position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/01/05/peak-motifs.2025-01-05.113808_2025-01-05.113808_VVhoIi/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 SMAD4 -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/01/05/peak-motifs.2025-01-05.113808_2025-01-05.113808_VVhoIi/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/2025/01/05/peak-motifs.2025-01-05.113808_2025-01-05.113808_VVhoIi/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2025/01/05/peak-motifs.2025-01-05.113808_2025-01-05.113808_VVhoIi/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 2888 Sum of sequence lengths 578557 Min sequence length 0 Max sequence length 1000 Average sequence length 200 Possible positions 575669 Oligonucleotide statistics: Total occurrences 545528 Position interval parameters: Position interval 20 Number of windows 50 Total positions 575669 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 3 60 2 -24 [-479,-460] -469.5 4 67 3 -23 [-459,-440] -449.5 4 80 4 -22 [-439,-420] -429.5 4 80 5 -21 [-419,-400] -409.5 4 80 6 -20 [-399,-380] -389.5 5 83 7 -19 [-379,-360] -369.5 6 111 8 -18 [-359,-340] -349.5 8 143 9 -17 [-339,-320] -329.5 14 201 10 -16 [-319,-300] -309.5 16 311 11 -15 [-299,-280] -289.5 19 366 12 -14 [-279,-260] -269.5 24 448 13 -13 [-259,-240] -249.5 34 568 14 -12 [-239,-220] -229.5 53 817 15 -11 [-219,-200] -209.5 77 1237 16 -10 [-199,-180] -189.5 122 2011 17 -9 [-179,-160] -169.5 197 3237 18 -8 [-159,-140] -149.5 322 5084 19 -7 [-139,-120] -129.5 569 8883 20 -6 [-119,-100] -109.5 1074 16237 21 -5 [-99,-80] -89.5 1837 29202 22 -4 [-79,-60] -69.5 2888 48072 23 -3 [-59,-40] -49.5 2888 57760 24 -2 [-39,-20] -29.5 2888 57760 25 -1 [-19,0] -9.5 2888 57760 26 0 [1,20] 10.5 2888 57760 27 1 [21,40] 30.5 2888 57760 28 2 [41,60] 50.5 2888 57760 29 3 [61,80] 70.5 2888 46119 30 4 [81,100] 90.5 1774 27649 31 5 [101,120] 110.5 1012 15231 32 6 [121,140] 130.5 542 8388 33 7 [141,160] 150.5 308 4837 34 8 [161,180] 170.5 193 3080 35 9 [181,200] 190.5 117 1921 36 10 [201,220] 210.5 73 1194 37 11 [221,240] 230.5 50 781 38 12 [241,260] 250.5 33 547 39 13 [261,280] 270.5 24 435 40 14 [281,300] 290.5 19 362 41 15 [301,320] 310.5 16 307 42 16 [321,340] 330.5 11 189 43 17 [341,360] 350.5 8 139 44 18 [361,380] 370.5 6 109 45 19 [381,400] 390.5 5 81 46 20 [401,420] 410.5 4 80 47 21 [421,440] 430.5 4 80 48 22 [441,460] 450.5 4 80 49 23 [461,480] 470.5 4 65 50 24 [481,500] 490.5 3 57 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| cc | cc | 46209 | 356.2 | 49 | 3.1e-48 | 5e-47 | 46.30 | 1 | 5 | 0 | 6 | 4 | 0 | 0 | 6 | 7 | 12 | 7 | 23 | 19 | 35 | 40 | 79 | 146 | 264 | 390 | 767 | 1345 | 2441 | 4152 | 5004 | 4876 | 4677 | 4744 | 4575 | 4516 | 3491 | 2042 | 1146 | 615 | 339 | 183 | 109 | 55 | 25 | 16 | 20 | 9 | 13 | 3 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 |
| gg | gg | 45975 | 313.9 | 49 | 2.5e-40 | 4e-39 | 38.40 | 2 | 1 | 2 | 3 | 3 | 0 | 0 | 3 | 2 | 7 | 22 | 11 | 22 | 35 | 48 | 72 | 111 | 236 | 376 | 637 | 1209 | 2228 | 3775 | 4529 | 4635 | 4476 | 4634 | 4836 | 4882 | 4098 | 2284 | 1225 | 692 | 345 | 224 | 137 | 72 | 44 | 28 | 12 | 3 | 5 | 7 | 2 | 2 | 0 | 0 | 0 | 0 | 0 | 0 |
| ct | ct | 41261 | 218.7 | 49 | 2.6e-23 | 4.2e-22 | 21.37 | 3 | 3 | 3 | 2 | 2 | 1 | 1 | 3 | 6 | 12 | 12 | 17 | 17 | 24 | 33 | 75 | 123 | 230 | 354 | 641 | 1205 | 2240 | 3658 | 4270 | 4160 | 4309 | 4167 | 4142 | 4043 | 3244 | 1911 | 1037 | 558 | 323 | 180 | 98 | 67 | 33 | 14 | 12 | 6 | 9 | 4 | 4 | 1 | 0 | 1 | 4 | 2 | 0 | 0 |
| tg | tg | 42856 | 209.7 | 49 | 9.0e-22 | 1.4e-20 | 19.84 | 4 | 4 | 7 | 3 | 6 | 5 | 1 | 7 | 3 | 6 | 12 | 12 | 20 | 24 | 37 | 57 | 143 | 213 | 347 | 634 | 1193 | 2158 | 3555 | 4292 | 4311 | 4482 | 4415 | 4468 | 4456 | 3450 | 2020 | 1062 | 606 | 343 | 208 | 130 | 76 | 33 | 17 | 11 | 2 | 14 | 7 | 2 | 1 | 0 | 1 | 1 | 1 | 0 | 0 |
| ca | ca | 42572 | 209.4 | 49 | 1.0e-21 | 1.6e-20 | 19.79 | 5 | 4 | 1 | 2 | 3 | 0 | 0 | 4 | 9 | 5 | 17 | 16 | 24 | 20 | 49 | 81 | 130 | 211 | 357 | 625 | 1198 | 2120 | 3483 | 4428 | 4373 | 4409 | 4524 | 4286 | 4349 | 3427 | 1969 | 1078 | 568 | 329 | 197 | 111 | 67 | 38 | 27 | 12 | 6 | 8 | 1 | 2 | 0 | 0 | 0 | 3 | 1 | 0 | 0 |
| aa | aa | 32185 | 207.6 | 49 | 2.0e-21 | 3.3e-20 | 19.49 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 7 | 7 | 18 | 18 | 23 | 43 | 52 | 120 | 160 | 290 | 469 | 998 | 1680 | 2904 | 3217 | 3187 | 3033 | 2982 | 3091 | 3304 | 2821 | 1692 | 901 | 493 | 271 | 185 | 97 | 53 | 28 | 11 | 4 | 11 | 3 | 5 | 2 | 0 | 0 | 0 | 1 | 1 | 0 | 0 |
| gc | gc | 39876 | 205.5 | 49 | 4.7e-21 | 7.5e-20 | 19.13 | 7 | 2 | 1 | 1 | 2 | 1 | 0 | 2 | 4 | 6 | 17 | 17 | 20 | 21 | 42 | 61 | 107 | 209 | 308 | 568 | 1084 | 1958 | 3255 | 4163 | 4111 | 4063 | 4192 | 4048 | 4072 | 3291 | 1879 | 1052 | 535 | 347 | 175 | 94 | 65 | 40 | 25 | 11 | 5 | 12 | 1 | 4 | 3 | 0 | 0 | 2 | 0 | 0 | 0 |
| tt | tt | 31941 | 195.7 | 49 | 2.0e-19 | 3.1e-18 | 17.50 | 8 | 0 | 2 | 0 | 2 | 0 | 0 | 1 | 1 | 5 | 6 | 5 | 5 | 18 | 25 | 63 | 100 | 197 | 331 | 510 | 942 | 1742 | 2801 | 3311 | 3217 | 3139 | 2958 | 3195 | 3238 | 2600 | 1652 | 852 | 422 | 225 | 155 | 86 | 48 | 30 | 13 | 6 | 14 | 11 | 7 | 0 | 0 | 0 | 1 | 0 | 5 | 0 | 0 |
| tc | tc | 33189 | 194.3 | 49 | 3.4e-19 | 5.4e-18 | 17.27 | 9 | 2 | 1 | 2 | 2 | 0 | 0 | 1 | 6 | 9 | 9 | 6 | 14 | 17 | 32 | 70 | 107 | 164 | 328 | 526 | 952 | 1834 | 3008 | 3431 | 3420 | 3472 | 3343 | 3275 | 3234 | 2554 | 1524 | 823 | 440 | 230 | 143 | 80 | 52 | 20 | 16 | 13 | 8 | 8 | 4 | 2 | 0 | 0 | 1 | 4 | 2 | 0 | 0 |
| ag | ag | 41241 | 161.2 | 49 | 7.0e-14 | 1.1e-12 | 11.95 | 10 | 6 | 0 | 8 | 1 | 0 | 0 | 5 | 2 | 2 | 17 | 18 | 16 | 28 | 52 | 80 | 124 | 215 | 331 | 576 | 1193 | 2060 | 3460 | 4188 | 4060 | 4194 | 4181 | 4159 | 4200 | 3415 | 2066 | 1117 | 617 | 335 | 206 | 137 | 64 | 42 | 22 | 11 | 10 | 11 | 6 | 2 | 1 | 0 | 0 | 1 | 1 | 1 | 0 |
| ac | ac | 28462 | 158.0 | 49 | 2.1e-13 | 3.4e-12 | 11.47 | 11 | 3 | 1 | 2 | 3 | 0 | 0 | 4 | 9 | 7 | 9 | 11 | 20 | 14 | 30 | 51 | 85 | 145 | 211 | 416 | 749 | 1399 | 2326 | 2952 | 3001 | 3010 | 3084 | 2933 | 2882 | 2237 | 1269 | 699 | 363 | 230 | 130 | 67 | 39 | 32 | 14 | 9 | 5 | 5 | 3 | 1 | 0 | 0 | 0 | 1 | 1 | 0 | 0 |
| gt | gt | 28885 | 149.0 | 49 | 5.0e-12 | 8e-11 | 10.10 | 12 | 3 | 4 | 3 | 3 | 5 | 1 | 3 | 1 | 2 | 9 | 4 | 10 | 15 | 34 | 49 | 101 | 138 | 255 | 447 | 763 | 1480 | 2437 | 2916 | 2931 | 3089 | 3015 | 3051 | 2938 | 2206 | 1307 | 723 | 384 | 214 | 130 | 97 | 47 | 19 | 19 | 7 | 6 | 10 | 8 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| cg | cg | 17813 | 123.2 | 49 | 2.6e-08 | 4.1e-07 | 6.39 | 13 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 2 | 7 | 6 | 6 | 12 | 9 | 24 | 27 | 44 | 79 | 132 | 243 | 429 | 854 | 1427 | 1886 | 1979 | 1869 | 1910 | 1847 | 1786 | 1418 | 797 | 456 | 223 | 144 | 72 | 39 | 27 | 21 | 11 | 8 | 5 | 8 | 1 | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| at | at | 23016 | 114.3 | 49 | 3.9e-07 | 6.3e-06 | 5.20 | 14 | 0 | 2 | 0 | 4 | 0 | 0 | 0 | 3 | 3 | 6 | 8 | 14 | 20 | 23 | 42 | 77 | 123 | 217 | 382 | 686 | 1289 | 1992 | 2294 | 2253 | 2213 | 2182 | 2229 | 2394 | 1925 | 1190 | 632 | 351 | 175 | 121 | 75 | 46 | 16 | 7 | 7 | 3 | 6 | 2 | 0 | 0 | 0 | 0 | 2 | 1 | 1 | 0 |
| ga | ga | 32984 | 113.2 | 49 | 5.5e-07 | 8.8e-06 | 5.06 | 15 | 6 | 1 | 7 | 4 | 0 | 0 | 4 | 5 | 5 | 11 | 14 | 19 | 26 | 32 | 54 | 104 | 156 | 241 | 473 | 946 | 1636 | 2763 | 3261 | 3326 | 3349 | 3279 | 3385 | 3451 | 2710 | 1689 | 835 | 508 | 265 | 171 | 109 | 60 | 23 | 15 | 11 | 9 | 11 | 4 | 3 | 0 | 0 | 0 | 1 | 1 | 1 | 0 |
| ta | ta | 17063 | 79.9 | 49 | 3.5e-03 | 0.056 | 1.25 | 16 | 0 | 2 | 0 | 1 | 0 | 0 | 0 | 0 | 2 | 5 | 8 | 8 | 16 | 20 | 37 | 54 | 105 | 148 | 288 | 503 | 965 | 1538 | 1693 | 1702 | 1643 | 1598 | 1674 | 1704 | 1362 | 897 | 492 | 236 | 140 | 90 | 57 | 33 | 19 | 5 | 4 | 3 | 4 | 5 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 |
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