; position-analysis -v 1 -i $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta -format fasta -sort -return html,chi,sig,distrib,exp_occ,graphs,rank,index -max_graphs 100 -2str -noov -seqtype dna -l 6 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 100 -img_format png -title ChIP-seq_FNR_E._coli_tunned_parameters_dyad -origin center -max_graphs 20 -o $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab ; Citation: van Helden, et al. (2000). Nucleic Acids Res 28, 1000-1010. ; Sequence file /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/data/sequences/peak-motifs_test_maxlen1000_purged_ml30_mis0.fasta ; Sequence format fasta ; Sequence type dna ; Output file /vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/positions_6nt/peak-motifs_positions-2str-noov_6nt_ci50.tab ; Oligo length 6 ; Lower threshold on occurrences 1 ; Occurrences counted on both strands ; Grouping reverse complements ; Background model estimation: homogeneous repartition ; Sequence statistics: ; Nb of sequences 109 ; Sum of sequence lengths 108923 ; Min sequence length 0 ; Max sequence length 1000 ; Average sequence length 999 ; Possible positions 216756 ; Oligonucleotide statistics: ; Total occurrences 107089 ; Total overlaps 229 ; Position interval parameters: ; Position interval 50 ; Number of windows 20 ; Total positions 108378 ; Degrees of freedom 19 ; K-mer clustering parameters: ; Number of clusters 0 ; Clustering method complete ; Position intervals: ; window [min,max] mid seq occ ; 1 -10 [-499,-450] -474.5 109 5412 ; 2 -9 [-449,-400] -424.5 109 5450 ; 3 -8 [-399,-350] -374.5 109 5450 ; 4 -7 [-349,-300] -324.5 109 5450 ; 5 -6 [-299,-250] -274.5 109 5450 ; 6 -5 [-249,-200] -224.5 109 5450 ; 7 -4 [-199,-150] -174.5 109 5450 ; 8 -3 [-149,-100] -124.5 109 5450 ; 9 -2 [-99,-50] -74.5 109 5450 ; 10 -1 [-49,0] -24.5 109 5450 ; 11 0 [1,50] 25.5 109 5450 ; 12 1 [51,100] 75.5 109 5450 ; 13 2 [101,150] 125.5 109 5450 ; 14 3 [151,200] 175.5 109 5450 ; 15 4 [201,250] 225.5 109 5450 ; 16 5 [251,300] 275.5 109 5450 ; 17 6 [301,350] 325.5 109 5450 ; 18 7 [351,400] 375.5 109 5450 ; 19 8 [401,450] 425.5 109 5450 ; 20 9 [451,500] 475.5 109 4866 ; ; Column headers ; 1 seq pattern sequence ; 2 id pattern identifier ; 3 occ pattern occurrences ; 4 over overlapping occurrences (discarded) ; 5 chi2 observed chi-square ; 6 df degrees of freedom ; 7 Pval P-value (probability for one word to be a false positive) ; 8 Eval E-value; expected number of false positives (Eval = Pval * nb_tests) ; 9 sig Significance (sig = -log10(Eval)) ; 10 rank rank of the pattern according to sorting criterion ; 11 -474.5 occurrences in window 1 [-499,-450] ; 12 -424.5 occurrences in window 2 [-449,-400] ; 13 -374.5 occurrences in window 3 [-399,-350] ; 14 -324.5 occurrences in window 4 [-349,-300] ; 15 -274.5 occurrences in window 5 [-299,-250] ; 16 -224.5 occurrences in window 6 [-249,-200] ; 17 -174.5 occurrences in window 7 [-199,-150] ; 18 -124.5 occurrences in window 8 [-149,-100] ; 19 -74.5 occurrences in window 9 [-99,-50] ; 20 -24.5 occurrences in window 10 [-49,0] ; 21 25.5 occurrences in window 11 [1,50] ; 22 75.5 occurrences in window 12 [51,100] ; 23 125.5 occurrences in window 13 [101,150] ; 24 175.5 occurrences in window 14 [151,200] ; 25 225.5 occurrences in window 15 [201,250] ; 26 275.5 occurrences in window 16 [251,300] ; 27 325.5 occurrences in window 17 [301,350] ; 28 375.5 occurrences in window 18 [351,400] ; 29 425.5 occurrences in window 19 [401,450] ; 30 475.5 occurrences in window 20 [451,500] #seq id occ over chi2 df Pval Eval sig rank -474.5 -424.5 -374.5 -324.5 -274.5 -224.5 -174.5 -124.5 -74.5 -24.5 25.5 75.5 125.5 175.5 225.5 275.5 325.5 375.5 425.5 475.5 atcaaa atcaaa|tttgat 45 0 68.2 19 1.8e-07 0.00037 3.43 1 6 4 1 4 10 4 7 1 5 7 22 4 10 5 4 8 4 4 3 2 aaaata aaaata|tatttt 66 0 52.0 19 6.6e-05 0.14 0.87 2 2 5 3 6 5 7 6 4 11 22 10 6 13 3 7 7 5 11 6 7 atcgcc atcgcc|ggcgat 57 0 49.3 19 1.7e-04 0.35 0.46 3 15 4 13 4 6 5 6 5 2 1 2 3 4 3 6 8 5 6 8 13 cggtac cggtac|gtaccg 34 0 45.8 18 3.2e-04 0.66 0.18 4 8 8 9 1 2 4 2 2 1 1 0 0 1 6 2 5 0 5 1 1 gcataa gcataa|ttatgc 32 0 45.7 18 3.2e-04 0.67 0.17 5 3 4 4 4 2 13 9 6 1 3 3 1 3 3 1 3 1 4 3 0 aaatga aaatga|tcattt 46 0 45.7 18 3.3e-04 0.68 0.17 6 1 2 3 2 1 8 8 5 6 3 12 12 2 4 5 6 7 3 1 2 aaatat aaatat|atattt 51 0 45.2 18 3.9e-04 0.82 0.09 7 2 3 0 2 7 5 3 2 8 17 7 8 7 6 6 6 4 5 9 3 aaatag aaatag|ctattt 25 0 44.9 18 4.3e-04 0.89 0.05 8 3 1 2 4 2 0 3 4 5 11 1 5 5 0 0 1 3 4 0 3 cccaaa cccaaa|tttggg 20 0 41.6 16 4.5e-04 0.94 0.03 9 0 1 0 2 4 0 1 8 2 2 4 3 1 2 0 0 2 1 1 0 atggga atggga|tcccat 11 0 41.4 15 2.8e-04 0.58 0.24 10 0 2 0 0 0 1 0 2 2 1 0 1 1 2 0 7 0 0 0 3 ccctag ccctag|ctaggg 1 0 18.9 1 1.4e-05 0.029 1.54 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 cctagc cctagc|gctagg 3 0 16.9 1 3.9e-05 0.08 1.10 12 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 2 0 ; Host name biow ; Job started 2014-09-05.202802 ; Job done 2014-09-05.202807 ; Seconds 4.59 ; user 4.59 ; system 0.03 ; cuser 0 ; csystem 0