; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/04/30/tmp_sequence_2026-04-30.003956_1z6pcR.fasta.purged -format fasta -lth occ_sig 0 -uth rank 50 -return occ,proba,rank -2str -noov -quick_if_possible -seqtype dna -bg upstream-noorf -org Actinidia_chinensis.Red5_PS1_1.69.0.60 -pseudo 0.01 -l 6 -o $RSAT/public_html/tmp/www-data/2026/04/30/oligo-analysis_2026-04-30.003956_EgnUdf_6nt.tab
; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42.
; Program version 1.169
; Quick counting mode
; Detection of over-represented words (right-tail test)
; Oligomer length 6
; Input file $RSAT/public_html/tmp/www-data/2026/04/30/tmp_sequence_2026-04-30.003956_1z6pcR.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/04/30/oligo-analysis_2026-04-30.003956_EgnUdf_6nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Actinidia_chinensis.Red5_PS1_1.69.0.60
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Actinidia_chinensis.Red5_PS1_1.69.0.60/oligo-frequencies/6nt_upstream-noorf_Actinidia_chinensis.Red5_PS1_1.69.0.60-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 4.80769230769231e-06
; Sequence type DNA
; Nb of sequences 16
; Sum of sequence lengths 3405
; 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 3315
; total overlapping occurrences 20
; total non overlapping occ 3295
; alphabet size 4
; nb possible oligomers 2080
; oligomers tested for significance 2080
; Sequences:
; 07110 200
; 0155 200
; 02070 200
; PhoP 200
; PhoP2 200
; 03920 200
; 0330 200
; 01390 200
; 05970 200
; 1740 200
; 05655 405
; 02485 200
; 02830 200
; 01745 200
; 2045 200
; 7210 200
;
; column headers
; 1 seq oligomer sequence
; 2 id 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 id exp_freq occ exp_occ occ_P occ_E occ_sig rank ovl_occ forbocc
cgcgcc cgcgcc|ggcgcg 0.0000579627511 17 0.19 1.5e-27 3.1e-24 23.51 1 0 85
ccgcgc ccgcgc|gcgcgg 0.0000323060001 14 0.11 2.6e-25 5.5e-22 21.26 2 1 70
cggcgc cggcgc|gcgccg 0.0000439350902 12 0.15 1.6e-19 3.4e-16 15.47 3 0 60
ctgcgc ctgcgc|gcgcag 0.0000485276145 11 0.16 4e-17 8.3e-14 13.08 4 0 55
cgccgc cgccgc|gcggcg 0.0000701488553 10 0.23 1e-13 2.1e-10 9.67 5 1 50
cgcggc cgcggc|gccgcg 0.0000371827153 8 0.12 1.2e-12 2.4e-09 8.61 6 0 40
gcgcga gcgcga|tcgcgc 0.0000423322537 8 0.14 3.3e-12 6.8e-09 8.17 7 0 40
cgcgca cgcgca|tgcgcg 0.0000512672144 8 0.17 1.5e-11 3.1e-08 7.51 8 1 40
cgcagc cgcagc|gctgcg 0.0000562235031 8 0.19 3e-11 6.3e-08 7.20 9 0 40
gcccgc gcccgc|gcgggc 0.0000608387626 8 0.20 5.6e-11 1.2e-07 6.93 10 0 40
ccgggc ccgggc|gcccgg 0.0000617709087 8 0.20 6.3e-11 1.3e-07 6.88 11 0 40
gcggcc gcggcc|ggccgc 0.0000643172588 8 0.21 8.7e-11 1.8e-07 6.74 12 0 40
cgcgaa cgcgaa|ttcgcg 0.0000667044620 8 0.22 1.2e-10 2.4e-07 6.62 13 1 40
cccgcg cccgcg|cgcggg 0.0000406157409 7 0.13 1.4e-10 2.9e-07 6.53 14 0 35
ccggcc ccggcc|ggccgg 0.0001159831575 9 0.38 3.5e-10 7.4e-07 6.13 15 0 45
gcgccc gcgccc|gggcgc 0.0000471976013 7 0.16 3.9e-10 8.2e-07 6.09 16 0 35
gcgcca gcgcca|tggcgc 0.0000782085081 8 0.26 4e-10 8.3e-07 6.08 17 0 40
cctgcg cctgcg|cgcagg 0.0000509830235 7 0.17 6.7e-10 1.4e-06 5.86 18 0 35
agcgcc agcgcc|ggcgct 0.0000549844309 7 0.18 1.1e-09 2.3e-06 5.63 19 0 35
ccggcg ccggcg|cgccgg 0.0000564508557 7 0.19 1.3e-09 2.8e-06 5.55 20 1 35
acggcg acggcg|cgccgt 0.0000695918412 7 0.23 5.6e-09 1.2e-05 4.93 21 0 35
cggccc cggccc|gggccg 0.0001103561784 8 0.37 5.7e-09 1.2e-05 4.93 22 0 40
cccggc cccggc|gccggg 0.0000699442379 7 0.23 5.8e-09 1.2e-05 4.92 23 0 35
ccgcaa ccgcaa|ttgcgg 0.0001144485268 8 0.38 7.5e-09 1.6e-05 4.80 24 0 40
ccgccg ccgccg|cggcgg 0.0000784926990 7 0.26 1.3e-08 2.6e-05 4.58 25 1 35
cccgca cccgca|tgcggg 0.0000812777695 7 0.27 1.6e-08 3.3e-05 4.48 26 0 35
accccg accccg|cggggt 0.0000963171499 7 0.32 5.1e-08 1.1e-04 3.98 27 0 35
caccgg caccgg|ccggtg 0.0000984201622 7 0.33 5.8e-08 1.2e-04 3.92 28 0 35
agcccg agcccg|cgggct 0.0001032968775 7 0.34 8.1e-08 1.7e-04 3.77 29 0 35
cgggga cgggga|tccccg 0.0001066162267 7 0.35 1e-07 2.1e-04 3.68 30 0 35
cgctgc cgctgc|gcagcg 0.0000643399940 6 0.21 1.1e-07 2.3e-04 3.65 31 0 30
gccgcc gccgcc|ggcggc 0.0001085941951 7 0.36 1.1e-07 2.3e-04 3.63 32 0 35
gccgca gccgca|tgcggc 0.0000663179624 6 0.22 1.3e-07 2.7e-04 3.57 33 0 30
ccgtgc ccgtgc|gcacgg 0.0001117543975 7 0.37 1.4e-07 2.8e-04 3.55 34 0 35
aagcgc aagcgc|gcgctt 0.0000713424569 6 0.24 2e-07 4.1e-04 3.39 35 0 30
acgcgc acgcgc|gcgcgt 0.0000757417315 6 0.25 2.8e-07 5.8e-04 3.24 36 0 30
ccaccc ccaccc|gggtgg 0.0004240346842 11 1.41 2.9e-07 6.0e-04 3.22 37 0 55
ccgcac ccgcac|gtgcgg 0.0000807662259 6 0.27 4.1e-07 8.4e-04 3.07 38 0 30
cgctga cgctga|tcagcg 0.0000826077827 6 0.27 4.6e-07 9.6e-04 3.02 39 0 30
ccccgg ccccgg|ccgggg 0.0000835285610 6 0.28 4.9e-07 1.0e-03 2.99 40 0 30
gcggga gcggga|tcccgc 0.0000892919517 6 0.30 7.2e-07 1.5e-03 2.82 41 0 30
ccccgc ccccgc|gcgggg 0.0000899285393 6 0.30 7.5e-07 1.6e-03 2.81 42 0 30
cagcgc cagcgc|gcgctg 0.0000484480411 5 0.16 7.8e-07 1.6e-03 2.79 43 0 25
cgggcc cgggcc|ggcccg 0.0000930205359 6 0.31 9.1e-07 1.9e-03 2.72 44 1 30
accggc accggc|gccggt 0.0000941004611 6 0.31 9.8e-07 2.0e-03 2.69 45 0 30
cgggag cgggag|ctcccg 0.0000961693706 6 0.32 1.1e-06 2.3e-03 2.64 46 0 30
tccgca tccgca|tgcgga 0.0000964649291 6 0.32 1.1e-06 2.3e-03 2.63 47 0 30
accgcg accgcg|cgcggt 0.0000526995364 5 0.17 1.2e-06 2.4e-03 2.61 48 0 25
cacccc cacccc|ggggtg 0.0003938081441 10 1.31 1.2e-06 2.5e-03 2.60 49 0 50
cccgga cccgga|tccggg 0.0001086396656 6 0.36 2.2e-06 4.6e-03 2.34 50 0 30
; Host name rsat
; Job started 2026-04-30.003956
; Job done 2026-04-30.003956
; Seconds 0.26
; user 0.26
; system 0.03
; cuser 0.08
; csystem 0