position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.203737_2025-04-28.203737_n2namY/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 TnaA_WD_PRE -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.203737_2025-04-28.203737_n2namY/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/2025/04/28/peak-motifs.2025-04-28.203737_2025-04-28.203737_n2namY/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.203737_2025-04-28.203737_n2namY/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 35 Sum of sequence lengths 10554 Min sequence length 0 Max sequence length 1000 Average sequence length 301 Possible positions 10519 Sequences: # length ID 1 240 TnaA-WD_peak_2::chr2L:5009637-5009877(.) 2 304 TnaA-WD_peak_4::chr2L:6078941-6079245(.) 3 369 TnaA-WD_peak_5::chr2L:6081240-6081609(.) 4 309 TnaA-WD_peak_6::chr2L:6088361-6088670(.) 5 308 TnaA-WD_peak_7::chr2L:6480724-6481032(.) 6 240 TnaA-WD_peak_12::chr2L:8365857-8366097(.) 7 548 TnaA-WD_peak_17::chr2L:14615881-14616429(.) 8 223 TnaA-WD_peak_18::chr2L:16257528-16257751(.) 9 687 TnaA-WD_peak_28::chr2R:6093057-6093744(.) 10 206 TnaA-WD_peak_29::chr2R:12869631-12869837(.) 11 210 TnaA-WD_peak_30::chr2R:14503804-14504014(.) 12 326 TnaA-WD_peak_31::chr2R:15847975-15848301(.) 13 229 TnaA-WD_peak_32::chr2R:15931900-15932129(.) 14 243 TnaA-WD_peak_33::chr2R:18639518-18639761(.) 15 311 TnaA-WD_peak_35::chr2R:21501874-21502185(.) 16 1000 TnaA-WD_peak_46::chr3L:10871817-10873573(.) 17 236 TnaA-WD_peak_53::chr3L:18412375-18412611(.) 18 215 TnaA-WD_peak_59::chr3R:5648696-5648911(.) 19 221 TnaA-WD_peak_60::chr3R:5650178-5650399(.) 20 411 TnaA-WD_peak_62::chr3R:6822427-6822838(.) 21 204 TnaA-WD_peak_65::chr3R:9540796-9541000(.) 22 228 TnaA-WD_peak_68::chr3R:15408302-15408530(.) 23 272 TnaA-WD_peak_69::chr3R:17718233-17718505(.) 24 377 TnaA-WD_peak_70::chr3R:17890901-17891278(.) 25 215 TnaA-WD_peak_71::chr3R:18412826-18413041(.) 26 216 TnaA-WD_peak_73::chr3R:21097749-21097965(.) 27 255 TnaA-WD_peak_77::chr3R:29063656-29063911(.) 28 280 TnaA-WD_peak_84::chr4:43674-43954(.) 29 230 TnaA-WD_peak_114::chrX:2270655-2270885(.) 30 253 TnaA-WD_peak_115::chrX:5420805-5421058(.) 31 346 TnaA-WD_peak_116::chrX:5737857-5738203(.) 32 216 TnaA-WD_peak_117::chrX:10744996-10745212(.) 33 211 TnaA-WD_peak_118::chrX:17827457-17827668(.) 34 205 TnaA-WD_peak_119::chrX:17887108-17887313(.) 35 210 TnaA-WD_peak_120::chrX:18370845-18371055(.) Oligonucleotide statistics: Total occurrences 10519 Position interval parameters: Position interval 20 Number of windows 50 Total positions 10519 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 2 24 9 -17 [-339,-320] -329.5 2 40 10 -16 [-319,-300] -309.5 2 40 11 -15 [-299,-280] -289.5 2 40 12 -14 [-279,-260] -269.5 3 54 13 -13 [-259,-240] -249.5 3 60 14 -12 [-239,-220] -229.5 3 60 15 -11 [-219,-200] -209.5 4 66 16 -10 [-199,-180] -189.5 6 94 17 -9 [-179,-160] -169.5 8 138 18 -8 [-159,-140] -149.5 12 217 19 -7 [-139,-120] -129.5 17 293 20 -6 [-119,-100] -109.5 35 525 21 -5 [-99,-80] -89.5 35 700 22 -4 [-79,-60] -69.5 35 700 23 -3 [-59,-40] -49.5 35 700 24 -2 [-39,-20] -29.5 35 700 25 -1 [-19,0] -9.5 35 700 26 0 [1,20] 10.5 35 700 27 1 [21,40] 30.5 35 700 28 2 [41,60] 50.5 35 700 29 3 [61,80] 70.5 35 700 30 4 [81,100] 90.5 35 700 31 5 [101,120] 110.5 35 492 32 6 [121,140] 130.5 16 285 33 7 [141,160] 150.5 12 211 34 8 [161,180] 170.5 8 132 35 9 [181,200] 190.5 6 90 36 10 [201,220] 210.5 4 64 37 11 [221,240] 230.5 3 60 38 12 [241,260] 250.5 3 60 39 13 [261,280] 270.5 3 53 40 14 [281,300] 290.5 2 40 41 15 [301,320] 310.5 2 40 42 16 [321,340] 330.5 2 40 43 17 [341,360] 350.5 2 22 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 | 855 | 95.7 | 49 | 7.5e-05 | 0.0012 | 2.92 | 1 | 0 | 0 | 1 | 0 | 2 | 1 | 4 | 4 | 2 | 0 | 2 | 2 | 4 | 1 | 2 | 7 | 8 | 28 | 32 | 55 | 77 | 61 | 54 | 30 | 27 | 41 | 46 | 59 | 65 | 93 | 53 | 33 | 16 | 13 | 13 | 6 | 5 | 2 | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 1 | 2 | 0 | 0 | 0 |
| aa | aa | 800 | 75.8 | 49 | 8.4e-03 | 0.13 | 0.87 | 2 | 1 | 0 | 1 | 2 | 1 | 2 | 1 | 3 | 0 | 0 | 1 | 7 | 7 | 4 | 3 | 8 | 10 | 18 | 23 | 54 | 64 | 49 | 42 | 25 | 46 | 29 | 62 | 46 | 78 | 65 | 61 | 25 | 22 | 14 | 3 | 6 | 2 | 4 | 4 | 0 | 0 | 2 | 1 | 1 | 0 | 1 | 0 | 1 | 0 | 1 |
| cg | cg | 696 | 29.5 | 49 | 9.9e-01 | 16 | -1.20 | 3 | 2 | 2 | 1 | 0 | 1 | 1 | 0 | 1 | 2 | 2 | 3 | 4 | 4 | 5 | 5 | 11 | 6 | 17 | 14 | 30 | 41 | 48 | 40 | 58 | 61 | 58 | 39 | 54 | 35 | 39 | 32 | 11 | 13 | 10 | 5 | 4 | 3 | 3 | 6 | 3 | 2 | 5 | 0 | 2 | 3 | 0 | 2 | 2 | 3 | 3 |
| tc | tc | 560 | 27.6 | 49 | 9.9e-01 | 16 | -1.20 | 4 | 1 | 0 | 1 | 1 | 0 | 5 | 1 | 2 | 2 | 3 | 1 | 3 | 6 | 3 | 5 | 6 | 11 | 7 | 16 | 29 | 34 | 31 | 34 | 51 | 40 | 39 | 30 | 47 | 46 | 21 | 23 | 11 | 7 | 9 | 5 | 5 | 2 | 5 | 2 | 2 | 3 | 0 | 3 | 1 | 0 | 1 | 1 | 1 | 1 | 2 |
| gg | gg | 590 | 26.8 | 49 | 1.0e+00 | 16 | -1.20 | 5 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 2 | 10 | 7 | 3 | 3 | 3 | 2 | 2 | 3 | 10 | 18 | 12 | 21 | 30 | 34 | 37 | 36 | 40 | 59 | 37 | 45 | 37 | 39 | 25 | 18 | 10 | 12 | 3 | 1 | 5 | 3 | 2 | 3 | 3 | 3 | 0 | 1 | 3 | 0 | 2 | 1 | 2 | 1 |
| ga | ga | 615 | 22.4 | 49 | 1.0e+00 | 16 | -1.20 | 6 | 1 | 0 | 1 | 1 | 1 | 1 | 0 | 2 | 5 | 3 | 1 | 3 | 2 | 2 | 3 | 8 | 4 | 20 | 16 | 26 | 32 | 39 | 47 | 45 | 52 | 41 | 46 | 36 | 28 | 40 | 31 | 13 | 16 | 9 | 4 | 2 | 3 | 6 | 6 | 1 | 0 | 3 | 2 | 2 | 2 | 0 | 3 | 3 | 2 | 1 |
| gt | gt | 584 | 20.8 | 49 | 1.0e+00 | 16 | -1.20 | 7 | 0 | 2 | 1 | 0 | 3 | 1 | 0 | 0 | 3 | 0 | 0 | 4 | 1 | 6 | 2 | 3 | 12 | 6 | 14 | 34 | 42 | 42 | 45 | 47 | 30 | 40 | 39 | 35 | 45 | 26 | 29 | 20 | 15 | 6 | 5 | 3 | 4 | 2 | 1 | 4 | 0 | 2 | 1 | 1 | 1 | 2 | 1 | 1 | 2 | 1 |
| ta | ta | 603 | 20.7 | 49 | 1.0e+00 | 16 | -1.20 | 8 | 0 | 0 | 2 | 2 | 1 | 0 | 3 | 1 | 0 | 0 | 0 | 2 | 4 | 3 | 5 | 2 | 8 | 16 | 18 | 41 | 39 | 34 | 32 | 40 | 41 | 48 | 49 | 38 | 45 | 51 | 31 | 12 | 13 | 6 | 2 | 2 | 1 | 4 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | 1 | 0 | 0 | 0 |
| ac | ac | 532 | 20.7 | 49 | 1.0e+00 | 16 | -1.20 | 9 | 3 | 0 | 0 | 2 | 1 | 0 | 3 | 0 | 2 | 1 | 2 | 2 | 2 | 4 | 3 | 5 | 5 | 9 | 21 | 23 | 51 | 47 | 28 | 34 | 37 | 32 | 37 | 31 | 33 | 40 | 21 | 11 | 12 | 4 | 6 | 3 | 2 | 2 | 0 | 1 | 2 | 2 | 0 | 3 | 3 | 0 | 0 | 1 | 0 | 1 |
| ag | ag | 581 | 19.5 | 49 | 1.0e+00 | 16 | -1.20 | 10 | 0 | 1 | 1 | 1 | 3 | 1 | 0 | 2 | 4 | 2 | 0 | 4 | 4 | 0 | 4 | 6 | 8 | 14 | 14 | 30 | 28 | 32 | 57 | 42 | 36 | 33 | 41 | 31 | 33 | 32 | 29 | 17 | 14 | 6 | 5 | 3 | 5 | 6 | 6 | 3 | 6 | 5 | 1 | 1 | 2 | 2 | 1 | 2 | 1 | 2 |
| ct | ct | 543 | 17.6 | 49 | 1.0e+00 | 16 | -1.20 | 11 | 1 | 2 | 0 | 1 | 1 | 2 | 2 | 2 | 1 | 6 | 5 | 3 | 2 | 3 | 6 | 4 | 8 | 9 | 24 | 23 | 43 | 38 | 31 | 42 | 36 | 35 | 33 | 41 | 41 | 32 | 22 | 14 | 4 | 4 | 6 | 2 | 2 | 3 | 3 | 0 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | 0 | 0 |
| gc | gc | 832 | 16.8 | 49 | 1.0e+00 | 16 | -1.20 | 12 | 2 | 4 | 1 | 1 | 2 | 1 | 0 | 1 | 1 | 7 | 8 | 4 | 4 | 5 | 6 | 9 | 10 | 14 | 20 | 37 | 46 | 56 | 64 | 64 | 62 | 62 | 54 | 57 | 43 | 49 | 29 | 19 | 12 | 10 | 8 | 7 | 5 | 4 | 9 | 5 | 8 | 7 | 1 | 0 | 2 | 4 | 1 | 2 | 3 | 2 |
| cc | cc | 494 | 16.7 | 49 | 1.0e+00 | 16 | -1.20 | 13 | 4 | 5 | 4 | 2 | 0 | 1 | 0 | 1 | 2 | 1 | 5 | 4 | 2 | 10 | 9 | 7 | 9 | 3 | 8 | 22 | 26 | 33 | 28 | 31 | 34 | 31 | 22 | 36 | 33 | 29 | 23 | 14 | 13 | 5 | 5 | 2 | 5 | 1 | 4 | 6 | 2 | 2 | 3 | 3 | 1 | 0 | 0 | 0 | 2 | 1 |
| ca | ca | 683 | 14.9 | 49 | 1.0e+00 | 16 | -1.20 | 14 | 3 | 1 | 1 | 3 | 1 | 2 | 3 | 0 | 2 | 2 | 2 | 4 | 6 | 3 | 5 | 5 | 9 | 8 | 19 | 26 | 50 | 54 | 51 | 46 | 48 | 38 | 47 | 40 | 46 | 38 | 22 | 17 | 13 | 8 | 8 | 7 | 6 | 5 | 2 | 5 | 9 | 4 | 2 | 2 | 2 | 3 | 0 | 2 | 0 | 3 |
| tg | tg | 757 | 14.8 | 49 | 1.0e+00 | 16 | -1.20 | 15 | 1 | 3 | 1 | 1 | 3 | 0 | 0 | 2 | 3 | 4 | 6 | 3 | 2 | 5 | 3 | 4 | 10 | 11 | 22 | 33 | 56 | 57 | 60 | 53 | 48 | 53 | 55 | 45 | 45 | 45 | 28 | 29 | 15 | 7 | 7 | 5 | 7 | 3 | 3 | 4 | 0 | 2 | 2 | 0 | 0 | 4 | 2 | 2 | 3 | 0 |
| at | at | 794 | 13.5 | 49 | 1.0e+00 | 16 | -1.20 | 16 | 1 | 0 | 3 | 2 | 0 | 2 | 3 | 1 | 1 | 2 | 1 | 2 | 7 | 4 | 3 | 6 | 10 | 19 | 20 | 41 | 41 | 45 | 50 | 56 | 62 | 61 | 63 | 59 | 47 | 61 | 33 | 21 | 16 | 9 | 5 | 6 | 3 | 7 | 3 | 2 | 3 | 0 | 4 | 1 | 0 | 1 | 3 | 2 | 1 | 1 |
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