position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.113356_2026-01-05.113356_6ezgHe/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 DAR_8C_control_vs_Nr5a2_knockdown -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.113356_2026-01-05.113356_6ezgHe/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/2026/01/05/peak-motifs.2026-01-05.113356_2026-01-05.113356_6ezgHe/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.113356_2026-01-05.113356_6ezgHe/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 6584 Sum of sequence lengths 1523591 Min sequence length 0 Max sequence length 1000 Average sequence length 231 Possible positions 1523591 Oligonucleotide statistics: Total occurrences 1152589 Position interval parameters: Position interval 20 Number of windows 50 Total positions 1523591 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 6 102 2 -24 [-479,-460] -469.5 7 138 3 -23 [-459,-440] -449.5 11 182 4 -22 [-439,-420] -429.5 12 230 5 -21 [-419,-400] -409.5 13 250 6 -20 [-399,-380] -389.5 13 260 7 -19 [-379,-360] -369.5 15 283 8 -18 [-359,-340] -349.5 20 339 9 -17 [-339,-320] -329.5 28 489 10 -16 [-319,-300] -309.5 41 737 11 -15 [-299,-280] -289.5 67 1079 12 -14 [-279,-260] -269.5 118 1905 13 -13 [-259,-240] -249.5 177 2984 14 -12 [-239,-220] -229.5 270 4560 15 -11 [-219,-200] -209.5 393 6709 16 -10 [-199,-180] -189.5 576 9724 17 -9 [-179,-160] -169.5 863 14489 18 -8 [-159,-140] -149.5 1637 24038 19 -7 [-139,-120] -129.5 2493 41990 20 -6 [-119,-100] -109.5 3536 60703 21 -5 [-99,-80] -89.5 4848 84532 22 -4 [-79,-60] -69.5 6528 114258 23 -3 [-59,-40] -49.5 6584 131680 24 -2 [-39,-20] -29.5 6584 131680 25 -1 [-19,0] -9.5 6584 131680 26 0 [1,20] 10.5 6584 131680 27 1 [21,40] 30.5 6584 131680 28 2 [41,60] 50.5 6584 131680 29 3 [61,80] 70.5 6424 112595 30 4 [81,100] 90.5 4773 83229 31 5 [101,120] 110.5 3481 59653 32 6 [121,140] 130.5 2457 41127 33 7 [141,160] 150.5 1588 23311 34 8 [161,180] 170.5 851 14195 35 9 [181,200] 190.5 566 9532 36 10 [201,220] 210.5 389 6592 37 11 [221,240] 230.5 267 4481 38 12 [241,260] 250.5 174 2929 39 13 [261,280] 270.5 115 1857 40 14 [281,300] 290.5 66 1053 41 15 [301,320] 310.5 40 725 42 16 [321,340] 330.5 28 482 43 17 [341,360] 350.5 20 335 44 18 [361,380] 370.5 15 282 45 19 [381,400] 390.5 13 260 46 20 [401,420] 410.5 13 249 47 21 [421,440] 430.5 12 230 48 22 [441,460] 450.5 11 177 49 23 [461,480] 470.5 7 136 50 24 [481,500] 490.5 5 100 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| c | c | 283754 | 232.0 | 49 | 1.3e-25 | 5.3e-25 | 24.27 | 1 | 21 | 44 | 40 | 48 | 44 | 51 | 70 | 99 | 111 | 141 | 234 | 395 | 533 | 839 | 1298 | 1787 | 2694 | 4482 | 8224 | 11452 | 16024 | 21447 | 24691 | 24251 | 24201 | 24157 | 24198 | 24916 | 21187 | 15329 | 10708 | 7589 | 4269 | 2511 | 1743 | 1177 | 801 | 591 | 396 | 234 | 179 | 102 | 66 | 64 | 65 | 76 | 65 | 45 | 35 | 30 |
| a | a | 291195 | 168.6 | 49 | 4.9e-15 | 2e-14 | 13.71 | 2 | 31 | 39 | 45 | 52 | 46 | 78 | 76 | 82 | 109 | 148 | 234 | 377 | 587 | 913 | 1296 | 1950 | 2860 | 4605 | 7793 | 11340 | 16103 | 22031 | 25227 | 25205 | 25299 | 25146 | 25104 | 25371 | 21444 | 15694 | 11216 | 7676 | 4367 | 2651 | 1957 | 1283 | 846 | 556 | 432 | 229 | 157 | 104 | 92 | 60 | 73 | 67 | 56 | 40 | 23 | 25 |
| t | t | 295248 | 143.4 | 49 | 3.4e-11 | 1.4e-10 | 9.86 | 3 | 25 | 24 | 33 | 44 | 57 | 59 | 69 | 63 | 113 | 175 | 258 | 413 | 610 | 882 | 1342 | 1945 | 2860 | 4711 | 7952 | 11693 | 16168 | 22178 | 25516 | 25435 | 25601 | 25628 | 25638 | 25856 | 22122 | 16212 | 11072 | 7651 | 4324 | 2695 | 1784 | 1242 | 874 | 654 | 373 | 232 | 159 | 101 | 77 | 76 | 60 | 55 | 46 | 34 | 33 | 24 |
| g | g | 282392 | 112.6 | 49 | 6.5e-07 | 2.6e-06 | 5.59 | 4 | 25 | 31 | 35 | 36 | 49 | 53 | 60 | 75 | 117 | 183 | 205 | 339 | 561 | 817 | 1201 | 1862 | 2738 | 4499 | 7678 | 11295 | 15685 | 21292 | 24321 | 24044 | 23948 | 24446 | 24316 | 24809 | 21506 | 15334 | 11109 | 7556 | 4168 | 2633 | 1704 | 1191 | 751 | 552 | 358 | 210 | 140 | 119 | 60 | 52 | 51 | 47 | 43 | 38 | 29 | 21 |
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