; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/04/30/tmp_sequence_2026-04-30.111533_YCQqp0.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 Plasmodium_berghei.PBANKA01.34 -pseudo 0.01 -l 6 -o $RSAT/public_html/tmp/www-data/2026/04/30/oligo-analysis_2026-04-30.111533_Jw8Wrp_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/2026/04/30/tmp_sequence_2026-04-30.111533_YCQqp0.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/04/30/oligo-analysis_2026-04-30.111533_Jw8Wrp_6nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Plasmodium_berghei.PBANKA01.34
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/oligo-frequencies/6nt_upstream-noorf_Plasmodium_berghei.PBANKA01.34-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 4.80769230769231e-06
; Sequence type DNA
; Nb of sequences 7
; Sum of sequence lengths 590
; 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 561
; total overlapping occurrences 24
; total non overlapping occ 537
; alphabet size 4
; nb possible oligomers 2080
; oligomers tested for significance 2080
; Sequences:
; gp11_Padj 80
; gp12 85
; gp13 85
; gp14 85
; gp15 85
; gp16 85
; gp17 85
;
; 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
cttcta cttcta|tagaag 0.0002281007525 4 0.13 1e-05 2.1e-02 1.68 1 0 20
tatcga tatcga|tcgata 0.0002836589497 4 0.16 2.3e-05 4.8e-02 1.31 2 0 20
agaaga agaaga|tcttct 0.0002997750681 4 0.17 2.9e-05 6.0e-02 1.22 3 0 20
ttagaa ttagaa|ttctaa 0.0007932251641 5 0.44 9.9e-05 2.1e-01 0.69 4 0 25
ggtcac ggtcac|gtgacc 0.0000281336530 2 0.02 0.00012 2.6e-01 0.59 5 0 10
cgaaaa cgaaaa|ttttcg 0.0008598101792 5 0.48 0.00014 3.0e-01 0.52 6 0 25
gaaaga gaaaga|tctttc 0.0004779005862 4 0.27 0.00017 3.6e-01 0.45 7 0 20
gataga gataga|tctatc 0.0002043506834 3 0.11 0.00023 4.8e-01 0.32 8 0 15
gaaaaa gaaaaa|tttttc 0.0047469755030 10 2.66 0.00043 9.0e-01 0.05 9 0 50
; Host name rsat
; Job started 2026-04-30.111534
; Job done 2026-04-30.111534
; Seconds 0.2
; user 0.21
; system 0.03
; cuser 0.1
; csystem 0.02
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/04/30/tmp_sequence_2026-04-30.111533_YCQqp0.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 Plasmodium_berghei.PBANKA01.34 -pseudo 0.01 -l 7 -o $RSAT/public_html/tmp/www-data/2026/04/30/oligo-analysis_2026-04-30.111533_Jw8Wrp_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/2026/04/30/tmp_sequence_2026-04-30.111533_YCQqp0.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/04/30/oligo-analysis_2026-04-30.111533_Jw8Wrp_7nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Plasmodium_berghei.PBANKA01.34
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/oligo-frequencies/7nt_upstream-noorf_Plasmodium_berghei.PBANKA01.34-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 1.220703125e-06
; Sequence type DNA
; Nb of sequences 7
; Sum of sequence lengths 590
; 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 548
; total overlapping occurrences 18
; total non overlapping occ 530
; alphabet size 4
; nb possible oligomers 8192
; oligomers tested for significance 8170
; Sequences:
; gp11_Padj 80
; gp12 85
; gp13 85
; gp14 85
; gp15 85
; gp16 85
; gp17 85
;
; 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
agtgacc agtgacc|ggtcact 0.0000076398806 2 0.0042 8.7e-06 7.1e-02 1.15 1 0 12
atttttc atttttc|gaaaaat 0.0013807019428 7 0.76 1.4e-05 1.2e-01 0.94 2 0 42
tcgataa tcgataa|ttatcga 0.0001097048024 3 0.06 3.4e-05 2.8e-01 0.55 3 0 18
tatcgaa tatcgaa|ttcgata 0.0001392330188 3 0.08 7e-05 5.7e-01 0.25 4 0 18
; Host name rsat
; Job started 2026-04-30.111534
; Job done 2026-04-30.111535
; Seconds 0.58
; user 0.58
; system 0.01
; cuser 0.07
; csystem 0.02
; oligo-analysis -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/04/30/tmp_sequence_2026-04-30.111533_YCQqp0.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 Plasmodium_berghei.PBANKA01.34 -pseudo 0.01 -l 8 -o $RSAT/public_html/tmp/www-data/2026/04/30/oligo-analysis_2026-04-30.111533_Jw8Wrp_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/2026/04/30/tmp_sequence_2026-04-30.111533_YCQqp0.fasta.purged
; Input format fasta
; Output file $RSAT/public_html/tmp/www-data/2026/04/30/oligo-analysis_2026-04-30.111533_Jw8Wrp_8nt.tab
; Discard overlapping matches
; Counted on both strands
; grouped by pairs of reverse complements
; Background model upstream-noorf
; Organism Plasmodium_berghei.PBANKA01.34
; Background estimation method Frequency file
; Expected frequency file $RSAT/public_html/data/genomes/Plasmodium_berghei.PBANKA01.34/oligo-frequencies/8nt_upstream-noorf_Plasmodium_berghei.PBANKA01.34-noov-2str.freq
; Pseudo-frequency 0.01
; Pseudo-frequency per oligo 3.03988326848249e-07
; Sequence type DNA
; Nb of sequences 7
; Sum of sequence lengths 590
; 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 544
; total overlapping occurrences 9
; total non overlapping occ 535
; alphabet size 4
; nb possible oligomers 32896
; oligomers tested for significance 31561
; Sequences:
; gp11_Padj 80
; gp12 85
; gp13 85
; gp14 85
; gp15 85
; gp16 85
; gp17 85
;
; 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
aagtgacc aagtgacc|ggtcactt 0.0000041447141 2 0.0023 2.5e-06 8.0e-02 1.10 1 0 14
ttatcgaa ttatcgaa|ttcgataa 0.0000504467978 3 0.03 3.4e-06 1.1e-01 0.97 2 0 21
tcgataaa tcgataaa|tttatcga 0.0000632492172 3 0.03 6.6e-06 2.1e-01 0.68 3 0 21
gatattta gatattta|taaatatc 0.0002115439092 4 0.12 6.6e-06 2.1e-01 0.68 4 0 28
gtcactta gtcactta|taagtgac 0.0000084121873 2 0.0046 1e-05 3.3e-01 0.48 5 0 14
tatttaaa tatttaaa|tttaaata 0.0010189498286 6 0.55 2.5e-05 7.7e-01 0.11 6 0 42
aagaaaga aagaaaga|tctttctt 0.0000990959917 3 0.05 2.5e-05 7.9e-01 0.10 7 0 21
; Host name rsat
; Job started 2026-04-30.111535
; Job done 2026-04-30.111537
; Seconds 2.42
; user 2.42
; system 0.06
; cuser 0.11
; csystem 0.03