; position-analysis -v 1 -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 20 -1str -ovlp -seqtype dna -l 2 -ci 20 -img_format png -title STAT1_motif_Analysis -origin center -o $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.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/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab ; Oligo length 2 ; Occurrences counted on a single strands ; 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 480000 ; Oligonucleotide statistics: ; Total occurrences 478613 ; Class parameters: ; Class interval 20 ; Number of classes 11 ; Total positions 480000 ; Degrees of freedom 10 ; Sequences per class: ; class [min max] mid seq occ ; 1 [-119 -100] -109.5 2400 2400 ; 2 [-99 -80] -89.5 2400 48000 ; 3 [-79 -60] -69.5 2400 48000 ; 4 [-59 -40] -49.5 2400 48000 ; 5 [-39 -20] -29.5 2400 48000 ; 6 [-19 0] -9.5 2400 48000 ; 7 [1 20] 10.5 2400 48000 ; 8 [21 40] 30.5 2400 48000 ; 9 [41 60] 50.5 2400 48000 ; 10 [61 80] 70.5 2400 48000 ; 11 [81 100] 90.5 2400 45600 ; ; 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 -109.5 observed class occurrences ; 11 -89.5 observed class occurrences ; 12 -69.5 observed class occurrences ; 13 -49.5 observed class occurrences ; 14 -29.5 observed class occurrences ; 15 -9.5 observed class occurrences ; 16 10.5 observed class occurrences ; 17 30.5 observed class occurrences ; 18 50.5 observed class occurrences ; 19 70.5 observed class occurrences ; 20 90.5 observed class occurrences #seq id occ chi2 df Pval Eval sig rank -109.5 -89.5 -69.5 -49.5 -29.5 -9.5 10.5 30.5 50.5 70.5 90.5 tt tt 36914 75.5 10 3.8e-12 6.1e-11 10.21 1 175 3604 3515 3567 3718 4047 3802 3716 3466 3633 3671 ta ta 19733 52.3 10 1.0e-07 1.6e-06 5.79 2 79 2083 1999 1949 1998 1816 1866 1843 2041 2061 1998 gc gc 28517 48.7 10 4.6e-07 7.3e-06 5.14 3 131 2951 2979 2846 2855 2651 2626 2886 2902 2975 2715 aa aa 36559 40.4 10 1.4e-05 0.00023 3.64 4 184 3670 3596 3486 3497 3765 3919 3719 3612 3611 3500 ga ga 30545 26.2 10 3.5e-03 0.057 1.25 5 122 3095 3038 3059 3051 3130 3219 3084 2994 2967 2786 tc tc 30493 22.5 10 1.3e-02 0.21 0.69 6 142 2925 3024 3066 3004 3229 3133 3096 3025 2977 2872 ct ct 36152 16.8 10 7.8e-02 1.3 -0.10 7 215 3611 3617 3671 3606 3548 3464 3648 3621 3653 3498 ac ac 23336 16.2 10 9.3e-02 1.5 -0.17 8 110 2394 2356 2330 2399 2254 2303 2249 2411 2261 2269 ca ca 34851 14.1 10 1.7e-01 2.7 -0.44 9 188 3471 3545 3516 3519 3358 3460 3450 3601 3402 3341 at at 25683 11.2 10 3.4e-01 5.5 -0.74 10 139 2595 2579 2486 2587 2549 2661 2482 2582 2546 2477 tg tg 34920 10.8 10 3.8e-01 6 -0.78 11 176 3507 3531 3495 3475 3410 3382 3567 3485 3595 3297 cc cc 35103 10.5 10 4.0e-01 6.4 -0.81 12 181 3463 3545 3606 3584 3559 3474 3520 3430 3491 3250 cg cg 11448 10.2 10 4.3e-01 6.8 -0.83 13 69 1180 1123 1142 1142 1190 1153 1143 1159 1124 1023 gg gg 34887 8.8 10 5.5e-01 8.9 -0.95 14 175 3467 3462 3480 3377 3472 3486 3510 3574 3582 3302 gt gt 23372 8.7 10 5.6e-01 9 -0.96 15 117 2260 2329 2392 2343 2303 2302 2328 2374 2421 2203 ag ag 36100 8.5 10 5.8e-01 9.2 -0.96 16 194 3641 3636 3694 3594 3501 3582 3623 3643 3625 3367 ; Host name rsat ; Job started 2013-01-11.110715 ; Job done 2013-01-11.110724 ; Seconds 6.87 ; user 6.87 ; system 0.01 ; cuser 2.15 ; csystem 0.16