peak-motifs dmrl_meedicago_up2_w

peak-motifs  -v 1 -title dmrl_meedicago_up2_w_nicotinana -i $RSAT/public_html/tmp/www-data/2026/05/29/peak-motifs.2026-05-29.141217_2026-05-29.141217_KPnZGR/peak-motifspeak_seq -ctrl $RSAT/public_html/tmp/www-data/2026/05/29/peak-motifs.2026-05-29.141217_2026-05-29.141217_KPnZGR/peak-motifscontrol_seq -markov auto -disco oligos,dyads -nmotifs 10 -minol 6 -maxol 8 -merge_lengths -2str -origin end -offset -200 -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2026/05/29/peak-motifs.2026-05-29.141217_2026-05-29.141217_KPnZGR

Sequence composition (test sequences)

Nb of peaks: 13
Total seq. size: 9 kb
Min length: 455 bp
Mean length: 682.077 bp
Max length: 701 bp [ seq: converted purged ]
[ lengths: list distrib graph ]

Nucleotide composition profiles

Transition frequencies
Position profiles

[ 1nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Dinucleotide composition profiles

Transition frequencies
Position profiles

[ 2nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Sequence composition (ctrl sequences)

Nb of peaks: 34262
Total seq. size: 19694 kb
Min length: 201 bp
Mean length: 574.793 bp
Max length: 701 bp [ seq: converted purged ]
[ lengths: list distrib graph ]

Nucleotide composition profiles

Transition frequencies
Position profiles

[ 1nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Dinucleotide composition profiles

Transition frequencies
Position profiles

[ 2nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

motif discovery

oligos_6-8nt

oligos_6-8nt_m1	assembly: actcag (sig=0.44; e-value=0.36)	RC: ctgagt
oligos_6-8nt_m2	assembly: cgctac (sig=0.34; e-value=0.46)	RC: gtagcg
oligos_6-8nt_m3	assembly: acctctta (sig=0.22; e-value=0.6)	RC: taagaggt
oligos_6-8nt_m4	: (sig=; e-value=1)	RC:
oligos_6-8nt_m5	: (sig=; e-value=1)	RC:
oligos_6-8nt_m6	: (sig=; e-value=1)	RC:
oligos_6-8nt_m7	: (sig=; e-value=1)	RC:
oligos_6-8nt_m8	: (sig=; e-value=1)	RC:
oligos_6-8nt_m9	: (sig=; e-value=1)	RC:
oligos_6-8nt_m10	: (sig=; e-value=1)	RC:

[ discovered words: text ]
[ assembly: text sig matrices ]
[ matrices: tab format transfac format ]

dyads_test_vs_ctrl

dyads_test_vs_ctrl_m1	assembly: gcannnnnnnngcc (sig=2.84; e-value=0.0014)	RC: ggcnnnnnnnntgc
dyads_test_vs_ctrl_m2	assembly: acannnnnnnnnnnnnnctc (sig=2.84; e-value=0.0014)	RC: gagnnnnnnnnnnnnnntgt
dyads_test_vs_ctrl_m3	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m4	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m5	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m6	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m7	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m8	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m9	: (sig=; e-value=1)	RC:
dyads_test_vs_ctrl_m10	: (sig=; e-value=1)	RC:

[ discovered words: text ]
[ assembly: text sig matrices ]
[ matrices: tab format transfac format ]

Motif discovery

Motif 1 oligos_6-8nt_m1

k-mer sig=0.44; evalue=0.36

hRACTCaGmw

WKCTGAGTYD

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 4 (30.77%)
Max nb of predicted sites per peak: 4
(BVRB_4g096340|Beta_vulgaris.RefBeet-1.2.2.60|BVRB_4g096340)
Mean nb of predicted sites per peak: 1.75

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 2 oligos_6-8nt_m2

k-mer sig=0.34; evalue=0.46

asCGCtaCcw

WGGTAGCGST

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 6 (46.15%)
Max nb of predicted sites per peak: 1
(gene-LOC110794951|Spinacia_oleracea.GCF020520425.1.RefSeq|gene-LOC110794951)
Mean nb of predicted sites per peak: 1.00

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 3 oligos_6-8nt_m3

k-mer sig=0.22; evalue=0.6

kyACCTCTTaam

KTTAAGAGGTRM

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 5 (38.46%)
Max nb of predicted sites per peak: 2
(gene-LSAT_8X33320|Lactuca_sativa.Lsat_Salinas_v7.60|gene-LSAT_8X33320)
Mean nb of predicted sites per peak: 1.60

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 4 dyads_test_vs_ctrl_m1

k-mer sig=2.84; evalue=0.0014

skGCayGawkCrkGCCgt

ACGGCMYGMWTCRTGCMS

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 9 (69.23%)
Max nb of predicted sites per peak: 3
(Csa_6G366300|Cucumis_sativus.ASM407v2.60|Csa_6G366300)
Mean nb of predicted sites per peak: 1.89

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 5 dyads_test_vs_ctrl_m2

k-mer sig=2.84; evalue=0.0014

scGsmGSmscwGmSsmKSCckCbk

MVGMGGSMKSSKCWGSKSCKSCGS

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 10 (76.92%)
Max nb of predicted sites per peak: 5
(Csa_6G366300|Cucumis_sativus.ASM407v2.60|Csa_6G366300)
Mean nb of predicted sites per peak: 2.20

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Word significance table
Word comparisons		[tab] [html] [heatmap]
Comparisons between discovered motifs
Discovered motifs versus discovered motifs		[ Discovered motif(s): tf ] [ table: html txt ] [ alignments (logo): html text ] [ clustering: html ] [ graph: gml (for CytoScape) ]

Log files
Parameters and files		[txt] [html]
Time log		[time table] [time log] [html]

RSAT - peak-motifs result

Analysis: dmrl_meedicago_up2_w_nicotinana (29/05/2026 14:24)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results