position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/02/27/peak-motifs.2025-02-27.144751_2025-02-27.144751_AomCLd/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta -format fasta -sort -return html,chi,sig,distrib,graphs,rank,index -max_graphs 20 -1str -ovlp -seqtype dna -l 2 -ci 20 -img_format png -title pH_responsive_promoters -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/02/27/peak-motifs.2025-02-27.144751_2025-02-27.144751_AomCLd/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab Citation: van Helden, et al. (2000). Nucleic Acids Res 28, 1000-1010. Sequence file $RSAT/public_html/tmp/www-data/2025/02/27/peak-motifs.2025-02-27.144751_2025-02-27.144751_AomCLd/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2025/02/27/peak-motifs.2025-02-27.144751_2025-02-27.144751_AomCLd/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab Oligo length 2 Occurrences counted on a single strands Conditions of applicability checked. Background model estimation: homogeneous repartition Sequence statistics: Nb of sequences 6 Sum of sequence lengths 1200 Min sequence length 0 Max sequence length 200 Average sequence length 200 Possible positions 1194 Sequences: # length ID 1 200 S0785_RS07145_up200bp 2 200 S0785_RS03160_up200bp 3 200 SO785_RS01125_up200bp 4 200 SO785_RS00500_up200bp 5 200 S0785_RS09380_up200bp 6 200 S0785_RS08845_up200bp Oligonucleotide statistics: Total occurrences 1194 Position interval parameters: Position interval 20 Number of windows 10 Total positions 1194 Degrees of freedom 9 K-mer clustering parameters: Number of clusters 0 Clustering method complete Position intervals: window [min,max] mid seq occ 1 -5 [-99,-80] -89.5 6 120 2 -4 [-79,-60] -69.5 6 120 3 -3 [-59,-40] -49.5 6 120 4 -2 [-39,-20] -29.5 6 120 5 -1 [-19,0] -9.5 6 120 6 0 [1,20] 10.5 6 120 7 1 [21,40] 30.5 6 120 8 2 [41,60] 50.5 6 120 9 3 [61,80] 70.5 6 120 10 4 [81,100] 90.5 6 114 Column headers 1 seq pattern sequence 2 id pattern identifier 3 occ pattern occurrences 4 chi2 observed chi-square 5 df degrees of freedom 6 Pval P-value (probability for one word to be a false positive) 7 Eval E-value; expected number of false positives (Eval = Pval * nb_tests) 8 sig Significance (sig = -log10(Eval)) 9 rank rank of the pattern according to sorting criterion 10 -89.5 occurrences in window 1 [-99,-80] 11 -69.5 occurrences in window 2 [-79,-60] 12 -49.5 occurrences in window 3 [-59,-40] 13 -29.5 occurrences in window 4 [-39,-20] 14 -9.5 occurrences in window 5 [-19,0] 15 10.5 occurrences in window 6 [1,20] 16 30.5 occurrences in window 7 [21,40] 17 50.5 occurrences in window 8 [41,60] 18 70.5 occurrences in window 9 [61,80] 19 90.5 occurrences in window 10 [81,100]
| seq | id | occ | chi2 | df | Pval | Eval | sig | rank | -89.5 | -69.5 | -49.5 | -29.5 | -9.5 | 10.5 | 30.5 | 50.5 | 70.5 | 90.5 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ga | ga | 79 | 21.3 | 9 | 1.2e-02 | 0.18 | 0.73 | 1 | 6 | 4 | 7 | 8 | 12 | 6 | 7 | 6 | 5 | 18 |
| ag | ag | 68 | 16.2 | 9 | 6.2e-02 | 1 | 0.00 | 2 | 6 | 7 | 5 | 6 | 13 | 4 | 2 | 8 | 5 | 12 |
| tt | tt | 167 | 14.9 | 9 | 9.3e-02 | 1.5 | -0.17 | 3 | 21 | 14 | 7 | 20 | 10 | 22 | 23 | 18 | 18 | 14 |
| aa | aa | 173 | 12.0 | 9 | 2.1e-01 | 3.4 | -0.53 | 4 | 13 | 21 | 20 | 18 | 23 | 17 | 12 | 13 | 25 | 11 |
| ta | ta | 144 | 9.5 | 9 | 3.9e-01 | 6.3 | -0.80 | 5 | 16 | 18 | 14 | 20 | 11 | 13 | 8 | 15 | 19 | 10 |
| tc | tc | 50 | 9.3 | 9 | 4.1e-01 | 6.5 | -0.81 | 6 | 5 | 5 | 9 | 3 | 5 | 9 | 6 | 4 | 2 | 2 |
| ct | ct | 58 | 8.9 | 9 | 4.5e-01 | 7.1 | -0.85 | 7 | 4 | 7 | 9 | 3 | 7 | 8 | 7 | 6 | 6 | 1 |
| tg | tg | 64 | 8.5 | 9 | 4.8e-01 | 7.7 | -0.89 | 8 | 8 | 5 | 6 | 6 | 7 | 4 | 12 | 6 | 3 | 7 |
| ac | ac | 53 | 6.6 | 9 | 6.8e-01 | 11 | -1.04 | 9 | 5 | 7 | 5 | 2 | 4 | 5 | 8 | 6 | 8 | 3 |
| ca | ca | 52 | 6.0 | 9 | 7.4e-01 | 12 | -1.08 | 10 | 6 | 6 | 7 | 2 | 4 | 5 | 9 | 6 | 5 | 2 |
| at | at | 153 | 4.2 | 9 | 9.0e-01 | 14 | -1.16 | 11 | 17 | 13 | 20 | 19 | 12 | 14 | 16 | 13 | 14 | 15 |
| gg | gg | 32 | 0.0 | 9 | 1.0e+00 | 16 | -1.20 | 12 | 3 | 0 | 3 | 2 | 2 | 1 | 2 | 5 | 0 | 14 |
| cc | cc | 11 | 0.0 | 9 | 1.0e+00 | 16 | -1.20 | 13 | 0 | 3 | 2 | 1 | 0 | 3 | 2 | 0 | 0 | 0 |
| gc | gc | 25 | 0.0 | 9 | 1.0e+00 | 16 | -1.20 | 14 | 3 | 1 | 3 | 2 | 4 | 2 | 2 | 6 | 2 | 0 |
| cg | cg | 18 | 0.0 | 9 | 1.0e+00 | 16 | -1.20 | 15 | 1 | 2 | 1 | 2 | 1 | 3 | 1 | 2 | 3 | 2 |
| gt | gt | 47 | 0.0 | 9 | 1.0e+00 | 16 | -1.20 | 16 | 6 | 7 | 2 | 6 | 5 | 4 | 3 | 6 | 5 | 3 |
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