; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/03/24/matrix-scan_2026-03-24.231552_wBNLbz.matrix -pseudo 1 -decimals 1 -2str -origin end -bgfile $RSAT/public_html/data/genomes/Drosophila_melanogaster/oligo-frequencies/2nt_upstream-noorf_Drosophila_melanogaster-ovlp-1str.freq -bg_pseudo 0.01 -return limits -return sites -return pval -lth score 1 -uth pval 1e-4 -i $RSAT/public_html/tmp/www-data/2026/03/24/tmp_sequence_2026-03-24.231552_zTt6Qg.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	bg	$RSAT/public_html/data/genomes/Drosophila_melanogaster/oligo-frequencies/2nt_upstream-noorf_Drosophila_melanogaster-ovlp-1str.freq
;	input	$RSAT/public_html/tmp/www-data/2026/03/24/tmp_sequence_2026-03-24.231552_zTt6Qg.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/03/24/matrix-scan_2026-03-24.231552_wBNLbz.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	file
;	Markov order  	1
;	Strand        	sensitive
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.30375
;		c	0.20054
;		g	0.19828
;		t	0.29742
; Thresholds	lower	upper
;	pval  	NA	0.0001
;	score 	1    	NA
; Output columns
;	1	seq_id
;	2	ft_type
;	3	ft_name
;	4	strand
;	5	start
;	6	end
;	7	sequence
;	8	weight
#seq_id	ft_type	ft_name	strand	start	end	sequence	weight	Pval	ln_Pval	sig
dm3_flyBaseGene_CG2328-RA	limit	START_END	D	-5500	-1	.	0	0	0	0
dm3_flyBaseGene_CG2328-RA	site	ttk	D	-5221	-5215	CAGGACC	8.6	2.3e-05	-10.677	4.637
dm3_flyBaseGene_CG2328-RA	site	eve	R	-4205	-4191	CCAATGATTAGCGGT	7.5	7.7e-05	-9.465	4.111
dm3_flyBaseGene_CG2328-RA	site	hb	D	-4042	-4035	TTTTTATG	7.3	7.6e-05	-9.485	4.119
dm3_flyBaseGene_CG2328-RA	site	kni	R	-3701	-3694	GATCTAGT	7.1	7.6e-06	-11.783	5.117
dm3_flyBaseGene_CG2328-RA	site	hb	D	-3567	-3560	TTTTTATG	7.3	7.6e-05	-9.485	4.119
dm3_flyBaseGene_CG2328-RA	site	Stat92E	D	-3543	-3535	TTCGCGGAA	10.1	4.1e-06	-12.405	5.388
dm3_flyBaseGene_CG2328-RA	site	kni	R	-3476	-3469	GATCTACT	6.9	1.5e-05	-11.108	4.824
dm3_flyBaseGene_CG2328-RA	site	Stat92E	R	-3422	-3414	TTCGGGGAA	9.8	7.2e-06	-11.845	5.144
dm3_flyBaseGene_CG2328-RA	site	kni	D	-3335	-3328	GCTCTACT	6.1	8.7e-05	-9.352	4.062
dm3_flyBaseGene_CG2328-RA	site	hb	R	-3110	-3103	TTTTTATG	7.3	7.6e-05	-9.485	4.119
dm3_flyBaseGene_CG2328-RA	site	hb	D	-2594	-2587	TTTTTATG	7.3	7.6e-05	-9.485	4.119
dm3_flyBaseGene_CG2328-RA	site	Kr	R	-1203	-1196	AACCCGGT	7.1	8.3e-05	-9.395	4.080
dm3_flyBaseGene_CG2328-RA	site	gt	R	-1039	-1030	TTATGACTTT	7.8	3.3e-05	-10.328	4.485
dm3_flyBaseGene_CG2328-RA	site	hb	R	-1034	-1027	TTTTTATG	7.3	7.6e-05	-9.485	4.119
dm3_flyBaseGene_CG2328-RA	site	Kr	D	-913	-906	AACCCGTT	8.0	4.5e-05	-10.008	4.346
dm3_flyBaseGene_CG2328-RA	site	ttk	R	-785	-779	CAGGACC	8.6	2.3e-05	-10.677	4.637
dm3_flyBaseGene_CG2328-RA	site	eve	D	-620	-606	CAAATGGTTATGGCT	7.8	5.8e-05	-9.759	4.238
dm3_flyBaseGene_CG2328-RA	site	eve	R	-527	-513	CGCACGTTTAACAGC	7.6	7.0e-05	-9.572	4.157
dm3_flyBaseGene_CG2328-RA	site	gt	R	-516	-507	TTATGCCGCA	7.2	9.3e-05	-9.284	4.032
dm3_flyBaseGene_CG2328-RA	site	ttk	D	-195	-189	CAGGACC	8.6	2.3e-05	-10.677	4.637
dm3_flyBaseGene_CG2328-RA	site	ttk	R	-181	-175	CAGGACC	8.6	2.3e-05	-10.677	4.637
dm3_flyBaseGene_CG2328-RA	site	ttk	R	-139	-133	CAGGACC	8.6	2.3e-05	-10.677	4.637
dm3_flyBaseGene_CG2328-RA	site	eve	D	-116	-102	CGCCTCGTTATCGCC	10.9	1.4e-06	-13.488	5.858
dm3_flyBaseGene_CG2328-RA	site	eve	D	-60	-46	CGCACGATTAGCACC	12.6	4.8e-08	-16.860	7.322
;
; Matrices
;	matrix	name   	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	Kr     	8	4	1	-22.800	8.400	31.200	a:0.304 c:0.201 g:0.198 t:0.297 
;	2	Med    	6	4	1	-14.400	7.400	21.800	a:0.304 c:0.201 g:0.198 t:0.297 
;	3	Stat92E	9	4	1	-12.500	10.700	23.200	a:0.304 c:0.201 g:0.198 t:0.297 
;	4	bcd    	6	4	1	-17.700	6.600	24.300	a:0.304 c:0.201 g:0.198 t:0.297 
;	5	eve    	15	4	1	-33.100	14.000	47.100	a:0.304 c:0.201 g:0.198 t:0.297 
;	6	gt     	10	4	1	-22.000	8.700	30.700	a:0.304 c:0.201 g:0.198 t:0.297 
;	7	hb     	8	4	1	-25.500	7.900	33.400	a:0.304 c:0.201 g:0.198 t:0.297 
;	8	kni    	8	4	1	-12.700	6.200	18.900	a:0.304 c:0.201 g:0.198 t:0.297 
;	9	pan    	8	4	1	-18.100	7.300	25.400	a:0.304 c:0.201 g:0.198 t:0.297 
;	10	prd    	8	4	1	-18.500	8.300	26.800	a:0.304 c:0.201 g:0.198 t:0.297 
;	11	tin    	6	4	1	-15.000	7.200	22.200	a:0.304 c:0.201 g:0.198 t:0.297 
;	12	ttk    	7	4	1	-15.400	8.400	23.800	a:0.304 c:0.201 g:0.198 t:0.297 
; Number of sequences scanned	1
; Sum of sequence lengths	5500
; N residues           	0
; Matches per matrix
;	matrix	name   	matches	scored
;	1	Kr             	2	10986
;	2	Med            	0	10990
;	3	Stat92E        	2	10984
;	4	bcd            	0	10990
;	5	eve            	5	10972
;	6	gt             	2	10982
;	7	hb             	5	10986
;	8	kni            	3	10986
;	9	pan            	0	10986
;	10	prd            	0	10986
;	11	tin            	0	10990
;	12	ttk            	5	10988
;		TOTAL          	24	131826
; Host name	rsat
; Job started	2026-03-24.231552
; Job done	2026-03-24.231601
; Seconds	8.71
;	user	8.71
;	system	0.03
;	cuser	0
;	csystem	0