; oligo-analysis  -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/04/18/tmp_sequence_2026-04-18.211625_pHkZbY.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/2026/04/18/oligo-analysis_2026-04-18.211625_Igd2np_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/2026/04/18/tmp_sequence_2026-04-18.211625_pHkZbY.fasta.purged
; Input format                 	fasta
; Output file                  	$RSAT/public_html/tmp/www-data/2026/04/18/oligo-analysis_2026-04-18.211625_Igd2np_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              	1
; Sum of sequence lengths      	3189
; 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      	3182
; total overlapping occurrences	32
; total non overlapping occ    	3150
; alphabet size                	4
; nb possible oligomers        	32896
; oligomers tested for significance	32896
; Sequences:
;	Armadillos	3189
;
; 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
cagctgca	cagctgca|tgcagctg	0.0000117786615	3	0.04	8.5e-06	2.8e-01	0.55	1	0	21
gaacttgc	gaacttgc|gcaagttc	0.0000148234761	3	0.05	1.7e-05	5.5e-01	0.26	2	0	21
; Host name	rsat
; Job started	2026-04-18.211627
; Job done	2026-04-18.211630
; Seconds	2.65
;	user	2.65
;	system	0.1
;	cuser	0.13
;	csystem	0.02