position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.084429_2026-01-22.084429_vEeoc0/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 1 -ci 20 -img_format png -title WT48h_hupA_sensitive -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.084429_2026-01-22.084429_vEeoc0/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab Citation: van Helden, et al. (2000). Nucleic Acids Res 28, 1000-1010. Sequence file $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.084429_2026-01-22.084429_vEeoc0/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.084429_2026-01-22.084429_vEeoc0/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab Oligo length 1 Occurrences counted on a single strands Conditions of applicability checked. Background model estimation: homogeneous repartition Sequence statistics: Nb of sequences 493 Sum of sequence lengths 239920 Min sequence length 0 Max sequence length 1000 Average sequence length 486 Possible positions 239920 Oligonucleotide statistics: Total occurrences 237298 Position interval parameters: Position interval 20 Number of windows 50 Total positions 239920 Degrees of freedom 49 K-mer clustering parameters: Number of clusters 0 Clustering method complete Position intervals: window [min,max] mid seq occ 1 -25 [-499,-480] -489.5 28 520 2 -24 [-479,-460] -469.5 30 567 3 -23 [-459,-440] -449.5 33 635 4 -22 [-439,-420] -429.5 39 710 5 -21 [-419,-400] -409.5 44 831 6 -20 [-399,-380] -389.5 54 975 7 -19 [-379,-360] -369.5 64 1198 8 -18 [-359,-340] -349.5 73 1371 9 -17 [-339,-320] -329.5 88 1603 10 -16 [-319,-300] -309.5 111 2015 11 -15 [-299,-280] -289.5 137 2556 12 -14 [-279,-260] -269.5 171 3077 13 -13 [-259,-240] -249.5 200 3676 14 -12 [-239,-220] -229.5 240 4448 15 -11 [-219,-200] -209.5 283 5286 16 -10 [-199,-180] -189.5 342 6289 17 -9 [-179,-160] -169.5 399 7427 18 -8 [-159,-140] -149.5 447 8514 19 -7 [-139,-120] -129.5 486 9376 20 -6 [-119,-100] -109.5 493 9815 21 -5 [-99,-80] -89.5 493 9860 22 -4 [-79,-60] -69.5 493 9860 23 -3 [-59,-40] -49.5 493 9860 24 -2 [-39,-20] -29.5 493 9860 25 -1 [-19,0] -9.5 493 9860 26 0 [1,20] 10.5 493 9860 27 1 [21,40] 30.5 493 9860 28 2 [41,60] 50.5 493 9860 29 3 [61,80] 70.5 493 9860 30 4 [81,100] 90.5 493 9860 31 5 [101,120] 110.5 493 9809 32 6 [121,140] 130.5 483 9343 33 7 [141,160] 150.5 445 8455 34 8 [161,180] 170.5 393 7371 35 9 [181,200] 190.5 341 6238 36 10 [201,220] 210.5 283 5241 37 11 [221,240] 230.5 238 4412 38 12 [241,260] 250.5 199 3652 39 13 [261,280] 270.5 168 3042 40 14 [281,300] 290.5 136 2529 41 15 [301,320] 310.5 111 1995 42 16 [321,340] 330.5 87 1589 43 17 [341,360] 350.5 73 1362 44 18 [361,380] 370.5 64 1188 45 19 [381,400] 390.5 53 963 46 20 [401,420] 410.5 44 824 47 21 [421,440] 430.5 39 704 48 22 [441,460] 450.5 33 631 49 23 [461,480] 470.5 29 564 50 24 [481,500] 490.5 28 519 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 -489.5 occurrences in window 1 [-499,-480] 11 -469.5 occurrences in window 2 [-479,-460] 12 -449.5 occurrences in window 3 [-459,-440] 13 -429.5 occurrences in window 4 [-439,-420] 14 -409.5 occurrences in window 5 [-419,-400] 15 -389.5 occurrences in window 6 [-399,-380] 16 -369.5 occurrences in window 7 [-379,-360] 17 -349.5 occurrences in window 8 [-359,-340] 18 -329.5 occurrences in window 9 [-339,-320] 19 -309.5 occurrences in window 10 [-319,-300] 20 -289.5 occurrences in window 11 [-299,-280] 21 -269.5 occurrences in window 12 [-279,-260] 22 -249.5 occurrences in window 13 [-259,-240] 23 -229.5 occurrences in window 14 [-239,-220] 24 -209.5 occurrences in window 15 [-219,-200] 25 -189.5 occurrences in window 16 [-199,-180] 26 -169.5 occurrences in window 17 [-179,-160] 27 -149.5 occurrences in window 18 [-159,-140] 28 -129.5 occurrences in window 19 [-139,-120] 29 -109.5 occurrences in window 20 [-119,-100] 30 -89.5 occurrences in window 21 [-99,-80] 31 -69.5 occurrences in window 22 [-79,-60] 32 -49.5 occurrences in window 23 [-59,-40] 33 -29.5 occurrences in window 24 [-39,-20] 34 -9.5 occurrences in window 25 [-19,0] 35 10.5 occurrences in window 26 [1,20] 36 30.5 occurrences in window 27 [21,40] 37 50.5 occurrences in window 28 [41,60] 38 70.5 occurrences in window 29 [61,80] 39 90.5 occurrences in window 30 [81,100] 40 110.5 occurrences in window 31 [101,120] 41 130.5 occurrences in window 32 [121,140] 42 150.5 occurrences in window 33 [141,160] 43 170.5 occurrences in window 34 [161,180] 44 190.5 occurrences in window 35 [181,200] 45 210.5 occurrences in window 36 [201,220] 46 230.5 occurrences in window 37 [221,240] 47 250.5 occurrences in window 38 [241,260] 48 270.5 occurrences in window 39 [261,280] 49 290.5 occurrences in window 40 [281,300] 50 310.5 occurrences in window 41 [301,320] 51 330.5 occurrences in window 42 [321,340] 52 350.5 occurrences in window 43 [341,360] 53 370.5 occurrences in window 44 [361,380] 54 390.5 occurrences in window 45 [381,400] 55 410.5 occurrences in window 46 [401,420] 56 430.5 occurrences in window 47 [421,440] 57 450.5 occurrences in window 48 [441,460] 58 470.5 occurrences in window 49 [461,480] 59 490.5 occurrences in window 50 [481,500]
| seq | id | occ | chi2 | df | Pval | Eval | sig | rank | -489.5 | -469.5 | -449.5 | -429.5 | -409.5 | -389.5 | -369.5 | -349.5 | -329.5 | -309.5 | -289.5 | -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 | 290.5 | 310.5 | 330.5 | 350.5 | 370.5 | 390.5 | 410.5 | 430.5 | 450.5 | 470.5 | 490.5 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| a | a | 34258 | 53.3 | 49 | 3.1e-01 | 1.2 | -0.10 | 1 | 78 | 86 | 94 | 111 | 114 | 153 | 175 | 207 | 219 | 273 | 366 | 459 | 523 | 606 | 754 | 885 | 1013 | 1210 | 1344 | 1402 | 1418 | 1412 | 1418 | 1463 | 1434 | 1452 | 1497 | 1385 | 1384 | 1342 | 1390 | 1343 | 1213 | 977 | 841 | 735 | 652 | 498 | 431 | 330 | 292 | 232 | 230 | 190 | 135 | 133 | 87 | 97 | 96 | 79 |
| g | g | 83812 | 43.2 | 49 | 7.1e-01 | 2.8 | -0.45 | 2 | 176 | 205 | 217 | 269 | 325 | 334 | 415 | 493 | 554 | 739 | 945 | 1057 | 1221 | 1569 | 1898 | 2181 | 2577 | 2948 | 3266 | 3402 | 3395 | 3415 | 3402 | 3388 | 3369 | 3397 | 3402 | 3456 | 3409 | 3437 | 3444 | 3334 | 2942 | 2677 | 2228 | 1803 | 1575 | 1317 | 1059 | 889 | 732 | 582 | 460 | 422 | 345 | 280 | 279 | 215 | 204 | 164 |
| t | t | 34802 | 39.7 | 49 | 8.3e-01 | 3.3 | -0.52 | 3 | 86 | 84 | 102 | 107 | 123 | 129 | 167 | 198 | 266 | 283 | 349 | 460 | 568 | 657 | 777 | 922 | 1036 | 1211 | 1349 | 1412 | 1397 | 1448 | 1426 | 1456 | 1504 | 1457 | 1432 | 1453 | 1462 | 1444 | 1375 | 1312 | 1222 | 1062 | 894 | 769 | 589 | 520 | 444 | 384 | 270 | 239 | 181 | 153 | 149 | 127 | 109 | 82 | 76 | 80 |
| c | c | 84426 | 36.1 | 49 | 9.2e-01 | 3.7 | -0.56 | 4 | 180 | 192 | 222 | 223 | 269 | 359 | 441 | 473 | 564 | 720 | 896 | 1099 | 1339 | 1574 | 1794 | 2241 | 2718 | 3045 | 3290 | 3474 | 3528 | 3470 | 3476 | 3406 | 3406 | 3414 | 3408 | 3421 | 3445 | 3498 | 3467 | 3203 | 2948 | 2597 | 2250 | 1914 | 1580 | 1286 | 1077 | 906 | 695 | 536 | 491 | 423 | 334 | 284 | 229 | 237 | 188 | 196 |
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