position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/08/17/peak-motifs.2025-08-17.121427_2025-08-17.121427_PAZ7BE/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 Set_2_TOP150 -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/08/17/peak-motifs.2025-08-17.121427_2025-08-17.121427_PAZ7BE/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/2025/08/17/peak-motifs.2025-08-17.121427_2025-08-17.121427_PAZ7BE/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2025/08/17/peak-motifs.2025-08-17.121427_2025-08-17.121427_PAZ7BE/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 150 Sum of sequence lengths 15000 Min sequence length 0 Max sequence length 100 Average sequence length 100 Possible positions 14850 Oligonucleotide statistics: Total occurrences 14537 Position interval parameters: Position interval 20 Number of windows 6 Total positions 14850 Degrees of freedom 5 K-mer clustering parameters: Number of clusters 0 Clustering method complete Position intervals: window [min,max] mid seq occ 1 -3 [-59,-40] -49.5 150 1500 2 -2 [-39,-20] -29.5 150 3000 3 -1 [-19,0] -9.5 150 3000 4 0 [1,20] 10.5 150 3000 5 1 [21,40] 30.5 150 3000 6 2 [41,60] 50.5 150 1350 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 -49.5 occurrences in window 1 [-59,-40] 11 -29.5 occurrences in window 2 [-39,-20] 12 -9.5 occurrences in window 3 [-19,0] 13 10.5 occurrences in window 4 [1,20] 14 30.5 occurrences in window 5 [21,40] 15 50.5 occurrences in window 6 [41,60]
| seq | id | occ | chi2 | df | Pval | Eval | sig | rank | -49.5 | -29.5 | -9.5 | 10.5 | 30.5 | 50.5 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ac | ac | 812 | 14.8 | 5 | 1.1e-02 | 0.18 | 0.74 | 1 | 89 | 178 | 170 | 183 | 123 | 69 |
| tt | tt | 755 | 14.1 | 5 | 1.5e-02 | 0.24 | 0.62 | 2 | 65 | 174 | 177 | 126 | 152 | 61 |
| gc | gc | 1281 | 12.4 | 5 | 3.0e-02 | 0.47 | 0.32 | 3 | 125 | 211 | 281 | 268 | 275 | 121 |
| ta | ta | 524 | 10.9 | 5 | 5.4e-02 | 0.86 | 0.07 | 4 | 57 | 119 | 89 | 86 | 118 | 55 |
| at | at | 717 | 10.3 | 5 | 6.8e-02 | 1.1 | -0.04 | 5 | 71 | 164 | 120 | 131 | 160 | 71 |
| gg | gg | 1004 | 9.8 | 5 | 8.1e-02 | 1.3 | -0.11 | 6 | 116 | 205 | 170 | 204 | 203 | 106 |
| aa | aa | 755 | 8.1 | 5 | 1.5e-01 | 2.4 | -0.39 | 7 | 80 | 154 | 134 | 148 | 151 | 88 |
| ga | ga | 876 | 7.6 | 5 | 1.8e-01 | 2.9 | -0.46 | 8 | 95 | 187 | 154 | 197 | 162 | 81 |
| cg | cg | 1022 | 7.2 | 5 | 2.0e-01 | 3.3 | -0.52 | 9 | 94 | 184 | 233 | 216 | 205 | 90 |
| gt | gt | 878 | 4.5 | 5 | 4.8e-01 | 7.7 | -0.89 | 10 | 85 | 183 | 179 | 187 | 181 | 63 |
| ca | ca | 1040 | 4.3 | 5 | 5.1e-01 | 8.1 | -0.91 | 11 | 106 | 217 | 215 | 226 | 192 | 84 |
| tc | tc | 931 | 4.1 | 5 | 5.4e-01 | 8.6 | -0.94 | 12 | 90 | 207 | 189 | 169 | 191 | 85 |
| ct | ct | 946 | 3.7 | 5 | 5.9e-01 | 9.5 | -0.98 | 13 | 98 | 186 | 205 | 172 | 192 | 93 |
| tg | tg | 1100 | 3.6 | 5 | 6.1e-01 | 9.7 | -0.99 | 14 | 115 | 203 | 226 | 241 | 217 | 98 |
| ag | ag | 905 | 3.4 | 5 | 6.4e-01 | 10 | -1.01 | 15 | 93 | 185 | 176 | 183 | 198 | 70 |
| cc | cc | 991 | 3.0 | 5 | 7.1e-01 | 11 | -1.05 | 16 | 101 | 202 | 217 | 183 | 200 | 88 |
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