position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 1 -ci 20 -img_format png -title fetch-sequences_Schmidt_2011_mm9_CEBPA_SWEMBL_R0.12_702peaks_1slk_20151103_065518 -origin center -o $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/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 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab Oligo length 1 Occurrences counted on a single strands Background model estimation: homogeneous repartition Sequence statistics: Nb of sequences 689 Sum of sequence lengths 192449 Min sequence length 0 Max sequence length 582 Average sequence length 279 Possible positions 192449 Oligonucleotide statistics: Total occurrences 188626 Position interval parameters: Position interval 20 Number of windows 30 Total positions 192449 Degrees of freedom 29 K-mer clustering parameters: Number of clusters 0 Clustering method complete Position intervals: window [min,max] mid seq occ 1 -15 [-299,-280] -289.5 1 12 2 -14 [-279,-260] -269.5 2 32 3 -13 [-259,-240] -249.5 3 48 4 -12 [-239,-220] -229.5 5 72 5 -11 [-219,-200] -209.5 10 126 6 -10 [-199,-180] -189.5 21 303 7 -9 [-179,-160] -169.5 74 852 8 -8 [-159,-140] -149.5 261 3168 9 -7 [-139,-120] -129.5 640 9497 10 -6 [-119,-100] -109.5 688 13575 11 -5 [-99,-80] -89.5 689 13776 12 -4 [-79,-60] -69.5 689 13780 13 -3 [-59,-40] -49.5 689 13780 14 -2 [-39,-20] -29.5 689 13780 15 -1 [-19,0] -9.5 689 13780 16 0 [1,20] 10.5 689 13780 17 1 [21,40] 30.5 689 13780 18 2 [41,60] 50.5 689 13780 19 3 [61,80] 70.5 689 13780 20 4 [81,100] 90.5 689 13774 21 5 [101,120] 110.5 688 13528 22 6 [121,140] 130.5 638 9113 23 7 [141,160] 150.5 251 2971 24 8 [161,180] 170.5 70 796 25 9 [181,200] 190.5 21 290 26 10 [201,220] 210.5 8 120 27 11 [221,240] 230.5 5 70 28 12 [241,260] 250.5 3 46 29 13 [261,280] 270.5 2 30 30 14 [281,300] 290.5 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 -289.5 occurrences in window 1 [-299,-280] 11 -269.5 occurrences in window 2 [-279,-260] 12 -249.5 occurrences in window 3 [-259,-240] 13 -229.5 occurrences in window 4 [-239,-220] 14 -209.5 occurrences in window 5 [-219,-200] 15 -189.5 occurrences in window 6 [-199,-180] 16 -169.5 occurrences in window 7 [-179,-160] 17 -149.5 occurrences in window 8 [-159,-140] 18 -129.5 occurrences in window 9 [-139,-120] 19 -109.5 occurrences in window 10 [-119,-100] 20 -89.5 occurrences in window 11 [-99,-80] 21 -69.5 occurrences in window 12 [-79,-60] 22 -49.5 occurrences in window 13 [-59,-40] 23 -29.5 occurrences in window 14 [-39,-20] 24 -9.5 occurrences in window 15 [-19,0] 25 10.5 occurrences in window 16 [1,20] 26 30.5 occurrences in window 17 [21,40] 27 50.5 occurrences in window 18 [41,60] 28 70.5 occurrences in window 19 [61,80] 29 90.5 occurrences in window 20 [81,100] 30 110.5 occurrences in window 21 [101,120] 31 130.5 occurrences in window 22 [121,140] 32 150.5 occurrences in window 23 [141,160] 33 170.5 occurrences in window 24 [161,180] 34 190.5 occurrences in window 25 [181,200] 35 210.5 occurrences in window 26 [201,220] 36 230.5 occurrences in window 27 [221,240] 37 250.5 occurrences in window 28 [241,260] 38 270.5 occurrences in window 29 [261,280] 39 290.5 occurrences in window 30 [281,300]
| seq | id | occ | chi2 | df | Pval | Eval | sig | rank | -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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| a | a | 53476 | 63.0 | 28 | 1.7e-04 | 0.00066 | 3.18 | 1 | 2 | 12 | 16 | 22 | 47 | 91 | 248 | 958 | 2867 | 3852 | 3957 | 3773 | 3637 | 3776 | 3806 | 3747 | 3805 | 3751 | 3747 | 3779 | 3780 | 2557 | 870 | 229 | 73 | 32 | 22 | 13 | 5 | 2 |
| t | t | 52687 | 41.6 | 28 | 4.7e-02 | 0.19 | 0.73 | 2 | 6 | 9 | 12 | 13 | 25 | 70 | 242 | 882 | 2596 | 3693 | 3675 | 3765 | 3872 | 3777 | 3675 | 3790 | 3752 | 3677 | 3760 | 3807 | 3745 | 2559 | 875 | 225 | 99 | 36 | 19 | 11 | 13 | 7 |
| g | g | 41288 | 27.7 | 27 | 4.3e-01 | 1.7 | -0.23 | 3 | 3 | 5 | 10 | 18 | 28 | 78 | 192 | 638 | 2006 | 2905 | 3035 | 2952 | 3004 | 2975 | 2991 | 2957 | 2857 | 3017 | 3023 | 2912 | 2891 | 1908 | 582 | 186 | 57 | 25 | 19 | 10 | 4 | 0 |
| c | c | 41175 | 24.5 | 27 | 6.0e-01 | 2.4 | -0.38 | 4 | 1 | 6 | 10 | 19 | 26 | 64 | 170 | 668 | 1904 | 2892 | 2867 | 3030 | 2993 | 2932 | 2952 | 2925 | 3026 | 3004 | 2925 | 2976 | 2906 | 1992 | 613 | 155 | 61 | 27 | 10 | 12 | 8 | 1 |
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