position-analysis -v 1 -i peaks-rm-orig/data/sequences/peaks_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 analysis_M11 -origin end -offset 0 -o peaks-rm-orig/results/composition/peaks_test_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_test_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file peaks-rm-orig/results/composition/peaks_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 269 Sum of sequence lengths 54069 Min sequence length 0 Max sequence length 201 Average sequence length 201 Possible positions 54069 Oligonucleotide statistics: Total occurrences 40726 Position interval parameters: Position interval 20 Number of windows 11 Total positions 54069 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] -209.5 269 538 2 -10 [-199,-180] -189.5 269 5380 3 -9 [-179,-160] -169.5 269 5380 4 -8 [-159,-140] -149.5 269 5380 5 -7 [-139,-120] -129.5 269 5380 6 -6 [-119,-100] -109.5 269 5380 7 -5 [-99,-80] -89.5 269 5380 8 -4 [-79,-60] -69.5 269 5380 9 -3 [-59,-40] -49.5 269 5380 10 -2 [-39,-20] -29.5 269 5380 11 -1 [-19,0] -9.5 269 5111 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| c | c | 10211 | 32.0 | 10 | 4.0e-04 | 0.0016 | 2.80 | 1 | 77 | 927 | 927 | 1033 | 1043 | 989 | 1029 | 1034 | 1074 | 1076 | 1002 |
| t | t | 11807 | 31.3 | 10 | 5.3e-04 | 0.0021 | 2.68 | 2 | 141 | 1137 | 1099 | 1086 | 1136 | 1248 | 1169 | 1186 | 1196 | 1208 | 1201 |
| a | a | 11651 | 13.8 | 10 | 1.8e-01 | 0.74 | 0.13 | 3 | 118 | 1235 | 1186 | 1208 | 1170 | 1158 | 1124 | 1129 | 1099 | 1125 | 1099 |
| g | g | 7057 | 11.2 | 10 | 3.4e-01 | 1.4 | -0.14 | 4 | 64 | 679 | 724 | 691 | 654 | 669 | 744 | 724 | 704 | 714 | 690 |
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