; compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_footprintDB
; Program version       	1.118
; Quick mode 
; Input files
;	file1 	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf
;	file2 	/var/www/html/rsat/public_html/motif_databases/footprintDB/footprintDB.motif.tf
; Output files
;	alignments_1ton	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_footprintDB_alignments_1ton.tab
;	match_table_txt	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_footprintDB.tab
;	alignments_1ton_html	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_footprintDB_alignments_1ton.html
;	prefix       	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_footprintDB
;	match_table_html	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_footprintDB.html
;	html_index   	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_footprintDB_index.html
; Matrices
;	file1	1 matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.tf
;		file1	1	30	37
;	file2	13863 matrices	/var/www/html/rsat/public_html/motif_databases/footprintDB/footprintDB.motif.tf
;		file2		1		17		1.01
;		file2		2		7		96
;		file2		3		8		5
;		file2		4		8		3
;		file2		5		8		5
;		file2		6		8		1
;		file2		7		8		2
;		file2		8		8		2
;		file2		9		8		6
;		file2		10		8		2
;		file2		11		8		8
;		...	13853 more matrices
; Column content
;	1	id1          	Identifier of the first matrix
;	2	id2          	Identifier of the second matrix
;	3	name1        	Name of the first matrix
;	4	name2        	Name of the second matrix
;	5	cor          	Pearson coefficient of correlation between frequency matrices
;	6	Ncor         	Normalized correlation. Ncor = cor * Wr
;	7	w1           	Width of the first matrix
;	8	w2           	Width of the second matrix
;	9	w            	Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset)
;	10	W            	Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w
;	11	Wr           	Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W
;	12	wr1          	Alignment length relative to the width of the first matrix. wr1 = w/w1
;	13	wr2          	Alignment length relative to the width of the second matrix. wr2 = w/w2
;	14	strand       	"strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct;  R=reverse)
;	15	offset       	shift of the second matrix relative to the first matrix (negative:left; positive: right)
#id1	id2	name1	name2	cor	Ncor	w1	w2	w	W	Wr	wr1	wr2	strand	offset
dyads_m3	MYB39.ampDAP/M0559/AthalianaCistrome	dyads_m3	MYB39.ampDAP:M0559:AthalianaCistrome	0.707	0.420	30	21	19	32	0.5938	0.6333	0.9048	R	-2
; Host name	rsat
; Job started	2025-03-02.091234
; Job done	2025-03-02.091240
; Seconds	5.62
;	user	5.62
;	system	0.13
;	cuser	0.57
;	csystem	0.08
