position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/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 m12 -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/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/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.093750_2025-06-19.093750_1W0rgp/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 80 Sum of sequence lengths 21335 Min sequence length 0 Max sequence length 1000 Average sequence length 266 Possible positions 21255 Sequences: # length ID 1 1000 CHLRE_08g358526v5 2 100 CHLRE_10g451950v5 3 140 CHLRE_13g577100v5 4 141 CHLRE_03g164000v5 5 200 CHLRE_06g262250v5 6 100 CHLRE_07g324600v5 7 102 CHLRE_03g146187v5 8 480 CHLRE_16g651350v5 9 110 CHLRE_17g731950v5 10 770 CHLRE_09g405050v5 11 94 CHLRE_03g203850v5 12 1000 CHLRE_08g373050v5 13 100 CHLRE_03g145607v5 14 1000 CHLRE_16g649466v5 15 133 CHLRE_03g145547v5 16 1000 CHLRE_09g416750v5 17 94 CHLRE_06g269950v5 18 100 CHLRE_01g000300v5 19 100 CHLRE_12g487850v5 20 390 CHLRE_07g318350v5 21 48 CHLRE_12g510850v5 22 98 CHLRE_06g306300v5 23 102 CHLRE_12g514750v5 24 100 CHLRE_14g619100v5 25 120 CHLRE_06g299650v5 26 52 CHLRE_06g308500v5 27 440 CHLRE_04g231222v5 28 140 CHLRE_13g583600v5 29 205 CHLRE_12g539000v5 30 437 CHLRE_03g206929v5 31 270 CHLRE_12g538450v5 32 110 CHLRE_10g464600v5 33 200 CHLRE_02g144450v5 34 54 CHLRE_06g297200v5 35 114 CHLRE_04g215250v5 36 152 CHLRE_09g390763v5 37 49 CHLRE_16g672800v5 38 120 CHLRE_03g189950v5 39 164 CHLRE_04g214500v5 40 152 CHLRE_12g507400v5 41 378 CHLRE_06g283050v5 42 48 CHLRE_13g605150v5 43 429 CHLRE_17g708750v5 44 610 CHLRE_09g402552v5 45 94 CHLRE_06g274650v5 46 154 CHLRE_12g523200v5 47 1000 CHLRE_06g256300v5 48 100 CHLRE_17g722150v5 49 148 CHLRE_14g626900v5 50 536 CHLRE_01g052100v5 51 170 CHLRE_09g396213v5 52 1000 CHLRE_03g191050v5 53 100 CHLRE_10g462250v5 54 401 CHLRE_09g387171v5 55 107 CHLRE_12g511900v5 56 117 CHLRE_17g701200v5 57 109 CHLRE_13g568900v5 58 100 CHLRE_02g115200v5 59 815 CHLRE_09g397697v5 60 138 CHLRE_12g537800v5 61 261 CHLRE_12g498900v5 62 377 CHLRE_17g710150v5 63 110 CHLRE_04g218050v5 64 340 CHLRE_09g408550v5 65 164 CHLRE_11g468300v5 66 100 CHLRE_14g619133v5 67 133 CHLRE_03g180850v5 68 545 CHLRE_12g522450v5 69 150 CHLRE_16g665400v5 70 54 CHLRE_16g656400v5 71 158 CHLRE_03g145247v5 72 794 CHLRE_13g603900v5 73 100 CHLRE_05g233800v5 74 130 CHLRE_12g549100v5 75 162 CHLRE_11g467567v5 76 48 CHLRE_07g357200v5 77 100 CHLRE_04g214502v5 78 100 CHLRE_09g409100v5 79 94 CHLRE_11g467710v5 80 580 CHLRE_14g624350v5 Oligonucleotide statistics: Total occurrences 20904 Position interval parameters: Position interval 20 Number of windows 50 Total positions 21255 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 6 120 2 -24 [-479,-460] -469.5 6 120 3 -23 [-459,-440] -449.5 6 120 4 -22 [-439,-420] -429.5 6 120 5 -21 [-419,-400] -409.5 7 128 6 -20 [-399,-380] -389.5 9 164 7 -19 [-379,-360] -369.5 9 180 8 -18 [-359,-340] -349.5 9 180 9 -17 [-339,-320] -329.5 9 180 10 -16 [-319,-300] -309.5 10 186 11 -15 [-299,-280] -289.5 11 210 12 -14 [-279,-260] -269.5 13 241 13 -13 [-259,-240] -249.5 13 260 14 -12 [-239,-220] -229.5 14 280 15 -11 [-219,-200] -209.5 18 335 16 -10 [-199,-180] -189.5 21 395 17 -9 [-179,-160] -169.5 22 430 18 -8 [-159,-140] -149.5 22 440 19 -7 [-139,-120] -129.5 24 467 20 -6 [-119,-100] -109.5 25 483 21 -5 [-99,-80] -89.5 31 552 22 -4 [-79,-60] -69.5 44 781 23 -3 [-59,-40] -49.5 73 1230 24 -2 [-39,-20] -29.5 80 1499 25 -1 [-19,0] -9.5 80 1600 26 0 [1,20] 10.5 80 1600 27 1 [21,40] 30.5 80 1487 28 2 [41,60] 50.5 73 1176 29 3 [61,80] 70.5 44 754 30 4 [81,100] 90.5 30 543 31 5 [101,120] 110.5 25 481 32 6 [121,140] 130.5 24 462 33 7 [141,160] 150.5 22 440 34 8 [161,180] 170.5 22 429 35 9 [181,200] 190.5 21 386 36 10 [201,220] 210.5 17 329 37 11 [221,240] 230.5 14 279 38 12 [241,260] 250.5 13 260 39 13 [261,280] 270.5 13 238 40 14 [281,300] 290.5 11 209 41 15 [301,320] 310.5 10 183 42 16 [321,340] 330.5 9 180 43 17 [341,360] 350.5 9 180 44 18 [361,380] 370.5 9 180 45 19 [381,400] 390.5 9 158 46 20 [401,420] 410.5 7 126 47 21 [421,440] 430.5 6 120 48 22 [441,460] 450.5 6 120 49 23 [461,480] 470.5 6 120 50 24 [481,500] 490.5 6 114 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| gg | gg | 1804 | 136.0 | 49 | 4.1e-10 | 6.6e-09 | 8.18 | 1 | 8 | 8 | 16 | 4 | 9 | 11 | 25 | 22 | 23 | 22 | 14 | 14 | 15 | 23 | 25 | 34 | 39 | 30 | 34 | 35 | 38 | 73 | 112 | 171 | 160 | 155 | 92 | 67 | 42 | 55 | 42 | 32 | 46 | 27 | 45 | 28 | 23 | 18 | 10 | 19 | 34 | 21 | 18 | 8 | 10 | 12 | 8 | 6 | 9 | 12 |
| cc | cc | 1805 | 129.2 | 49 | 3.7e-09 | 5.9e-08 | 7.23 | 2 | 15 | 9 | 13 | 4 | 8 | 11 | 12 | 19 | 14 | 18 | 30 | 21 | 28 | 29 | 43 | 58 | 41 | 47 | 46 | 53 | 74 | 68 | 59 | 118 | 120 | 148 | 127 | 85 | 72 | 42 | 31 | 37 | 26 | 36 | 27 | 35 | 19 | 17 | 27 | 16 | 13 | 20 | 15 | 11 | 7 | 8 | 1 | 6 | 14 | 7 |
| aa | aa | 999 | 85.5 | 49 | 9.7e-04 | 0.016 | 1.81 | 3 | 6 | 6 | 11 | 10 | 4 | 9 | 11 | 5 | 6 | 8 | 10 | 11 | 4 | 5 | 22 | 21 | 23 | 17 | 12 | 21 | 18 | 29 | 82 | 75 | 79 | 67 | 63 | 63 | 49 | 19 | 25 | 32 | 12 | 19 | 26 | 8 | 15 | 11 | 13 | 16 | 9 | 8 | 2 | 10 | 7 | 7 | 4 | 3 | 3 | 3 |
| tt | tt | 985 | 82.8 | 49 | 1.8e-03 | 0.029 | 1.54 | 4 | 3 | 3 | 7 | 1 | 1 | 2 | 6 | 8 | 7 | 6 | 2 | 12 | 2 | 17 | 18 | 14 | 13 | 21 | 24 | 28 | 28 | 40 | 64 | 75 | 73 | 78 | 96 | 71 | 41 | 19 | 16 | 22 | 13 | 23 | 14 | 12 | 14 | 14 | 15 | 11 | 8 | 2 | 9 | 10 | 10 | 2 | 3 | 1 | 2 | 4 |
| cg | cg | 1572 | 63.7 | 49 | 7.7e-02 | 1.2 | -0.09 | 5 | 13 | 8 | 6 | 14 | 8 | 15 | 13 | 15 | 22 | 16 | 12 | 12 | 14 | 23 | 27 | 18 | 39 | 35 | 29 | 35 | 34 | 68 | 87 | 115 | 134 | 119 | 105 | 70 | 47 | 36 | 41 | 32 | 36 | 26 | 31 | 30 | 24 | 21 | 13 | 16 | 15 | 25 | 17 | 14 | 2 | 8 | 8 | 6 | 12 | 6 |
| tc | tc | 995 | 58.9 | 49 | 1.6e-01 | 2.5 | -0.40 | 6 | 6 | 5 | 4 | 2 | 3 | 6 | 7 | 6 | 5 | 6 | 5 | 15 | 11 | 14 | 21 | 23 | 21 | 22 | 30 | 31 | 29 | 44 | 34 | 58 | 73 | 66 | 82 | 74 | 33 | 28 | 15 | 23 | 23 | 24 | 20 | 20 | 14 | 11 | 13 | 7 | 7 | 10 | 12 | 3 | 7 | 3 | 5 | 5 | 5 | 4 |
| ac | ac | 1244 | 58.7 | 49 | 1.6e-01 | 2.6 | -0.41 | 7 | 11 | 12 | 7 | 13 | 16 | 14 | 13 | 15 | 13 | 10 | 12 | 14 | 19 | 17 | 19 | 20 | 24 | 28 | 27 | 28 | 35 | 55 | 67 | 79 | 90 | 85 | 96 | 62 | 51 | 28 | 34 | 17 | 22 | 24 | 17 | 18 | 12 | 22 | 15 | 15 | 14 | 8 | 10 | 8 | 2 | 5 | 8 | 5 | 3 | 5 |
| gt | gt | 1098 | 58.2 | 49 | 1.7e-01 | 2.7 | -0.44 | 8 | 2 | 2 | 6 | 6 | 7 | 10 | 10 | 11 | 16 | 5 | 9 | 14 | 17 | 16 | 18 | 13 | 22 | 16 | 30 | 29 | 31 | 41 | 84 | 62 | 71 | 85 | 71 | 63 | 40 | 26 | 18 | 24 | 24 | 24 | 22 | 17 | 14 | 14 | 17 | 9 | 8 | 11 | 6 | 12 | 15 | 5 | 13 | 4 | 2 | 6 |
| ct | ct | 1193 | 57.8 | 49 | 1.8e-01 | 2.9 | -0.47 | 9 | 7 | 12 | 5 | 5 | 10 | 7 | 10 | 12 | 6 | 14 | 11 | 16 | 13 | 20 | 19 | 22 | 25 | 31 | 33 | 39 | 32 | 44 | 60 | 74 | 73 | 60 | 98 | 79 | 47 | 42 | 28 | 26 | 24 | 28 | 15 | 23 | 15 | 12 | 14 | 7 | 8 | 7 | 14 | 12 | 8 | 7 | 5 | 5 | 4 | 5 |
| ta | ta | 640 | 57.2 | 49 | 2.0e-01 | 3.1 | -0.50 | 10 | 3 | 4 | 2 | 7 | 7 | 9 | 4 | 7 | 1 | 4 | 8 | 7 | 10 | 9 | 8 | 9 | 10 | 16 | 19 | 14 | 13 | 24 | 54 | 37 | 29 | 35 | 41 | 56 | 28 | 19 | 18 | 14 | 14 | 15 | 6 | 8 | 9 | 12 | 10 | 6 | 5 | 1 | 5 | 7 | 5 | 2 | 4 | 3 | 2 | 0 |
| ga | ga | 1067 | 49.9 | 49 | 4.4e-01 | 7 | -0.84 | 11 | 6 | 9 | 3 | 7 | 7 | 11 | 10 | 9 | 10 | 9 | 11 | 5 | 9 | 5 | 15 | 17 | 19 | 24 | 21 | 16 | 36 | 33 | 73 | 87 | 102 | 83 | 64 | 47 | 40 | 24 | 31 | 21 | 27 | 18 | 22 | 21 | 14 | 10 | 11 | 11 | 6 | 4 | 10 | 7 | 10 | 7 | 5 | 8 | 7 | 5 |
| at | at | 901 | 49.5 | 49 | 4.5e-01 | 7.2 | -0.86 | 12 | 4 | 2 | 4 | 5 | 0 | 4 | 2 | 5 | 4 | 6 | 8 | 8 | 13 | 10 | 12 | 19 | 15 | 17 | 26 | 14 | 21 | 33 | 54 | 57 | 79 | 73 | 61 | 71 | 34 | 22 | 25 | 24 | 23 | 20 | 17 | 11 | 13 | 16 | 13 | 10 | 5 | 3 | 7 | 7 | 7 | 3 | 2 | 5 | 4 | 3 |
| tg | tg | 1546 | 46.7 | 49 | 5.7e-01 | 9.1 | -0.96 | 13 | 4 | 7 | 9 | 7 | 7 | 6 | 13 | 15 | 20 | 14 | 13 | 18 | 21 | 23 | 16 | 30 | 29 | 27 | 37 | 34 | 46 | 44 | 114 | 96 | 126 | 115 | 99 | 87 | 58 | 40 | 37 | 39 | 32 | 34 | 27 | 24 | 23 | 18 | 18 | 15 | 6 | 12 | 11 | 20 | 15 | 11 | 12 | 6 | 3 | 8 |
| ag | ag | 1223 | 46.1 | 49 | 5.9e-01 | 9.4 | -0.97 | 14 | 6 | 9 | 6 | 7 | 13 | 15 | 14 | 5 | 5 | 7 | 14 | 11 | 15 | 11 | 20 | 24 | 22 | 27 | 24 | 24 | 29 | 43 | 84 | 97 | 82 | 101 | 81 | 66 | 45 | 37 | 23 | 22 | 25 | 22 | 21 | 19 | 19 | 10 | 12 | 11 | 11 | 7 | 10 | 7 | 16 | 7 | 6 | 12 | 9 | 10 |
| ca | ca | 1655 | 39.2 | 49 | 8.4e-01 | 13 | -1.13 | 15 | 11 | 11 | 10 | 13 | 14 | 17 | 12 | 9 | 11 | 13 | 12 | 22 | 27 | 24 | 24 | 36 | 36 | 33 | 34 | 34 | 41 | 67 | 76 | 111 | 121 | 136 | 137 | 95 | 58 | 46 | 33 | 30 | 30 | 31 | 32 | 19 | 20 | 26 | 19 | 20 | 16 | 14 | 12 | 9 | 8 | 6 | 8 | 12 | 7 | 12 |
| gc | gc | 2177 | 32.5 | 49 | 9.7e-01 | 15 | -1.19 | 16 | 15 | 13 | 11 | 15 | 14 | 17 | 18 | 17 | 17 | 26 | 19 | 21 | 26 | 34 | 28 | 37 | 52 | 49 | 41 | 48 | 47 | 75 | 116 | 167 | 168 | 174 | 154 | 111 | 69 | 60 | 57 | 47 | 43 | 38 | 39 | 36 | 31 | 28 | 18 | 20 | 18 | 27 | 22 | 22 | 9 | 13 | 8 | 13 | 14 | 15 |
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