; compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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/peak-motifs_motifs_disco_compa.tab
; 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/peak-motifs_motifs_discovered.tf
;	file2 	/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/peak-motifs_motifs_discovered.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/peak-motifs_motifs_disco_compa_alignments_1ton.tab
;	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/peak-motifs_motifs_disco_compa
;	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/peak-motifs_motifs_disco_compa.tab
;	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/peak-motifs_motifs_disco_compa.html
;	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/peak-motifs_motifs_disco_compa_alignments_1ton.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/peak-motifs_motifs_disco_compa_index.html
; Matrices
;	file1	5 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/peak-motifs_motifs_discovered.tf
;		file1	1	10	36
;		file1	2	11	42
;		file1	3	13	28
;		file1	4	20	31
;		file1	5	30	37
;	file2	5 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/peak-motifs_motifs_discovered.tf
;		file2		1		10		36
;		file2		2		11		42
;		file2		3		13		28
;		file2		4		20		31
;		file2		5		30		37
; 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
oligos_7nt_mkv2_m1	oligos_7nt_mkv2_m1	oligos_7nt_mkv2_m1	oligos_7nt_mkv2_m1	1.000	1.000	11	11	11	11	1.0000	1.0000	1.0000	D	0
dyads_m1	dyads_m1	dyads_m1	dyads_m1	1.000	1.000	13	13	13	13	1.0000	1.0000	1.0000	D	0
dyads_m3	dyads_m3	dyads_m3	dyads_m3	1.000	1.000	30	30	30	30	1.0000	1.0000	1.0000	D	0
oligos_6nt_mkv2_m1	oligos_6nt_mkv2_m1	oligos_6nt_mkv2_m1	oligos_6nt_mkv2_m1	1.000	1.000	10	10	10	10	1.0000	1.0000	1.0000	D	0
dyads_m2	dyads_m2	dyads_m2	dyads_m2	1.000	1.000	20	20	20	20	1.0000	1.0000	1.0000	D	0
; Host name	rsat
; Job started	2025-03-02.091205
; Job done	2025-03-02.091206
; Seconds	0.15
;	user	0.15
;	system	0.06
;	cuser	1.18
;	csystem	0.2
