ...ACCCGGAtg AmCCGGATg.. 2542_MA0280.1_JASPAR_CORE_2009_ 2542_MA0280.1_JASPAR_CORE_2009_ D 6 0.5000 0.962 0.481 .....CCGGAt. CCGGar Total maches= 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: 32 (29.36%) Max nb of predicted sites per peak: 3  (?_gi|49175990|ref|NC_000913.2|_2944763_2946198_+) Mean nb of predicted sites per peak: 1.19	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 14   dyads_m1	wyAtCGCCAGCGygg CCRCGCTGGCGATRW	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wyAtCGCCAGCGygg Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor wyAtCGCCAGCGygg 4955_brk_DrosophilaTF_1.1_ 4955_brk_DrosophilaTF_1.1_ R 7 0.4667 0.889 0.415 ..ATCGCCA...... RRCGCCA 1772_MA0213.1_JASPAR_CORE_2009_ 1772_MA0213.1_JASPAR_CORE_2009_ R 8 0.5333 0.784 0.418 ..ATCGCCAG..... RGCGCCRS 6287_1qqa_A_3D-footprint_20130124_ 6287_1qqa_A_3D-footprint_20130124_ R 8 0.5333 0.759 0.405 ....CGCCAGCG... CGCNTGCG Total maches= 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 (40.37%) Max nb of predicted sites per peak: 2  (?_gi|49175990|ref|NC_000913.2|_3150987_3152126_+) Mean nb of predicted sites per peak: 1.16	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 15   dyads_m2	mkCCTGGCGATwm KWATCGCCAGGMK	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor mkCCTGGCGATwm Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor mkCCTGGCGATwm 4955_brk_DrosophilaTF_1.1_ 4955_brk_DrosophilaTF_1.1_ D 7 0.5385 0.835 0.449 ....TGGCGAT.. TGGCGyY 2843_PF0156.1_JASPAR_CORE_2009_ 2843_PF0156.1_JASPAR_CORE_2009_ R 9 0.5294 0.839 0.444 mkCCTGGCG.... ....CMCCTGGYG 2606_MA0368.1_JASPAR_CORE_2009_ 2606_MA0368.1_JASPAR_CORE_2009_ R 7 0.5385 0.760 0.409 ..CCTGGCG.... CTTGGCR Total maches= 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: 41 (37.61%) Max nb of predicted sites per peak: 4  (?_gi|49175990|ref|NC_000913.2|_695647_696755_+) Mean nb of predicted sites per peak: 1.32	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 16   dyads_m3	bwtCCTGACsk MSGTCAGGAWV	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor bwtCCTGACsk Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor bwtCCTGACsk 1785_MA0227.1_JASPAR_CORE_2009_ 1785_MA0227.1_JASPAR_CORE_2009_ D 6 0.5455 0.902 0.492 .....TGACnk TGACAk 1810_MA0252.1_JASPAR_CORE_2009_ 1810_MA0252.1_JASPAR_CORE_2009_ D 6 0.5455 0.881 0.480 .....TGACnk TGACAs 7677_TGIF1_si_HOCOMOCO_v9_ 7677_TGIF1_si_HOCOMOCO_v9_ D 6 0.5455 0.874 0.477 .....TGACnk TGACAg Total maches= 59 (56 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: 49 (44.95%) Max nb of predicted sites per peak: 4  (?_gi|49175990|ref|NC_000913.2|_3084066_3085778_+) Mean nb of predicted sites per peak: 1.47	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 17   dyads_m4	ymTCCAGAccr YGGTCTGGAKR	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ymTCCAGAccr Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor ymTCCAGAccr 1921_PB0060.1_JASPAR_CORE_2009_ 1921_PB0060.1_JASPAR_CORE_2009_ D 11 0.6471 0.832 0.538 ymTCCAGAccr ..watCCAGACrk.... 3697_UP00000_UniPROBE_20120919_ 3697_UP00000_UniPROBE_20120919_ D 11 0.6471 0.832 0.538 ymTCCAGAccr ..wawCCAGACrk.... 2481_MA0092.1_JASPAR_CORE_2009_ 2481_MA0092.1_JASPAR_CORE_2009_ R 10 0.9091 0.846 0.769 ymTCCAGAcc. AWKCCAGAYS Total maches= 16 (13 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: 39 (35.78%) Max nb of predicted sites per peak: 4  (?_gi|49175990|ref|NC_000913.2|_2904443_2906681_+) Mean nb of predicted sites per peak: 1.36	[ view in genome browser : ] [ sites: text BED (UCSC track) ] [ distribution: text ] [ sites per peak: text ] [ enrichment: text graph ]
Motif 18   dyads_m5	rgrCGCTGGAdg CHTCCAGCGYCY	[ matrix: tab format transfac format ]
regulonDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rgrCGCTGGAdg Total maches= 0		No match
footprintDB name id strand Nb overlap % Pearson Normalized aligned col. motif aligned col. match       columns aligned correlation cor rgrCGCTGGAdg 2742_PF0055.1_JASPAR_CORE_2009_ 2742_PF0055.1_JASPAR_CORE_2009_ D 6 0.5000 0.840 0.420 ......TGGAwr TGGAAA 2533_MA0267.1_JASPAR_CORE_2009_ 2533_MA0267.1_JASPAR_CORE_2009_ R 7 0.5833 0.777 0.453 ...CGCTGGA.. TGCTGGK Total maches= 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: 38 (34.86%) Max nb of predicted sites per peak: 2  (?_gi|49175990|ref|NC_000913.2|_3491374_3492566_+) 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 ChIP-seq_FNR_E._coli_tunned_parameters_dyad -i $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,dyads,positions -nmotifs 5 -minol 6 -maxol 8 -no_merge_lengths -2str -origin center -motif_db regulonDB tf $RSAT/public_html/data/motif_databases/REGULONDB/regulonDB_2014-04-11.tf -motif_db footprintDB tf $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -scan_markov 1 -source galaxy -task purge,seqlen,composition,disco,merge_words,collect_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/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR