position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/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 2 -ci 20 -img_format png -title reg -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/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/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/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 23 Sum of sequence lengths 10099 Min sequence length 0 Max sequence length 1089 Average sequence length 439 Possible positions 10076 Sequences: # length ID 1 200 NZ_CP037899.1:7618-7818 2 511 NZ_CP037899.1:230205-230716 3 456 NZ_CP037899.1:644474-644930 4 456 NZ_CP037899.1:644474-644930 5 321 NZ_CP037899.1:645307-645628 6 1089 NZ_CP037899.1:949092-950181 7 1089 NZ_CP037899.1:949092-950181 8 1089 NZ_CP037899.1:949092-950181 9 221 NZ_CP037899.1:953361-953582 10 263 NZ_CP037899.1:1134619-1134882 11 385 NZ_CP037899.1:1164899-1165284 12 385 NZ_CP037899.1:1164899-1165284 13 245 NZ_CP037899.1:1277211-1277456 14 436 NZ_CP037899.1:1329900-1330336 15 436 NZ_CP037899.1:1329900-1330336 16 332 NZ_CP037899.1:1343835-1344167 17 353 NZ_CP037899.1:1508893-1509246 18 341 NZ_CP037899.1:1530412-1530753 19 345 NZ_CP037899.1:1640064-1640409 20 200 NZ_CP037899.1:1679730-1679930 21 422 NZ_CP037899.1:1681794-1682216 22 324 NZ_CP037899.1:2093304-2093628 23 200 NZ_CP037899.1:2135546-2135746 Oligonucleotide statistics: Total occurrences 6626 Position interval parameters: Position interval 20 Number of windows 56 Total positions 10076 Degrees of freedom 55 K-mer clustering parameters: Number of clusters 0 Clustering method complete Position intervals: window [min,max] mid seq occ 1 -28 [-559,-540] -549.5 3 15 2 -27 [-539,-520] -529.5 3 60 3 -26 [-519,-500] -509.5 3 60 4 -25 [-499,-480] -489.5 3 60 5 -24 [-479,-460] -469.5 3 60 6 -23 [-459,-440] -449.5 3 60 7 -22 [-439,-420] -429.5 3 60 8 -21 [-419,-400] -409.5 3 60 9 -20 [-399,-380] -389.5 3 60 10 -19 [-379,-360] -369.5 3 60 11 -18 [-359,-340] -349.5 3 60 12 -17 [-339,-320] -329.5 3 60 13 -16 [-319,-300] -309.5 3 60 14 -15 [-299,-280] -289.5 3 60 15 -14 [-279,-260] -269.5 3 60 16 -13 [-259,-240] -249.5 4 76 17 -12 [-239,-220] -229.5 6 96 18 -11 [-219,-200] -209.5 9 168 19 -10 [-199,-180] -189.5 11 206 20 -9 [-179,-160] -169.5 17 270 21 -8 [-159,-140] -149.5 17 340 22 -7 [-139,-120] -129.5 19 355 23 -6 [-119,-100] -109.5 20 391 24 -5 [-99,-80] -89.5 23 460 25 -4 [-79,-60] -69.5 23 460 26 -3 [-59,-40] -49.5 23 460 27 -2 [-39,-20] -29.5 23 460 28 -1 [-19,0] -9.5 23 460 29 0 [1,20] 10.5 23 460 30 1 [21,40] 30.5 23 460 31 2 [41,60] 50.5 23 460 32 3 [61,80] 70.5 23 460 33 4 [81,100] 90.5 23 457 34 5 [101,120] 110.5 20 389 35 6 [121,140] 130.5 19 351 36 7 [141,160] 150.5 17 339 37 8 [161,180] 170.5 16 261 38 9 [181,200] 190.5 11 202 39 10 [201,220] 210.5 9 163 40 11 [221,240] 230.5 6 94 41 12 [241,260] 250.5 4 74 42 13 [261,280] 270.5 3 60 43 14 [281,300] 290.5 3 60 44 15 [301,320] 310.5 3 60 45 16 [321,340] 330.5 3 60 46 17 [341,360] 350.5 3 60 47 18 [361,380] 370.5 3 60 48 19 [381,400] 390.5 3 60 49 20 [401,420] 410.5 3 60 50 21 [421,440] 430.5 3 60 51 22 [441,460] 450.5 3 60 52 23 [461,480] 470.5 3 60 53 24 [481,500] 490.5 3 60 54 25 [501,520] 510.5 3 60 55 26 [521,540] 530.5 3 60 56 27 [541,560] 550.5 3 9 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 -549.5 occurrences in window 1 [-559,-540] 11 -529.5 occurrences in window 2 [-539,-520] 12 -509.5 occurrences in window 3 [-519,-500] 13 -489.5 occurrences in window 4 [-499,-480] 14 -469.5 occurrences in window 5 [-479,-460] 15 -449.5 occurrences in window 6 [-459,-440] 16 -429.5 occurrences in window 7 [-439,-420] 17 -409.5 occurrences in window 8 [-419,-400] 18 -389.5 occurrences in window 9 [-399,-380] 19 -369.5 occurrences in window 10 [-379,-360] 20 -349.5 occurrences in window 11 [-359,-340] 21 -329.5 occurrences in window 12 [-339,-320] 22 -309.5 occurrences in window 13 [-319,-300] 23 -289.5 occurrences in window 14 [-299,-280] 24 -269.5 occurrences in window 15 [-279,-260] 25 -249.5 occurrences in window 16 [-259,-240] 26 -229.5 occurrences in window 17 [-239,-220] 27 -209.5 occurrences in window 18 [-219,-200] 28 -189.5 occurrences in window 19 [-199,-180] 29 -169.5 occurrences in window 20 [-179,-160] 30 -149.5 occurrences in window 21 [-159,-140] 31 -129.5 occurrences in window 22 [-139,-120] 32 -109.5 occurrences in window 23 [-119,-100] 33 -89.5 occurrences in window 24 [-99,-80] 34 -69.5 occurrences in window 25 [-79,-60] 35 -49.5 occurrences in window 26 [-59,-40] 36 -29.5 occurrences in window 27 [-39,-20] 37 -9.5 occurrences in window 28 [-19,0] 38 10.5 occurrences in window 29 [1,20] 39 30.5 occurrences in window 30 [21,40] 40 50.5 occurrences in window 31 [41,60] 41 70.5 occurrences in window 32 [61,80] 42 90.5 occurrences in window 33 [81,100] 43 110.5 occurrences in window 34 [101,120] 44 130.5 occurrences in window 35 [121,140] 45 150.5 occurrences in window 36 [141,160] 46 170.5 occurrences in window 37 [161,180] 47 190.5 occurrences in window 38 [181,200] 48 210.5 occurrences in window 39 [201,220] 49 230.5 occurrences in window 40 [221,240] 50 250.5 occurrences in window 41 [241,260] 51 270.5 occurrences in window 42 [261,280] 52 290.5 occurrences in window 43 [281,300] 53 310.5 occurrences in window 44 [301,320] 54 330.5 occurrences in window 45 [321,340] 55 350.5 occurrences in window 46 [341,360] 56 370.5 occurrences in window 47 [361,380] 57 390.5 occurrences in window 48 [381,400] 58 410.5 occurrences in window 49 [401,420] 59 430.5 occurrences in window 50 [421,440] 60 450.5 occurrences in window 51 [441,460] 61 470.5 occurrences in window 52 [461,480] 62 490.5 occurrences in window 53 [481,500] 63 510.5 occurrences in window 54 [501,520] 64 530.5 occurrences in window 55 [521,540] 65 550.5 occurrences in window 56 [541,560]
| seq | id | occ | chi2 | df | Pval | Eval | sig | rank | -549.5 | -529.5 | -509.5 | -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 | 510.5 | 530.5 | 550.5 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| tt | tt | 662 | 94.1 | 55 | 8.1e-04 | 0.013 | 1.89 | 1 | 1 | 1 | 2 | 2 | 2 | 0 | 0 | 1 | 2 | 1 | 2 | 2 | 0 | 0 | 0 | 1 | 3 | 4 | 4 | 23 | 38 | 41 | 17 | 32 | 35 | 40 | 33 | 38 | 32 | 47 | 46 | 40 | 26 | 44 | 36 | 20 | 16 | 7 | 10 | 4 | 1 | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | 0 |
| aa | aa | 772 | 89.0 | 55 | 2.5e-03 | 0.04 | 1.39 | 2 | 0 | 2 | 1 | 4 | 1 | 2 | 1 | 1 | 2 | 1 | 2 | 4 | 0 | 2 | 2 | 1 | 3 | 8 | 24 | 9 | 24 | 25 | 38 | 55 | 39 | 51 | 42 | 54 | 48 | 41 | 63 | 40 | 36 | 33 | 24 | 24 | 15 | 10 | 10 | 3 | 2 | 1 | 2 | 4 | 2 | 2 | 2 | 1 | 1 | 0 | 2 | 3 | 1 | 2 | 2 | 0 |
| at | at | 596 | 61.2 | 55 | 2.6e-01 | 4.2 | -0.62 | 3 | 0 | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 1 | 1 | 2 | 1 | 1 | 0 | 1 | 3 | 1 | 5 | 10 | 18 | 14 | 23 | 29 | 34 | 31 | 48 | 43 | 36 | 40 | 36 | 30 | 35 | 31 | 21 | 28 | 25 | 13 | 10 | 8 | 1 | 2 | 1 | 0 | 1 | 1 | 0 | 1 | 2 | 1 | 0 | 1 | 0 | 1 | 2 | 0 | 0 |
| cc | cc | 324 | 40.1 | 55 | 9.3e-01 | 15 | -1.17 | 4 | 1 | 1 | 3 | 1 | 0 | 1 | 1 | 2 | 0 | 0 | 2 | 0 | 0 | 1 | 0 | 3 | 5 | 4 | 5 | 13 | 10 | 8 | 23 | 18 | 22 | 11 | 14 | 13 | 14 | 16 | 8 | 21 | 25 | 8 | 12 | 17 | 8 | 5 | 1 | 0 | 3 | 2 | 1 | 2 | 3 | 1 | 1 | 0 | 3 | 4 | 1 | 4 | 0 | 0 | 2 | 0 |
| ta | ta | 516 | 39.2 | 55 | 9.5e-01 | 15 | -1.18 | 5 | 0 | 1 | 0 | 1 | 1 | 0 | 2 | 0 | 2 | 3 | 0 | 1 | 3 | 0 | 1 | 2 | 1 | 8 | 8 | 14 | 15 | 20 | 26 | 32 | 29 | 38 | 27 | 26 | 27 | 34 | 30 | 27 | 23 | 19 | 33 | 18 | 13 | 10 | 4 | 2 | 1 | 1 | 1 | 0 | 0 | 0 | 1 | 2 | 1 | 1 | 0 | 2 | 2 | 1 | 2 | 0 |
| tg | tg | 376 | 30.9 | 55 | 1.0e+00 | 16 | -1.20 | 6 | 0 | 2 | 1 | 2 | 2 | 2 | 0 | 1 | 2 | 1 | 3 | 1 | 1 | 0 | 3 | 2 | 1 | 5 | 5 | 11 | 15 | 19 | 9 | 19 | 15 | 26 | 23 | 25 | 18 | 19 | 16 | 13 | 29 | 17 | 11 | 9 | 7 | 6 | 9 | 4 | 5 | 2 | 0 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 3 | 0 | 2 | 3 | 0 | 1 |
| ct | ct | 384 | 28.7 | 55 | 1.0e+00 | 16 | -1.20 | 7 | 1 | 2 | 2 | 1 | 0 | 2 | 0 | 1 | 1 | 0 | 2 | 1 | 3 | 1 | 1 | 2 | 4 | 9 | 2 | 13 | 19 | 10 | 21 | 21 | 23 | 18 | 22 | 14 | 22 | 21 | 14 | 20 | 29 | 18 | 11 | 14 | 9 | 8 | 5 | 3 | 4 | 0 | 0 | 0 | 0 | 3 | 1 | 1 | 0 | 1 | 2 | 0 | 1 | 0 | 0 | 1 |
| tc | tc | 388 | 23.7 | 55 | 1.0e+00 | 16 | -1.20 | 8 | 0 | 3 | 1 | 0 | 0 | 1 | 0 | 2 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 3 | 5 | 7 | 3 | 12 | 14 | 13 | 21 | 20 | 26 | 19 | 20 | 13 | 26 | 17 | 18 | 24 | 25 | 20 | 14 | 15 | 12 | 9 | 5 | 2 | 0 | 0 | 0 | 1 | 2 | 2 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | 0 |
| gg | gg | 338 | 22.8 | 55 | 1.0e+00 | 16 | -1.20 | 9 | 1 | 2 | 2 | 2 | 3 | 3 | 1 | 2 | 4 | 2 | 1 | 1 | 1 | 6 | 2 | 3 | 5 | 2 | 5 | 6 | 12 | 10 | 10 | 14 | 16 | 11 | 21 | 24 | 15 | 14 | 13 | 17 | 21 | 17 | 9 | 7 | 11 | 5 | 9 | 2 | 3 | 1 | 2 | 2 | 2 | 1 | 1 | 2 | 2 | 0 | 1 | 1 | 2 | 2 | 4 | 0 |
| ca | ca | 350 | 22.5 | 55 | 1.0e+00 | 16 | -1.20 | 10 | 0 | 1 | 2 | 0 | 1 | 1 | 3 | 1 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 6 | 10 | 9 | 12 | 10 | 16 | 18 | 20 | 15 | 22 | 17 | 23 | 17 | 17 | 23 | 21 | 12 | 10 | 20 | 9 | 4 | 3 | 5 | 1 | 2 | 2 | 2 | 2 | 1 | 0 | 2 | 0 | 2 | 2 | 1 | 0 | 0 | 1 | 0 |
| gt | gt | 299 | 21.9 | 55 | 1.0e+00 | 16 | -1.20 | 11 | 0 | 3 | 0 | 2 | 1 | 1 | 1 | 2 | 2 | 4 | 1 | 0 | 1 | 0 | 3 | 2 | 3 | 5 | 4 | 6 | 12 | 15 | 9 | 13 | 16 | 16 | 7 | 12 | 13 | 14 | 16 | 12 | 15 | 22 | 14 | 6 | 9 | 7 | 5 | 3 | 0 | 3 | 0 | 1 | 1 | 0 | 2 | 0 | 2 | 2 | 2 | 1 | 4 | 2 | 2 | 0 |
| gc | gc | 316 | 21.0 | 55 | 1.0e+00 | 16 | -1.20 | 12 | 1 | 0 | 1 | 0 | 0 | 2 | 3 | 2 | 1 | 0 | 1 | 1 | 1 | 1 | 2 | 1 | 4 | 2 | 5 | 7 | 12 | 9 | 8 | 18 | 19 | 13 | 17 | 21 | 17 | 15 | 17 | 16 | 21 | 7 | 8 | 15 | 7 | 5 | 3 | 5 | 6 | 1 | 2 | 1 | 1 | 3 | 2 | 4 | 1 | 2 | 1 | 1 | 1 | 0 | 1 | 1 |
| ag | ag | 402 | 19.9 | 55 | 1.0e+00 | 16 | -1.20 | 13 | 0 | 0 | 2 | 1 | 3 | 1 | 3 | 2 | 1 | 4 | 0 | 1 | 3 | 2 | 1 | 2 | 4 | 7 | 11 | 3 | 16 | 16 | 18 | 21 | 22 | 15 | 16 | 20 | 22 | 24 | 27 | 22 | 15 | 16 | 14 | 15 | 14 | 6 | 5 | 5 | 1 | 0 | 4 | 2 | 2 | 1 | 2 | 1 | 0 | 0 | 1 | 2 | 2 | 1 | 3 | 0 |
| ga | ga | 398 | 13.8 | 55 | 1.0e+00 | 16 | -1.20 | 14 | 0 | 0 | 1 | 2 | 4 | 1 | 1 | 1 | 0 | 2 | 2 | 1 | 3 | 3 | 1 | 4 | 3 | 8 | 8 | 9 | 11 | 19 | 20 | 20 | 18 | 21 | 25 | 25 | 22 | 21 | 22 | 21 | 17 | 15 | 10 | 12 | 9 | 8 | 6 | 3 | 2 | 0 | 3 | 2 | 1 | 1 | 2 | 0 | 1 | 0 | 1 | 1 | 1 | 3 | 1 | 0 |
| cg | cg | 237 | 10.0 | 55 | 1.0e+00 | 16 | -1.20 | 15 | 0 | 1 | 0 | 0 | 0 | 1 | 2 | 2 | 1 | 0 | 1 | 1 | 0 | 2 | 2 | 3 | 5 | 3 | 2 | 7 | 6 | 7 | 11 | 12 | 17 | 7 | 11 | 12 | 11 | 9 | 12 | 14 | 9 | 9 | 7 | 11 | 4 | 7 | 1 | 2 | 2 | 2 | 1 | 1 | 1 | 2 | 3 | 2 | 4 | 2 | 0 | 2 | 1 | 1 | 1 | 0 |
| ac | ac | 268 | 9.6 | 55 | 1.0e+00 | 16 | -1.20 | 16 | 0 | 1 | 2 | 1 | 1 | 2 | 1 | 0 | 1 | 0 | 0 | 2 | 2 | 1 | 0 | 2 | 1 | 7 | 7 | 10 | 10 | 10 | 15 | 13 | 12 | 11 | 17 | 10 | 10 | 15 | 11 | 15 | 14 | 11 | 10 | 11 | 5 | 4 | 2 | 3 | 1 | 3 | 2 | 0 | 1 | 1 | 0 | 1 | 1 | 3 | 1 | 2 | 0 | 1 | 1 | 0 |
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