peak-motifs Si_module

Sequence composition (test sequences)

Nb of peaks: 566
Total seq. size: 515 kb
Min length: 1 bp
Mean length: 910.489 bp
Max length: 1000 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: 17911
Total seq. size: 16456 kb
Min length: 1 bp
Mean length: 918.776 bp
Max length: 1000 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_6nt_test_vs_ctrl

oligos_6nt_test_vs_ctrl_m1	assembly: cgcggc (sig=2.24; e-value=0.0058)	RC: gccgcg
oligos_6nt_test_vs_ctrl_m2	assembly: ttataa (sig=2.15; e-value=0.0071)	RC: ttataa
oligos_6nt_test_vs_ctrl_m3	assembly: cccgca (sig=0.61; e-value=0.25)	RC: tgcggg
oligos_6nt_test_vs_ctrl_m4	assembly: cctccg (sig=0.51; e-value=0.31)	RC: cggagg
oligos_6nt_test_vs_ctrl_m5	assembly: tggggga (sig=0.36; e-value=0.44)	RC: tccccca

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

oligos_7nt_test_vs_ctrl

oligos_7nt_test_vs_ctrl_m1	assembly: cccccaa (sig=2.54; e-value=0.0029)	RC: ttggggg
oligos_7nt_test_vs_ctrl_m2	assembly: gagtactc (sig=0.63; e-value=0.23)	RC: gagtactc
oligos_7nt_test_vs_ctrl_m3	assembly: atctagat (sig=0.08; e-value=0.83)	RC: atctagat
oligos_7nt_test_vs_ctrl_m4	: (sig=; e-value=1)	RC:
oligos_7nt_test_vs_ctrl_m5	: (sig=; e-value=1)	RC:

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

Motif discovery

Motif 1 oligos_6nt_test_vs_ctrl_m1

k-mer sig=2.24; evalue=0.0058

ssCGCGGCss

SSGCCGCGSS

[ 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: 246 (43.46%)
Max nb of predicted sites per peak: 7
(SETIT_037689mg)
Mean nb of predicted sites per peak: 2.08

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

Motif 2 oligos_6nt_test_vs_ctrl_m2

k-mer sig=2.15; evalue=0.0071

wwTTATAAww

WWTTATAAWW

[ 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: 159 (28.09%)
Max nb of predicted sites per peak: 12
(SETIT_014052mg)
Mean nb of predicted sites per peak: 2.94

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

Motif 3 oligos_6nt_test_vs_ctrl_m3

k-mer sig=0.61; evalue=0.25

svCCCGCAss

SSTGCGGGBS

[ 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: 159 (28.09%)
Max nb of predicted sites per peak: 4
(SETIT_026108mg)
Mean nb of predicted sites per peak: 1.32

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

Motif 4 oligos_6nt_test_vs_ctrl_m4

k-mer sig=0.51; evalue=0.31

ckCCTCCGyc

GRCGGAGGMG

[ 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: 227 (40.11%)
Max nb of predicted sites per peak: 8
(SETIT_014577mg)
Mean nb of predicted sites per peak: 1.69

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

Motif 5 oligos_6nt_test_vs_ctrl_m5

k-mer sig=0.36; evalue=0.44

ggTGGGGGAgg

CCTCCCCCACC

[ 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: 179 (31.63%)
Max nb of predicted sites per peak: 5
(SETIT_020939mg)
Mean nb of predicted sites per peak: 1.45

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

Motif 6 oligos_7nt_test_vs_ctrl_m1

k-mer sig=2.54; evalue=0.0029

cwCCCCCAAcy

RGTTGGGGGWG

[ 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: 104 (18.37%)
Max nb of predicted sites per peak: 3
(SETIT_039805mg)
Mean nb of predicted sites per peak: 1.20

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

Motif 7 oligos_7nt_test_vs_ctrl_m2

k-mer sig=0.63; evalue=0.23

wkGAGTACTCmw

WKGAGTACTCMW

[ 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: 82 (14.49%)
Max nb of predicted sites per peak: 6
(SETIT_020992mg)
Mean nb of predicted sites per peak: 2.22

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

Motif 8 oligos_7nt_test_vs_ctrl_m3

k-mer sig=0.08; evalue=0.83

rwATCTAGATdy

RHATCTAGATWY

[ 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: 93 (16.43%)
Max nb of predicted sites per peak: 8
(SETIT_016485mg)
Mean nb of predicted sites per peak: 2.47

[ 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: Si_module_2 (25/03/2025 04:25)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results