; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/05/11/tmp_sequence_2026-05-11.134158_jt9VCY.fasta.purged -format fasta -lth occ_sig 0 -uth rank 50 -return freq,mseq,occ,proba,rank,ratio,zscore -1str -noov -quick_if_possible -seqtype dna -markov 2 -pseudo 0.01 -l 6 -o $RSAT/public_html/tmp/www-data/2026/05/11/oligo-analysis_2026-05-11.134158_qgrcwl_6nt.tab
; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42.
; Program version 1.169
; Slow counting mode
; Detection of over-represented words (right-tail test)
; Oligomer length 6
; Input file $RSAT/public_html/tmp/www-data/2026/05/11/tmp_sequence_2026-05-11.134158_jt9VCY.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/05/11/oligo-analysis_2026-05-11.134158_qgrcwl_6nt.tab
; Discard overlapping matches
; Counted on a single strand
; Background model Markov
; Background estimation method Markov model estimated from input sequences
; Markov chain order 2
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 2.44140625e-06
; Sequence type DNA
; Nb of sequences 500
; Sum of sequence lengths 100000
; discarded residues 320 (other letters than ACGT)
; discarded occurrences 320 (contain discarded residues)
; nb possible positions 97180
; total oligo occurrences 97180
; total overlapping occurrences 733
; total non overlapping occ 96447
; alphabet size 4
; nb possible oligomers 4096
; oligomers tested for significance 4093
;
; column headers
; 1 seq oligomer sequence
; 2 id oligomer identifier
; 3 obs_freq observed relative frequency
; 4 exp_freq expected relative frequency
; 5 occ observed occurrences
; 6 exp_occ expected occurrences
; 7 occ_P occurrence probability (binomial)
; 8 occ_E E-value for occurrences (binomial)
; 9 occ_sig occurrence significance (binomial)
; 10 rank rank
; 11 ovl_occ number of overlapping occurrences (discarded from the count)
; 12 forbocc forbidden positions (to avoid self-overlap)
; 13 zscore z-score (Gaussian approximation)
; 14 exp_var estimation of the variance on occurrences
; 15 ratio observed/expected ratio
; 16 ms number of matching sequences
; 17 exp_ms expected number of matching sequences
; 18 ms_P matching sequence probability (binomial)
; 19 ms_E E-value for matching sequences (binomial)
; 20 ms_sig matching sequenc significance (binomial)
; 21 ms_freq proportion of matching sequences (sequences with at least one occurrence)
; 22 exp_msf expected proportion matching sequences
; 23 ms_rati observed/expected numbers of matching sequences
#seq id obs_freq exp_freq occ exp_occ occ_P occ_E occ_sig rank ovl_occ forbocc zscore exp_var ratio ms exp_ms ms_P ms_E ms_sig ms_freq exp_msf ms_rati
tttctt tttctt 0.0018522329697 0.0012367670946 180 120.19 2.1e-07 8.8e-04 3.06 1 8 885 5.46 120.189 1.4976 137 106.89 0.00083 3.4 -0.5 0.27400 0.21379 1.28165
atcaag atcaag 0.0006688619057 0.0003542159453 65 34.42 2.2e-06 9.0e-03 2.05 2 0 318 5.21 34.423 1.8883 63 33.27 1.1e-06 0.0044 2.4 0.12600 0.06654 1.89359
tatata tatata 0.0015126569253 0.0010201723903 147 99.14 4.2e-06 1.7e-02 1.77 3 35 729 4.81 99.140 1.4827 121 89.97 0.00030 1.2 -0.1 0.24200 0.17994 1.34487
tccttt tccttt 0.0009158263017 0.0005641017323 89 54.82 1.4e-05 5.6e-02 1.25 4 0 441 4.62 54.819 1.6235 79 51.93 0.00012 0.5 0.3 0.15800 0.10387 1.52113
tctttt tctttt 0.0017287507718 0.0012450307404 168 120.99 3e-05 1.2e-01 0.91 5 4 825 4.27 120.992 1.3885 134 107.52 0.00286 12 -1.1 0.26800 0.21505 1.24622
ttcttt ttcttt 0.0017184605886 0.0012367670946 167 120.19 3.1e-05 1.3e-01 0.90 6 5 809 4.27 120.189 1.3895 135 106.89 0.00166 6.8 -0.8 0.27000 0.21379 1.26294
aaggaa aaggaa 0.0008849557522 0.0005573756181 86 54.17 4e-05 1.6e-01 0.79 7 0 409 4.33 54.166 1.5877 78 51.35 0.00014 0.58 0.2 0.15600 0.10270 1.51903
aagaaa aagaaa 0.0016155587569 0.0011752686536 157 114.21 8.5e-05 3.5e-01 0.46 8 8 778 4.00 114.213 1.3746 132 102.16 0.00078 3.2 -0.5 0.26400 0.20432 1.29208
tattat tattat 0.0009569870344 0.0006356992621 93 61.78 0.00013 5.2e-01 0.29 9 2 449 3.97 61.777 1.5054 85 58.13 0.00024 0.98 0.0 0.17000 0.11626 1.46222
aaaggg aaaggg 0.0004939287919 0.0002824531653 48 27.45 0.00024 9.8e-01 0.01 10 0 240 3.92 27.449 1.7487 45 26.71 0.00054 2.2 -0.3 0.09000 0.05343 1.68460
; Host name rsat
; Job started 2026-05-11.134158
; Job done 2026-05-11.134159
; Seconds 0.59
; user 0.59
; system 0.02
; cuser 0
; csystem 0
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/05/11/tmp_sequence_2026-05-11.134158_jt9VCY.fasta.purged -format fasta -lth occ_sig 0 -uth rank 50 -return freq,mseq,occ,proba,rank,ratio,zscore -1str -noov -quick_if_possible -seqtype dna -markov 2 -pseudo 0.01 -l 7 -o $RSAT/public_html/tmp/www-data/2026/05/11/oligo-analysis_2026-05-11.134158_qgrcwl_7nt.tab
; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42.
; Program version 1.169
; Slow counting mode
; Detection of over-represented words (right-tail test)
; Oligomer length 7
; Input file $RSAT/public_html/tmp/www-data/2026/05/11/tmp_sequence_2026-05-11.134158_jt9VCY.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/05/11/oligo-analysis_2026-05-11.134158_qgrcwl_7nt.tab
; Discard overlapping matches
; Counted on a single strand
; Background model Markov
; Background estimation method Markov model estimated from input sequences
; Markov chain order 2
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 6.103515625e-07
; Sequence type DNA
; Nb of sequences 500
; Sum of sequence lengths 100000
; discarded residues 320 (other letters than ACGT)
; discarded occurrences 320 (contain discarded residues)
; nb possible positions 96680
; total oligo occurrences 96680
; total overlapping occurrences 434
; total non overlapping occ 96246
; alphabet size 4
; nb possible oligomers 16384
; oligomers tested for significance 15396
;
; column headers
; 1 seq oligomer sequence
; 2 id oligomer identifier
; 3 obs_freq observed relative frequency
; 4 exp_freq expected relative frequency
; 5 occ observed occurrences
; 6 exp_occ expected occurrences
; 7 occ_P occurrence probability (binomial)
; 8 occ_E E-value for occurrences (binomial)
; 9 occ_sig occurrence significance (binomial)
; 10 rank rank
; 11 ovl_occ number of overlapping occurrences (discarded from the count)
; 12 forbocc forbidden positions (to avoid self-overlap)
; 13 zscore z-score (Gaussian approximation)
; 14 exp_var estimation of the variance on occurrences
; 15 ratio observed/expected ratio
; 16 ms number of matching sequences
; 17 exp_ms expected number of matching sequences
; 18 ms_P matching sequence probability (binomial)
; 19 ms_E E-value for matching sequences (binomial)
; 20 ms_sig matching sequenc significance (binomial)
; 21 ms_freq proportion of matching sequences (sequences with at least one occurrence)
; 22 exp_msf expected proportion matching sequences
; 23 ms_rati observed/expected numbers of matching sequences
#seq id obs_freq exp_freq occ exp_occ occ_P occ_E occ_sig rank ovl_occ forbocc zscore exp_var ratio ms exp_ms ms_P ms_E ms_sig ms_freq exp_msf ms_rati
ttttctt ttttctt 0.0009309060819 0.0004906926829 90 47.44 2.4e-08 3.8e-04 3.42 1 2 529 6.18 47.440 1.8971 74 45.27 2.2e-05 0.35 0.5 0.14800 0.09054 1.63465
tttcttt tttcttt 0.0009102192801 0.0004906926829 88 47.44 8.9e-08 1.4e-03 2.86 2 1 510 5.89 47.440 1.8550 77 45.27 3.5e-06 0.058 1.2 0.15400 0.09054 1.70092
atatata atatata 0.0006930078610 0.0003615487579 67 34.95 9.5e-07 1.5e-02 1.84 3 20 402 5.42 34.955 1.9168 59 33.77 2.6e-05 0.43 0.4 0.11800 0.06753 1.74729
gaaaatg gaaaatg 0.0003206454282 0.0001274808789 31 12.32 5.7e-06 8.7e-02 1.06 4 0 177 5.32 12.325 2.5152 30 12.17 8.4e-06 0.14 0.9 0.06000 0.02435 2.46407
tcctttt tcctttt 0.0004654530410 0.0002236145429 45 21.62 7.4e-06 1.1e-01 0.94 5 0 270 5.03 21.619 2.0815 40 21.16 0.00012 1.9 -0.3 0.08000 0.04232 1.89030
ttctttt ttctttt 0.0008274720728 0.0004906926829 80 47.44 1e-05 1.6e-01 0.81 6 2 475 4.73 47.440 1.6863 71 45.27 0.00012 1.9 -0.3 0.14200 0.09054 1.56838
tcttgtt tcttgtt 0.0003309888291 0.0001391690580 32 13.45 1.2e-05 1.9e-01 0.73 7 0 192 5.06 13.455 2.3783 31 13.28 1.7e-05 0.27 0.6 0.06200 0.02655 2.33498
tatataa tatataa 0.0005688870501 0.0003012466997 55 29.12 1.2e-05 1.9e-01 0.72 8 0 330 4.79 29.125 1.8884 53 28.30 1.1e-05 0.18 0.7 0.10600 0.05659 1.87301
tatatat tatatat 0.0006206040546 0.0003426965616 60 33.13 1.7e-05 2.6e-01 0.58 9 19 357 4.67 33.132 1.8109 55 32.06 8.1e-05 1.3 -0.1 0.11000 0.06413 1.71535
ttattat ttattat 0.0003930492346 0.0001865862821 38 18.04 2.8e-05 4.3e-01 0.37 10 2 224 4.70 18.039 2.1065 34 17.72 0.00029 4.7 -0.7 0.06800 0.03544 1.91882
ttttttc ttttttc 0.0009102192801 0.0005785421589 88 55.93 4.5e-05 6.9e-01 0.16 11 0 516 4.29 55.933 1.5733 73 52.93 0.00318 52 -1.7 0.14600 0.10587 1.37911
ctctttt ctctttt 0.0004447662391 0.0002289489701 43 22.13 5.5e-05 8.4e-01 0.07 12 0 258 4.43 22.135 1.9426 40 21.65 0.00018 3 -0.5 0.08000 0.04331 1.84720
; Host name rsat
; Job started 2026-05-11.134159
; Job done 2026-05-11.134200
; Seconds 1.15
; user 1.15
; system 0.04
; cuser 0
; csystem 0
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/05/11/tmp_sequence_2026-05-11.134158_jt9VCY.fasta.purged -format fasta -lth occ_sig 0 -uth rank 50 -return freq,mseq,occ,proba,rank,ratio,zscore -1str -noov -quick_if_possible -seqtype dna -markov 2 -pseudo 0.01 -l 8 -o $RSAT/public_html/tmp/www-data/2026/05/11/oligo-analysis_2026-05-11.134158_qgrcwl_8nt.tab
; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42.
; Program version 1.169
; Slow counting mode
; Detection of over-represented words (right-tail test)
; Oligomer length 8
; Input file $RSAT/public_html/tmp/www-data/2026/05/11/tmp_sequence_2026-05-11.134158_jt9VCY.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/05/11/oligo-analysis_2026-05-11.134158_qgrcwl_8nt.tab
; Discard overlapping matches
; Counted on a single strand
; Background model Markov
; Background estimation method Markov model estimated from input sequences
; Markov chain order 2
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 1.52587890625e-07
; Sequence type DNA
; Nb of sequences 500
; Sum of sequence lengths 100000
; discarded residues 320 (other letters than ACGT)
; discarded occurrences 320 (contain discarded residues)
; nb possible positions 96180
; total oligo occurrences 96180
; total overlapping occurrences 247
; total non overlapping occ 95933
; alphabet size 4
; nb possible oligomers 65536
; oligomers tested for significance 41529
;
; column headers
; 1 seq oligomer sequence
; 2 id oligomer identifier
; 3 obs_freq observed relative frequency
; 4 exp_freq expected relative frequency
; 5 occ observed occurrences
; 6 exp_occ expected occurrences
; 7 occ_P occurrence probability (binomial)
; 8 occ_E E-value for occurrences (binomial)
; 9 occ_sig occurrence significance (binomial)
; 10 rank rank
; 11 ovl_occ number of overlapping occurrences (discarded from the count)
; 12 forbocc forbidden positions (to avoid self-overlap)
; 13 zscore z-score (Gaussian approximation)
; 14 exp_var estimation of the variance on occurrences
; 15 ratio observed/expected ratio
; 16 ms number of matching sequences
; 17 exp_ms expected number of matching sequences
; 18 ms_P matching sequence probability (binomial)
; 19 ms_E E-value for matching sequences (binomial)
; 20 ms_sig matching sequenc significance (binomial)
; 21 ms_freq proportion of matching sequences (sequences with at least one occurrence)
; 22 exp_msf expected proportion matching sequences
; 23 ms_rati observed/expected numbers of matching sequences
#seq id obs_freq exp_freq occ exp_occ occ_P occ_E occ_sig rank ovl_occ forbocc zscore exp_var ratio ms exp_ms ms_P ms_E ms_sig ms_freq exp_msf ms_rati
catatata catatata 0.0002911208151 0.0000703856513 28 6.77 8.8e-10 3.7e-05 4.44 1 0 196 8.16 6.770 4.1361 26 6.72 9e-09 0.00059 3.2 0.05200 0.01345 3.86657
ttcttgtt ttcttgtt 0.0002079434394 0.0000548007102 20 5.27 7.7e-07 3.2e-02 1.50 2 0 140 6.42 5.271 3.7945 20 5.24 5.7e-07 0.038 1.4 0.04000 0.01049 3.81447
gaaaatga gaaaatga 0.0001663547515 0.0000370307679 16 3.56 1.1e-06 4.8e-02 1.32 3 0 97 6.59 3.562 4.4923 15 3.55 4.4e-06 0.29 0.5 0.03000 0.00710 4.22651
cttttctt cttttctt 0.0002911208151 0.0001006401852 28 9.68 1.2e-06 5.1e-02 1.29 4 0 194 5.89 9.680 2.8927 28 9.59 7.3e-07 0.048 1.3 0.05600 0.01917 2.92063
tttctttt tttctttt 0.0004366812227 0.0001947371240 42 18.73 2.5e-06 1.1e-01 0.98 5 1 294 5.38 18.730 2.2424 39 18.39 1.2e-05 0.8 0.1 0.07800 0.03677 2.12128
ttttcttt ttttcttt 0.0004366812227 0.0001947371240 42 18.73 2.5e-06 1.1e-01 0.98 6 0 280 5.38 18.730 2.2424 37 18.39 6.1e-05 4 -0.6 0.07400 0.03677 2.01250
tttttttc tttttttc 0.0004782699106 0.0002296172828 46 22.08 5.8e-06 2.4e-01 0.62 7 0 318 5.09 22.085 2.0829 39 21.61 0.00035 23 -1.4 0.07800 0.04321 1.80502
ttgttttc ttgttttc 0.0002079434394 0.0000645966334 20 6.21 8.5e-06 3.5e-01 0.45 8 0 140 5.53 6.213 3.2191 18 6.17 7.1e-05 4.6 -0.7 0.03600 0.01235 2.91514
gctgccgg gctgccgg 0.0000519858598 0.0000027494683 5 0.26 8.7e-06 3.6e-01 0.44 9 0 35 9.21 0.264 18.9076 5 0.26 8.5e-06 0.56 0.3 0.01000 0.00053 18.91258
tatatata tatatata 0.0002911208151 0.0001136856815 28 10.93 1.1e-05 4.7e-01 0.33 10 11 196 5.16 10.934 2.5608 25 10.82 0.00013 8.3 -0.9 0.05000 0.02163 2.31135
atatatat atatatat 0.0003015179871 0.0001214735002 29 11.68 1.4e-05 5.8e-01 0.23 11 11 203 5.07 11.683 2.4822 27 11.55 5.7e-05 3.7 -0.6 0.05400 0.02310 2.33795
tccttttc tccttttc 0.0001663547515 0.0000466399633 16 4.49 2e-05 8.1e-01 0.09 12 0 112 5.44 4.486 3.5668 15 4.47 6.1e-05 4 -0.6 0.03000 0.00893 3.35881
; Host name rsat
; Job started 2026-05-11.134200
; Job done 2026-05-11.134203
; Seconds 2.98
; user 2.99
; system 0.08
; cuser 0
; csystem 0