; oligo-analysis  -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/04/30/tmp_sequence_2026-04-30.004019_wylSsU.fasta.purged -format fasta -lth occ_sig 0 -uth rank 50 -return occ,proba,rank -2str -noov -quick_if_possible -seqtype dna -markov 2 -pseudo 0.01 -l 7 -o $RSAT/public_html/tmp/www-data/2026/04/30/oligo-analysis_2026-04-30.004019_vQuY1P_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_2026-04-30.004019_wylSsU.fasta.purged
; Input format                 	fasta
; Output file                  	$RSAT/public_html/tmp/www-data/2026/04/30/oligo-analysis_2026-04-30.004019_vQuY1P_7nt.tab
; Discard overlapping matches
; Counted on both strands
; 	grouped by pairs of reverse complements
; Background model             	Markov
; Background estimation method 	Markov model estimated from input sequences
; Markov chain order           	2
; Pseudo-frequency             	0.01
; Pseudo-frequency per oligo   	1.220703125e-06
; Sequence type                	DNA
; Nb of sequences              	16
; Sum of sequence lengths      	3405
; 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      	3298
; total overlapping occurrences	16
; total non overlapping occ    	3282
; alphabet size                	4
; nb possible oligomers        	8192
; oligomers tested for significance	2421
; Sequences:
;	07110	200
;	0155	200
;	02070	200
;	PhoP	200
;	PhoP2	200
;	03920	200
;	0330	200
;	01390	200
;	05970	200
;	1740	200
;	05655	405
;	02485	200
;	02830	200
;	01745	200
;	2045	200
;	7210	200
;
; 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
cgacgac	cgacgac|gtcgtcg	0.0000331229219	4	0.11	5.4e-06	1.3e-02	1.88	1	0	24
acgacga	acgacga|tcgtcgt	0.0000365622512	4	0.12	8e-06	1.9e-02	1.71	2	0	24
cgtcgtc	cgtcgtc|gacgacg	0.0000398084316	4	0.13	1.1e-05	2.7e-02	1.57	3	0	24
ccacccc	ccacccc|ggggtgg	0.0002739815762	7	0.90	4.4e-05	1.1e-01	0.97	4	0	42
caccccg	caccccg|cggggtg	0.0003753724262	7	1.24	0.00030	7.3e-01	0.14	5	0	42
; Host name	rsat
; Job started	2026-04-30.004020
; Job done	2026-04-30.004020
; Seconds	0.52
;	user	0.52
;	system	0.02
;	cuser	0.08
;	csystem	0