; position-analysis -v 2 -i $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/data/sequences/peak-motifs_test_purged_ml30_mis0.fasta -format fasta -sort -return chi,sig,distrib,graphs,rank -max_graphs 50 -2str -noov -seqtype dna -l 7 -ci 50 -lth_occ 1 -lth_sig 0 -uth_rank 50 -img_format png -title STAT1_motif_Analysis -origin center -max_graphs 20 -o $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab ; Citation: van Helden, et al. (2000). Nucleic Acids Res 28, 1000-1010. ; Sequence file /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/data/sequences/peak-motifs_test_purged_ml30_mis0.fasta ; Sequence format fasta ; Sequence type dna ; Output file /home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/positions_7nt/peak-motifs_positions-2str-noov_7nt_ci50.tab ; Oligo length 7 ; Lower threshold on occurrences 1 ; Occurrences counted on both strands ; grouped by pairs of reverse complements ; Sequence statistics: ; Nb of sequences 2400 ; Sum of sequence lengths 482400 ; Min sequence length 0 ; Max sequence length 201 ; Average sequence length 201 ; Possible positions 936000 ; Oligonucleotide statistics: ; Total occurrences 465125 ; Total overlaps 1380 ; Class parameters: ; Class interval 50 ; Number of classes 5 ; Total positions 468000 ; Degrees of freedom 4 ; Sequences per class: ; class [min max] mid seq occ ; 1 [-149 -100] -124.5 2400 2400 ; 2 [-99 -50] -74.5 2400 120000 ; 3 [-49 0] -24.5 2400 120000 ; 4 [1 50] 25.5 2400 120000 ; 5 [51 100] 75.5 2400 105600 ; ; 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 -124.5 observed class occurrences ; 12 -74.5 observed class occurrences ; 13 -24.5 observed class occurrences ; 14 25.5 observed class occurrences ; 15 75.5 observed class occurrences #seq id occ over chi2 df Pval Eval sig rank -124.5 -74.5 -24.5 25.5 75.5 tccagga tccagga|tcctgga 650 0 225.9 3 1.1e-48 8.7e-45 44.06 1 1 65 275 249 60 ccaggaa ccaggaa|ttcctgg 750 0 222.4 3 6.2e-48 5.1e-44 43.29 2 1 91 320 265 73 cctggaa cctggaa|ttccagg 644 0 212.9 3 6.7e-46 5.5e-42 41.26 3 0 68 273 241 62 ccgggaa ccgggaa|ttcccgg 335 0 182.1 3 3.1e-39 2.5e-35 34.60 4 1 20 166 126 22 ctgggaa ctgggaa|ttcccag 558 0 179.1 3 1.4e-38 1.1e-34 33.95 5 2 66 234 209 47 tcccgga tcccgga|tccggga 278 0 154.3 3 3.2e-33 2.6e-29 28.58 6 0 21 145 95 17 tcccaga tcccaga|tctggga 449 0 152.5 3 7.5e-33 6.2e-29 28.21 7 1 46 196 163 43 cccagaa cccagaa|ttctggg 445 0 147.3 3 1.0e-31 8.4e-28 27.08 8 2 43 193 161 46 cccggaa cccggaa|ttccggg 274 0 127.5 3 1.8e-27 1.5e-23 22.82 9 2 24 136 93 19 caggaaa caggaaa|tttcctg 560 0 122.3 3 2.4e-26 2e-22 21.70 10 0 79 224 192 65 ctggaaa ctggaaa|tttccag 479 0 112.1 3 4.0e-24 3.2e-20 19.49 11 2 59 187 174 57 cgggaag cgggaag|cttcccg 183 0 94.4 3 2.5e-20 2e-16 15.69 12 1 10 94 61 17 tgggaaa tgggaaa|tttccca 400 0 90.9 3 1.4e-19 1.1e-15 14.94 13 1 57 164 134 44 catttcc catttcc|ggaaatg 443 0 87.4 3 7.7e-19 6.3e-15 14.20 14 1 62 170 155 55 cgggaaa cgggaaa|tttcccg 181 0 85.6 3 2.0e-18 1.6e-14 13.79 15 0 15 85 69 12 atttccc atttccc|gggaaat 277 0 73.1 3 9.1e-16 7.5e-12 11.13 16 0 32 115 97 33 gatttcc gatttcc|ggaaatc 208 0 66.9 3 2.0e-14 1.6e-10 9.79 17 0 25 98 62 23 ccagaaa ccagaaa|tttctgg 307 0 66.5 3 2.3e-14 1.9e-10 9.72 18 0 31 121 105 50 gaaatca gaaatca|tgatttc 223 0 65.8 3 3.3e-14 2.7e-10 9.57 19 0 23 94 80 26 cctgtaa cctgtaa|ttacagg 174 0 52.6 3 2.2e-11 1.8e-07 6.74 20 0 20 70 67 17 tacagga tacagga|tcctgta 177 0 51.4 3 4.0e-11 3.3e-07 6.49 21 0 25 68 70 14 ctggaag ctggaag|cttccag 309 0 51.4 3 4.0e-11 3.3e-07 6.48 22 0 51 113 108 37 ggaaacc ggaaacc|ggtttcc 201 0 48.7 3 1.5e-10 1.3e-06 5.90 23 1 28 84 67 21 acaggaa acaggaa|ttcctgt 309 0 46.5 3 4.5e-10 3.7e-06 5.43 24 1 52 107 111 38 ccggaaa ccggaaa|tttccgg 138 0 46.0 3 5.7e-10 4.7e-06 5.33 25 0 19 65 42 12 cttttcc cttttcc|ggaaaag 281 1 45.4 3 7.7e-10 6.3e-06 5.20 26 2 39 110 88 42 aggaaat aggaaat|atttcct 376 0 45.3 3 7.9e-10 6.5e-06 5.19 27 1 67 139 117 52 caggaag caggaag|cttcctg 463 0 44.0 3 1.5e-09 1.3e-05 4.90 28 1 88 163 144 67 attccgg attccgg|ccggaat 64 0 41.6 3 4.9e-09 4e-05 4.40 29 0 3 36 20 5 gaagtca gaagtca|tgacttc 158 0 41.1 3 6.2e-09 5.1e-05 4.29 30 0 18 67 53 20 agaaatg agaaatg|catttct 250 0 40.4 3 8.8e-09 7.2e-05 4.14 31 1 48 82 94 25 gtttcca gtttcca|tggaaac 205 0 40.0 3 1.1e-08 8.7e-05 4.06 32 0 34 81 68 22 acgggaa acgggaa|ttcccgt 82 0 39.2 3 1.5e-08 0.00013 3.90 33 0 9 37 33 3 cgtttcc cgtttcc|ggaaacg 95 0 38.1 3 2.7e-08 0.00022 3.66 34 0 11 47 29 8 gaattcc gaattcc|ggaattc 189 0 38.1 3 2.7e-08 0.00022 3.65 35 0 23 71 68 27 gaaatga gaaatga|tcatttc 263 0 37.6 3 3.4e-08 0.00028 3.55 36 0 52 97 85 29 attcctg attcctg|caggaat 268 0 37.3 3 4.0e-08 0.00033 3.49 37 1 42 89 98 38 tccaaga tccaaga|tcttgga 177 0 36.6 3 5.6e-08 0.00046 3.34 38 1 28 73 56 19 acttccc acttccc|gggaagt 183 0 35.8 3 8.4e-08 0.00069 3.16 39 0 29 68 66 20 gaaacca gaaacca|tggtttc 192 0 35.5 3 9.6e-08 0.00079 3.10 40 0 30 82 52 28 tgactca tgactca|tgagtca 616 0 34.8 3 1.3e-07 0.0011 2.96 41 4 119 197 192 104 attcccg attcccg|cgggaat 76 0 34.7 3 1.4e-07 0.0011 2.95 42 0 7 25 38 6 atttcca atttcca|tggaaat 244 0 34.5 3 1.5e-07 0.0013 2.90 43 2 38 85 86 33 aggaaac aggaaac|gtttcct 239 0 34.3 3 1.7e-07 0.0014 2.86 44 0 35 89 78 37 atttctg atttctg|cagaaat 218 0 33.8 3 2.2e-07 0.0018 2.75 45 2 33 85 68 30 agaaatc agaaatc|gatttct 150 0 32.6 3 3.8e-07 0.0031 2.50 46 0 17 62 48 23 gacgtca gacgtca|tgacgtc 56 0 32.3 3 4.6e-07 0.0038 2.42 47 0 10 3 32 11 tactgga tactgga|tccagta 124 0 32.1 3 5.1e-07 0.0042 2.38 48 0 17 47 48 12 gggaaac gggaaac|gtttccc 211 0 31.8 3 5.9e-07 0.0048 2.32 49 1 41 79 68 22 ctttccc ctttccc|gggaaag 261 0 31.6 3 6.2e-07 0.0051 2.29 50 1 54 90 87 29 ; Host name rsat ; Job started 2013-01-11.110739 ; Job done 2013-01-11.110757 ; Seconds 14.28 ; user 14.28 ; system 0.04 ; cuser 2.72 ; csystem 0.25