; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/01/11/tmp_sequence_2026-01-11.092254_h65UZI.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 Oryza_sativa.IRGSP-1.0.60 -pseudo 0.01 -l 4 -o $RSAT/public_html/tmp/www-data/2026/01/11/oligo-analysis_2026-01-11.092254_jcmBZe_4nt.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 4
; Input file $RSAT/public_html/tmp/www-data/2026/01/11/tmp_sequence_2026-01-11.092254_h65UZI.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/01/11/oligo-analysis_2026-01-11.092254_jcmBZe_4nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Oryza_sativa.IRGSP-1.0.60
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.60/oligo-frequencies/4nt_upstream-noorf_Oryza_sativa.IRGSP-1.0.60-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 7.35294117647059e-05
; Sequence type DNA
; Nb of sequences 0
; Sum of sequence lengths 0
; 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 0
; total overlapping occurrences 0
; total non overlapping occ 0
; alphabet size 4
; nb possible oligomers 136
; oligomers tested for significance 136
; Sequences:
;
; 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
; Host name rsat
; Job started 2026-01-11.092255
; Job done 2026-01-11.092255
; Seconds 0.1
; user 0.1
; system 0
; cuser 0.1
; csystem 0.01
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/01/11/tmp_sequence_2026-01-11.092254_h65UZI.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 Oryza_sativa.IRGSP-1.0.60 -pseudo 0.01 -l 5 -o $RSAT/public_html/tmp/www-data/2026/01/11/oligo-analysis_2026-01-11.092254_jcmBZe_5nt.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 5
; Input file $RSAT/public_html/tmp/www-data/2026/01/11/tmp_sequence_2026-01-11.092254_h65UZI.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/01/11/oligo-analysis_2026-01-11.092254_jcmBZe_5nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Oryza_sativa.IRGSP-1.0.60
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.60/oligo-frequencies/5nt_upstream-noorf_Oryza_sativa.IRGSP-1.0.60-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 1.953125e-05
; Sequence type DNA
; Nb of sequences 0
; Sum of sequence lengths 0
; 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 0
; total overlapping occurrences 0
; total non overlapping occ 0
; alphabet size 4
; nb possible oligomers 512
; oligomers tested for significance 512
; Sequences:
;
; 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
; Host name rsat
; Job started 2026-01-11.092255
; Job done 2026-01-11.092256
; Seconds 0.11
; user 0.11
; system 0.01
; cuser 0.1
; csystem 0.01
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/01/11/tmp_sequence_2026-01-11.092254_h65UZI.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 Oryza_sativa.IRGSP-1.0.60 -pseudo 0.01 -l 6 -o $RSAT/public_html/tmp/www-data/2026/01/11/oligo-analysis_2026-01-11.092254_jcmBZe_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/2026/01/11/tmp_sequence_2026-01-11.092254_h65UZI.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/01/11/oligo-analysis_2026-01-11.092254_jcmBZe_6nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Oryza_sativa.IRGSP-1.0.60
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.60/oligo-frequencies/6nt_upstream-noorf_Oryza_sativa.IRGSP-1.0.60-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 4.80769230769231e-06
; Sequence type DNA
; Nb of sequences 0
; Sum of sequence lengths 0
; 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 0
; total overlapping occurrences 0
; total non overlapping occ 0
; alphabet size 4
; nb possible oligomers 2080
; oligomers tested for significance 2080
; Sequences:
;
; 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
; Host name rsat
; Job started 2026-01-11.092256
; Job done 2026-01-11.092256
; Seconds 0.24
; user 0.24
; system 0
; cuser 0.07
; csystem 0.01
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/01/11/tmp_sequence_2026-01-11.092254_h65UZI.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 Oryza_sativa.IRGSP-1.0.60 -pseudo 0.01 -l 7 -o $RSAT/public_html/tmp/www-data/2026/01/11/oligo-analysis_2026-01-11.092254_jcmBZe_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/2026/01/11/tmp_sequence_2026-01-11.092254_h65UZI.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/01/11/oligo-analysis_2026-01-11.092254_jcmBZe_7nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Oryza_sativa.IRGSP-1.0.60
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.60/oligo-frequencies/7nt_upstream-noorf_Oryza_sativa.IRGSP-1.0.60-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 1.220703125e-06
; Sequence type DNA
; Nb of sequences 0
; Sum of sequence lengths 0
; 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 0
; total overlapping occurrences 0
; total non overlapping occ 0
; alphabet size 4
; nb possible oligomers 8192
; oligomers tested for significance 8192
; Sequences:
;
; 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
; Host name rsat
; Job started 2026-01-11.092256
; Job done 2026-01-11.092257
; Seconds 0.51
; user 0.51
; system 0.02
; cuser 0.08
; csystem 0.01
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/01/11/tmp_sequence_2026-01-11.092254_h65UZI.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 Oryza_sativa.IRGSP-1.0.60 -pseudo 0.01 -l 8 -o $RSAT/public_html/tmp/www-data/2026/01/11/oligo-analysis_2026-01-11.092254_jcmBZe_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/2026/01/11/tmp_sequence_2026-01-11.092254_h65UZI.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/01/11/oligo-analysis_2026-01-11.092254_jcmBZe_8nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Oryza_sativa.IRGSP-1.0.60
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Oryza_sativa.IRGSP-1.0.60/oligo-frequencies/8nt_upstream-noorf_Oryza_sativa.IRGSP-1.0.60-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 3.03988326848249e-07
; Sequence type DNA
; Nb of sequences 0
; Sum of sequence lengths 0
; 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 0
; total overlapping occurrences 0
; total non overlapping occ 0
; alphabet size 4
; nb possible oligomers 32896
; oligomers tested for significance 32896
; Sequences:
;
; 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
; Host name rsat
; Job started 2026-01-11.092257
; Job done 2026-01-11.092259
; Seconds 2.03
; user 2.03
; system 0.06
; cuser 0.13
; csystem 0.01