position-analysis -v 1 -i Myogenin_Rep2_motifs50/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 1 -ci 20 -img_format png -title Myogeni_Rep2_motifs50 -origin center -offset 0 -o Myogenin_Rep2_motifs50/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 Myogenin_Rep2_motifs50/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file Myogenin_Rep2_motifs50/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 3375 Sum of sequence lengths 515697 Min sequence length 0 Max sequence length 1101 Average sequence length 152 Possible positions 515697 Oligonucleotide statistics: Total occurrences 493095 Position interval parameters: Position interval 20 Number of windows 56 Total positions 515697 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 1 11 2 -27 [-539,-520] -529.5 1 20 3 -26 [-519,-500] -509.5 1 20 4 -25 [-499,-480] -489.5 1 20 5 -24 [-479,-460] -469.5 1 20 6 -23 [-459,-440] -449.5 1 20 7 -22 [-439,-420] -429.5 1 20 8 -21 [-419,-400] -409.5 1 20 9 -20 [-399,-380] -389.5 1 20 10 -19 [-379,-360] -369.5 2 24 11 -18 [-359,-340] -349.5 2 40 12 -17 [-339,-320] -329.5 2 40 13 -16 [-319,-300] -309.5 2 40 14 -15 [-299,-280] -289.5 2 40 15 -14 [-279,-260] -269.5 2 40 16 -13 [-259,-240] -249.5 3 58 17 -12 [-239,-220] -229.5 6 96 18 -11 [-219,-200] -209.5 8 138 19 -10 [-199,-180] -189.5 13 225 20 -9 [-179,-160] -169.5 33 427 21 -8 [-159,-140] -149.5 80 1177 22 -7 [-139,-120] -129.5 172 2464 23 -6 [-119,-100] -109.5 381 5382 24 -5 [-99,-80] -89.5 1089 13963 25 -4 [-79,-60] -69.5 2488 35525 26 -3 [-59,-40] -49.5 3375 64876 27 -2 [-39,-20] -29.5 3375 67500 28 -1 [-19,0] -9.5 3375 67500 29 0 [1,20] 10.5 3375 67500 30 1 [21,40] 30.5 3375 67500 31 2 [41,60] 50.5 3375 63599 32 3 [61,80] 70.5 2381 34128 33 4 [81,100] 90.5 1044 13272 34 5 [101,120] 110.5 366 5153 35 6 [121,140] 130.5 168 2373 36 7 [141,160] 150.5 76 1135 37 8 [161,180] 170.5 31 407 38 9 [181,200] 190.5 13 222 39 10 [201,220] 210.5 8 136 40 11 [221,240] 230.5 6 94 41 12 [241,260] 250.5 3 58 42 13 [261,280] 270.5 2 40 43 14 [281,300] 290.5 2 40 44 15 [301,320] 310.5 2 40 45 16 [321,340] 330.5 2 40 46 17 [341,360] 350.5 2 40 47 18 [361,380] 370.5 2 24 48 19 [381,400] 390.5 1 20 49 20 [401,420] 410.5 1 20 50 21 [421,440] 430.5 1 20 51 22 [441,460] 450.5 1 20 52 23 [461,480] 470.5 1 20 53 24 [481,500] 490.5 1 20 54 25 [501,520] 510.5 1 20 55 26 [521,540] 530.5 1 20 56 27 [541,560] 550.5 1 10 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| c | c | 145281 | 331.6 | 55 | 3.7e-41 | 1.5e-40 | 39.82 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 9 | 18 | 29 | 36 | 103 | 290 | 662 | 1459 | 3842 | 9882 | 18352 | 19359 | 19639 | 19302 | 19120 | 17734 | 9386 | 3565 | 1372 | 636 | 297 | 79 | 56 | 29 | 16 | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 3 |
| g | g | 144470 | 330.6 | 55 | 5.6e-41 | 2.2e-40 | 39.65 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 9 | 23 | 66 | 92 | 291 | 690 | 1516 | 3954 | 9941 | 18216 | 19338 | 19122 | 19134 | 19093 | 17679 | 9265 | 3625 | 1364 | 608 | 248 | 85 | 48 | 36 | 18 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| a | a | 101166 | 326.2 | 55 | 3.6e-40 | 1.4e-39 | 38.84 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 12 | 25 | 30 | 60 | 254 | 444 | 1088 | 2911 | 7579 | 13510 | 13324 | 12746 | 12683 | 12659 | 12489 | 6925 | 2626 | 1047 | 428 | 200 | 57 | 40 | 14 | 7 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| t | t | 102178 | 218.8 | 55 | 2.1e-21 | 8.5e-21 | 20.07 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 9 | 17 | 21 | 35 | 84 | 189 | 462 | 1058 | 2820 | 7152 | 12828 | 13007 | 12928 | 13047 | 13442 | 13249 | 7240 | 2769 | 974 | 456 | 227 | 68 | 30 | 37 | 17 | 7 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 5 |
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