position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/12/18/peak-motifs.2025-12-18.192302_2025-12-18.192302_HeMbBV/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 HA_CTRL_1 -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/12/18/peak-motifs.2025-12-18.192302_2025-12-18.192302_HeMbBV/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/2025/12/18/peak-motifs.2025-12-18.192302_2025-12-18.192302_HeMbBV/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2025/12/18/peak-motifs.2025-12-18.192302_2025-12-18.192302_HeMbBV/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 1290 Sum of sequence lengths 86321 Min sequence length 0 Max sequence length 521 Average sequence length 66 Possible positions 85031 Oligonucleotide statistics: Total occurrences 79991 Position interval parameters: Position interval 20 Number of windows 27 Total positions 85031 Degrees of freedom 26 K-mer clustering parameters: Number of clusters 0 Clustering method complete Position intervals: window [min,max] mid seq occ 1 -14 [-279,-260] -269.5 1 1 2 -13 [-259,-240] -249.5 2 29 3 -12 [-239,-220] -229.5 2 40 4 -11 [-219,-200] -209.5 3 60 5 -10 [-199,-180] -189.5 5 88 6 -9 [-179,-160] -169.5 5 100 7 -8 [-159,-140] -149.5 13 205 8 -7 [-139,-120] -129.5 18 306 9 -6 [-119,-100] -109.5 26 430 10 -5 [-99,-80] -89.5 38 643 11 -4 [-79,-60] -69.5 77 1096 12 -3 [-59,-40] -49.5 186 2457 13 -2 [-39,-20] -29.5 1290 12524 14 -1 [-19,0] -9.5 1290 25800 15 0 [1,20] 10.5 1290 25800 16 1 [21,40] 30.5 1290 10348 17 2 [41,60] 50.5 166 2254 18 3 [61,80] 70.5 73 1027 19 4 [81,100] 90.5 37 620 20 5 [101,120] 110.5 23 413 21 6 [121,140] 130.5 18 295 22 7 [141,160] 150.5 13 187 23 8 [161,180] 170.5 5 100 24 9 [181,200] 190.5 5 84 25 10 [201,220] 210.5 3 58 26 11 [221,240] 230.5 2 40 27 12 [241,260] 250.5 2 26 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 -269.5 occurrences in window 1 [-279,-260] 11 -249.5 occurrences in window 2 [-259,-240] 12 -229.5 occurrences in window 3 [-239,-220] 13 -209.5 occurrences in window 4 [-219,-200] 14 -189.5 occurrences in window 5 [-199,-180] 15 -169.5 occurrences in window 6 [-179,-160] 16 -149.5 occurrences in window 7 [-159,-140] 17 -129.5 occurrences in window 8 [-139,-120] 18 -109.5 occurrences in window 9 [-119,-100] 19 -89.5 occurrences in window 10 [-99,-80] 20 -69.5 occurrences in window 11 [-79,-60] 21 -49.5 occurrences in window 12 [-59,-40] 22 -29.5 occurrences in window 13 [-39,-20] 23 -9.5 occurrences in window 14 [-19,0] 24 10.5 occurrences in window 15 [1,20] 25 30.5 occurrences in window 16 [21,40] 26 50.5 occurrences in window 17 [41,60] 27 70.5 occurrences in window 18 [61,80] 28 90.5 occurrences in window 19 [81,100] 29 110.5 occurrences in window 20 [101,120] 30 130.5 occurrences in window 21 [121,140] 31 150.5 occurrences in window 22 [141,160] 32 170.5 occurrences in window 23 [161,180] 33 190.5 occurrences in window 24 [181,200] 34 210.5 occurrences in window 25 [201,220] 35 230.5 occurrences in window 26 [221,240] 36 250.5 occurrences in window 27 [241,260]
| seq | id | occ | chi2 | df | Pval | Eval | sig | rank | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| tt | tt | 7457 | 55.8 | 26 | 5.9e-04 | 0.0095 | 2.02 | 1 | 0 | 1 | 3 | 1 | 4 | 2 | 25 | 34 | 32 | 30 | 71 | 169 | 1153 | 2283 | 2332 | 895 | 179 | 88 | 49 | 44 | 25 | 16 | 5 | 7 | 5 | 3 | 1 |
| cg | cg | 911 | 55.5 | 26 | 6.6e-04 | 0.011 | 1.97 | 2 | 0 | 0 | 0 | 1 | 0 | 0 | 2 | 3 | 6 | 11 | 27 | 28 | 129 | 224 | 280 | 113 | 33 | 21 | 15 | 10 | 4 | 1 | 0 | 2 | 0 | 0 | 1 |
| aa | aa | 7939 | 48.0 | 26 | 5.4e-03 | 0.087 | 1.06 | 3 | 0 | 1 | 4 | 5 | 7 | 8 | 34 | 23 | 36 | 63 | 104 | 225 | 1157 | 2519 | 2430 | 947 | 170 | 60 | 57 | 28 | 30 | 17 | 6 | 4 | 3 | 0 | 1 |
| gg | gg | 4463 | 37.2 | 26 | 7.2e-02 | 1.1 | -0.06 | 4 | 0 | 0 | 1 | 6 | 7 | 9 | 15 | 18 | 32 | 36 | 72 | 121 | 636 | 1330 | 1315 | 545 | 133 | 78 | 39 | 34 | 14 | 11 | 3 | 2 | 4 | 1 | 1 |
| ta | ta | 5059 | 29.8 | 26 | 2.8e-01 | 4.4 | -0.65 | 5 | 0 | 1 | 2 | 1 | 5 | 4 | 9 | 14 | 20 | 33 | 53 | 131 | 765 | 1556 | 1578 | 643 | 106 | 42 | 31 | 23 | 21 | 4 | 5 | 5 | 5 | 2 | 0 |
| ca | ca | 5843 | 28.6 | 26 | 3.3e-01 | 5.3 | -0.72 | 6 | 0 | 3 | 1 | 6 | 10 | 11 | 13 | 25 | 35 | 56 | 80 | 195 | 836 | 1701 | 1826 | 720 | 160 | 64 | 31 | 23 | 17 | 18 | 4 | 5 | 1 | 1 | 1 |
| ct | ct | 5567 | 27.7 | 26 | 3.8e-01 | 6 | -0.78 | 7 | 0 | 6 | 3 | 3 | 4 | 4 | 12 | 18 | 26 | 36 | 47 | 140 | 872 | 1762 | 1628 | 672 | 147 | 61 | 47 | 32 | 18 | 9 | 9 | 4 | 2 | 1 | 4 |
| gt | gt | 3904 | 25.6 | 26 | 4.9e-01 | 7.8 | -0.89 | 8 | 0 | 0 | 3 | 1 | 5 | 3 | 10 | 11 | 22 | 23 | 35 | 83 | 594 | 1205 | 1210 | 471 | 106 | 55 | 25 | 8 | 12 | 6 | 8 | 5 | 0 | 1 | 2 |
| tc | tc | 4723 | 24.7 | 26 | 5.4e-01 | 8.6 | -0.93 | 9 | 0 | 4 | 3 | 2 | 5 | 4 | 6 | 16 | 24 | 30 | 45 | 119 | 746 | 1451 | 1414 | 601 | 130 | 45 | 25 | 24 | 11 | 6 | 5 | 1 | 1 | 2 | 3 |
| at | at | 5984 | 24.6 | 26 | 5.4e-01 | 8.7 | -0.94 | 10 | 0 | 0 | 2 | 3 | 7 | 7 | 9 | 24 | 27 | 42 | 73 | 170 | 889 | 1782 | 1876 | 769 | 135 | 58 | 26 | 32 | 23 | 8 | 6 | 5 | 5 | 5 | 1 |
| ag | ag | 5748 | 21.3 | 26 | 7.3e-01 | 12 | -1.07 | 11 | 0 | 3 | 6 | 9 | 9 | 12 | 19 | 22 | 31 | 55 | 76 | 176 | 834 | 1723 | 1760 | 688 | 159 | 59 | 36 | 21 | 20 | 18 | 4 | 3 | 4 | 0 | 1 |
| tg | tg | 5658 | 19.3 | 26 | 8.2e-01 | 13 | -1.12 | 12 | 0 | 1 | 3 | 4 | 5 | 7 | 11 | 26 | 30 | 38 | 61 | 141 | 847 | 1760 | 1699 | 670 | 147 | 80 | 44 | 23 | 19 | 13 | 13 | 7 | 2 | 2 | 5 |
| gc | gc | 3546 | 18.0 | 26 | 8.8e-01 | 14 | -1.15 | 13 | 0 | 1 | 1 | 4 | 4 | 8 | 8 | 13 | 18 | 33 | 55 | 112 | 520 | 1032 | 1085 | 407 | 101 | 51 | 35 | 17 | 14 | 14 | 7 | 3 | 1 | 0 | 2 |
| ga | ga | 4886 | 17.7 | 26 | 8.9e-01 | 14 | -1.15 | 14 | 0 | 1 | 6 | 8 | 6 | 9 | 16 | 20 | 33 | 47 | 71 | 164 | 706 | 1461 | 1447 | 595 | 132 | 56 | 38 | 26 | 19 | 11 | 3 | 3 | 4 | 2 | 2 |
| cc | cc | 4250 | 14.2 | 26 | 9.7e-01 | 16 | -1.19 | 15 | 1 | 4 | 1 | 3 | 5 | 7 | 7 | 23 | 25 | 30 | 60 | 134 | 596 | 1313 | 1251 | 532 | 121 | 52 | 34 | 27 | 12 | 8 | 1 | 2 | 0 | 0 | 1 |
| ac | ac | 4053 | 8.2 | 26 | 1.0e+00 | 16 | -1.20 | 16 | 0 | 3 | 1 | 3 | 5 | 5 | 9 | 16 | 28 | 37 | 56 | 130 | 579 | 1204 | 1233 | 507 | 106 | 48 | 30 | 21 | 16 | 7 | 1 | 6 | 1 | 1 | 0 |
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