; oligo-analysis  -v 1 -sort -i $RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.142027_92dU7W.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 6 -o $RSAT/public_html/tmp/www-data/2026/06/17/oligo-analysis_2026-06-17.142027_KBUGvS_6nt.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              	6
; Input file                   	$RSAT/public_html/tmp/www-data/2026/06/17/tmp_sequence_2026-06-17.142027_92dU7W.fasta.purged
; Input format                 	fasta
; Output file                  	$RSAT/public_html/tmp/www-data/2026/06/17/oligo-analysis_2026-06-17.142027_KBUGvS_6nt.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   	4.80769230769231e-06
; Sequence type                	DNA
; Nb of sequences              	1
; Sum of sequence lengths      	20509
; 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      	20506
; total overlapping occurrences	147
; total non overlapping occ    	20359
; alphabet size                	4
; nb possible oligomers        	2080
; oligomers tested for significance	1999
; Sequences:
;	3-UTseq836-UTL128-SPB	20509
;
; 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
cagatg	cagatg|catctg	0.0005020552446	28	10.30	3.8e-06	7.6e-03	2.12	1	0	140
ggtgaa	ggtgaa|ttcacc	0.0005023750146	26	10.30	2.9e-05	5.7e-02	1.24	2	0	130
aacgcc	aacgcc|ggcgtt	0.0001631529996	13	3.35	4.9e-05	9.7e-02	1.01	3	0	65
tcaaca	tcaaca|tgttga	0.0009224330046	38	18.92	7.3e-05	1.5e-01	0.84	4	0	190
ctcccc	ctcccc|ggggag	0.0002090566266	14	4.29	0.00015	3.1e-01	0.51	5	0	70
cttcaa	cttcaa|ttgaag	0.0013128563346	47	26.92	0.00028	5.6e-01	0.25	6	0	235
taaaga	taaaga|tcttta	0.0014250302646	50	29.22	0.00029	5.8e-01	0.24	7	0	250
cgatta	cgatta|taatcg	0.0004323117246	21	8.86	0.00036	7.2e-01	0.14	8	0	105
cccttc	cccttc|gaaggg	0.0004057203246	20	8.32	0.00041	8.2e-01	0.09	9	0	100
; Host name	rsat
; Job started	2026-06-17.142028
; Job done	2026-06-17.142028
; Seconds	0.33
;	user	0.33
;	system	0.02
;	cuser	0.11
;	csystem	0.01