position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/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 Promoter_regions_2000 -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/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/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/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 9 Sum of sequence lengths 9000 Min sequence length 0 Max sequence length 1000 Average sequence length 1000 Possible positions 9000 Sequences: # length ID 1 1000 TraesCS3A02G230000 2 1000 TraesCS3B02G448000 3 1000 TraesCS2B02G533400 4 1000 TraesCS2A02G004600 5 1000 TraesCS1A02G362100 6 1000 TraesCS1A02G333800 7 1000 TraesCS4B02G198000 8 1000 TraesCS2B02G538800 9 1000 TraesCS6A02G024100 Oligonucleotide statistics: Total occurrences 8807 Position interval parameters: Position interval 20 Number of windows 50 Total positions 9000 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 9 180 2 -24 [-479,-460] -469.5 9 180 3 -23 [-459,-440] -449.5 9 180 4 -22 [-439,-420] -429.5 9 180 5 -21 [-419,-400] -409.5 9 180 6 -20 [-399,-380] -389.5 9 180 7 -19 [-379,-360] -369.5 9 180 8 -18 [-359,-340] -349.5 9 180 9 -17 [-339,-320] -329.5 9 180 10 -16 [-319,-300] -309.5 9 180 11 -15 [-299,-280] -289.5 9 180 12 -14 [-279,-260] -269.5 9 180 13 -13 [-259,-240] -249.5 9 180 14 -12 [-239,-220] -229.5 9 180 15 -11 [-219,-200] -209.5 9 180 16 -10 [-199,-180] -189.5 9 180 17 -9 [-179,-160] -169.5 9 180 18 -8 [-159,-140] -149.5 9 180 19 -7 [-139,-120] -129.5 9 180 20 -6 [-119,-100] -109.5 9 180 21 -5 [-99,-80] -89.5 9 180 22 -4 [-79,-60] -69.5 9 180 23 -3 [-59,-40] -49.5 9 180 24 -2 [-39,-20] -29.5 9 180 25 -1 [-19,0] -9.5 9 180 26 0 [1,20] 10.5 9 180 27 1 [21,40] 30.5 9 180 28 2 [41,60] 50.5 9 180 29 3 [61,80] 70.5 9 180 30 4 [81,100] 90.5 9 180 31 5 [101,120] 110.5 9 180 32 6 [121,140] 130.5 9 180 33 7 [141,160] 150.5 9 180 34 8 [161,180] 170.5 9 180 35 9 [181,200] 190.5 9 180 36 10 [201,220] 210.5 9 180 37 11 [221,240] 230.5 9 180 38 12 [241,260] 250.5 9 180 39 13 [261,280] 270.5 9 180 40 14 [281,300] 290.5 9 180 41 15 [301,320] 310.5 9 180 42 16 [321,340] 330.5 9 180 43 17 [341,360] 350.5 9 180 44 18 [361,380] 370.5 9 180 45 19 [381,400] 390.5 9 180 46 20 [401,420] 410.5 9 180 47 21 [421,440] 430.5 9 180 48 22 [441,460] 450.5 9 180 49 23 [461,480] 470.5 9 180 50 24 [481,500] 490.5 9 180 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 | 2582 | 77.9 | 49 | 5.4e-03 | 0.021 | 1.67 | 1 | 37 | 41 | 38 | 50 | 49 | 61 | 57 | 43 | 42 | 56 | 47 | 64 | 59 | 56 | 48 | 41 | 60 | 43 | 40 | 43 | 51 | 45 | 41 | 43 | 41 | 40 | 40 | 45 | 45 | 45 | 53 | 64 | 50 | 65 | 60 | 61 | 55 | 51 | 51 | 63 | 55 | 64 | 62 | 61 | 53 | 65 | 57 | 59 | 49 | 73 |
| t | t | 1996 | 70.4 | 49 | 2.4e-02 | 0.097 | 1.01 | 2 | 36 | 45 | 44 | 42 | 46 | 35 | 42 | 39 | 36 | 50 | 44 | 46 | 32 | 46 | 55 | 57 | 28 | 36 | 49 | 37 | 25 | 34 | 37 | 36 | 49 | 40 | 39 | 44 | 45 | 30 | 32 | 30 | 46 | 34 | 47 | 48 | 45 | 45 | 42 | 36 | 35 | 21 | 43 | 37 | 52 | 34 | 29 | 36 | 41 | 39 |
| g | g | 2228 | 66.1 | 49 | 5.2e-02 | 0.21 | 0.68 | 3 | 55 | 59 | 60 | 45 | 52 | 61 | 51 | 62 | 57 | 42 | 48 | 34 | 40 | 50 | 42 | 53 | 45 | 50 | 37 | 34 | 36 | 35 | 41 | 40 | 40 | 32 | 37 | 49 | 45 | 53 | 50 | 39 | 47 | 38 | 29 | 33 | 44 | 45 | 42 | 43 | 43 | 44 | 44 | 42 | 44 | 44 | 45 | 46 | 45 | 36 |
| a | a | 2001 | 59.3 | 49 | 1.5e-01 | 0.6 | 0.23 | 4 | 52 | 35 | 38 | 43 | 33 | 23 | 30 | 36 | 45 | 32 | 41 | 36 | 49 | 28 | 35 | 29 | 47 | 43 | 34 | 46 | 48 | 46 | 41 | 41 | 30 | 48 | 44 | 37 | 45 | 52 | 45 | 47 | 37 | 43 | 44 | 38 | 36 | 39 | 45 | 38 | 47 | 51 | 31 | 40 | 31 | 37 | 49 | 39 | 45 | 32 |
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