position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2021/02/16/peak-motifs.2021-02-16.144431_2021-02-16.144431_tXA9Xd/data/sequences/peak-motifs_test_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 Oct4_Chen2008_sites_from_Jaspar -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2021/02/16/peak-motifs.2021-02-16.144431_2021-02-16.144431_tXA9Xd/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/2021/02/16/peak-motifs.2021-02-16.144431_2021-02-16.144431_tXA9Xd/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2021/02/16/peak-motifs.2021-02-16.144431_2021-02-16.144431_tXA9Xd/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 1000 Sum of sequence lengths 409090 Min sequence length 0 Max sequence length 839 Average sequence length 409 Possible positions 409090 Oligonucleotide statistics: Total occurrences 405037 Position interval parameters: Position interval 20 Number of windows 42 Total positions 409090 Degrees of freedom 41 K-mer clustering parameters: Number of clusters 0 Clustering method complete Position intervals: window [min,max] mid seq occ 1 -21 [-419,-400] -409.5 1 20 2 -20 [-399,-380] -389.5 3 30 3 -19 [-379,-360] -369.5 5 85 4 -18 [-359,-340] -349.5 10 150 5 -17 [-339,-320] -329.5 24 371 6 -16 [-319,-300] -309.5 48 761 7 -15 [-299,-280] -289.5 84 1352 8 -14 [-279,-260] -269.5 137 2288 9 -13 [-259,-240] -249.5 227 3843 10 -12 [-239,-220] -229.5 341 5913 11 -11 [-219,-200] -209.5 485 8587 12 -10 [-199,-180] -189.5 619 11481 13 -9 [-179,-160] -169.5 772 14333 14 -8 [-159,-140] -149.5 891 17088 15 -7 [-139,-120] -129.5 972 19016 16 -6 [-119,-100] -109.5 995 19764 17 -5 [-99,-80] -89.5 999 19970 18 -4 [-79,-60] -69.5 1000 19996 19 -3 [-59,-40] -49.5 1000 20000 20 -2 [-39,-20] -29.5 1000 20000 21 -1 [-19,0] -9.5 1000 20000 22 0 [1,20] 10.5 1000 20000 23 1 [21,40] 30.5 1000 20000 24 2 [41,60] 50.5 1000 20000 25 3 [61,80] 70.5 1000 19994 26 4 [81,100] 90.5 999 19968 27 5 [101,120] 110.5 995 19744 28 6 [121,140] 130.5 972 18937 29 7 [141,160] 150.5 891 16964 30 8 [161,180] 170.5 772 14184 31 9 [181,200] 190.5 619 11336 32 10 [201,220] 210.5 485 8437 33 11 [221,240] 230.5 341 5801 34 12 [241,260] 250.5 227 3757 35 13 [261,280] 270.5 137 2234 36 14 [281,300] 290.5 84 1316 37 15 [301,320] 310.5 48 738 38 16 [321,340] 330.5 24 356 39 17 [341,360] 350.5 10 145 40 18 [361,380] 370.5 5 84 41 19 [381,400] 390.5 3 28 42 20 [401,420] 410.5 1 19 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 -409.5 occurrences in window 1 [-419,-400] 11 -389.5 occurrences in window 2 [-399,-380] 12 -369.5 occurrences in window 3 [-379,-360] 13 -349.5 occurrences in window 4 [-359,-340] 14 -329.5 occurrences in window 5 [-339,-320] 15 -309.5 occurrences in window 6 [-319,-300] 16 -289.5 occurrences in window 7 [-299,-280] 17 -269.5 occurrences in window 8 [-279,-260] 18 -249.5 occurrences in window 9 [-259,-240] 19 -229.5 occurrences in window 10 [-239,-220] 20 -209.5 occurrences in window 11 [-219,-200] 21 -189.5 occurrences in window 12 [-199,-180] 22 -169.5 occurrences in window 13 [-179,-160] 23 -149.5 occurrences in window 14 [-159,-140] 24 -129.5 occurrences in window 15 [-139,-120] 25 -109.5 occurrences in window 16 [-119,-100] 26 -89.5 occurrences in window 17 [-99,-80] 27 -69.5 occurrences in window 18 [-79,-60] 28 -49.5 occurrences in window 19 [-59,-40] 29 -29.5 occurrences in window 20 [-39,-20] 30 -9.5 occurrences in window 21 [-19,0] 31 10.5 occurrences in window 22 [1,20] 32 30.5 occurrences in window 23 [21,40] 33 50.5 occurrences in window 24 [41,60] 34 70.5 occurrences in window 25 [61,80] 35 90.5 occurrences in window 26 [81,100] 36 110.5 occurrences in window 27 [101,120] 37 130.5 occurrences in window 28 [121,140] 38 150.5 occurrences in window 29 [141,160] 39 170.5 occurrences in window 30 [161,180] 40 190.5 occurrences in window 31 [181,200] 41 210.5 occurrences in window 32 [201,220] 42 230.5 occurrences in window 33 [221,240] 43 250.5 occurrences in window 34 [241,260] 44 270.5 occurrences in window 35 [261,280] 45 290.5 occurrences in window 36 [281,300] 46 310.5 occurrences in window 37 [301,320] 47 330.5 occurrences in window 38 [321,340] 48 350.5 occurrences in window 39 [341,360] 49 370.5 occurrences in window 40 [361,380] 50 390.5 occurrences in window 41 [381,400] 51 410.5 occurrences in window 42 [401,420]
| seq | id | occ | chi2 | df | Pval | Eval | sig | rank | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| c | c | 97472 | 71.5 | 41 | 2.2e-03 | 0.0088 | 2.05 | 1 | 4 | 10 | 15 | 39 | 84 | 168 | 288 | 569 | 918 | 1424 | 2062 | 2651 | 3361 | 4077 | 4607 | 4855 | 4820 | 4923 | 4799 | 4710 | 4830 | 4729 | 4758 | 4890 | 4828 | 4788 | 4727 | 4443 | 3849 | 3219 | 2683 | 2042 | 1324 | 827 | 517 | 316 | 147 | 81 | 44 | 30 | 10 | 6 |
| a | a | 104970 | 70.4 | 41 | 2.9e-03 | 0.011 | 1.94 | 2 | 11 | 4 | 18 | 29 | 102 | 194 | 375 | 599 | 1001 | 1523 | 2221 | 3037 | 3792 | 4470 | 5036 | 5187 | 5216 | 5196 | 5208 | 5038 | 5070 | 5128 | 5071 | 4943 | 4986 | 5067 | 4857 | 4680 | 4356 | 3693 | 2908 | 2185 | 1519 | 990 | 573 | 347 | 191 | 75 | 36 | 25 | 8 | 5 |
| g | g | 97891 | 57.7 | 41 | 4.3e-02 | 0.17 | 0.76 | 3 | 1 | 6 | 27 | 38 | 81 | 168 | 329 | 531 | 918 | 1409 | 2097 | 2722 | 3370 | 3995 | 4499 | 4663 | 4754 | 4783 | 4742 | 4818 | 4688 | 5040 | 4905 | 4846 | 4864 | 4673 | 4674 | 4474 | 4150 | 3495 | 2744 | 1969 | 1356 | 933 | 504 | 292 | 185 | 99 | 28 | 9 | 7 | 5 |
| t | t | 104704 | 47.9 | 41 | 2.1e-01 | 0.86 | 0.07 | 4 | 4 | 10 | 25 | 44 | 98 | 211 | 340 | 566 | 970 | 1514 | 2121 | 2891 | 3622 | 4407 | 4723 | 4929 | 5086 | 5013 | 5080 | 5250 | 5300 | 5038 | 5182 | 5183 | 5067 | 5085 | 5082 | 4969 | 4375 | 3632 | 2895 | 2181 | 1542 | 942 | 589 | 359 | 215 | 101 | 37 | 20 | 3 | 3 |
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