; matrix-scan  -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/07/17/matrix-scan_2026-07-17.091403_9l6izy.matrix -pseudo 1 -decimals 1 -2str -origin end -bginput -markov 1 -bg_pseudo 0.01 -return limits -return sites -return pval -lth score 1 -uth pval 1e-4 -i $RSAT/public_html/tmp/www-data/2026/07/17/tmp_sequence_2026-07-17.091403_Q4woG9.fasta -seq_format fasta -n score
; Slow counting mode            
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/07/17/tmp_sequence_2026-07-17.091403_Q4woG9.fasta
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/07/17/matrix-scan_2026-07-17.091403_9l6izy.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	input
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.23831
;		c	0.24916
;		g	0.23168
;		t	0.28085
; 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	8.2	3.3e-05	-10.330	4.486
dm3_flyBaseGene_CG2328-RA	site	ttk	R	-5123	-5117	CAGGACA	8.0	5.9e-05	-9.737	4.229
dm3_flyBaseGene_CG2328-RA	site	kni	D	-4306	-4299	GTTCTACT	6.1	1.0e-04	-9.181	3.987
dm3_flyBaseGene_CG2328-RA	site	eve	R	-4205	-4191	CCAATGATTAGCGGT	7.5	7.7e-05	-9.466	4.111
dm3_flyBaseGene_CG2328-RA	site	hb	D	-4042	-4035	TTTTTATG	7.7	5.1e-05	-9.885	4.293
dm3_flyBaseGene_CG2328-RA	site	gt	D	-4039	-4030	TTATGAGTTT	7.5	6.6e-05	-9.623	4.179
dm3_flyBaseGene_CG2328-RA	site	kni	R	-3701	-3694	GATCTAGT	7.2	6.9e-06	-11.890	5.164
dm3_flyBaseGene_CG2328-RA	site	hb	D	-3567	-3560	TTTTTATG	7.7	5.1e-05	-9.885	4.293
dm3_flyBaseGene_CG2328-RA	site	Stat92E	D	-3543	-3535	TTCGCGGAA	9.7	6.6e-06	-11.935	5.183
dm3_flyBaseGene_CG2328-RA	site	ttk	R	-3528	-3522	CAGGACA	8.0	5.9e-05	-9.737	4.229
dm3_flyBaseGene_CG2328-RA	site	kni	R	-3476	-3469	GATCTACT	7.0	1.3e-05	-11.221	4.873
dm3_flyBaseGene_CG2328-RA	site	Stat92E	R	-3422	-3414	TTCGGGGAA	9.2	1.2e-05	-11.313	4.913
dm3_flyBaseGene_CG2328-RA	site	hb	R	-3110	-3103	TTTTTATG	7.7	5.1e-05	-9.885	4.293
dm3_flyBaseGene_CG2328-RA	site	hb	D	-2594	-2587	TTTTTATG	7.7	5.1e-05	-9.885	4.293
dm3_flyBaseGene_CG2328-RA	site	gt	D	-1367	-1358	TTATTAGTCA	7.7	5.4e-05	-9.832	4.270
dm3_flyBaseGene_CG2328-RA	site	gt	R	-1039	-1030	TTATGACTTT	8.4	1.9e-05	-10.862	4.717
dm3_flyBaseGene_CG2328-RA	site	hb	R	-1034	-1027	TTTTTATG	7.7	5.1e-05	-9.885	4.293
dm3_flyBaseGene_CG2328-RA	site	Kr	D	-913	-906	AACCCGTT	7.8	5.5e-05	-9.805	4.258
dm3_flyBaseGene_CG2328-RA	site	ttk	R	-785	-779	CAGGACC	8.2	3.3e-05	-10.330	4.486
dm3_flyBaseGene_CG2328-RA	site	eve	D	-620	-606	CAAATGGTTATGGCT	7.8	5.8e-05	-9.753	4.236
dm3_flyBaseGene_CG2328-RA	site	eve	R	-527	-513	CGCACGTTTAACAGC	8.1	4.3e-05	-10.056	4.367
dm3_flyBaseGene_CG2328-RA	site	ttk	D	-195	-189	CAGGACC	8.2	3.3e-05	-10.330	4.486
dm3_flyBaseGene_CG2328-RA	site	ttk	R	-181	-175	CAGGACC	8.2	3.3e-05	-10.330	4.486
dm3_flyBaseGene_CG2328-RA	site	ttk	R	-139	-133	CAGGACC	8.2	3.3e-05	-10.330	4.486
dm3_flyBaseGene_CG2328-RA	site	eve	D	-116	-102	CGCCTCGTTATCGCC	9.5	9.2e-06	-11.600	5.038
dm3_flyBaseGene_CG2328-RA	site	eve	D	-60	-46	CGCACGATTAGCACC	12.7	3.6e-08	-17.141	7.444
;
; Matrices
;	matrix	name   	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	Kr     	8	4	1	-23.000	8.400	31.400	a:0.238 c:0.249 g:0.232 t:0.281 
;	2	Med    	6	4	1	-14.400	6.800	21.200	a:0.238 c:0.249 g:0.232 t:0.281 
;	3	Stat92E	9	4	1	-12.500	10.400	22.900	a:0.238 c:0.249 g:0.232 t:0.281 
;	4	bcd    	6	4	1	-17.600	6.800	24.400	a:0.238 c:0.249 g:0.232 t:0.281 
;	5	eve    	15	4	1	-33.100	13.400	46.500	a:0.238 c:0.249 g:0.232 t:0.281 
;	6	gt     	10	4	1	-22.000	9.100	31.100	a:0.238 c:0.249 g:0.232 t:0.281 
;	7	hb     	8	4	1	-25.500	8.400	33.900	a:0.238 c:0.249 g:0.232 t:0.281 
;	8	kni    	8	4	1	-13.100	6.400	19.500	a:0.238 c:0.249 g:0.232 t:0.281 
;	9	pan    	8	4	1	-18.300	7.800	26.100	a:0.238 c:0.249 g:0.232 t:0.281 
;	10	prd    	8	4	1	-18.500	7.800	26.300	a:0.238 c:0.249 g:0.232 t:0.281 
;	11	tin    	6	4	1	-15.000	7.400	22.400	a:0.238 c:0.249 g:0.232 t:0.281 
;	12	ttk    	7	4	1	-15.400	7.900	23.300	a:0.238 c:0.249 g:0.232 t:0.281 
; Number of sequences scanned	1
; Sum of sequence lengths	5500
; N residues           	0
; Matches per matrix
;	matrix	name   	matches	scored
;	1	Kr             	1	10986
;	2	Med            	0	10990
;	3	Stat92E        	2	10984
;	4	bcd            	0	10990
;	5	eve            	5	10972
;	6	gt             	3	10982
;	7	hb             	5	10986
;	8	kni            	3	10986
;	9	pan            	0	10986
;	10	prd            	0	10986
;	11	tin            	0	10990
;	12	ttk            	7	10988
;		TOTAL          	26	131826
; Host name	rsat
; Job started	2026-07-17.091403
; Job done	2026-07-17.091412
; Seconds	8.71
;	user	8.71
;	system	0.03
;	cuser	0.11
;	csystem	0.01