position-analysis -v 1 -i $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.083405_2026-04-21.083405_7S6poV/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 2 -ci 20 -img_format png -title Gordonia_ -origin center -offset 0 -o $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.083405_2026-04-21.083405_7S6poV/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 $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.083405_2026-04-21.083405_7S6poV/data/sequences/peak-motifs_test_maxlen1000_purged_ml40_mis3.fasta Sequence format fasta Sequence type dna Output file $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.083405_2026-04-21.083405_7S6poV/results/composition/peak-motifs_test_profiles-1str-ovlp_2nt_ci20.tab Oligo length 2 Occurrences counted on a single strands Conditions of applicability checked. Background model estimation: homogeneous repartition Sequence statistics: Nb of sequences 36 Sum of sequence lengths 900 Min sequence length 0 Max sequence length 25 Average sequence length 25 Possible positions 864 Sequences: # length ID 1 25 gene1 2 25 gene2 3 25 gene3 4 25 gene4 5 25 gene5 6 25 gene6 7 25 gene7 8 25 gene8 9 25 gene9 10 25 gene10 11 25 gene11 12 25 GENE12 13 25 GENE13 14 25 GENE14 15 25 GENE15 16 25 GENE16 17 25 GENE17 18 25 GENE18 19 25 GENE19 20 25 GENE20 21 25 GENE21 22 25 GENE22 23 25 GENE23 24 25 GENE24 25 25 GENE25 26 25 GENE26 27 25 GENE27 28 25 GENE28 29 25 GENE29 30 25 GENE30 31 25 GENE31 32 25 GENE32 33 25 GENE33 34 25 GENE34 35 25 GENE35 36 25 GENE36 Oligonucleotide statistics: Total occurrences 864 Position interval parameters: Position interval 20 Number of windows 2 Total positions 864 Degrees of freedom 1 K-mer clustering parameters: Number of clusters 0 Clustering method complete Position intervals: window [min,max] mid seq occ 1 -1 [-19,0] -9.5 36 468 2 0 [1,20] 10.5 36 396 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 -9.5 occurrences in window 1 [-19,0] 11 10.5 occurrences in window 2 [1,20]
| seq | id | occ | chi2 | df | Pval | Eval | sig | rank | -9.5 | 10.5 |
|---|---|---|---|---|---|---|---|---|---|---|
| ac | ac | 56 | 5.0 | 1 | 2.5e-02 | 0.41 | 0.39 | 1 | 22 | 34 |
| at | at | 36 | 4.7 | 1 | 3.0e-02 | 0.48 | 0.32 | 2 | 26 | 10 |
| gc | gc | 58 | 4.0 | 1 | 4.6e-02 | 0.73 | 0.14 | 3 | 39 | 19 |
| ta | ta | 17 | 3.4 | 1 | 6.5e-02 | 1 | -0.02 | 4 | 13 | 4 |
| gg | gg | 100 | 2.7 | 1 | 1.0e-01 | 1.6 | -0.21 | 5 | 46 | 54 |
| cg | cg | 71 | 1.7 | 1 | 1.9e-01 | 3 | -0.48 | 6 | 44 | 27 |
| tt | tt | 19 | 1.1 | 1 | 2.9e-01 | 4.7 | -0.67 | 7 | 8 | 11 |
| tg | tg | 46 | 0.8 | 1 | 3.6e-01 | 5.8 | -0.76 | 8 | 28 | 18 |
| cc | cc | 55 | 0.6 | 1 | 4.5e-01 | 7.2 | -0.86 | 9 | 27 | 28 |
| aa | aa | 53 | 0.6 | 1 | 4.6e-01 | 7.3 | -0.86 | 10 | 26 | 27 |
| ag | ag | 64 | 0.4 | 1 | 5.0e-01 | 8.1 | -0.91 | 11 | 32 | 32 |
| ct | ct | 37 | 0.4 | 1 | 5.2e-01 | 8.3 | -0.92 | 12 | 22 | 15 |
| ga | ga | 81 | 0.2 | 1 | 6.8e-01 | 11 | -1.03 | 13 | 42 | 39 |
| gt | gt | 48 | 0.1 | 1 | 7.7e-01 | 12 | -1.09 | 14 | 27 | 21 |
| ca | ca | 59 | 0.1 | 1 | 8.0e-01 | 13 | -1.11 | 15 | 31 | 28 |
| tc | tc | 64 | 0.0 | 1 | 9.3e-01 | 15 | -1.17 | 16 | 35 | 29 |
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