; matrix-scan  -v 1 -quick -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2026/06/02/matrix-scan_2026-06-02.080732_UxuZsd.matrix -pseudo 1 -decimals 1 -2str -origin end -bgfile $RSAT/public_html/data/genomes/Komagataella_pastoris.GCA_000027005.1.62/oligo-frequencies/2nt_upstream-noorf_Komagataella_pastoris.GCA_000027005.1.62-ovlp-1str.freq -bg_pseudo 0.01 -return limits -return pval -uth pval 0.0002 -i $RSAT/public_html/tmp/www-data/2026/06/02/tmp_sequence_2026-06-02.080732_1W3nVe.fasta -seq_format fasta -n score
; Quick counting mode           
; Input files
;	input	$RSAT/public_html/tmp/www-data/2026/06/02/tmp_sequence_2026-06-02.080732_1W3nVe.fasta
;	bg	$RSAT/public_html/data/genomes/Komagataella_pastoris.GCA_000027005.1.62/oligo-frequencies/2nt_upstream-noorf_Komagataella_pastoris.GCA_000027005.1.62-ovlp-1str.freq
; Matrix files
;	matrix 1	$RSAT/public_html/tmp/www-data/2026/06/02/matrix-scan_2026-06-02.080732_UxuZsd.matrix
; Sequence format      	fasta
; Pseudo counts        	1
; Background model
;	Method        	file
;	Markov order  	1
;	Strand        	sensitive
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.29272
;		c	0.21166
;		g	0.19264
;		t	0.30299
; Thresholds	lower	upper
;	pval  	NA	0.0002
; 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
PAS_c121_0015|PAS_c121_0015	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr1-1_0135|PAS_chr1-1_0135	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr1-4_0040|PAS_chr1-4_0040	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr1-4_0355|PAS_chr1-4_0355	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0103|PAS_chr2-1_0103	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0177|PAS_chr2-1_0177	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0235|PAS_chr2-1_0235	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0579|PAS_chr2-1_0579	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0580|PAS_chr2-1_0580	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0668|PAS_chr2-1_0668	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0685|PAS_chr2-1_0685	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-1_0787|PAS_chr2-1_0787	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr2-2_0420|PAS_chr2-2_0420	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_0505|PAS_chr3_0505	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr3_0886|PAS_chr3_0886	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0005|PAS_chr4_0005	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0077|PAS_chr4_0077	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0185|PAS_chr4_0185	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0290|PAS_chr4_0290	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0337|PAS_chr4_0337	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0399|PAS_chr4_0399	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_chr4_0570|PAS_chr4_0570	limit	START_END	D	-800	-1	.	0	0	0	0
PAS_c121_0015|PAS_c121_0015	site	AFT1	D	-614	-605	TTTCGCACCC	7.9	6.0e-05	-9.721	4.222
PAS_chr1-1_0135|PAS_chr1-1_0135	site	AFT1	D	-324	-315	CTATGCACCC	7.8	6.5e-05	-9.641	4.187
PAS_chr2-1_0580|PAS_chr2-1_0580	site	AFT1	R	-164	-155	TTTTGCACCA	6.1	2.0e-04	-8.517	3.699
PAS_chr4_0077|PAS_chr4_0077	site	AFT1	D	-643	-634	CTTTACACCC	6.7	1.4e-04	-8.874	3.854
PAS_chr4_0337|PAS_chr4_0337	site	AFT1	R	-369	-360	GATTGCACAC	6.7	1.4e-04	-8.874	3.854
PAS_chr4_0570|PAS_chr4_0570	site	AFT1	D	-463	-454	CAGGGCACCC	6.9	1.3e-04	-8.948	3.886
PAS_chr1-4_0355|PAS_chr1-4_0355	site	AFT2	D	-9	-4	ACACCC	8.3	1.7e-04	-8.680	3.770
PAS_chr2-1_0177|PAS_chr2-1_0177	site	AFT2	D	-657	-652	ACACCC	8.3	1.7e-04	-8.680	3.770
PAS_chr2-1_0579|PAS_chr2-1_0579	site	AFT2	R	-157	-152	ACACCC	8.3	1.7e-04	-8.680	3.770
PAS_chr4_0077|PAS_chr4_0077	site	AFT2	D	-639	-634	ACACCC	8.3	1.7e-04	-8.680	3.770
PAS_chr4_0570|PAS_chr4_0570	site	AFT2	R	-605	-600	ACACCC	8.3	1.7e-04	-8.680	3.770
;
; Matrices
;	matrix	name	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	AFT1	10	4	0	-27.500	11.800	39.300	a:0.293 c:0.212 g:0.193 t:0.303 
;	2	AFT2	6	4	0	-27.700	8.300	36.000	a:0.293 c:0.212 g:0.193 t:0.303 
; Number of sequences scanned	22
; Sum of sequence lengths	17600
; N residues           	0
; Matches per matrix
;	matrix	name	matches	scored
;	1	AFT1           	6	0
;	2	AFT2           	5	0
;		TOTAL          	11	0
; Host name	rsat
; Job started	2026-06-02.080733
; Job done	2026-06-02.080734
; Seconds	0.33
;	user	0.33
;	system	0.05
;	cuser	0.57
;	csystem	0.07