position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/03/19/peak-motifs.2025-03-19.101854_2025-03-19.101854_hlFw6q/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 2 -ci 20 -img_format png -title pr_genes -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/03/19/peak-motifs.2025-03-19.101854_2025-03-19.101854_hlFw6q/results/composition/peak-motifs_test_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/2025/03/19/peak-motifs.2025-03-19.101854_2025-03-19.101854_hlFw6q/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2025/03/19/peak-motifs.2025-03-19.101854_2025-03-19.101854_hlFw6q/results/composition/peak-motifs_test_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 4 Sum of sequence lengths 4000 Min sequence length 0 Max sequence length 1000 Average sequence length 1000 Possible positions 3996 Sequences: # length ID 1 1000 PR1 2 1000 PR4 3 1000 PR5 4 1000 PR2 Oligonucleotide statistics: Total occurrences 3996 Position interval parameters: Position interval 20 Number of windows 50 Total positions 3996 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 4 80 2 -24 [-479,-460] -469.5 4 80 3 -23 [-459,-440] -449.5 4 80 4 -22 [-439,-420] -429.5 4 80 5 -21 [-419,-400] -409.5 4 80 6 -20 [-399,-380] -389.5 4 80 7 -19 [-379,-360] -369.5 4 80 8 -18 [-359,-340] -349.5 4 80 9 -17 [-339,-320] -329.5 4 80 10 -16 [-319,-300] -309.5 4 80 11 -15 [-299,-280] -289.5 4 80 12 -14 [-279,-260] -269.5 4 80 13 -13 [-259,-240] -249.5 4 80 14 -12 [-239,-220] -229.5 4 80 15 -11 [-219,-200] -209.5 4 80 16 -10 [-199,-180] -189.5 4 80 17 -9 [-179,-160] -169.5 4 80 18 -8 [-159,-140] -149.5 4 80 19 -7 [-139,-120] -129.5 4 80 20 -6 [-119,-100] -109.5 4 80 21 -5 [-99,-80] -89.5 4 80 22 -4 [-79,-60] -69.5 4 80 23 -3 [-59,-40] -49.5 4 80 24 -2 [-39,-20] -29.5 4 80 25 -1 [-19,0] -9.5 4 80 26 0 [1,20] 10.5 4 80 27 1 [21,40] 30.5 4 80 28 2 [41,60] 50.5 4 80 29 3 [61,80] 70.5 4 80 30 4 [81,100] 90.5 4 80 31 5 [101,120] 110.5 4 80 32 6 [121,140] 130.5 4 80 33 7 [141,160] 150.5 4 80 34 8 [161,180] 170.5 4 80 35 9 [181,200] 190.5 4 80 36 10 [201,220] 210.5 4 80 37 11 [221,240] 230.5 4 80 38 12 [241,260] 250.5 4 80 39 13 [261,280] 270.5 4 80 40 14 [281,300] 290.5 4 80 41 15 [301,320] 310.5 4 80 42 16 [321,340] 330.5 4 80 43 17 [341,360] 350.5 4 80 44 18 [361,380] 370.5 4 80 45 19 [381,400] 390.5 4 80 46 20 [401,420] 410.5 4 80 47 21 [421,440] 430.5 4 80 48 22 [441,460] 450.5 4 80 49 23 [461,480] 470.5 4 80 50 24 [481,500] 490.5 4 76 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| tt | tt | 597 | 97.2 | 49 | 5.0e-05 | 0.0008 | 3.10 | 1 | 12 | 11 | 16 | 8 | 10 | 6 | 18 | 15 | 8 | 11 | 19 | 15 | 13 | 13 | 11 | 10 | 16 | 5 | 13 | 19 | 10 | 12 | 10 | 14 | 13 | 22 | 20 | 7 | 8 | 12 | 12 | 14 | 11 | 18 | 14 | 22 | 18 | 4 | 5 | 6 | 10 | 4 | 7 | 4 | 7 | 7 | 11 | 19 | 18 | 9 |
| aa | aa | 614 | 94.9 | 49 | 9.3e-05 | 0.0015 | 2.83 | 2 | 6 | 16 | 5 | 11 | 9 | 20 | 7 | 8 | 12 | 17 | 6 | 11 | 6 | 9 | 19 | 11 | 11 | 15 | 9 | 9 | 15 | 23 | 6 | 15 | 13 | 12 | 11 | 24 | 10 | 14 | 12 | 16 | 5 | 19 | 17 | 9 | 9 | 14 | 18 | 18 | 9 | 11 | 15 | 18 | 17 | 17 | 10 | 10 | 4 | 6 |
| ta | ta | 491 | 27.7 | 49 | 9.9e-01 | 16 | -1.20 | 3 | 9 | 9 | 7 | 10 | 13 | 8 | 15 | 13 | 8 | 13 | 9 | 8 | 10 | 13 | 9 | 12 | 12 | 8 | 12 | 7 | 11 | 9 | 13 | 11 | 13 | 13 | 8 | 9 | 17 | 10 | 9 | 11 | 8 | 7 | 8 | 9 | 6 | 10 | 9 | 8 | 8 | 9 | 8 | 7 | 11 | 11 | 8 | 7 | 8 | 10 |
| at | at | 520 | 26.5 | 49 | 1.0e+00 | 16 | -1.20 | 4 | 10 | 9 | 9 | 12 | 8 | 10 | 15 | 11 | 12 | 15 | 14 | 10 | 9 | 10 | 10 | 14 | 12 | 13 | 8 | 9 | 8 | 12 | 13 | 11 | 14 | 15 | 9 | 9 | 12 | 8 | 10 | 9 | 11 | 11 | 8 | 13 | 9 | 12 | 8 | 9 | 11 | 9 | 6 | 6 | 11 | 12 | 12 | 7 | 10 | 5 |
| tc | tc | 204 | 0.0 | 49 | 1.0e+00 | 16 | -1.20 | 5 | 5 | 4 | 5 | 4 | 5 | 3 | 4 | 2 | 3 | 4 | 2 | 6 | 4 | 2 | 2 | 5 | 3 | 5 | 1 | 5 | 5 | 2 | 5 | 6 | 8 | 3 | 6 | 0 | 3 | 4 | 5 | 4 | 8 | 6 | 5 | 5 | 4 | 5 | 4 | 2 | 6 | 2 | 2 | 2 | 6 | 3 | 4 | 3 | 5 | 7 |
| cg | cg | 53 | 0.0 | 49 | 1.0e+00 | 16 | -1.20 | 6 | 1 | 1 | 1 | 1 | 3 | 1 | 1 | 2 | 0 | 1 | 1 | 0 | 5 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 2 | 1 | 3 | 0 | 2 | 1 | 3 | 0 | 1 | 1 | 1 | 1 | 0 | 3 | 3 | 0 | 4 | 1 | 2 | 0 |
| ag | ag | 163 | 0.0 | 49 | 1.0e+00 | 16 | -1.20 | 7 | 4 | 1 | 7 | 5 | 2 | 3 | 3 | 4 | 5 | 2 | 3 | 3 | 4 | 4 | 3 | 2 | 3 | 4 | 2 | 4 | 4 | 2 | 4 | 1 | 3 | 2 | 2 | 3 | 8 | 3 | 5 | 2 | 3 | 1 | 3 | 2 | 2 | 4 | 6 | 4 | 2 | 6 | 2 | 5 | 1 | 5 | 2 | 2 | 2 | 4 |
| gg | gg | 80 | 0.0 | 49 | 1.0e+00 | 16 | -1.20 | 8 | 0 | 1 | 5 | 2 | 4 | 2 | 1 | 0 | 1 | 0 | 3 | 5 | 5 | 0 | 3 | 2 | 2 | 1 | 0 | 2 | 2 | 0 | 2 | 0 | 1 | 0 | 1 | 1 | 2 | 1 | 0 | 1 | 4 | 0 | 5 | 0 | 1 | 4 | 0 | 4 | 3 | 2 | 1 | 1 | 1 | 2 | 1 | 0 | 1 | 0 |
| gt | gt | 190 | 0.0 | 49 | 1.0e+00 | 16 | -1.20 | 9 | 8 | 4 | 6 | 2 | 2 | 3 | 4 | 4 | 5 | 2 | 3 | 4 | 7 | 6 | 4 | 7 | 4 | 3 | 5 | 6 | 3 | 2 | 5 | 2 | 2 | 3 | 2 | 2 | 5 | 4 | 5 | 3 | 2 | 3 | 2 | 2 | 3 | 4 | 5 | 6 | 2 | 4 | 5 | 2 | 4 | 4 | 6 | 4 | 3 | 2 |
| gc | gc | 77 | 0.0 | 49 | 1.0e+00 | 16 | -1.20 | 10 | 4 | 1 | 2 | 3 | 2 | 3 | 1 | 3 | 2 | 0 | 1 | 2 | 3 | 0 | 2 | 1 | 1 | 4 | 1 | 1 | 1 | 0 | 2 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 2 | 4 | 0 | 1 | 1 | 2 | 0 | 1 | 3 | 3 | 0 | 0 | 2 | 1 | 1 | 2 | 3 | 4 | 3 |
| ca | ca | 209 | 0.0 | 49 | 1.0e+00 | 16 | -1.20 | 11 | 5 | 4 | 4 | 5 | 2 | 5 | 1 | 2 | 3 | 2 | 3 | 7 | 3 | 5 | 4 | 5 | 3 | 8 | 2 | 7 | 5 | 8 | 6 | 1 | 3 | 3 | 4 | 7 | 0 | 5 | 2 | 2 | 4 | 3 | 1 | 2 | 4 | 6 | 9 | 2 | 8 | 7 | 5 | 4 | 3 | 5 | 2 | 7 | 5 | 6 |
| cc | cc | 95 | 0.0 | 49 | 1.0e+00 | 16 | -1.20 | 12 | 0 | 3 | 0 | 2 | 7 | 2 | 2 | 1 | 3 | 1 | 0 | 0 | 2 | 5 | 1 | 0 | 1 | 2 | 1 | 1 | 2 | 2 | 1 | 7 | 2 | 0 | 3 | 0 | 1 | 2 | 1 | 1 | 2 | 2 | 1 | 0 | 1 | 2 | 2 | 1 | 1 | 3 | 4 | 7 | 0 | 1 | 0 | 3 | 1 | 8 |
| ct | ct | 185 | 0.0 | 49 | 1.0e+00 | 16 | -1.20 | 13 | 5 | 4 | 2 | 5 | 7 | 3 | 4 | 3 | 3 | 3 | 1 | 2 | 2 | 2 | 3 | 2 | 2 | 3 | 6 | 3 | 4 | 0 | 3 | 7 | 4 | 1 | 6 | 2 | 4 | 5 | 5 | 6 | 6 | 3 | 6 | 4 | 2 | 3 | 2 | 4 | 3 | 3 | 5 | 4 | 6 | 1 | 3 | 3 | 6 | 9 |
| ac | ac | 168 | 0.0 | 49 | 1.0e+00 | 16 | -1.20 | 14 | 2 | 4 | 2 | 2 | 5 | 3 | 1 | 2 | 1 | 2 | 2 | 2 | 2 | 6 | 2 | 2 | 2 | 2 | 7 | 3 | 4 | 6 | 4 | 1 | 1 | 1 | 3 | 8 | 1 | 6 | 2 | 3 | 1 | 1 | 2 | 1 | 4 | 4 | 6 | 2 | 4 | 9 | 8 | 8 | 3 | 2 | 3 | 5 | 5 | 6 |
| ga | ga | 150 | 0.0 | 49 | 1.0e+00 | 16 | -1.20 | 15 | 1 | 3 | 4 | 5 | 1 | 3 | 1 | 4 | 6 | 4 | 6 | 1 | 3 | 1 | 2 | 1 | 3 | 2 | 4 | 1 | 3 | 1 | 1 | 2 | 2 | 2 | 2 | 4 | 5 | 1 | 5 | 2 | 3 | 3 | 3 | 5 | 6 | 4 | 2 | 3 | 4 | 6 | 5 | 5 | 3 | 4 | 5 | 1 | 2 | 0 |
| tg | tg | 200 | 0.0 | 49 | 1.0e+00 | 16 | -1.20 | 16 | 8 | 5 | 5 | 3 | 0 | 5 | 2 | 6 | 8 | 3 | 7 | 4 | 2 | 4 | 5 | 5 | 5 | 4 | 9 | 3 | 2 | 1 | 4 | 2 | 0 | 3 | 3 | 3 | 2 | 4 | 4 | 3 | 5 | 3 | 2 | 4 | 6 | 4 | 2 | 7 | 5 | 4 | 7 | 2 | 3 | 5 | 7 | 5 | 4 | 1 |
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