; oligo-analysis -v 1 -quick -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 -lth ratio 1 -lth occ_sig 0 -uth rank 50 -return occ,proba,rank -2str -noov -seqtype dna -l 7 -markov 4 -pseudo 0.01 -o $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/oligos_7nt_mkv4/peak-motifs_oligos-2str-noov_7nt_mkv4.tab ; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42. ; Program version 1.165 ; Quick counting mode ; Detection of over-represented words (right-tail test) ; Oligomer length 7 ; Input file $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 ; Input format fasta ; Output file $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/oligos_7nt_mkv4/peak-motifs_oligos-2str-noov_7nt_mkv4.tab ; Discard overlapping matches ; Counted on both strands ; grouped by pairs of reverse complements ; Background model Markov ; Background estimation method Markov model estimated from input sequences ; Markov chain order 4 ; Pseudo-frequency 0.01 ; Pseudo-frequency per oligo 1.220703125e-06 ; Sequence type DNA ; Nb of sequences 2400 ; Sum of sequence lengths 482400 ; discarded residues NA (quick mode) (other letters than ACGT) ; discarded occurrences NA (quick mode) (contain discarded residues) ; nb possible positions NA (quick mode) ; total oligo occurrences 466505 ; total overlapping occurrences 3858 ; total non overlapping occ 462647 ; alphabet size 4 ; nb possible oligomers 8192 ; oligomers tested for significance 8186 ; Threshold values ; Parameter Lower Upper ; ratio 1 none ; ms_P none 1 ; occ_sig 0 none ; occ_P none 1 ; rank none 50 ; ; column headers ; 1 seq oligomer sequence ; 2 identifier oligomer identifier ; 3 exp_freq expected relative frequency ; 4 occ observed occurrences ; 5 exp_occ expected occurrences ; 6 occ_P occurrence probability (binomial) ; 7 occ_E E-value for occurrences (binomial) ; 8 occ_sig occurrence significance (binomial) ; 9 rank rank ; 10 ovl_occ number of overlapping occurrences (discarded from the count) ; 11 forbocc forbidden positions (to avoid self-overlap) #seq identifier exp_freq occ exp_occ occ_P occ_E occ_sig rank ovl_occ forbocc tccagga tccagga|tcctgga 0.0005671097468 650 264.56 9.8e-89 8.0e-85 84.09 1 0 3900 tgactca tgactca|tgagtca 0.0005588590087 616 260.71 4.5e-78 3.7e-74 73.43 2 0 3696 cctggaa cctggaa|ttccagg 0.0007125768040 644 332.42 6.7e-52 5.5e-48 47.26 3 0 3864 tcccgga tcccgga|tccggga 0.0002202192883 278 102.73 3.1e-46 2.5e-42 41.59 4 0 1668 cccagaa cccagaa|ttctggg 0.0004555244602 445 212.50 4.6e-44 3.8e-40 39.43 5 0 2670 tcccaga tcccaga|tctggga 0.0004616644699 449 215.37 5.5e-44 4.5e-40 39.35 6 0 2694 ccaggaa ccaggaa|ttcctgg 0.0009381268836 750 437.64 4.9e-42 4.1e-38 37.39 7 0 4500 ccgggaa ccgggaa|ttcccgg 0.0003325075055 333 155.12 2.3e-35 1.9e-31 30.72 8 2 1998 cccggaa cccggaa|ttccggg 0.0002749412087 274 128.26 4.1e-29 3.3e-25 24.48 9 0 1644 ccccacc ccccacc|ggtgggg 0.0002499400792 256 116.60 5.7e-29 4.6e-25 24.33 10 4 1536 ctgggaa ctgggaa|ttcccag 0.0007645699022 558 356.68 4.2e-23 3.5e-19 18.46 11 0 3348 catttcc catttcc|ggaaatg 0.0006166666664 443 287.68 1.3e-17 1.1e-13 12.98 12 0 2658 tacagga tacagga|tcctgta 0.0001876946718 177 87.56 3.2e-17 2.6e-13 12.58 13 0 1062 tgaatca tgaatca|tgattca 0.0001977403065 182 92.25 1.1e-16 8.9e-13 12.05 14 0 1092 atgagtc atgagtc|gactcat 0.0002605697684 219 121.56 1.3e-15 1.0e-11 10.99 15 0 1314 ctccacc ctccacc|ggtggag 0.0001766914112 162 82.43 6.6e-15 5.4e-11 10.27 16 0 972 cccaccc cccaccc|gggtggg 0.0003158212025 250 147.33 9e-15 7.4e-11 10.13 17 4 1500 cccctcc cccctcc|ggagggg 0.0003287177271 247 153.35 2.3e-12 1.8e-08 7.73 18 5 1482 ctcctcc ctcctcc|ggaggag 0.0003245142681 244 151.39 2.9e-12 2.3e-08 7.63 19 13 1464 atgactc atgactc|gagtcat 0.0003727105276 271 173.87 5.9e-12 4.8e-08 7.32 20 0 1626 aaaacaa aaaacaa|ttgtttt 0.0003384284060 249 157.88 1.3e-11 1.1e-07 6.96 21 13 1494 tactgga tactgga|tccagta 0.0001375100466 124 64.15 2.3e-11 1.9e-07 6.73 22 0 744 ccctgcc ccctgcc|ggcaggg 0.0003615703174 260 168.67 4.3e-11 3.6e-07 6.45 23 4 1560 ccactcc ccactcc|ggagtgg 0.0001500441851 131 70.00 5e-11 4.1e-07 6.39 24 0 786 cctgtaa cctgtaa|ttacagg 0.0002187933148 174 102.07 6.1e-11 5.0e-07 6.30 25 0 1044 cctcccc cctcccc|ggggagg 0.0003700558755 264 172.63 6.5e-11 5.4e-07 6.27 26 2 1584 tgactaa tgactaa|ttagtca 0.0001761093771 147 82.16 7.6e-11 6.2e-07 6.21 27 0 882 ccccgcc ccccgcc|ggcgggg 0.0002482027504 189 115.79 2.8e-10 2.3e-06 5.65 28 4 1134 aaccaca aaccaca|tgtggtt 0.0001749724748 144 81.63 2.9e-10 2.4e-06 5.62 29 0 864 ccggaac ccggaac|gttccgg 0.0001009518991 94 47.09 1.2e-09 9.4e-06 5.02 30 2 564 catgtga catgtga|tcacatg 0.0001790050378 143 83.51 2.1e-09 1.7e-05 4.76 31 2 858 tccaaga tccaaga|tcttgga 0.0002351516667 177 109.70 2.2e-09 1.8e-05 4.75 32 0 1062 tatgcaa tatgcaa|ttgcata 0.0000791440981 77 36.92 5.7e-09 4.7e-05 4.33 33 0 462 ctggaaa ctggaaa|tttccag 0.0007861892989 479 366.76 1.2e-08 9.8e-05 4.01 34 0 2874 ccgcccc ccgcccc|ggggcgg 0.0002678235068 192 124.94 1.6e-08 1.3e-04 3.89 35 2 1152 ccctccc ccctccc|gggaggg 0.0004541378109 297 211.86 2e-08 1.6e-04 3.79 36 10 1782 cactccc cactccc|gggagtg 0.0001896191972 145 88.46 2.2e-08 1.8e-04 3.74 37 0 870 cgggaag cgggaag|cttcccg 0.0002540627161 183 118.52 2.4e-08 2.0e-04 3.70 38 0 1098 cgcctcc cgcctcc|ggaggcg 0.0001367887523 112 63.81 3.1e-08 2.6e-04 3.59 39 1 672 attagtc attagtc|gactaat 0.0000950801331 85 44.36 3.9e-08 3.2e-04 3.50 40 0 510 aagaaaa aagaaaa|ttttctt 0.0004351286434 284 202.99 4.6e-08 3.8e-04 3.42 41 5 1704 ccttttc ccttttc|gaaaagg 0.0003106325195 214 144.91 4.8e-08 4.0e-04 3.40 42 0 1284 cccgccc cccgccc|gggcggg 0.0003379410574 229 157.65 5.9e-08 4.8e-04 3.32 43 3 1374 cctgccc cctgccc|gggcagg 0.0003835984434 254 178.95 7.5e-08 6.1e-04 3.21 44 5 1524 tgcacaa tgcacaa|ttgtgca 0.0001127269181 95 52.59 9.3e-08 7.6e-04 3.12 45 0 570 gagtcac gagtcac|gtgactc 0.0003710621254 246 173.10 1.1e-07 8.8e-04 3.06 46 0 1476 cacaccc cacaccc|gggtgtg 0.0002535022391 179 118.26 1.2e-07 1.0e-03 3.00 47 0 1074 cgcaggc cgcaggc|gcctgcg 0.0000905220431 80 42.23 1.5e-07 1.2e-03 2.92 48 0 480 gtggaga gtggaga|tctccac 0.0001368548134 109 63.84 1.7e-07 1.4e-03 2.85 49 0 654 cggttcc cggttcc|ggaaccg 0.0000569200915 57 26.55 2e-07 1.6e-03 2.79 50 0 342 ; Host name rsat ; Job started 2013-01-11.110725 ; Job done 2013-01-11.110728 ; Seconds 2.8 ; user 2.8 ; system 0.02 ; cuser 0.28 ; csystem 0.01