position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/04/17/peak-motifs.2025-04-17.044940_2025-04-17.044940_gWHOHM/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 dve-1_lys -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/04/17/peak-motifs.2025-04-17.044940_2025-04-17.044940_gWHOHM/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/2025/04/17/peak-motifs.2025-04-17.044940_2025-04-17.044940_gWHOHM/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2025/04/17/peak-motifs.2025-04-17.044940_2025-04-17.044940_gWHOHM/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 39 Sum of sequence lengths 11775 Min sequence length 0 Max sequence length 1000 Average sequence length 301 Possible positions 11736 Sequences: # length ID 1 378 test_peak_287 2 310 test_peak_11570 3 291 test_peak_13295 4 172 test_peak_16208 5 249 test_peak_13153 6 289 test_peak_1997 7 282 test_peak_14288 8 313 test_peak_16134 9 464 test_peak_16135 10 282 test_peak_1275 11 614 test_peak_17558 12 198 test_peak_16479 13 290 test_peak_937 14 175 test_peak_13782 15 234 test_peak_13799 16 371 test_peak_4371 17 219 test_peak_13379 18 253 test_peak_16626 19 248 test_peak_16627 20 180 test_peak_10790 21 235 test_peak_13945 22 237 test_peak_13759 23 348 test_peak_16632 24 182 test_peak_8067 25 281 test_peak_11110 26 199 test_peak_8610 27 517 test_peak_5475 28 243 test_peak_11638 29 203 test_peak_7766 30 264 test_peak_9852 31 178 test_peak_10310 32 172 test_peak_65 33 181 test_peak_13305 34 465 test_peak_3838 35 1000 test_peak_13152 36 180 test_peak_16143 37 584 test_peak_15749 38 288 test_peak_15750 39 206 test_peak_3849 Oligonucleotide statistics: Total occurrences 11645 Position interval parameters: Position interval 20 Number of windows 50 Total positions 11736 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 1 20 2 -24 [-479,-460] -469.5 1 20 3 -23 [-459,-440] -449.5 1 20 4 -22 [-439,-420] -429.5 1 20 5 -21 [-419,-400] -409.5 1 20 6 -20 [-399,-380] -389.5 1 20 7 -19 [-379,-360] -369.5 1 20 8 -18 [-359,-340] -349.5 1 20 9 -17 [-339,-320] -329.5 1 20 10 -16 [-319,-300] -309.5 2 28 11 -15 [-299,-280] -289.5 3 52 12 -14 [-279,-260] -269.5 3 60 13 -13 [-259,-240] -249.5 4 79 14 -12 [-239,-220] -229.5 6 105 15 -11 [-219,-200] -209.5 6 120 16 -10 [-199,-180] -189.5 8 136 17 -9 [-179,-160] -169.5 9 174 18 -8 [-159,-140] -149.5 18 239 19 -7 [-139,-120] -129.5 23 390 20 -6 [-119,-100] -109.5 29 531 21 -5 [-99,-80] -89.5 39 693 22 -4 [-79,-60] -69.5 39 780 23 -3 [-59,-40] -49.5 39 780 24 -2 [-39,-20] -29.5 39 780 25 -1 [-19,0] -9.5 39 780 26 0 [1,20] 10.5 39 780 27 1 [21,40] 30.5 39 780 28 2 [41,60] 50.5 39 780 29 3 [61,80] 70.5 39 780 30 4 [81,100] 90.5 39 674 31 5 [101,120] 110.5 28 517 32 6 [121,140] 130.5 22 379 33 7 [141,160] 150.5 15 221 34 8 [161,180] 170.5 9 173 35 9 [181,200] 190.5 8 131 36 10 [201,220] 210.5 6 120 37 11 [221,240] 230.5 6 102 38 12 [241,260] 250.5 4 77 39 13 [261,280] 270.5 3 60 40 14 [281,300] 290.5 3 51 41 15 [301,320] 310.5 2 25 42 16 [321,340] 330.5 1 20 43 17 [341,360] 350.5 1 20 44 18 [361,380] 370.5 1 20 45 19 [381,400] 390.5 1 20 46 20 [401,420] 410.5 1 20 47 21 [421,440] 430.5 1 20 48 22 [441,460] 450.5 1 20 49 23 [461,480] 470.5 1 20 50 24 [481,500] 490.5 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 -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 | 1484 | 132.9 | 49 | 1.1e-09 | 1.8e-08 | 7.74 | 1 | 1 | 3 | 7 | 2 | 2 | 2 | 1 | 1 | 1 | 5 | 3 | 7 | 6 | 16 | 12 | 22 | 16 | 21 | 51 | 69 | 92 | 76 | 78 | 75 | 67 | 72 | 72 | 114 | 132 | 141 | 93 | 70 | 33 | 23 | 19 | 20 | 14 | 15 | 12 | 3 | 4 | 2 | 2 | 1 | 1 | 3 | 0 | 1 | 1 | 0 |
| aa | aa | 1305 | 73.2 | 49 | 1.4e-02 | 0.23 | 0.65 | 2 | 4 | 2 | 3 | 2 | 2 | 3 | 1 | 0 | 0 | 2 | 5 | 5 | 10 | 9 | 19 | 13 | 16 | 46 | 53 | 56 | 94 | 118 | 93 | 74 | 74 | 72 | 74 | 86 | 73 | 59 | 54 | 59 | 39 | 13 | 15 | 9 | 6 | 7 | 6 | 3 | 0 | 2 | 5 | 0 | 2 | 5 | 4 | 5 | 3 | 0 |
| gc | gc | 449 | 42.3 | 49 | 7.4e-01 | 12 | -1.07 | 3 | 1 | 0 | 1 | 1 | 1 | 1 | 0 | 2 | 0 | 1 | 3 | 1 | 2 | 4 | 5 | 4 | 13 | 7 | 10 | 16 | 23 | 14 | 31 | 29 | 39 | 38 | 41 | 38 | 35 | 17 | 13 | 9 | 6 | 10 | 8 | 5 | 5 | 6 | 1 | 2 | 0 | 1 | 0 | 1 | 1 | 1 | 1 | 0 | 1 | 0 |
| ag | ag | 637 | 36.7 | 49 | 9.0e-01 | 14 | -1.16 | 4 | 1 | 1 | 0 | 2 | 0 | 1 | 1 | 0 | 1 | 0 | 7 | 4 | 7 | 8 | 4 | 8 | 14 | 15 | 22 | 27 | 24 | 46 | 40 | 46 | 52 | 45 | 62 | 38 | 23 | 30 | 23 | 15 | 14 | 10 | 9 | 7 | 8 | 4 | 2 | 3 | 0 | 0 | 4 | 2 | 1 | 1 | 2 | 1 | 1 | 1 |
| tg | tg | 738 | 32.5 | 49 | 9.7e-01 | 15 | -1.19 | 5 | 1 | 2 | 2 | 0 | 0 | 2 | 1 | 1 | 2 | 1 | 6 | 5 | 2 | 10 | 11 | 12 | 8 | 13 | 19 | 30 | 33 | 33 | 47 | 54 | 51 | 58 | 60 | 51 | 42 | 38 | 26 | 26 | 18 | 11 | 8 | 11 | 13 | 6 | 3 | 4 | 3 | 1 | 2 | 2 | 2 | 1 | 1 | 2 | 1 | 2 |
| ac | ac | 578 | 30.4 | 49 | 9.8e-01 | 16 | -1.20 | 6 | 1 | 1 | 1 | 0 | 5 | 2 | 1 | 0 | 0 | 2 | 2 | 2 | 4 | 3 | 6 | 6 | 5 | 10 | 22 | 32 | 37 | 41 | 38 | 30 | 50 | 55 | 42 | 32 | 39 | 23 | 23 | 17 | 10 | 9 | 2 | 1 | 3 | 1 | 5 | 2 | 2 | 1 | 0 | 0 | 2 | 3 | 1 | 1 | 1 | 2 |
| gt | gt | 608 | 29.8 | 49 | 9.9e-01 | 16 | -1.20 | 7 | 0 | 0 | 1 | 0 | 0 | 0 | 2 | 0 | 2 | 2 | 3 | 7 | 4 | 10 | 5 | 10 | 8 | 5 | 14 | 21 | 22 | 34 | 40 | 46 | 39 | 49 | 47 | 51 | 44 | 34 | 22 | 19 | 10 | 9 | 9 | 7 | 8 | 5 | 3 | 2 | 2 | 1 | 2 | 2 | 1 | 0 | 0 | 2 | 4 | 0 |
| tc | tc | 822 | 29.2 | 49 | 9.9e-01 | 16 | -1.20 | 8 | 1 | 1 | 1 | 1 | 0 | 0 | 3 | 3 | 2 | 2 | 2 | 6 | 5 | 5 | 7 | 10 | 16 | 15 | 23 | 38 | 48 | 63 | 53 | 72 | 57 | 44 | 45 | 61 | 67 | 53 | 37 | 22 | 6 | 10 | 5 | 12 | 5 | 5 | 6 | 2 | 1 | 2 | 0 | 1 | 1 | 0 | 1 | 1 | 1 | 0 |
| gg | gg | 381 | 28.0 | 49 | 9.9e-01 | 16 | -1.20 | 9 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | 3 | 2 | 2 | 4 | 5 | 4 | 5 | 8 | 4 | 4 | 2 | 12 | 8 | 19 | 19 | 35 | 33 | 16 | 33 | 29 | 22 | 27 | 17 | 19 | 15 | 8 | 3 | 4 | 1 | 2 | 5 | 1 | 0 | 2 | 1 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 2 |
| cg | cg | 472 | 25.9 | 49 | 1.0e+00 | 16 | -1.20 | 10 | 1 | 0 | 0 | 0 | 1 | 0 | 2 | 2 | 1 | 2 | 0 | 2 | 5 | 2 | 5 | 3 | 7 | 8 | 11 | 18 | 30 | 22 | 28 | 34 | 37 | 36 | 35 | 43 | 47 | 22 | 15 | 13 | 5 | 8 | 6 | 2 | 0 | 4 | 1 | 2 | 2 | 1 | 0 | 2 | 1 | 1 | 1 | 0 | 3 | 1 |
| ga | ga | 783 | 25.8 | 49 | 1.0e+00 | 16 | -1.20 | 11 | 2 | 3 | 0 | 1 | 0 | 2 | 1 | 1 | 2 | 2 | 5 | 3 | 9 | 5 | 9 | 10 | 9 | 18 | 33 | 34 | 40 | 55 | 46 | 56 | 62 | 52 | 64 | 48 | 32 | 39 | 28 | 26 | 19 | 14 | 7 | 8 | 5 | 4 | 2 | 6 | 1 | 1 | 3 | 3 | 3 | 2 | 2 | 1 | 1 | 4 |
| at | at | 955 | 25.1 | 49 | 1.0e+00 | 16 | -1.20 | 12 | 1 | 3 | 1 | 4 | 2 | 2 | 1 | 2 | 3 | 1 | 3 | 3 | 5 | 8 | 10 | 6 | 13 | 26 | 28 | 46 | 70 | 70 | 67 | 61 | 57 | 54 | 51 | 51 | 61 | 63 | 51 | 30 | 21 | 17 | 13 | 12 | 9 | 2 | 4 | 8 | 3 | 2 | 1 | 2 | 0 | 0 | 2 | 2 | 0 | 3 |
| ca | ca | 716 | 22.9 | 49 | 1.0e+00 | 16 | -1.20 | 13 | 0 | 1 | 1 | 2 | 5 | 1 | 0 | 1 | 1 | 0 | 4 | 3 | 5 | 5 | 6 | 7 | 18 | 14 | 22 | 43 | 48 | 47 | 55 | 44 | 51 | 56 | 53 | 41 | 43 | 32 | 34 | 20 | 8 | 10 | 5 | 6 | 9 | 2 | 6 | 2 | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 1 |
| ta | ta | 667 | 21.9 | 49 | 1.0e+00 | 16 | -1.20 | 14 | 1 | 1 | 1 | 3 | 2 | 2 | 2 | 0 | 1 | 2 | 1 | 3 | 4 | 7 | 5 | 4 | 8 | 16 | 15 | 28 | 40 | 54 | 46 | 39 | 45 | 45 | 35 | 35 | 46 | 45 | 40 | 15 | 14 | 12 | 11 | 7 | 6 | 3 | 3 | 6 | 2 | 2 | 1 | 1 | 1 | 0 | 3 | 2 | 1 | 1 |
| cc | cc | 384 | 20.6 | 49 | 1.0e+00 | 16 | -1.20 | 15 | 2 | 0 | 0 | 1 | 0 | 0 | 1 | 2 | 2 | 1 | 1 | 0 | 5 | 3 | 2 | 8 | 9 | 6 | 17 | 20 | 20 | 23 | 37 | 30 | 28 | 26 | 27 | 22 | 18 | 22 | 11 | 9 | 2 | 5 | 4 | 4 | 3 | 3 | 0 | 3 | 2 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 1 | 2 |
| ct | ct | 666 | 16.2 | 49 | 1.0e+00 | 16 | -1.20 | 16 | 3 | 1 | 1 | 1 | 0 | 2 | 2 | 2 | 0 | 3 | 3 | 4 | 2 | 5 | 6 | 9 | 10 | 13 | 18 | 25 | 33 | 45 | 39 | 57 | 55 | 45 | 43 | 47 | 51 | 39 | 28 | 14 | 8 | 9 | 6 | 8 | 6 | 5 | 5 | 3 | 0 | 2 | 0 | 0 | 3 | 2 | 2 | 1 | 0 | 0 |
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