; oligo-analysis  -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.141420_XRUSe9.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 5 -o $RSAT/public_html/tmp/www-data/2026/06/17/oligo-analysis_2026-06-17.141420_y6Waxm_5nt.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              	5
; Input file                   	$RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.141420_XRUSe9.fasta.purged
; Input format                 	fasta
; Output file                  	$RSAT/public_html/tmp/www-data/2026/06/17/oligo-analysis_2026-06-17.141420_y6Waxm_5nt.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   	1.953125e-05
; Sequence type                	DNA
; Nb of sequences              	1
; Sum of sequence lengths      	6935
; 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      	6221
; total overlapping occurrences	141
; total non overlapping occ    	6080
; alphabet size                	4
; nb possible oligomers        	512
; oligomers tested for significance	496
; Sequences:
;	2-UTseq835-UTL128-PhiB002	6935
;
; 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
gccgc	gccgc|gcggc	0.0006461938600	19	4.02	5.5e-08	2.7e-05	4.57	1	0	76
agcgg	agcgg|ccgct	0.0014373266200	25	8.94	7.6e-06	3.8e-03	2.42	2	0	100
gtcaa	gtcaa|ttgac	0.0018255135400	29	11.36	8.2e-06	4.1e-03	2.39	3	0	116
acgat	acgat|atcgt	0.0008920603600	16	5.55	0.00022	1.1e-01	0.96	4	0	64
aatcg	aatcg|cgatt	0.0007332029800	13	4.56	0.00090	4.5e-01	0.35	5	0	52
agccg	agccg|cggct	0.0008346453100	14	5.19	0.00099	4.9e-01	0.31	6	0	56
ccagc	ccagc|gctgg	0.0009830314600	15	6.12	0.00167	8.3e-01	0.08	7	0	60
; Host name	rsat
; Job started	2026-06-17.141420
; Job done	2026-06-17.141420
; Seconds	0.2
;	user	0.2
;	system	0.01
;	cuser	0.07
;	csystem	0.02