; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/05/16/tmp_sequence_2026-05-16.130401_3KrsvU.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 Arabidopsis_thaliana.TAIR10.60 -pseudo 0.01 -l 7 -o $RSAT/public_html/tmp/www-data/2026/05/16/oligo-analysis_2026-05-16.130401_1F38HQ_7nt.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 7
; Input file $RSAT/public_html/tmp/www-data/2026/05/16/tmp_sequence_2026-05-16.130401_3KrsvU.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/05/16/oligo-analysis_2026-05-16.130401_1F38HQ_7nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Arabidopsis_thaliana.TAIR10.60
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Arabidopsis_thaliana.TAIR10.60/oligo-frequencies/7nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 1.220703125e-06
; Sequence type DNA
; Nb of sequences 1012
; Sum of sequence lengths 506000
; 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 492706
; total overlapping occurrences 8442
; total non overlapping occ 484264
; alphabet size 4
; nb possible oligomers 8192
; oligomers tested for significance 8192
;
; 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
acacgtg acacgtg|cacgtgt 0.0001028912072 151 50.70 4.7e-30 3.8e-26 25.42 1 52 906
acgtgtc acgtgtc|gacacgt 0.0000900062325 135 44.35 6.4e-28 5.2e-24 23.28 2 9 810
acgtggc acgtggc|gccacgt 0.0000675330245 112 33.27 7.5e-27 6.2e-23 22.21 3 3 672
cacgtgg cacgtgg|ccacgtg 0.0000702509489 106 34.61 1.7e-22 1.4e-18 17.85 4 19 636
cgtgtca cgtgtca|tgacacg 0.0000662998922 89 32.67 3.5e-16 2.9e-12 11.54 5 2 534
aacacgt aacacgt|acgtgtt 0.0001145682157 115 56.45 5.5e-12 4.5e-08 7.34 6 5 690
acacgta acacgta|tacgtgt 0.0000990659804 100 48.81 9.2e-11 7.6e-07 6.12 7 0 600
cgtggca cgtggca|tgccacg 0.0000463432808 58 22.83 5.2e-10 4.3e-06 5.37 8 0 348
cgccacg cgccacg|cgtggcg 0.0000221084552 35 10.89 5.1e-09 4.2e-05 4.38 9 0 210
acgtgga acgtgga|tccacgt 0.0000836392430 82 41.21 1.4e-08 1.2e-04 3.94 10 1 492
acacaca acacaca|tgtgtgt 0.0002339303942 177 115.26 5.7e-08 4.7e-04 3.33 11 48 1062
ccacgta ccacgta|tacgtgg 0.0000538679048 58 26.54 8.8e-08 7.2e-04 3.14 12 0 348
cacgtca cacgtca|tgacgtg 0.0000734973585 72 36.21 1e-07 8.5e-04 3.07 13 0 432
acgtgta acgtgta|tacacgt 0.0000972036988 87 47.89 2.5e-07 2.0e-03 2.69 14 0 522
atgcatg atgcatg|catgcat 0.0002103750497 159 103.65 2.7e-07 2.2e-03 2.65 15 56 954
agagaga agagaga|tctctct 0.0003787101987 257 186.59 6.1e-07 5.0e-03 2.30 16 101 1542
atacgtg atacgtg|cacgtat 0.0000779265686 72 38.39 8.4e-07 6.9e-03 2.16 17 0 432
gtgtgta gtgtgta|tacacac 0.0001378467345 111 67.92 1e-06 8.3e-03 2.08 18 0 666
cacgtac cacgtac|gtacgtg 0.0000502188397 52 24.74 1.2e-06 9.7e-03 2.01 19 0 312
cacgtag cacgtag|ctacgtg 0.0000409829300 43 20.19 6.8e-06 5.6e-02 1.25 20 0 258
agacacg agacacg|cgtgtct 0.0000551513690 52 27.17 1.5e-05 1.2e-01 0.92 21 1 312
caacacg caacacg|cgtgttg 0.0000554785266 52 27.33 1.7e-05 1.4e-01 0.85 22 0 312
gcatgca gcatgca|tgcatgc 0.0000829597619 69 40.87 3.8e-05 3.1e-01 0.51 23 35 414
acgtgat acgtgat|atcacgt 0.0000860048439 70 42.38 6.3e-05 5.2e-01 0.29 24 0 420
cacgtga cacgtga|tcacgtg 0.0000751834783 63 37.04 6.4e-05 5.3e-01 0.28 25 14 378
acgtaga acgtaga|tctacgt 0.0000737993502 62 36.36 6.8e-05 5.6e-01 0.25 26 2 372
gtgacac gtgacac|gtgtcac 0.0000633303082 55 31.20 7.4e-05 6.1e-01 0.22 27 0 330
acatgca acatgca|tgcatgt 0.0002215990706 151 109.18 8.7e-05 7.2e-01 0.15 28 5 906
; Host name rsat
; Job started 2026-05-16.130404
; Job done 2026-05-16.130405
; Seconds 0.88
; user 0.88
; system 0.02
; cuser 0.21
; csystem 0.03