; oligo-analysis  -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.152659_QktSSh.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_2026-06-17.152659_iu21Lq_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_2026-06-17.152659_QktSSh.fasta.purged
; Input format                 	fasta
; Output file                  	$RSAT/public_html/tmp/www-data/2026/06/17/oligo-analysis_2026-06-17.152659_iu21Lq_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      	10667
; 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      	10511
; total overlapping occurrences	212
; total non overlapping occ    	10299
; alphabet size                	4
; nb possible oligomers        	512
; oligomers tested for significance	500
; Sequences:
;	5-UTseq838-UTL300-PhiB002	10667
;
; 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	0.0004280869600	20	4.50	6.6e-08	3.3e-05	4.48	1	0	80
agcgg	agcgg|ccgct	0.0011192425900	32	11.76	8.1e-07	4.0e-04	3.39	2	0	128
gtcaa	gtcaa|ttgac	0.0016582223500	34	17.43	0.00028	1.4e-01	0.85	3	0	136
acgat	acgat|atcgt	0.0012546429100	27	13.19	0.00055	2.8e-01	0.56	4	0	108
gagga	gagga|tcctc	0.0031930441000	54	33.56	0.00069	3.5e-01	0.46	5	6	216
gacta	gacta|tagtc	0.0015364137400	30	16.15	0.00129	6.4e-01	0.19	6	0	120
gcagc	gcagc|gctgc	0.0010929422500	23	11.49	0.00179	8.9e-01	0.05	7	0	92
; Host name	rsat
; Job started	2026-06-17.152700
; Job done	2026-06-17.152700
; Seconds	0.16
;	user	0.16
;	system	0.01
;	cuser	0.08
;	csystem	0