position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.044641_2025-04-28.044641_ntYsd5/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 1 -ci 20 -img_format png -title TnaA_WD_Filtered -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_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.2025-04-28.044641_2025-04-28.044641_ntYsd5/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.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab Oligo length 1 Occurrences counted on a single strands Conditions of applicability checked. Background model estimation: homogeneous repartition Sequence statistics: Nb of sequences 65 Sum of sequence lengths 18842 Min sequence length 0 Max sequence length 1000 Average sequence length 289 Possible positions 18842 Sequences: # length ID 1 229 TnaA-WD_peak_1::chr2L:1980697-1980926(.) 2 240 TnaA-WD_peak_2::chr2L:5009637-5009877(.) 3 254 TnaA-WD_peak_3::chr2L:5724522-5724776(.) 4 304 TnaA-WD_peak_4::chr2L:6078941-6079245(.) 5 369 TnaA-WD_peak_5::chr2L:6081240-6081609(.) 6 309 TnaA-WD_peak_6::chr2L:6088361-6088670(.) 7 308 TnaA-WD_peak_7::chr2L:6480724-6481032(.) 8 233 TnaA-WD_peak_9::chr2L:6967485-6967718(.) 9 1000 TnaA-WD_peak_10::chr2L:7297537-7298811(.) 10 245 TnaA-WD_peak_11::chr2L:7885325-7885570(.) 11 240 TnaA-WD_peak_12::chr2L:8365857-8366097(.) 12 279 TnaA-WD_peak_13::chr2L:8541545-8541824(.) 13 548 TnaA-WD_peak_17::chr2L:14615881-14616429(.) 14 223 TnaA-WD_peak_18::chr2L:16257528-16257751(.) 15 221 TnaA-WD_peak_19::chr2L:18590758-18590979(.) 16 272 TnaA-WD_peak_20::chr2L:18859202-18859474(.) 17 257 TnaA-WD_peak_21::chr2L:19045200-19045457(.) 18 260 TnaA-WD_peak_22::chr2L:19430519-19430779(.) 19 687 TnaA-WD_peak_28::chr2R:6093057-6093744(.) 20 206 TnaA-WD_peak_29::chr2R:12869631-12869837(.) 21 210 TnaA-WD_peak_30::chr2R:14503804-14504014(.) 22 326 TnaA-WD_peak_31::chr2R:15847975-15848301(.) 23 229 TnaA-WD_peak_32::chr2R:15931900-15932129(.) 24 243 TnaA-WD_peak_33::chr2R:18639518-18639761(.) 25 200 TnaA-WD_peak_34::chr2R:20245291-20245491(.) 26 311 TnaA-WD_peak_35::chr2R:21501874-21502185(.) 27 224 TnaA-WD_peak_37::chr2R:22937652-22937876(.) 28 249 TnaA-WD_peak_39::chr2R:23856847-23857096(.) 29 210 TnaA-WD_peak_42::chr3L:3814081-3814291(.) 30 238 TnaA-WD_peak_43::chr3L:8203015-8203253(.) 31 1000 TnaA-WD_peak_46::chr3L:10871817-10873573(.) 32 203 TnaA-WD_peak_47::chr3L:12277533-12277736(.) 33 210 TnaA-WD_peak_49::chr3L:16531460-16531670(.) 34 236 TnaA-WD_peak_53::chr3L:18412375-18412611(.) 35 303 TnaA-WD_peak_54::chr3L:18672996-18673299(.) 36 249 TnaA-WD_peak_56::chr3L:20302291-20302540(.) 37 261 TnaA-WD_peak_57::chr3R:938882-939143(.) 38 424 TnaA-WD_peak_61::chr3R:6820109-6820533(.) 39 411 TnaA-WD_peak_62::chr3R:6822427-6822838(.) 40 428 TnaA-WD_peak_63::chr3R:7474566-7474994(.) 41 204 TnaA-WD_peak_65::chr3R:9540796-9541000(.) 42 242 TnaA-WD_peak_66::chr3R:9563562-9563804(.) 43 200 TnaA-WD_peak_67::chr3R:15385232-15385432(.) 44 228 TnaA-WD_peak_68::chr3R:15408302-15408530(.) 45 272 TnaA-WD_peak_69::chr3R:17718233-17718505(.) 46 215 TnaA-WD_peak_71::chr3R:18412826-18413041(.) 47 216 TnaA-WD_peak_73::chr3R:21097749-21097965(.) 48 255 TnaA-WD_peak_77::chr3R:29063656-29063911(.) 49 223 TnaA-WD_peak_78::chr3R:29591720-29591943(.) 50 255 TnaA-WD_peak_80::chr3R:29924272-29924527(.) 51 302 TnaA-WD_peak_81::chr3R:30039578-30039880(.) 52 239 TnaA-WD_peak_82::chr3R:30046108-30046347(.) 53 280 TnaA-WD_peak_84::chr4:43674-43954(.) 54 205 TnaA-WD_peak_111::chrX:655978-656183(.) 55 278 TnaA-WD_peak_112::chrX:1033062-1033340(.) 56 284 TnaA-WD_peak_113::chrX:1512779-1513063(.) 57 230 TnaA-WD_peak_114::chrX:2270655-2270885(.) 58 253 TnaA-WD_peak_115::chrX:5420805-5421058(.) 59 346 TnaA-WD_peak_116::chrX:5737857-5738203(.) 60 216 TnaA-WD_peak_117::chrX:10744996-10745212(.) 61 211 TnaA-WD_peak_118::chrX:17827457-17827668(.) 62 205 TnaA-WD_peak_119::chrX:17887108-17887313(.) 63 210 TnaA-WD_peak_120::chrX:18370845-18371055(.) 64 213 TnaA-WD_peak_121::chrX:19866021-19866234(.) 65 211 TnaA-WD_peak_123::chrX:23105922-23106133(.) Oligonucleotide statistics: Total occurrences 18382 Position interval parameters: Position interval 20 Number of windows 50 Total positions 18842 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 2 40 2 -24 [-479,-460] -469.5 2 40 3 -23 [-459,-440] -449.5 2 40 4 -22 [-439,-420] -429.5 2 40 5 -21 [-419,-400] -409.5 2 40 6 -20 [-399,-380] -389.5 2 40 7 -19 [-379,-360] -369.5 2 40 8 -18 [-359,-340] -349.5 3 44 9 -17 [-339,-320] -329.5 3 60 10 -16 [-319,-300] -309.5 3 60 11 -15 [-299,-280] -289.5 3 60 12 -14 [-279,-260] -269.5 4 74 13 -13 [-259,-240] -249.5 4 80 14 -12 [-239,-220] -229.5 4 80 15 -11 [-219,-200] -209.5 7 112 16 -10 [-199,-180] -189.5 8 145 17 -9 [-179,-160] -169.5 10 178 18 -8 [-159,-140] -149.5 17 283 19 -7 [-139,-120] -129.5 34 510 20 -6 [-119,-100] -109.5 63 983 21 -5 [-99,-80] -89.5 65 1300 22 -4 [-79,-60] -69.5 65 1300 23 -3 [-59,-40] -49.5 65 1300 24 -2 [-39,-20] -29.5 65 1300 25 -1 [-19,0] -9.5 65 1300 26 0 [1,20] 10.5 65 1300 27 1 [21,40] 30.5 65 1300 28 2 [41,60] 50.5 65 1300 29 3 [61,80] 70.5 65 1300 30 4 [81,100] 90.5 65 1300 31 5 [101,120] 110.5 63 955 32 6 [121,140] 130.5 33 494 33 7 [141,160] 150.5 17 278 34 8 [161,180] 170.5 10 174 35 9 [181,200] 190.5 8 144 36 10 [201,220] 210.5 7 111 37 11 [221,240] 230.5 4 80 38 12 [241,260] 250.5 4 80 39 13 [261,280] 270.5 4 74 40 14 [281,300] 290.5 3 60 41 15 [301,320] 310.5 3 60 42 16 [321,340] 330.5 3 60 43 17 [341,360] 350.5 3 43 44 18 [361,380] 370.5 2 40 45 19 [381,400] 390.5 2 40 46 20 [401,420] 410.5 2 40 47 21 [421,440] 430.5 2 40 48 22 [441,460] 450.5 2 40 49 23 [461,480] 470.5 2 40 50 24 [481,500] 490.5 2 40 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| t | t | 4907 | 81.5 | 49 | 2.5e-03 | 0.0098 | 2.01 | 1 | 9 | 8 | 12 | 12 | 8 | 16 | 11 | 11 | 11 | 14 | 11 | 15 | 22 | 15 | 29 | 27 | 44 | 77 | 142 | 286 | 383 | 346 | 333 | 338 | 291 | 319 | 297 | 360 | 388 | 358 | 262 | 139 | 76 | 44 | 36 | 26 | 18 | 17 | 12 | 15 | 6 | 7 | 13 | 4 | 4 | 9 | 11 | 3 | 8 | 4 |
| c | c | 4237 | 77.0 | 49 | 6.5e-03 | 0.026 | 1.59 | 2 | 13 | 14 | 7 | 8 | 7 | 7 | 9 | 8 | 8 | 14 | 21 | 18 | 16 | 28 | 31 | 30 | 33 | 52 | 110 | 183 | 277 | 289 | 282 | 318 | 338 | 325 | 314 | 318 | 270 | 270 | 193 | 84 | 48 | 33 | 39 | 27 | 20 | 17 | 22 | 16 | 17 | 16 | 9 | 13 | 11 | 10 | 7 | 12 | 13 | 12 |
| g | g | 4228 | 63.6 | 49 | 7.9e-02 | 0.31 | 0.50 | 3 | 7 | 8 | 6 | 4 | 11 | 6 | 5 | 8 | 21 | 19 | 18 | 19 | 15 | 20 | 22 | 34 | 34 | 58 | 93 | 213 | 270 | 273 | 322 | 314 | 326 | 321 | 300 | 285 | 269 | 258 | 202 | 121 | 57 | 35 | 26 | 22 | 24 | 22 | 23 | 15 | 13 | 22 | 10 | 11 | 13 | 13 | 11 | 10 | 10 | 9 |
| a | a | 5010 | 51.7 | 49 | 3.7e-01 | 1.5 | -0.17 | 4 | 11 | 10 | 15 | 16 | 14 | 11 | 15 | 17 | 20 | 13 | 10 | 22 | 27 | 17 | 24 | 34 | 47 | 76 | 145 | 281 | 350 | 372 | 343 | 310 | 325 | 315 | 369 | 317 | 344 | 374 | 258 | 111 | 77 | 42 | 37 | 36 | 18 | 24 | 17 | 14 | 24 | 15 | 11 | 12 | 12 | 8 | 11 | 15 | 9 | 15 |
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