; 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