; dyad-analysis  -v 1 -i $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta -quick -format fasta -sort -lth ratio 1 -lth occ_sig 0 -uth rank 100 -return occ,proba,ratio,zscore,rank -2str -noov -seqtype dna -l 3 -sp 0-20 -bg monads -pseudo 0.01
; Citation: van Helden et al. (2000). Nucleic Acids Res. 28(8):1808-18.
; Program version              	1.78
; Input file                   	$RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta
; Sequence type                	DNA
; Nb of sequences              	23
; Sum of sequence lengths      	10099
; default return values        	occ,freq
; return values                	ratio,exp_freq,proba,zscore,exp_occ,occ,rank
; Discard overlapping matches
; Counted on both strands
; 	grouped by pairs of reverse complements
; Monad parameters             
; 	monad size                  	3
; 	monad positions              6608
; 	    valid                    	6608
; 	    discarded                	0 (contain other letters than ACGT)
; 	distinct monads              64
; Dyad parameters              
; 	dyad type                    any dyad
; 	minimal spacing              0
; 	maximal spacing              20
; 	distinct dyads               	43680
; 	dyads tested for significance	20066
;	Dyad counts per spacing
;		spacing	max_pos	occ	ovlps	ovl+occ	ACGT	nonACGT
;		sp 0		6471	87	6558	6471	NA
;		sp 1		6437	104	6541	6437	NA
;		sp 2		6407	118	6525	6407	NA
;		sp 3		6381	124	6505	6381	NA
;		sp 4		6360	129	6489	6360	NA
;		sp 5		6313	157	6470	6313	NA
;		sp 6		6290	164	6454	6290	NA
;		sp 7		6273	165	6438	6273	NA
;		sp 8		6254	168	6422	6254	NA
;		sp 9		6215	188	6403	6215	NA
;		sp 10		6200	179	6379	6200	NA
;		sp 11		6181	180	6361	6181	NA
;		sp 12		6155	192	6347	6155	NA
;		sp 13		6124	208	6332	6124	NA
;		sp 14		6086	230	6316	6086	NA
;		sp 15		6073	225	6298	6073	NA
;		sp 16		6055	226	6281	6055	NA
;		sp 17		6036	220	6256	6036	NA
;		sp 18		6015	230	6245	6015	NA
;		sp 19		6003	218	6221	6003	NA
;		sp 20		5993	208	6201	5993	NA
; Estimation of expected dyad frequencies
;	Background model	monads
;	Monad calibration from input sequences
; Sequences:
;	Analyzed by count-words
; column headers
;	1	sequence       	
;	2	identifier             	
;	3	expected_freq  	
;	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
;	11	all_occ        	number of non-overlapping + overlapping occurrences
;	12	zscore         	z-score (normal)
;	13	occ_var        	
;	14	ratio          	observed/expected ratio
;	15	ov_coef        	overlap coefficient
;	16	remark         	remark (dir_rep=direct repeat; rc_pal=reverse complementary palindrom)
#sequence  	identifier             	expected_freq	occ	exp_occ	occ_P	occ_E	occ_sig	rank	ovl_occ	all_occ	zscore	occ_var	ratio	ov_coef	remark
gcan{3}gga	gcan{3}gga|tccn{3}tgc	0.0004234906402	     12	   2.70	2.7e-05	5.3e-01	   0.27	      1	0	12	   5.67	   2.69	   4.44	 1.0000	
ggan{10}cga	ggan{10}cga|tcgn{10}tcc	0.0003176179801	     10	   1.97	4.1e-05	8.2e-01	   0.09	      2	0	10	   5.73	   1.96	   5.08	 1.0000	
accn{20}cag	accn{20}cag|ctgn{20}ggt	0.0002663419936	      9	   1.60	4.4e-05	8.9e-01	   0.05	      3	0	9	   5.87	   1.59	   5.64	 1.0000	
; Host name	rsat
; Job started	2025-03-02.091155
; Job done	2025-03-02.091159
; Seconds	3.75
;	user	3.75
;	system	0.04
;	cuser	0.28
;	csystem	0.03
