; matrix-scan  -quick -v 1 -seq_format fasta -i $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124448_2025-04-03.124448_OhsrJC/data/sequences/peak-motifs_test_maxlen1000.fasta -matrix_format transfac -m $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124448_2025-04-03.124448_OhsrJC/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4.tf -bg_format inclusive -bgfile $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124448_2025-04-03.124448_OhsrJC/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt -pseudo 1 -2str -decimals 1 -bg_pseudo 0.01 -n score -lth score 7.5 -origin center -offset 0 -return sites -o $RSAT/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124448_2025-04-03.124448_OhsrJC/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_sites.tab
; Quick counting mode           
; Input files
;	input	/var/www/html/rsat/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124448_2025-04-03.124448_OhsrJC/data/sequences/peak-motifs_test_maxlen1000.fasta
;	bg	/var/www/html/rsat/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124448_2025-04-03.124448_OhsrJC/results/composition/peak-motifs_test_inclusive-1str-ovlp_2nt.txt
; Matrix files
;	matrix 1	/var/www/html/rsat/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124448_2025-04-03.124448_OhsrJC/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4.tf
; Sequence format      	fasta
; Output files
;	output	/var/www/html/rsat/public_html/tmp/www-data/2025/04/03/peak-motifs.2025-04-03.124448_2025-04-03.124448_OhsrJC/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_sites.tab
; Pseudo counts        	1
; Background model
;	Method        	file
;	Markov order  	1
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.26461
;		c	0.24461
;		g	0.23830
;		t	0.25248
; Thresholds	lower	upper
;	score 	7.5  	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
ChrIII_A_nidulans_FGSC_A4:103141-103241(.)	site	oligos_7nt_mkv2_m4	D	-46	-36	TCCTATCTAGA	9.3
ChrIII_A_nidulans_FGSC_A4:209815-209915(.)	site	oligos_7nt_mkv2_m4	D	-23	-13	GCCTATCTAAA	10.5
ChrII_A_nidulans_FGSC_A4:3859-3959(.)	site	oligos_7nt_mkv2_m4	R	16	26	AACTATGTAGA	7.5
ChrII_A_nidulans_FGSC_A4:73725-73825(.)	site	oligos_7nt_mkv2_m4	R	19	29	GCCTATCTATA	10.3
ChrII_A_nidulans_FGSC_A4:919677-919777(.)	site	oligos_7nt_mkv2_m4	D	-16	-6	GCCTATCTAAA	10.5
ChrII_A_nidulans_FGSC_A4:924615-924715(.)	site	oligos_7nt_mkv2_m4	D	-29	-19	GCCTATCTAAA	10.5
ChrII_A_nidulans_FGSC_A4:1476944-1477044(.)	site	oligos_7nt_mkv2_m4	R	-3	7	ATCTATCTAAA	10.0
ChrII_A_nidulans_FGSC_A4:1476944-1477044(.)	site	oligos_7nt_mkv2_m4	D	10	20	TCCTATCTAGA	9.3
ChrII_A_nidulans_FGSC_A4:3802147-3802247(.)	site	oligos_7nt_mkv2_m4	R	16	26	GCCTATCTATA	10.3
ChrII_A_nidulans_FGSC_A4:4067322-4067422(.)	site	oligos_7nt_mkv2_m4	D	-25	-15	AACTATGTAGA	7.5
ChrIV_A_nidulans_FGSC_A4:154106-154206(.)	site	oligos_7nt_mkv2_m4	R	21	31	GCCTATCTAAA	10.5
ChrIV_A_nidulans_FGSC_A4:721457-721557(.)	site	oligos_7nt_mkv2_m4	R	23	33	GCCTATCTATA	10.3
ChrIV_A_nidulans_FGSC_A4:1061234-1061334(.)	site	oligos_7nt_mkv2_m4	D	-26	-16	GCCTATCTAAA	10.5
ChrIV_A_nidulans_FGSC_A4:1111262-1111362(.)	site	oligos_7nt_mkv2_m4	R	20	30	GCCTATCTAAA	10.5
ChrIV_A_nidulans_FGSC_A4:1967798-1967898(.)	site	oligos_7nt_mkv2_m4	R	-35	-25	ACCTATCGATA	8.0
ChrIV_A_nidulans_FGSC_A4:2780757-2780857(.)	site	oligos_7nt_mkv2_m4	D	-16	-6	GCCTATCTATA	10.3
ChrIV_A_nidulans_FGSC_A4:2861293-2861393(.)	site	oligos_7nt_mkv2_m4	R	-2	8	TCCTATCTAGA	9.3
ChrIV_A_nidulans_FGSC_A4:2861293-2861393(.)	site	oligos_7nt_mkv2_m4	D	11	21	ATCCATCTAAA	8.0
ChrI_A_nidulans_FGSC_A4:169876-169976(.)	site	oligos_7nt_mkv2_m4	D	-33	-23	GCCTATCTAAA	10.5
ChrVIII_A_nidulans_FGSC_A4:2967195-2967295(.)	site	oligos_7nt_mkv2_m4	R	-18	-8	GACTACCTATA	7.9
ChrVIII_A_nidulans_FGSC_A4:4914293-4914393(.)	site	oligos_7nt_mkv2_m4	R	-16	-6	TCCTATCTAGA	9.3
ChrVIII_A_nidulans_FGSC_A4:4914293-4914393(.)	site	oligos_7nt_mkv2_m4	D	-3	7	ATCCATCTAAA	8.0
ChrVII_A_nidulans_FGSC_A4:1935153-1935253(.)	site	oligos_7nt_mkv2_m4	D	-48	-38	GCCTATCTAAA	10.5
ChrVII_A_nidulans_FGSC_A4:3158896-3158996(.)	site	oligos_7nt_mkv2_m4	R	-22	-12	ATCCATCTAAA	8.0
ChrVII_A_nidulans_FGSC_A4:3158896-3158996(.)	site	oligos_7nt_mkv2_m4	D	-9	1	TCCTATCTAGA	9.3
ChrVII_A_nidulans_FGSC_A4:3620034-3620134(.)	site	oligos_7nt_mkv2_m4	R	23	33	GCCTATCTAAA	10.5
ChrVI_A_nidulans_FGSC_A4:1031852-1031952(.)	site	oligos_7nt_mkv2_m4	R	-49	-39	GACTACCTATA	7.9
ChrVI_A_nidulans_FGSC_A4:1130604-1130704(.)	site	oligos_7nt_mkv2_m4	D	-33	-23	AACTATCTAAG	9.0
ChrV_A_nidulans_FGSC_A4:127977-128077(.)	site	oligos_7nt_mkv2_m4	D	-24	-14	AACTATGTAGA	7.5
ChrV_A_nidulans_FGSC_A4:925415-925515(.)	site	oligos_7nt_mkv2_m4	R	-50	-40	AACTATCTAAG	9.0
ChrV_A_nidulans_FGSC_A4:925415-925515(.)	site	oligos_7nt_mkv2_m4	D	-8	2	AACTATGTAGA	7.5
ChrV_A_nidulans_FGSC_A4:3331030-3331130(.)	site	oligos_7nt_mkv2_m4	D	-38	-28	AACTATCTAAG	9.0
;
; Matrices
;	matrix	name              	ncol	nrow	pseudo	Wmin	Wmax	Wrange
;	1	oligos_7nt_mkv2_m4	11	4	0	-31.100	11.100	42.200	a:0.265 c:0.245 g:0.238 t:0.252 
; Number of sequences scanned	150
; Sum of sequence lengths	15000
; N residues           	0
; Matches per matrix
;	matrix	name              	matches	scored
;	1	oligos_7nt_mkv2_m4	32	0
;		TOTAL          	32	0
; Host name	rsat
; Job started	2025-04-03.124526
; Job done	2025-04-03.124526
; Seconds	0.15
;	user	0.15
;	system	0.01
;	cuser	0.11
;	csystem	0.01
