position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/05/22/peak-motifs.2025-05-22.140202_2025-05-22.140202_bQqV1Q/data/sequences/peak-motifs_ctrl_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 ELAV_activated_vs_repressed -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/05/22/peak-motifs.2025-05-22.140202_2025-05-22.140202_bQqV1Q/results/composition/peak-motifs_ctrl_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/2025/05/22/peak-motifs.2025-05-22.140202_2025-05-22.140202_bQqV1Q/data/sequences/peak-motifs_ctrl_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2025/05/22/peak-motifs.2025-05-22.140202_2025-05-22.140202_bQqV1Q/results/composition/peak-motifs_ctrl_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 354 Sum of sequence lengths 87792 Min sequence length 0 Max sequence length 544 Average sequence length 248 Possible positions 87438 Oligonucleotide statistics: Total occurrences 36363 Position interval parameters: Position interval 20 Number of windows 28 Total positions 87438 Degrees of freedom 27 K-mer clustering parameters: Number of clusters 0 Clustering method complete Position intervals: window [min,max] mid seq occ 1 -14 [-279,-260] -269.5 1 12 2 -13 [-259,-240] -249.5 1 20 3 -12 [-239,-220] -229.5 1 20 4 -11 [-219,-200] -209.5 1 20 5 -10 [-199,-180] -189.5 1 20 6 -9 [-179,-160] -169.5 1 20 7 -8 [-159,-140] -149.5 1 20 8 -7 [-139,-120] -129.5 352 1424 9 -6 [-119,-100] -109.5 352 7040 10 -5 [-99,-80] -89.5 352 7040 11 -4 [-79,-60] -69.5 352 7040 12 -3 [-59,-40] -49.5 354 7060 13 -2 [-39,-20] -29.5 354 7080 14 -1 [-19,0] -9.5 354 7080 15 0 [1,20] 10.5 354 7080 16 1 [21,40] 30.5 354 7080 17 2 [41,60] 50.5 354 7058 18 3 [61,80] 70.5 352 7040 19 4 [81,100] 90.5 352 7040 20 5 [101,120] 110.5 352 7040 21 6 [121,140] 130.5 352 1073 22 7 [141,160] 150.5 1 20 23 8 [161,180] 170.5 1 20 24 9 [181,200] 190.5 1 20 25 10 [201,220] 210.5 1 20 26 11 [221,240] 230.5 1 20 27 12 [241,260] 250.5 1 20 28 13 [261,280] 270.5 1 11 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 -269.5 occurrences in window 1 [-279,-260] 11 -249.5 occurrences in window 2 [-259,-240] 12 -229.5 occurrences in window 3 [-239,-220] 13 -209.5 occurrences in window 4 [-219,-200] 14 -189.5 occurrences in window 5 [-199,-180] 15 -169.5 occurrences in window 6 [-179,-160] 16 -149.5 occurrences in window 7 [-159,-140] 17 -129.5 occurrences in window 8 [-139,-120] 18 -109.5 occurrences in window 9 [-119,-100] 19 -89.5 occurrences in window 10 [-99,-80] 20 -69.5 occurrences in window 11 [-79,-60] 21 -49.5 occurrences in window 12 [-59,-40] 22 -29.5 occurrences in window 13 [-39,-20] 23 -9.5 occurrences in window 14 [-19,0] 24 10.5 occurrences in window 15 [1,20] 25 30.5 occurrences in window 16 [21,40] 26 50.5 occurrences in window 17 [41,60] 27 70.5 occurrences in window 18 [61,80] 28 90.5 occurrences in window 19 [81,100] 29 110.5 occurrences in window 20 [101,120] 30 130.5 occurrences in window 21 [121,140] 31 150.5 occurrences in window 22 [141,160] 32 170.5 occurrences in window 23 [161,180] 33 190.5 occurrences in window 24 [181,200] 34 210.5 occurrences in window 25 [201,220] 35 230.5 occurrences in window 26 [221,240] 36 250.5 occurrences in window 27 [241,260] 37 270.5 occurrences in window 28 [261,280]
| seq | id | occ | chi2 | df | Pval | Eval | sig | rank | -269.5 | -249.5 | -229.5 | -209.5 | -189.5 | -169.5 | -149.5 | -129.5 | -109.5 | -89.5 | -69.5 | -49.5 | -29.5 | -9.5 | 10.5 | 30.5 | 50.5 | 70.5 | 90.5 | 110.5 | 130.5 | 150.5 | 170.5 | 190.5 | 210.5 | 230.5 | 250.5 | 270.5 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| tt | tt | 3323 | 4682.8 | 27 | 0.0e+00 | 0 | 300 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 122 | 651 | 695 | 778 | 556 | 502 | 3 | 0 | 6 | 5 | 1 | 1 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| gc | gc | 2610 | 3583.6 | 27 | 0.0e+00 | 0 | 300 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 116 | 527 | 532 | 458 | 536 | 425 | 3 | 3 | 4 | 1 | 3 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| cg | cg | 2538 | 3566.2 | 27 | 0.0e+00 | 0 | 300 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 88 | 448 | 491 | 452 | 626 | 418 | 1 | 3 | 5 | 0 | 2 | 3 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| ca | ca | 2346 | 3312.2 | 27 | 0.0e+00 | 0 | 300 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 82 | 452 | 454 | 549 | 479 | 311 | 6 | 3 | 2 | 3 | 1 | 2 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| tg | tg | 2344 | 3282.3 | 27 | 0.0e+00 | 0 | 300 | 5 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 113 | 515 | 485 | 413 | 464 | 339 | 0 | 4 | 5 | 3 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| gt | gt | 2259 | 3182.9 | 27 | 0.0e+00 | 0 | 300 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 83 | 440 | 409 | 508 | 486 | 321 | 1 | 5 | 2 | 1 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| aa | aa | 3019 | 3084.9 | 27 | 0.0e+00 | 0 | 300 | 7 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 91 | 541 | 533 | 452 | 572 | 461 | 2 | 355 | 2 | 2 | 2 | 1 | 3 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 |
| tc | tc | 2844 | 2907.9 | 27 | 0.0e+00 | 0 | 300 | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 99 | 437 | 495 | 576 | 476 | 391 | 4 | 353 | 5 | 2 | 2 | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| ag | ag | 1941 | 2773.2 | 27 | 0.0e+00 | 0 | 300 | 9 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 93 | 391 | 352 | 465 | 366 | 262 | 2 | 4 | 2 | 2 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| ct | ct | 1975 | 2730.9 | 27 | 0.0e+00 | 0 | 300 | 10 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 97 | 427 | 409 | 367 | 351 | 310 | 3 | 1 | 4 | 2 | 2 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| ga | ga | 1951 | 2721.5 | 27 | 0.0e+00 | 0 | 300 | 11 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 79 | 398 | 384 | 357 | 439 | 281 | 0 | 3 | 5 | 3 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| at | at | 2488 | 2544.3 | 27 | 0.0e+00 | 0 | 300 | 12 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 92 | 447 | 454 | 446 | 379 | 306 | 1 | 1 | 5 | 355 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
| ac | ac | 1775 | 2476.3 | 27 | 0.0e+00 | 0 | 300 | 13 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 57 | 342 | 338 | 332 | 426 | 265 | 4 | 1 | 3 | 1 | 0 | 3 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| gg | gg | 1576 | 2171.1 | 27 | 0.0e+00 | 0 | 300 | 14 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 51 | 342 | 313 | 253 | 354 | 244 | 3 | 2 | 3 | 5 | 2 | 1 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| cc | cc | 1463 | 2001.6 | 27 | 0.0e+00 | 0 | 300 | 15 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 59 | 298 | 341 | 274 | 247 | 225 | 6 | 4 | 1 | 2 | 0 | 3 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| ta | ta | 1911 | 1972.3 | 27 | 0.0e+00 | 0 | 300 | 16 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 78 | 344 | 317 | 320 | 265 | 229 | 1 | 0 | 2 | 353 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
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