position-analysis -v 1 -i peaks-rm-orig/data/sequences/peaks_ctrl_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 analysis_M11 -origin end -offset 0 -o peaks-rm-orig/results/composition/peaks_ctrl_profiles-1str-ovlp_1nt_ci20.tab Citation: van Helden, et al. (2000). Nucleic Acids Res 28, 1000-1010. Sequence file peaks-rm-orig/data/sequences/peaks_ctrl_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file peaks-rm-orig/results/composition/peaks_ctrl_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 27107 Sum of sequence lengths 5448507 Min sequence length 0 Max sequence length 201 Average sequence length 201 Possible positions 5448507 Oligonucleotide statistics: Total occurrences 4534959 Position interval parameters: Position interval 20 Number of windows 11 Total positions 5448507 Degrees of freedom 10 K-mer clustering parameters: Number of clusters 0 Clustering method complete Position intervals: window [min,max] mid seq occ 1 -11 [-219,-200] -209.5 27107 54214 2 -10 [-199,-180] -189.5 27107 542140 3 -9 [-179,-160] -169.5 27107 542140 4 -8 [-159,-140] -149.5 27107 542140 5 -7 [-139,-120] -129.5 27107 542140 6 -6 [-119,-100] -109.5 27107 542140 7 -5 [-99,-80] -89.5 27107 542140 8 -4 [-79,-60] -69.5 27107 542140 9 -3 [-59,-40] -49.5 27107 542140 10 -2 [-39,-20] -29.5 27107 542140 11 -1 [-19,0] -9.5 27107 515033 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 -209.5 occurrences in window 1 [-219,-200] 11 -189.5 occurrences in window 2 [-199,-180] 12 -169.5 occurrences in window 3 [-179,-160] 13 -149.5 occurrences in window 4 [-159,-140] 14 -129.5 occurrences in window 5 [-139,-120] 15 -109.5 occurrences in window 6 [-119,-100] 16 -89.5 occurrences in window 7 [-99,-80] 17 -69.5 occurrences in window 8 [-79,-60] 18 -49.5 occurrences in window 9 [-59,-40] 19 -29.5 occurrences in window 10 [-39,-20] 20 -9.5 occurrences in window 11 [-19,0]
| seq | id | occ | chi2 | df | Pval | Eval | sig | rank | -209.5 | -189.5 | -169.5 | -149.5 | -129.5 | -109.5 | -89.5 | -69.5 | -49.5 | -29.5 | -9.5 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| a | a | 1311235 | 2440.9 | 10 | 0.0e+00 | 0 | 300 | 1 | 17029 | 139612 | 134411 | 131197 | 130071 | 129937 | 128438 | 126819 | 126948 | 126503 | 120270 |
| c | c | 1076408 | 1838.3 | 10 | 0.0e+00 | 0 | 300 | 2 | 8146 | 100907 | 102519 | 104146 | 105768 | 107910 | 109963 | 109824 | 110343 | 110397 | 106485 |
| g | g | 851911 | 913.0 | 10 | 0.0e+00 | 0 | 300 | 3 | 6713 | 89237 | 83295 | 83019 | 83960 | 83770 | 83400 | 83884 | 84156 | 86288 | 84189 |
| t | t | 1295405 | 389.6 | 10 | 1.6e-77 | 6.2e-77 | 76.21 | 4 | 14381 | 128629 | 128767 | 128252 | 127432 | 126972 | 126915 | 128280 | 129236 | 130278 | 126263 |
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