; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/05/16/tmp_sequence_2026-05-16.124744_SQuess.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_2026-05-16.124744_M92ZkP_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_2026-05-16.124744_SQuess.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/05/16/oligo-analysis_2026-05-16.124744_M92ZkP_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 440
; Sum of sequence lengths 220000
; 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 216034
; total overlapping occurrences 4521
; total non overlapping occ 211513
; 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
acgtgg acgtgg|ccacgt 0.0002373957950 90 51.29 6.4e-07 1.3e-03 2.88 1 8 450
acgtca acgtca|tgacgt 0.0002638553590 89 57.00 5.3e-05 1.1e-01 0.96 2 2 445
aagtct aagtct|agactt 0.0005953781311 175 128.62 5.9e-05 1.2e-01 0.91 3 0 875
cacgtc cacgtc|gacgtg 0.0001751379974 64 37.84 6.6e-05 1.4e-01 0.86 4 0 320
acgttg acgttg|caacgt 0.0002647842051 88 57.20 9.4e-05 2.0e-01 0.71 5 7 440
aaagac aaagac|gtcttt 0.0007922935200 221 171.16 0.00015 3.0e-01 0.52 6 0 1105
gagaca gagaca|tgtctc 0.0004481183567 133 96.81 0.00028 5.8e-01 0.23 7 0 665
aagact aagact|agtctt 0.0006139048467 174 132.62 0.00033 7.0e-01 0.16 8 0 870
aacgtg aacgtg|cacgtt 0.0002922730311 92 63.14 0.00039 8.0e-01 0.09 9 0 460
aaccac aaccac|gtggtt 0.0004496748016 132 97.15 0.00045 9.3e-01 0.03 10 0 660
; Host name rsat
; Job started 2026-05-16.124745
; Job done 2026-05-16.124746
; Seconds 0.35
; user 0.35
; system 0.02
; cuser 0.11
; csystem 0.01
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/05/16/tmp_sequence_2026-05-16.124744_SQuess.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_2026-05-16.124744_M92ZkP_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_2026-05-16.124744_SQuess.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/05/16/oligo-analysis_2026-05-16.124744_M92ZkP_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 440
; Sum of sequence lengths 220000
; 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 215308
; total overlapping occurrences 3623
; total non overlapping occ 211685
; 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
aaagacc aaagacc|ggtcttt 0.0001126052703 53 24.24 3e-07 2.5e-03 2.61 1 0 318
aacgtgg aacgtgg|ccacgtt 0.0000602852262 30 12.98 3.7e-05 3.0e-01 0.52 2 0 180
acgtgga acgtgga|tccacgt 0.0000836392430 37 18.01 5.8e-05 4.8e-01 0.32 3 1 222
gagccac gagccac|gtggctc 0.0000398001295 22 8.57 8.9e-05 7.3e-01 0.14 4 0 132
aaacgtg aaacgtg|cacgttt 0.0001197020728 47 25.77 0.00011 9.0e-01 0.04 5 0 282
; Host name rsat
; Job started 2026-05-16.124746
; Job done 2026-05-16.124747
; Seconds 0.8
; user 0.8
; system 0.03
; cuser 0.13
; csystem 0.02
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/05/16/tmp_sequence_2026-05-16.124744_SQuess.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_2026-05-16.124744_M92ZkP_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_2026-05-16.124744_SQuess.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/05/16/oligo-analysis_2026-05-16.124744_M92ZkP_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 440
; Sum of sequence lengths 220000
; 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 214942
; total overlapping occurrences 1772
; total non overlapping occ 213170
; 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
aaacgtgg aaacgtgg|ccacgttt 0.0000235552998 17 5.06 2.3e-05 7.6e-01 0.12 1 0 119
; Host name rsat
; Job started 2026-05-16.124747
; Job done 2026-05-16.124751
; Seconds 3.86
; user 3.86
; system 0.12
; cuser 0.27
; csystem 0.02