position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.143635_2026-01-05.143635_7Pttt5/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 SOX2 -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.143635_2026-01-05.143635_7Pttt5/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.2026-01-05.143635_2026-01-05.143635_7Pttt5/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.2026-01-05.143635_2026-01-05.143635_7Pttt5/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 9579 Sum of sequence lengths 3395865 Min sequence length 0 Max sequence length 1000 Average sequence length 354 Possible positions 3395865 Oligonucleotide statistics: Total occurrences 3252658 Position interval parameters: Position interval 20 Number of windows 50 Total positions 3395865 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] -489.5 189 3415 2 -24 [-479,-460] -469.5 220 4087 3 -23 [-459,-440] -449.5 261 4820 4 -22 [-439,-420] -429.5 307 5680 5 -21 [-419,-400] -409.5 359 6619 6 -20 [-399,-380] -389.5 445 8030 7 -19 [-379,-360] -369.5 531 9790 8 -18 [-359,-340] -349.5 628 11616 9 -17 [-339,-320] -329.5 757 13845 10 -16 [-319,-300] -309.5 923 16893 11 -15 [-299,-280] -289.5 1134 20647 12 -14 [-279,-260] -269.5 1412 25490 13 -13 [-259,-240] -249.5 1736 31606 14 -12 [-239,-220] -229.5 2146 38802 15 -11 [-219,-200] -209.5 2666 48300 16 -10 [-199,-180] -189.5 3287 59830 17 -9 [-179,-160] -169.5 4120 74245 18 -8 [-159,-140] -149.5 5175 93248 19 -7 [-139,-120] -129.5 6604 118361 20 -6 [-119,-100] -109.5 8512 151904 21 -5 [-99,-80] -89.5 9579 189141 22 -4 [-79,-60] -69.5 9579 191580 23 -3 [-59,-40] -49.5 9579 191580 24 -2 [-39,-20] -29.5 9579 191580 25 -1 [-19,0] -9.5 9579 191580 26 0 [1,20] 10.5 9579 191580 27 1 [21,40] 30.5 9579 191580 28 2 [41,60] 50.5 9579 191580 29 3 [61,80] 70.5 9579 191580 30 4 [81,100] 90.5 9579 188085 31 5 [101,120] 110.5 8415 149983 32 6 [121,140] 130.5 6526 116890 33 7 [141,160] 150.5 5103 92160 34 8 [161,180] 170.5 4076 73430 35 9 [181,200] 190.5 3258 59203 36 10 [201,220] 210.5 2644 47785 37 11 [221,240] 230.5 2122 38386 38 12 [241,260] 250.5 1720 31282 39 13 [261,280] 270.5 1392 25216 40 14 [281,300] 290.5 1120 20428 41 15 [301,320] 310.5 916 16729 42 16 [321,340] 330.5 745 13719 43 17 [341,360] 350.5 619 11510 44 18 [361,380] 370.5 525 9697 45 19 [381,400] 390.5 437 7940 46 20 [401,420] 410.5 355 6569 47 21 [421,440] 430.5 304 5626 48 22 [441,460] 450.5 259 4780 49 23 [461,480] 470.5 217 4052 50 24 [481,500] 490.5 189 3386 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 | 879338 | 460.7 | 49 | 0.0e+00 | 0 | 300 | 1 | 841 | 1002 | 1211 | 1355 | 1687 | 2009 | 2509 | 2850 | 3502 | 4318 | 5140 | 6445 | 8083 | 9996 | 12433 | 15360 | 19054 | 24119 | 31107 | 39533 | 49949 | 50406 | 50450 | 49733 | 50204 | 50146 | 50067 | 50069 | 50133 | 49339 | 39214 | 30136 | 23331 | 18451 | 14720 | 11915 | 9615 | 7800 | 6227 | 5070 | 4109 | 3254 | 2728 | 2424 | 1789 | 1513 | 1278 | 1052 | 863 | 799 |
| g | g | 876198 | 318.4 | 49 | 3.8e-41 | 1.5e-40 | 39.82 | 2 | 742 | 936 | 1125 | 1399 | 1592 | 1976 | 2357 | 2904 | 3302 | 4137 | 5117 | 6346 | 8043 | 9646 | 12137 | 15214 | 18933 | 23806 | 30480 | 39718 | 49024 | 49654 | 49886 | 50271 | 50009 | 49813 | 49980 | 49786 | 50019 | 48669 | 38776 | 30379 | 23947 | 19074 | 15257 | 12232 | 9823 | 7927 | 6263 | 4973 | 4158 | 3436 | 2857 | 2350 | 1882 | 1547 | 1298 | 1140 | 990 | 868 |
| a | a | 749649 | 284.4 | 49 | 6.4e-35 | 2.6e-34 | 33.59 | 3 | 784 | 935 | 1056 | 1303 | 1451 | 1814 | 2304 | 2606 | 3242 | 3853 | 4802 | 5990 | 7312 | 8842 | 10873 | 13610 | 16861 | 21046 | 26491 | 34112 | 42180 | 42730 | 42274 | 42463 | 42053 | 42217 | 41978 | 41397 | 41267 | 40966 | 32615 | 25230 | 19961 | 16188 | 13066 | 10492 | 8304 | 6857 | 5673 | 4402 | 3657 | 3027 | 2544 | 2027 | 1774 | 1382 | 1189 | 982 | 789 | 678 |
| t | t | 747473 | 227.5 | 49 | 8.3e-25 | 3.3e-24 | 23.48 | 4 | 759 | 858 | 1044 | 1206 | 1442 | 1742 | 2017 | 2552 | 3026 | 3680 | 4515 | 5533 | 6837 | 8698 | 10811 | 13043 | 16164 | 20393 | 25590 | 32814 | 41173 | 41395 | 41434 | 41582 | 41796 | 41867 | 41933 | 42706 | 42748 | 42166 | 33425 | 26066 | 20830 | 16364 | 13409 | 10874 | 8769 | 7144 | 5777 | 4744 | 3695 | 3020 | 2555 | 2163 | 1791 | 1455 | 1235 | 1030 | 928 | 675 |
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