position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/08/17/peak-motifs.2025-08-17.121447_2025-08-17.121447_Kvls6d/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_3_TOP150 -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/08/17/peak-motifs.2025-08-17.121447_2025-08-17.121447_Kvls6d/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.2025-08-17.121447_2025-08-17.121447_Kvls6d/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.2025-08-17.121447_2025-08-17.121447_Kvls6d/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 14346 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ta | ta | 572 | 11.5 | 5 | 4.2e-02 | 0.67 | 0.17 | 1 | 74 | 131 | 96 | 103 | 113 | 55 |
| at | at | 743 | 7.0 | 5 | 2.2e-01 | 3.5 | -0.55 | 2 | 78 | 160 | 136 | 131 | 159 | 79 |
| gt | gt | 882 | 6.9 | 5 | 2.3e-01 | 3.7 | -0.57 | 3 | 70 | 189 | 178 | 196 | 172 | 77 |
| ca | ca | 1041 | 6.1 | 5 | 3.0e-01 | 4.7 | -0.67 | 4 | 102 | 191 | 213 | 238 | 200 | 97 |
| cc | cc | 954 | 5.7 | 5 | 3.4e-01 | 5.5 | -0.74 | 5 | 109 | 201 | 193 | 167 | 193 | 91 |
| tg | tg | 1080 | 5.2 | 5 | 4.0e-01 | 6.3 | -0.80 | 6 | 96 | 211 | 237 | 222 | 206 | 108 |
| aa | aa | 781 | 4.9 | 5 | 4.3e-01 | 6.9 | -0.84 | 7 | 82 | 171 | 150 | 145 | 171 | 62 |
| ct | ct | 914 | 4.7 | 5 | 4.5e-01 | 7.3 | -0.86 | 8 | 102 | 180 | 195 | 194 | 164 | 79 |
| tt | tt | 742 | 3.3 | 5 | 6.6e-01 | 11 | -1.02 | 9 | 78 | 146 | 136 | 148 | 166 | 68 |
| gc | gc | 1160 | 2.6 | 5 | 7.6e-01 | 12 | -1.08 | 10 | 125 | 227 | 247 | 240 | 222 | 99 |
| cg | cg | 905 | 2.6 | 5 | 7.7e-01 | 12 | -1.09 | 11 | 91 | 192 | 182 | 171 | 194 | 75 |
| ag | ag | 972 | 2.4 | 5 | 7.9e-01 | 13 | -1.10 | 12 | 96 | 204 | 193 | 210 | 189 | 80 |
| ac | ac | 808 | 2.3 | 5 | 8.0e-01 | 13 | -1.11 | 13 | 91 | 154 | 168 | 166 | 154 | 75 |
| ga | ga | 916 | 1.4 | 5 | 9.3e-01 | 15 | -1.17 | 14 | 94 | 190 | 177 | 176 | 193 | 86 |
| tc | tc | 890 | 1.2 | 5 | 9.5e-01 | 15 | -1.18 | 15 | 94 | 173 | 190 | 177 | 177 | 79 |
| gg | gg | 986 | 0.7 | 5 | 9.8e-01 | 16 | -1.20 | 16 | 95 | 201 | 201 | 196 | 207 | 86 |
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