position-analysis -v 1 -i Myogenin_Rep3_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_Rep3_motifs50 -origin center -offset 0 -o Myogenin_Rep3_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_Rep3_motifs50/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file Myogenin_Rep3_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 536 Sum of sequence lengths 43082 Min sequence length 0 Max sequence length 751 Average sequence length 80 Possible positions 43082 Oligonucleotide statistics: Total occurrences 20700 Position interval parameters: Position interval 20 Number of windows 38 Total positions 43082 Degrees of freedom 37 K-mer clustering parameters: Number of clusters 0 Clustering method complete Position intervals: window [min,max] mid seq occ 1 -19 [-379,-360] -369.5 2 18 2 -18 [-359,-340] -349.5 2 40 3 -17 [-339,-320] -329.5 2 40 4 -16 [-319,-300] -309.5 2 40 5 -15 [-299,-280] -289.5 2 40 6 -14 [-279,-260] -269.5 2 40 7 -13 [-259,-240] -249.5 2 40 8 -12 [-239,-220] -229.5 4 51 9 -11 [-219,-200] -209.5 7 107 10 -10 [-199,-180] -189.5 8 150 11 -9 [-179,-160] -169.5 10 181 12 -8 [-159,-140] -149.5 14 234 13 -7 [-139,-120] -129.5 17 293 14 -6 [-119,-100] -109.5 20 358 15 -5 [-99,-80] -89.5 35 530 16 -4 [-79,-60] -69.5 73 1061 17 -3 [-59,-40] -49.5 160 2132 18 -2 [-39,-20] -29.5 486 5706 19 -1 [-19,0] -9.5 536 10720 20 0 [1,20] 10.5 536 10720 21 1 [21,40] 30.5 443 5382 22 2 [41,60] 50.5 152 2049 23 3 [61,80] 70.5 71 1023 24 4 [81,100] 90.5 35 515 25 5 [101,120] 110.5 20 354 26 6 [121,140] 130.5 16 292 27 7 [141,160] 150.5 13 230 28 8 [161,180] 170.5 10 179 29 9 [181,200] 190.5 8 150 30 10 [201,220] 210.5 7 103 31 11 [221,240] 230.5 4 49 32 12 [241,260] 250.5 2 40 33 13 [261,280] 270.5 2 40 34 14 [281,300] 290.5 2 40 35 15 [301,320] 310.5 2 40 36 16 [321,340] 330.5 2 40 37 17 [341,360] 350.5 2 40 38 18 [361,380] 370.5 1 15 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 -369.5 occurrences in window 1 [-379,-360] 11 -349.5 occurrences in window 2 [-359,-340] 12 -329.5 occurrences in window 3 [-339,-320] 13 -309.5 occurrences in window 4 [-319,-300] 14 -289.5 occurrences in window 5 [-299,-280] 15 -269.5 occurrences in window 6 [-279,-260] 16 -249.5 occurrences in window 7 [-259,-240] 17 -229.5 occurrences in window 8 [-239,-220] 18 -209.5 occurrences in window 9 [-219,-200] 19 -189.5 occurrences in window 10 [-199,-180] 20 -169.5 occurrences in window 11 [-179,-160] 21 -149.5 occurrences in window 12 [-159,-140] 22 -129.5 occurrences in window 13 [-139,-120] 23 -109.5 occurrences in window 14 [-119,-100] 24 -89.5 occurrences in window 15 [-99,-80] 25 -69.5 occurrences in window 16 [-79,-60] 26 -49.5 occurrences in window 17 [-59,-40] 27 -29.5 occurrences in window 18 [-39,-20] 28 -9.5 occurrences in window 19 [-19,0] 29 10.5 occurrences in window 20 [1,20] 30 30.5 occurrences in window 21 [21,40] 31 50.5 occurrences in window 22 [41,60] 32 70.5 occurrences in window 23 [61,80] 33 90.5 occurrences in window 24 [81,100] 34 110.5 occurrences in window 25 [101,120] 35 130.5 occurrences in window 26 [121,140] 36 150.5 occurrences in window 27 [141,160] 37 170.5 occurrences in window 28 [161,180] 38 190.5 occurrences in window 29 [181,200] 39 210.5 occurrences in window 30 [201,220] 40 230.5 occurrences in window 31 [221,240] 41 250.5 occurrences in window 32 [241,260] 42 270.5 occurrences in window 33 [261,280] 43 290.5 occurrences in window 34 [281,300] 44 310.5 occurrences in window 35 [301,320] 45 330.5 occurrences in window 36 [321,340] 46 350.5 occurrences in window 37 [341,360] 47 370.5 occurrences in window 38 [361,380]
| seq | id | occ | chi2 | df | Pval | Eval | sig | rank | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| g | g | 5190 | 261.7 | 37 | 1.2e-35 | 5e-35 | 34.30 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 6 | 9 | 3 | 5 | 11 | 29 | 97 | 267 | 744 | 1457 | 1442 | 699 | 224 | 95 | 33 | 20 | 17 | 9 | 6 | 10 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 |
| c | c | 5101 | 255.9 | 37 | 1.5e-34 | 6.1e-34 | 33.21 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 4 | 4 | 6 | 7 | 9 | 8 | 30 | 120 | 251 | 778 | 1427 | 1393 | 662 | 227 | 82 | 26 | 11 | 15 | 12 | 14 | 6 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 3 | 0 |
| t | t | 5192 | 229.2 | 37 | 1.5e-29 | 5.8e-29 | 28.24 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 5 | 7 | 10 | 7 | 6 | 16 | 52 | 95 | 254 | 736 | 1344 | 1456 | 772 | 242 | 90 | 39 | 13 | 10 | 7 | 7 | 12 | 9 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
| a | a | 5217 | 172.1 | 37 | 2.5e-19 | 1e-18 | 18.00 | 4 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 9 | 7 | 9 | 10 | 10 | 18 | 55 | 109 | 283 | 739 | 1457 | 1351 | 710 | 237 | 97 | 39 | 15 | 22 | 12 | 6 | 11 | 5 | 0 | 0 | 0 | 0 | 0 | 0 | 4 | 0 |
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