; compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.141641_hJU8mO/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -format2 tf -strand DR -lth cor 0.7 -lth Ncor 0.4 -uth match_rank 50 -return cor,Ncor,logoDP,NsEucl,NSW,match_rank,matrix_id,matrix_name,width,strand,offset,consensus,alignments_1ton -o $RSAT/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.141641_hJU8mO/compare-matrices.tab
; Program version       	1.118
; Slow mode 
; Input files
;	file2 	/var/www/html/rsat/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf
;	file1 	/var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.141641_hJU8mO/compare-matrices_query_matrices.transfac
; Output files
;	prefix       	/var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.141641_hJU8mO/compare-matrices
;	alignments_1ton_html	/var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.141641_hJU8mO/compare-matrices_alignments_1ton.html
;	html_index   	/var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.141641_hJU8mO/compare-matrices_index.html
;	alignments_1ton	/var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.141641_hJU8mO/compare-matrices_alignments_1ton.tab
;	match_table_txt	/var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.141641_hJU8mO/compare-matrices.tab
;	match_table_html	/var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.141641_hJU8mO/compare-matrices.html
; Matrices
;	file1	1 matrices	/var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.141641_hJU8mO/compare-matrices_query_matrices.transfac
;		file1	1	16	23	ccCGKCCCGTCCCGTy
;	file2	3463 matrices	/var/www/html/rsat/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf
;		file2		1		8		5		awmAGTTr
;		file2		2		8		3		rkTAGTTr
;		file2		3		8		5		wamaGTTr
;		file2		4		8		1		GTTAGTTA
;		file2		5		8		2		kwCwGTTr
;		file2		6		8		2		GTTAGTTr
;		file2		7		8		6		wwmaGTTr
;		file2		8		8		2		rsTkGTTr
;		file2		9		8		8		RkTwGKTr
;		file2		10		8		1		TACTGTTG
;		file2		11		8		4		WhhWGTTr
;		...	3453 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	logoDP       	Dot product between the logo matrices.
;	8	NSW          	Normalized Sandelin-Wasserman similarity. NSW = SW/w
;	9	NsEucl       	relative Euclidian similarity. NsEucl = (max(dEucl) - dEucl)/max(dEucl)
;	10	w1           	Width of the first matrix
;	11	w2           	Width of the second matrix
;	12	w            	Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset)
;	13	W            	Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w
;	14	Wr           	Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W
;	15	wr1          	Alignment length relative to the width of the first matrix. wr1 = w/w1
;	16	wr2          	Alignment length relative to the width of the second matrix. wr2 = w/w2
;	17	strand       	"strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct;  R=reverse)
;	18	offset       	shift of the second matrix relative to the first matrix (negative:left; positive: right)
;	19	consensus1   	IUPAC consensus of matrix 1 (dots represent non-aligned columns)
;	20	consensus2   	IUPAC consensus of matrix 2 (dots represent non-aligned columns)
;	21	rcor         	Matching rank for cor
;	22	rNcor        	Matching rank for Ncor
;	23	rlogoDP      	Matching rank for logoDP
;	24	rNsEucl      	Matching rank for NsEucl
;	25	rNSW         	Matching rank for NSW
;	26	rank_mean    	Mean of the matching ranks on all selected metrics
;	27	match_rank   	Rank of the match (sorting by rank_mean)
#id1	id2	name1	name2	cor	Ncor	logoDP	NSW	NsEucl	w1	w2	w	W	Wr	wr1	wr2	strand	offset	consensus1	consensus2	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank
; Host name	rsat
; Job started	2026-05-29.141641
; Job done	2026-05-29.141655
; Seconds	13.66
;	user	13.66
;	system	0.19
;	cuser	0
;	csystem	0.01