; 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 8 -o $RSAT/public_html/tmp/www-data/2026/04/30/oligo-analysis_2026-04-30.003956_EgnUdf_8nt.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 8
; 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_8nt.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/8nt_upstream-noorf_Actinidia_chinensis.Red5_PS1_1.69.0.60-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 3.03988326848249e-07
; 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 3281
; total overlapping occurrences 9
; total non overlapping occ 3272
; alphabet size 4
; nb possible oligomers 32896
; oligomers tested for significance 32896
; 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
ccgcgccg ccgcgccg|cggcgcgg 0.0000018066180 5 0.0059 6e-14 2.0e-09 8.70 1 0 35
acggcgcg acggcgcg|cgcgccgt 0.0000017724673 4 0.0058 4.7e-11 1.6e-06 5.81 2 0 28
gccgcgcc gccgcgcc|ggcgcggc 0.0000021936590 4 0.0072 1.1e-10 3.7e-06 5.44 3 0 28
agcgcagc agcgcagc|gctgcgct 0.0000025465493 4 0.0084 2e-10 6.6e-06 5.18 4 0 28
ccaccccg ccaccccg|cggggtgg 0.0000112208207 5 0.04 5.4e-10 1.8e-05 4.75 5 0 35
aagcgcag aagcgcag|ctgcgctt 0.0000039353434 4 0.01 1.1e-09 3.8e-05 4.42 6 0 28
ccggcgcg ccggcgcg|cgcgccgg 0.0000014423442 3 0.0047 1.8e-08 5.8e-04 3.24 7 0 21
gccggcgc gccggcgc|gcgccggc 0.0000014878783 3 0.0049 1.9e-08 6.3e-04 3.20 8 0 21
cctgcgcg cctgcgcg|cgcgcagg 0.0000016813989 3 0.0055 2.8e-08 9.2e-04 3.04 9 0 21
agggcgcg agggcgcg|cgcgccct 0.0000022961110 3 0.0075 7.1e-08 2.3e-03 2.63 10 0 21
gacgccgc gacgccgc|gcggcgtc 0.0000023644124 3 0.0078 7.7e-08 2.5e-03 2.59 11 0 21
agccgcgc agccgcgc|gcgcggct 0.0000023871795 3 0.0078 8e-08 2.6e-03 2.58 12 0 21
cgacgacg cgacgacg|cgtcgtcg 0.0000116647795 4 0.04 8.7e-08 2.8e-03 2.55 13 0 28
gcgccagc gcgccagc|gctggcgc 0.0000024896315 3 0.0082 9e-08 3.0e-03 2.53 14 0 21
acgacgac acgacgac|gtcgtcgt 0.0000122567245 4 0.04 1.1e-07 3.5e-03 2.46 15 0 28
aacggcgc aacggcgc|gcgccgtt 0.0000033320148 3 0.01 2.2e-07 7.1e-03 2.15 16 0 21
cggctggc cggctggc|gccagccg 0.0000035938366 3 0.01 2.7e-07 8.9e-03 2.05 17 0 21
ggcgctga ggcgctga|tcagcgcc 0.0000037190558 3 0.01 3e-07 9.9e-03 2.01 18 0 21
gacgacgc gacgacgc|gcgtcgtc 0.0000037190558 3 0.01 3e-07 9.9e-03 2.01 19 0 21
cagcgcca cagcgcca|tggcgctg 0.0000041630146 3 0.01 4.2e-07 1.4e-02 1.86 20 0 21
ccagccgc ccagccgc|gcggctgg 0.0000046069733 3 0.02 5.7e-07 1.9e-02 1.73 21 0 21
acctgcgc acctgcgc|gcgcaggt 0.0000047208089 3 0.02 6.1e-07 2.0e-02 1.70 22 0 21
caccccgg caccccgg|ccggggtg 0.0000057567127 3 0.02 1.1e-06 3.6e-02 1.44 23 0 21
gagcggcc gagcggcc|ggccgctc 0.0000066560139 3 0.02 1.7e-06 5.6e-02 1.25 24 0 21
gccggtga gccggtga|tcaccggc 0.0000068040000 3 0.02 1.8e-06 6.0e-02 1.22 25 0 21
cgacgccg cgacgccg|cggcgtcg 0.0000070202877 3 0.02 2e-06 6.6e-02 1.18 26 0 21
cgggctca cgggctca|tgagcccg 0.0000077488355 3 0.03 2.7e-06 8.8e-02 1.05 27 0 21
aaagcgca aaagcgca|tgcgcttt 0.0000078740545 3 0.03 2.8e-06 9.3e-02 1.03 28 0 21
acgacgcc acgacgcc|ggcgtcgt 0.0000079651230 3 0.03 2.9e-06 9.6e-02 1.02 29 0 21
aacgggga aacgggga|tccccgtt 0.0000090237940 3 0.03 4.2e-06 1.4e-01 0.86 30 0 21
cgccgggc cgccgggc|gcccggcg 0.0000013854263 2 0.0045 1e-05 3.4e-01 0.47 31 0 14
cgcccgcg cgcccgcg|cgcgggcg 0.0000014423442 2 0.0047 1.1e-05 3.7e-01 0.44 32 0 14
ccgcgcag ccgcgcag|ctgcgcgg 0.0000014878783 2 0.0049 1.2e-05 3.9e-01 0.41 33 0 14
cgctgcgc cgctgcgc|gcgcagcg 0.0000015447962 2 0.0051 1.3e-05 4.2e-01 0.38 34 0 14
gcggaaaa gcggaaaa|ttttccgc 0.0000133495461 3 0.04 1.4e-05 4.5e-01 0.35 35 0 21
ccgcggcg ccgcggcg|cgccgcgg 0.0000016472482 2 0.0054 1.5e-05 4.8e-01 0.32 36 0 14
cgccgcgc cgccgcgc|gcgcggcg 0.0000016813989 2 0.0055 1.5e-05 5.0e-01 0.30 37 0 14
cccggccc cccggccc|gggccggg 0.0000141122445 3 0.05 1.6e-05 5.3e-01 0.28 38 0 21
ccccgcgc ccccgcgc|gcgcgggg 0.0000018180016 2 0.006 1.8e-05 5.8e-01 0.23 39 0 14
cccgcggc cccgcggc|gccgcggg 0.0000019090701 2 0.0063 2e-05 6.4e-01 0.19 40 0 14
gcccgcga gcccgcga|tcgcgggc 0.0000019318371 2 0.0063 2e-05 6.6e-01 0.18 41 0 14
ggcgcgga ggcgcgga|tccgcgcc 0.0000019318371 2 0.0063 2e-05 6.6e-01 0.18 42 0 14
ccgcgccc ccgcgccc|gggcgcgg 0.0000021481248 2 0.007 2.5e-05 8.1e-01 0.09 43 0 14
ccgtgcgc ccgtgcgc|gcgcacgg 0.0000021936590 2 0.0072 2.6e-05 8.5e-01 0.07 44 0 14
cgcacggc cgcacggc|gccgtgcg 0.0000022847275 2 0.0075 2.8e-05 9.2e-01 0.04 45 0 14
atcgcgcc atcgcgcc|ggcgcgat 0.0000022961110 2 0.0075 2.8e-05 9.3e-01 0.03 46 0 14
acttttcc acttttcc|ggaaaagt 0.0000508583705 4 0.17 2.8e-05 9.3e-01 0.03 47 0 28
cgcgggga cgcgggga|tccccgcg 0.0000023188781 2 0.0076 2.9e-05 9.5e-01 0.02 48 0 14
gggcgcta gggcgcta|tagcgccc 0.0000023188781 2 0.0076 2.9e-05 9.5e-01 0.02 49 0 14
gggcgcga gggcgcga|tcgcgccc 0.0000023530288 2 0.0077 3e-05 9.8e-01 0.01 50 0 14
; Host name rsat
; Job started 2026-04-30.003957
; Job done 2026-04-30.004000
; Seconds 2.22
; user 2.22
; system 0.05
; cuser 0.14
; csystem 0.02