; dyad-analysis  -v 1 -i $RSAT/public_html/tmp/www-data/2025/09/18/peak-motifs.2025-09-18.095753_2025-09-18.095753_7F5dVY/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 -expfreq $RSAT/public_html/tmp/www-data/2025/09/18/peak-motifs.2025-09-18.095753_2025-09-18.095753_7F5dVY/results/dyads_test_vs_ctrl/peak-motifs_dyads_bg_from_ctrl-2str-noov_3nt_sp0-20_bg_monads.tab -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/2025/09/18/peak-motifs.2025-09-18.095753_2025-09-18.095753_7F5dVY/data/sequences/peak-motifs_test_purged_ml40_mis3.fasta
; Sequence type                	DNA
; Nb of sequences              	2996
; Sum of sequence lengths      	602196
; default return values        	freq,occ
; return values                	zscore,ratio,occ,exp_occ,rank,proba,exp_freq
; Discard overlapping matches
; Counted on both strands
; 	grouped by pairs of reverse complements
; Monad parameters             
; 	monad size                  	3
; 	monad positions              463427
; 	    valid                    	463427
; 	    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	27458
;	Dyad counts per spacing
;		spacing	max_pos	occ	ovlps	ovl+occ	ACGT	nonACGT
;		sp 0		450020	4845	454865	450020	NA
;		sp 1		446227	5832	452059	446227	NA
;		sp 2		442442	6824	449266	442442	NA
;		sp 3		439070	7334	446404	439070	NA
;		sp 4		435888	7747	443635	435888	NA
;		sp 5		432788	8031	440819	432788	NA
;		sp 6		429954	8108	438062	429954	NA
;		sp 7		426821	8490	435311	426821	NA
;		sp 8		423923	8631	432554	423923	NA
;		sp 9		420810	9018	429828	420810	NA
;		sp 10		417867	9273	427140	417867	NA
;		sp 11		414832	9581	424413	414832	NA
;		sp 12		411920	9818	421738	411920	NA
;		sp 13		409028	10000	419028	409028	NA
;		sp 14		406113	10235	416348	406113	NA
;		sp 15		403230	10390	413620	403230	NA
;		sp 16		400286	10697	410983	400286	NA
;		sp 17		397489	10827	408316	397489	NA
;		sp 18		394544	11121	405665	394544	NA
;		sp 19		391754	11284	403038	391754	NA
;		sp 20		388896	11491	400387	388896	NA
; Estimation of expected dyad frequencies
;	Background model	exp_freq_file
;	exp. freq. file       	$RSAT/public_html/tmp/www-data/2025/09/18/peak-motifs.2025-09-18.095753_2025-09-18.095753_7F5dVY/results/dyads_test_vs_ctrl/peak-motifs_dyads_bg_from_ctrl-2str-noov_3nt_sp0-20_bg_monads.tab
; 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
tcan{19}cca	tcan{19}cca|tggn{19}tga	0.0006682331672	    336	 261.78	6.1e-06	1.7e-01	   0.78	      1	6	342	   4.61	 259.51	   1.28	 1.0000	
agtn{9}ttc	agtn{9}ttc|gaan{9}act	0.0005145590616	    284	 216.53	6.7e-06	1.8e-01	   0.74	      2	2	286	   4.60	 215.08	   1.31	 1.0000	
tccn{16}aaa	tccn{16}aaa|tttn{16}gga	0.0006170942248	    316	 247.01	1.4e-05	3.9e-01	   0.41	      3	6	322	   4.41	 245.03	   1.28	 1.0000	
ccan{20}aac	ccan{20}aac|gttn{20}tgg	0.0006091027843	    304	 236.88	1.6e-05	4.4e-01	   0.36	      4	3	307	   4.37	 235.46	   1.28	 1.0010	
cttn{14}caa	cttn{14}caa|ttgn{14}aag	0.0006913466445	    353	 280.76	1.8e-05	5.0e-01	   0.30	      5	16	369	   4.33	 278.24	   1.26	 1.0000	
aagn{3}cta	aagn{3}cta|tagn{3}ctt	0.0003461685929	    205	 151.99	2.5e-05	6.8e-01	   0.17	      6	2	207	   4.31	 151.61	   1.35	 1.0010	
agcn{14}tcc	agcn{14}tcc|ggan{14}gct	0.0004961705510	    262	 201.50	2.5e-05	7.0e-01	   0.16	      7	5	267	   4.28	 200.20	   1.30	 1.0000	
gcan{18}caa	gcan{18}caa|ttgn{18}tgc	0.0006228905016	    312	 245.76	2.7e-05	7.5e-01	   0.13	      8	6	318	   4.24	 243.77	   1.27	 1.0000	
; Host name	rsat
; Job started	2025-09-18.095830
; Job done	2025-09-18.095837
; Seconds	5.77
;	user	5.77
;	system	0.07
;	cuser	1.87
;	csystem	0.02
