; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/04/21/tmp_sequence_2026-04-21.143933_X9Nc0W.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 Saccharomyces_cerevisiae -pseudo 0.01 -l 6 -o $RSAT/public_html/tmp/www-data/2026/04/21/oligo-analysis_2026-04-21.143933_QsMNau_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/2026/04/21/tmp_sequence_2026-04-21.143933_X9Nc0W.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/04/21/oligo-analysis_2026-04-21.143933_QsMNau_6nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Saccharomyces_cerevisiae
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Saccharomyces_cerevisiae/oligo-frequencies/6nt_upstream-noorf_Saccharomyces_cerevisiae-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 4.80769230769231e-06
; Sequence type DNA
; Nb of sequences 19
; Sum of sequence lengths 9485
; 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 9376
; total overlapping occurrences 207
; total non overlapping occ 9169
; alphabet size 4
; nb possible oligomers 2080
; oligomers tested for significance 2080
; Sequences:
; MET8 463
; MET32 547
; MET18 568
; MET30 177
; MET28 489
; MET6 687
; MET10 338
; MET13 380
; MET3 800
; MET14 800
; MET1 702
; MET17 800
; MET2 481
; MET4 800
; MET22 215
; MET7 250
; MET31 161
; MET12 384
; MET16 443
;
; 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
cacgtg cacgtg|cacgtg 0.0001566968513 17 1.47 4.8e-13 1.0e-09 9.00 1 0 85
acgtga acgtga|tcacgt 0.0003343411284 18 3.13 6.9e-09 1.4e-05 4.85 2 4 90
ccacag ccacag|ctgtgg 0.0002366037566 14 2.22 1e-07 2.1e-04 3.68 3 0 70
gccaca gccaca|tgtggc 0.0002894347684 15 2.71 1.9e-07 4.0e-04 3.40 4 0 75
actgtg actgtg|cacagt 0.0003762757441 16 3.53 1e-06 2.1e-03 2.68 5 0 80
cgtgca cgtgca|tgcacg 0.0002326414307 11 2.18 1.8e-05 3.8e-02 1.42 6 0 55
aactgt aactgt|acagtt 0.0006169870416 17 5.78 0.00011 2.4e-01 0.63 7 0 85
agtcat agtcat|atgact 0.0005040607539 15 4.73 0.00012 2.6e-01 0.59 8 0 75
tagtca tagtca|tgacta 0.0004611355567 14 4.32 0.00017 3.5e-01 0.46 9 0 70
agccac agccac|gtggct 0.0002597173242 10 2.44 0.00023 4.7e-01 0.33 10 0 50
cgtgac cgtgac|gtcacg 0.0001692442165 8 1.59 0.00025 5.1e-01 0.29 11 1 40
cgcgca cgcgca|tgcgcg 0.0001715555733 8 1.61 0.00027 5.6e-01 0.25 12 0 40
acgtgc acgtgc|gcacgt 0.0002276885234 9 2.13 0.00038 7.9e-01 0.10 13 0 45
gactca gactca|tgagtc 0.0002319810431 9 2.18 0.00043 9.0e-01 0.05 14 0 45
; Host name rsat
; Job started 2026-04-21.143934
; Job done 2026-04-21.143934
; Seconds 0.28
; user 0.28
; system 0.04
; cuser 0.07
; csystem 0.02
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/04/21/tmp_sequence_2026-04-21.143933_X9Nc0W.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 Saccharomyces_cerevisiae -pseudo 0.01 -l 7 -o $RSAT/public_html/tmp/www-data/2026/04/21/oligo-analysis_2026-04-21.143933_QsMNau_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/2026/04/21/tmp_sequence_2026-04-21.143933_X9Nc0W.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/04/21/oligo-analysis_2026-04-21.143933_QsMNau_7nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Saccharomyces_cerevisiae
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Saccharomyces_cerevisiae/oligo-frequencies/7nt_upstream-noorf_Saccharomyces_cerevisiae-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 1.220703125e-06
; Sequence type DNA
; Nb of sequences 19
; Sum of sequence lengths 9485
; 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 9315
; total overlapping occurrences 149
; total non overlapping occ 9166
; alphabet size 4
; nb possible oligomers 8192
; oligomers tested for significance 8192
; Sequences:
; MET8 463
; MET32 547
; MET18 568
; MET30 177
; MET28 489
; MET6 687
; MET10 338
; MET13 380
; MET3 800
; MET14 800
; MET1 702
; MET17 800
; MET2 481
; MET4 800
; MET22 215
; MET7 250
; MET31 161
; MET12 384
; MET16 443
;
; 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
cacgtga cacgtga|tcacgtg 0.0001115745941 17 1.04 2e-15 1.6e-11 10.78 1 4 102
aactgtg aactgtg|cacagtt 0.0001251617098 11 1.17 4.7e-08 3.8e-04 3.42 2 0 66
actgtgg actgtgg|ccacagt 0.0000810864320 9 0.76 1.1e-07 9.1e-04 3.04 3 0 54
acgtgac acgtgac|gtcacgt 0.0000747899638 8 0.70 7.4e-07 6.1e-03 2.22 4 1 48
cacgtgc cacgtgc|gcacgtg 0.0000668365302 7 0.62 4.2e-06 3.4e-02 1.47 5 0 42
ctgtggc ctgtggc|gccacag 0.0000684934956 7 0.64 4.9e-06 4.0e-02 1.40 6 0 42
agccaca agccaca|tgtggct 0.0000946735477 7 0.88 3.8e-05 3.1e-01 0.50 7 0 42
atgacta atgacta|tagtcat 0.0001692369875 9 1.58 4e-05 3.3e-01 0.48 8 0 54
tcatgaa tcatgaa|ttcatga 0.0001367604671 8 1.27 5.6e-05 4.6e-01 0.34 9 4 48
atgcgcg atgcgcg|cgcgcat 0.0000462901601 5 0.43 8.7e-05 7.1e-01 0.15 10 0 30
acgtgca acgtgca|tgcacgt 0.0000790980736 6 0.74 0.00012 9.7e-01 0.01 11 0 36
; Host name rsat
; Job started 2026-04-21.143934
; Job done 2026-04-21.143935
; Seconds 0.69
; user 0.69
; system 0.01
; cuser 0.12
; csystem 0.02
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/04/21/tmp_sequence_2026-04-21.143933_X9Nc0W.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 Saccharomyces_cerevisiae -pseudo 0.01 -l 8 -o $RSAT/public_html/tmp/www-data/2026/04/21/oligo-analysis_2026-04-21.143933_QsMNau_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/2026/04/21/tmp_sequence_2026-04-21.143933_X9Nc0W.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/04/21/oligo-analysis_2026-04-21.143933_QsMNau_8nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Saccharomyces_cerevisiae
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Saccharomyces_cerevisiae/oligo-frequencies/8nt_upstream-noorf_Saccharomyces_cerevisiae-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 3.03988326848249e-07
; Sequence type DNA
; Nb of sequences 19
; Sum of sequence lengths 9485
; 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 9329
; total overlapping occurrences 107
; total non overlapping occ 9222
; alphabet size 4
; nb possible oligomers 32896
; oligomers tested for significance 32896
; Sequences:
; MET8 463
; MET32 547
; MET18 568
; MET30 177
; MET28 489
; MET6 687
; MET10 338
; MET13 380
; MET3 800
; MET14 800
; MET1 702
; MET17 800
; MET2 481
; MET4 800
; MET22 215
; MET7 250
; MET31 161
; MET12 384
; MET16 443
;
; 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
aactgtgg aactgtgg|ccacagtt 0.0000334807653 8 0.31 1.7e-09 5.6e-05 4.25 1 0 56
gcacgtga gcacgtga|tcacgtgc 0.0000397843529 7 0.37 1.4e-07 4.6e-03 2.34 2 0 49
cacgtgac cacgtgac|gtcacgtg 0.0000434337984 7 0.41 2.5e-07 8.2e-03 2.09 3 1 49
cacgtgaa cacgtgaa|ttcacgtg 0.0000308266231 6 0.29 6.1e-07 2.0e-02 1.70 4 0 42
aaactgtg aaactgtg|cacagttt 0.0000557092058 7 0.52 1.3e-06 4.2e-02 1.37 5 0 49
actgtggc actgtggc|gccacagt 0.0000251865710 5 0.23 4.9e-06 1.6e-01 0.79 6 0 35
atcacgtg atcacgtg|cacgtgat 0.0000464197083 6 0.43 6.3e-06 2.1e-01 0.68 7 0 42
aagccaca aagccaca|tgtggctt 0.0000321536941 5 0.30 1.6e-05 5.2e-01 0.29 8 0 35
; Host name rsat
; Job started 2026-04-21.143935
; Job done 2026-04-21.143938
; Seconds 2.84
; user 2.84
; system 0.07
; cuser 0.13
; csystem 0.04