; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/05/16/tmp_sequence_2026-05-16.125221_V1BqtH.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_2026-05-16.125221_GFR1LJ_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_2026-05-16.125221_V1BqtH.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/05/16/oligo-analysis_2026-05-16.125221_GFR1LJ_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 486
; Sum of sequence lengths 243000
; 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 236480
; total overlapping occurrences 5068
; total non overlapping occ 231412
; 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
agaaga agaaga|tcttct 0.0013525885944 420 319.86 5e-08 1.0e-04 3.98 1 47 2100
aagaag aagaag|cttctt 0.0012397965441 375 293.19 2.5e-06 5.2e-03 2.28 2 37 1875
acagag acagag|ctctgt 0.0003910570769 136 92.48 1.3e-05 2.8e-02 1.55 3 0 680
ccttga ccttga|tcaagg 0.0003007581664 108 71.12 2.8e-05 5.9e-02 1.23 4 0 540
cagaga cagaga|tctctg 0.0004506789596 151 106.58 2.9e-05 6.1e-02 1.22 5 0 755
gaagaa gaagaa|ttcttc 0.0013322543944 387 315.05 4.9e-05 1.0e-01 1.00 6 51 1935
atctgc atctgc|gcagat 0.0002396802545 88 56.68 7e-05 1.5e-01 0.84 7 1 440
ctcttc ctcttc|gaagag 0.0005950517798 187 140.72 0.00011 2.3e-01 0.63 8 3 935
ctgaga ctgaga|tctcag 0.0002823569706 98 66.77 0.00020 4.2e-01 0.37 9 0 490
cagatc cagatc|gatctg 0.0002410107639 86 56.99 0.00020 4.3e-01 0.37 10 5 430
tctgca tctgca|tgcaga 0.0003074358173 105 72.70 0.00022 4.5e-01 0.34 11 5 525
acgaag acgaag|cttcgt 0.0002820306192 97 66.69 0.00029 6.1e-01 0.22 12 0 485
gaagac gaagac|gtcttc 0.0004224370152 136 99.90 0.00035 7.2e-01 0.14 13 0 680
cttcga cttcga|tcgaag 0.0002642068143 91 62.48 0.00042 8.7e-01 0.06 14 3 455
; Host name rsat
; Job started 2026-05-16.125222
; Job done 2026-05-16.125223
; Seconds 0.42
; user 0.42
; system 0.02
; cuser 0.11
; csystem 0.02
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/05/16/tmp_sequence_2026-05-16.125221_V1BqtH.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_2026-05-16.125221_GFR1LJ_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_2026-05-16.125221_V1BqtH.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/05/16/oligo-analysis_2026-05-16.125221_GFR1LJ_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 486
; Sum of sequence lengths 243000
; 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 235658
; total overlapping occurrences 4070
; total non overlapping occ 231588
; 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
acagaga acagaga|tctctgt 0.0001755705182 73 41.37 5.6e-06 4.6e-02 1.34 1 0 438
caacttg caacttg|caagttg 0.0001634405224 68 38.52 1.1e-05 9.1e-02 1.04 2 0 408
ctgtgcc ctgtgcc|ggcacag 0.0000164964447 15 3.89 1.4e-05 1.2e-01 0.93 3 0 90
acgtggg acgtggg|cccacgt 0.0000356980770 23 8.41 2.5e-05 2.0e-01 0.70 4 1 138
agaagag agaagag|ctcttct 0.0002637268983 95 62.15 6.5e-05 5.3e-01 0.28 5 2 570
ctgcaga ctgcaga|tctgcag 0.0000435498586 25 10.26 7e-05 5.7e-01 0.24 6 5 150
aagaaga aagaaga|tcttctt 0.0006334149443 198 149.27 8e-05 6.6e-01 0.18 7 32 1188
; Host name rsat
; Job started 2026-05-16.125223
; Job done 2026-05-16.125224
; Seconds 0.84
; user 0.84
; system 0.04
; cuser 0.14
; csystem 0.02
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/05/16/tmp_sequence_2026-05-16.125221_V1BqtH.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_2026-05-16.125221_GFR1LJ_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_2026-05-16.125221_V1BqtH.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/05/16/oligo-analysis_2026-05-16.125221_GFR1LJ_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 486
; Sum of sequence lengths 243000
; 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 235262
; total overlapping occurrences 2056
; total non overlapping occ 233206
; 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
ggcacaga ggcacaga|tctgtgcc 0.0000065446000 10 1.54 5.1e-06 1.7e-01 0.77 1 0 70
atgtggga atgtggga|tcccacat 0.0000313560644 22 7.38 1e-05 3.3e-01 0.48 2 0 154
aacagaga aacagaga|tctctgtt 0.0000768773007 38 18.09 2.9e-05 9.7e-01 0.01 3 0 266
; Host name rsat
; Job started 2026-05-16.125224
; Job done 2026-05-16.125228
; Seconds 4.02
; user 4.02
; system 0.15
; cuser 0.27
; csystem 0.03