; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/05/16/tmp_sequence_2026-05-16.124457_fWnOqA.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 6 -o $RSAT/public_html/tmp/www-data/2026/05/16/oligo-analysis_2026-05-16.124457_ceJlAB_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/2026/05/16/tmp_sequence_2026-05-16.124457_fWnOqA.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/05/16/oligo-analysis_2026-05-16.124457_ceJlAB_6nt.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/6nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 4.80769230769231e-06
; Sequence type DNA
; Nb of sequences 498
; Sum of sequence lengths 249000
; 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 243215
; total overlapping occurrences 5539
; total non overlapping occ 237676
; alphabet size 4
; nb possible oligomers 2080
; oligomers tested for significance 2080
;
; 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
aacgtg aacgtg|cacgtt 0.0002922730311 122 71.09 2.6e-08 5.4e-05 4.27 1 0 610
acgtga acgtga|tcacgt 0.0002991013056 116 72.75 1.8e-06 3.8e-03 2.42 2 3 580
acgtgc acgtgc|gcacgt 0.0001205118008 58 29.31 1.9e-06 3.9e-03 2.40 3 1 290
tatata tatata|tatata 0.0018867755601 559 458.89 3.3e-06 6.8e-03 2.17 4 332 2795
acgttg acgttg|caacgt 0.0002647842051 104 64.40 3.5e-06 7.3e-03 2.14 5 4 520
atataa atataa|ttatat 0.0027383266698 775 666.00 2e-05 4.1e-02 1.38 6 76 3875
caacta caacta|tagttg 0.0006827147754 220 166.05 3.7e-05 7.6e-02 1.12 7 0 1100
cacgta cacgta|tacgtg 0.0002556463671 95 62.18 6.6e-05 1.4e-01 0.87 8 1 475
aataat aataat|attatt 0.0028732101965 801 698.81 8.1e-05 1.7e-01 0.77 9 66 4005
tataaa tataaa|tttata 0.0027829614940 774 676.86 0.00013 2.8e-01 0.55 10 66 3870
aaagac aaagac|gtcttt 0.0007922935200 245 192.70 0.00016 3.4e-01 0.47 11 0 1225
cgcacg cgcacg|cgtgcg 0.0000537855000 28 13.08 0.00023 4.7e-01 0.33 12 0 140
agcgaa agcgaa|ttcgct 0.0001793052532 69 43.61 0.00023 4.8e-01 0.31 13 0 345
cgttga cgttga|tcaacg 0.0003099964203 107 75.40 0.00035 7.3e-01 0.14 14 0 535
acatgg acatgg|ccatgt 0.0004047387300 134 98.44 0.00038 7.9e-01 0.10 15 0 670
atatag atatag|ctatat 0.0012114541838 354 294.64 0.00043 8.9e-01 0.05 16 11 1770
; Host name rsat
; Job started 2026-05-16.124458
; Job done 2026-05-16.124458
; Seconds 0.4
; user 0.4
; system 0.01
; cuser 0.14
; csystem 0.02
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/05/16/tmp_sequence_2026-05-16.124457_fWnOqA.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_2026-05-16.124457_ceJlAB_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_2026-05-16.124457_fWnOqA.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/05/16/oligo-analysis_2026-05-16.124457_ceJlAB_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 498
; Sum of sequence lengths 249000
; 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 242336
; total overlapping occurrences 4452
; total non overlapping occ 237884
; 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
tatataa tatataa|ttatata 0.0009847318348 336 238.64 1.6e-09 1.3e-05 4.88 1 77 2016
caacgtg caacgtg|cacgttg 0.0000507724909 35 12.30 9.4e-08 7.7e-04 3.11 2 0 210
aacgtga aacgtga|tcacgtt 0.0001002991127 49 24.31 6.9e-06 5.7e-02 1.24 3 0 294
acgtgcg acgtgcg|cgcacgt 0.0000219071274 18 5.31 1.2e-05 9.8e-02 1.01 4 0 108
ctatata ctatata|tatatag 0.0004961597638 166 120.24 4.5e-05 3.7e-01 0.44 5 13 996
aacgtgc aacgtgc|gcacgtt 0.0000330808166 21 8.02 9.7e-05 7.9e-01 0.10 6 0 126
acacaca acacaca|tgtgtgt 0.0002339303942 87 56.69 0.00011 9.1e-01 0.04 7 33 522
; Host name rsat
; Job started 2026-05-16.124458
; Job done 2026-05-16.124459
; Seconds 0.8
; user 0.8
; system 0.03
; cuser 0.16
; csystem 0.02
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/05/16/tmp_sequence_2026-05-16.124457_fWnOqA.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 8 -o $RSAT/public_html/tmp/www-data/2026/05/16/oligo-analysis_2026-05-16.124457_ceJlAB_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/2026/05/16/tmp_sequence_2026-05-16.124457_fWnOqA.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/05/16/oligo-analysis_2026-05-16.124457_ceJlAB_8nt.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/8nt_upstream-noorf_Arabidopsis_thaliana.TAIR10.60-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 3.03988326848249e-07
; Sequence type DNA
; Nb of sequences 498
; Sum of sequence lengths 249000
; 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 241920
; total overlapping occurrences 2168
; total non overlapping occ 239752
; alphabet size 4
; nb possible oligomers 32896
; oligomers tested for significance 32896
;
; 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
acaacgtg acaacgtg|cacgttgt 0.0000153770788 16 3.72 2e-06 6.5e-02 1.18 1 0 112
tatataaa tatataaa|tttatata 0.0004578314173 161 110.76 4.5e-06 1.5e-01 0.83 2 7 1127
caacgtga caacgtga|tcacgttg 0.0000166855941 16 4.04 5.5e-06 1.8e-01 0.74 3 0 112
; Host name rsat
; Job started 2026-05-16.124459
; Job done 2026-05-16.124503
; Seconds 3.78
; user 3.79
; system 0.14
; cuser 0.25
; csystem 0.06