position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.200629_2026-02-26.200629_uoww0v/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 SMAD2_hela_hg38_SEACR_relaxed -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.200629_2026-02-26.200629_uoww0v/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/2026/02/26/peak-motifs.2026-02-26.200629_2026-02-26.200629_uoww0v/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.200629_2026-02-26.200629_uoww0v/results/composition/peak-motifs_test_profiles-1str-ovlp_1nt_ci20.tab Oligo length 1 Occurrences counted on a single strands Conditions of applicability checked. Background model estimation: homogeneous repartition Sequence statistics: Nb of sequences 226 Sum of sequence lengths 226000 Min sequence length 0 Max sequence length 1000 Average sequence length 1000 Possible positions 226000 Oligonucleotide statistics: Total occurrences 196612 Position interval parameters: Position interval 20 Number of windows 50 Total positions 226000 Degrees of freedom 49 K-mer clustering parameters: Number of clusters 0 Clustering method complete Position intervals: window [min,max] mid seq occ 1 -25 [-499,-480] -489.5 226 4520 2 -24 [-479,-460] -469.5 226 4520 3 -23 [-459,-440] -449.5 226 4520 4 -22 [-439,-420] -429.5 226 4520 5 -21 [-419,-400] -409.5 226 4520 6 -20 [-399,-380] -389.5 226 4520 7 -19 [-379,-360] -369.5 226 4520 8 -18 [-359,-340] -349.5 226 4520 9 -17 [-339,-320] -329.5 226 4520 10 -16 [-319,-300] -309.5 226 4520 11 -15 [-299,-280] -289.5 226 4520 12 -14 [-279,-260] -269.5 226 4520 13 -13 [-259,-240] -249.5 226 4520 14 -12 [-239,-220] -229.5 226 4520 15 -11 [-219,-200] -209.5 226 4520 16 -10 [-199,-180] -189.5 226 4520 17 -9 [-179,-160] -169.5 226 4520 18 -8 [-159,-140] -149.5 226 4520 19 -7 [-139,-120] -129.5 226 4520 20 -6 [-119,-100] -109.5 226 4520 21 -5 [-99,-80] -89.5 226 4520 22 -4 [-79,-60] -69.5 226 4520 23 -3 [-59,-40] -49.5 226 4520 24 -2 [-39,-20] -29.5 226 4520 25 -1 [-19,0] -9.5 226 4520 26 0 [1,20] 10.5 226 4520 27 1 [21,40] 30.5 226 4520 28 2 [41,60] 50.5 226 4520 29 3 [61,80] 70.5 226 4520 30 4 [81,100] 90.5 226 4520 31 5 [101,120] 110.5 226 4520 32 6 [121,140] 130.5 226 4520 33 7 [141,160] 150.5 226 4520 34 8 [161,180] 170.5 226 4520 35 9 [181,200] 190.5 226 4520 36 10 [201,220] 210.5 226 4520 37 11 [221,240] 230.5 226 4520 38 12 [241,260] 250.5 226 4520 39 13 [261,280] 270.5 226 4520 40 14 [281,300] 290.5 226 4520 41 15 [301,320] 310.5 226 4520 42 16 [321,340] 330.5 226 4520 43 17 [341,360] 350.5 226 4520 44 18 [361,380] 370.5 226 4520 45 19 [381,400] 390.5 226 4520 46 20 [401,420] 410.5 226 4520 47 21 [421,440] 430.5 226 4520 48 22 [441,460] 450.5 226 4520 49 23 [461,480] 470.5 226 4520 50 24 [481,500] 490.5 226 4520 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 -489.5 occurrences in window 1 [-499,-480] 11 -469.5 occurrences in window 2 [-479,-460] 12 -449.5 occurrences in window 3 [-459,-440] 13 -429.5 occurrences in window 4 [-439,-420] 14 -409.5 occurrences in window 5 [-419,-400] 15 -389.5 occurrences in window 6 [-399,-380] 16 -369.5 occurrences in window 7 [-379,-360] 17 -349.5 occurrences in window 8 [-359,-340] 18 -329.5 occurrences in window 9 [-339,-320] 19 -309.5 occurrences in window 10 [-319,-300] 20 -289.5 occurrences in window 11 [-299,-280] 21 -269.5 occurrences in window 12 [-279,-260] 22 -249.5 occurrences in window 13 [-259,-240] 23 -229.5 occurrences in window 14 [-239,-220] 24 -209.5 occurrences in window 15 [-219,-200] 25 -189.5 occurrences in window 16 [-199,-180] 26 -169.5 occurrences in window 17 [-179,-160] 27 -149.5 occurrences in window 18 [-159,-140] 28 -129.5 occurrences in window 19 [-139,-120] 29 -109.5 occurrences in window 20 [-119,-100] 30 -89.5 occurrences in window 21 [-99,-80] 31 -69.5 occurrences in window 22 [-79,-60] 32 -49.5 occurrences in window 23 [-59,-40] 33 -29.5 occurrences in window 24 [-39,-20] 34 -9.5 occurrences in window 25 [-19,0] 35 10.5 occurrences in window 26 [1,20] 36 30.5 occurrences in window 27 [21,40] 37 50.5 occurrences in window 28 [41,60] 38 70.5 occurrences in window 29 [61,80] 39 90.5 occurrences in window 30 [81,100] 40 110.5 occurrences in window 31 [101,120] 41 130.5 occurrences in window 32 [121,140] 42 150.5 occurrences in window 33 [141,160] 43 170.5 occurrences in window 34 [161,180] 44 190.5 occurrences in window 35 [181,200] 45 210.5 occurrences in window 36 [201,220] 46 230.5 occurrences in window 37 [221,240] 47 250.5 occurrences in window 38 [241,260] 48 270.5 occurrences in window 39 [261,280] 49 290.5 occurrences in window 40 [281,300] 50 310.5 occurrences in window 41 [301,320] 51 330.5 occurrences in window 42 [321,340] 52 350.5 occurrences in window 43 [341,360] 53 370.5 occurrences in window 44 [361,380] 54 390.5 occurrences in window 45 [381,400] 55 410.5 occurrences in window 46 [401,420] 56 430.5 occurrences in window 47 [421,440] 57 450.5 occurrences in window 48 [441,460] 58 470.5 occurrences in window 49 [461,480] 59 490.5 occurrences in window 50 [481,500]
| seq | id | occ | chi2 | df | Pval | Eval | sig | rank | -489.5 | -469.5 | -449.5 | -429.5 | -409.5 | -389.5 | -369.5 | -349.5 | -329.5 | -309.5 | -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 | 310.5 | 330.5 | 350.5 | 370.5 | 390.5 | 410.5 | 430.5 | 450.5 | 470.5 | 490.5 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| c | c | 40023 | 91.7 | 49 | 2.1e-04 | 0.00085 | 3.07 | 1 | 857 | 810 | 747 | 759 | 826 | 760 | 775 | 849 | 782 | 746 | 825 | 840 | 834 | 763 | 859 | 821 | 788 | 773 | 818 | 857 | 752 | 815 | 859 | 792 | 837 | 792 | 819 | 807 | 823 | 829 | 803 | 839 | 829 | 844 | 838 | 789 | 810 | 831 | 790 | 736 | 781 | 780 | 769 | 784 | 802 | 702 | 712 | 758 | 772 | 840 |
| t | t | 58727 | 79.3 | 49 | 4.0e-03 | 0.016 | 1.80 | 2 | 1183 | 1106 | 1157 | 1112 | 1129 | 1146 | 1194 | 1126 | 1144 | 1169 | 1152 | 1110 | 1181 | 1184 | 1176 | 1130 | 1208 | 1161 | 1226 | 1185 | 1214 | 1200 | 1129 | 1185 | 1117 | 1205 | 1177 | 1196 | 1160 | 1252 | 1243 | 1245 | 1268 | 1173 | 1088 | 1137 | 1105 | 1141 | 1221 | 1224 | 1159 | 1207 | 1216 | 1150 | 1189 | 1249 | 1216 | 1142 | 1144 | 1196 |
| g | g | 39493 | 67.3 | 49 | 4.2e-02 | 0.17 | 0.77 | 3 | 831 | 773 | 793 | 893 | 813 | 776 | 778 | 762 | 779 | 794 | 757 | 816 | 759 | 807 | 794 | 815 | 790 | 841 | 775 | 783 | 833 | 767 | 755 | 824 | 810 | 791 | 750 | 746 | 825 | 758 | 865 | 835 | 776 | 810 | 795 | 758 | 752 | 757 | 769 | 758 | 798 | 741 | 789 | 777 | 760 | 734 | 812 | 809 | 800 | 810 |
| a | a | 58369 | 38.0 | 49 | 8.7e-01 | 3.5 | -0.54 | 4 | 1180 | 1195 | 1185 | 1160 | 1182 | 1204 | 1122 | 1119 | 1181 | 1157 | 1175 | 1220 | 1201 | 1177 | 1136 | 1207 | 1129 | 1154 | 1156 | 1196 | 1210 | 1177 | 1186 | 1138 | 1159 | 1122 | 1161 | 1175 | 1206 | 1181 | 1135 | 1134 | 1170 | 1178 | 1208 | 1140 | 1156 | 1176 | 1140 | 1156 | 1180 | 1165 | 1079 | 1189 | 1142 | 1193 | 1120 | 1152 | 1195 | 1210 |
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