/var/www/html/rsat/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.105353_3PThzu/compare-matrices.tab 
 compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.105353_3PThzu/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/2026/04/09/compare-matrices_2026-04-09.105353_3PThzu/compare-matrices.tab
 Program version       	1.118
 Slow mode 
 Input files
	file2 	$RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf
	file1 	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.105353_3PThzu/compare-matrices_query_matrices.transfac
 Output files
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.105353_3PThzu/compare-matrices_alignments_1ton.html
	alignments_1ton	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.105353_3PThzu/compare-matrices_alignments_1ton.tab
	prefix       	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.105353_3PThzu/compare-matrices
	match_table_txt	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.105353_3PThzu/compare-matrices.tab
	html_index   	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.105353_3PThzu/compare-matrices_index.html
	match_table_html	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.105353_3PThzu/compare-matrices.html
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.105353_3PThzu/compare-matrices_query_matrices.transfac
		file1	1	21	768	wwtTAAATAAATTAAAATTww
	file2	3463 matrices	$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
positions_6nt_m2 ARID3_UN0388.1_JASPAR positions_6nt_m2 ARID3:UN0388.1:JASPAR 0.827 0.467 3.188 0.936 0.92996 21 15 13 23 0.5652 0.6190 0.8667 D 8 ........AAATTAAAATTww AAwwtrAAATYAA.. 3 5 5 1 2 3.2000 1
positions_6nt_m2 AT2G17410.DAP_M0147_AthalianaCistrome positions_6nt_m2 AT2G17410.DAP:M0147:AthalianaCistrome 0.827 0.467 3.188 0.936 0.92995 21 15 13 23 0.5652 0.6190 0.8667 D 8 ........AAATTAAAATTww AAwwtrAAATYAA.. 4 6 6 2 3 4.2000 2
positions_6nt_m2 AT1G20910.DAP_M0143_AthalianaCistrome positions_6nt_m2 AT1G20910.DAP:M0143:AthalianaCistrome 0.837 0.438 3.251 0.932 0.92156 21 11 11 21 0.5238 0.5238 1.0000 R 8 ........AAATTAAAATT.. AAATTRAWTTW 2 8 4 5 4 4.6000 3
positions_6nt_m2 TCX3_MA1682.2_JASPAR positions_6nt_m2 TCX3:MA1682.2:JASPAR 0.810 0.463 4.283 0.915 0.91590 21 12 12 21 0.5714 0.5714 1.0000 D 8 ........AAATTAAAATTw. AAATTCAAATww 5 7 2 8 6 5.6000 4
positions_6nt_m2 AHL25_AHL25_3_ArabidopsisPBM positions_6nt_m2 AHL25:AHL25_3:ArabidopsisPBM 0.847 0.403 2.111 0.944 0.92535 21 10 10 21 0.4762 0.4762 1.0000 R 4 ....AAATAAATTA....... WAWTWWWWTW 1 13 10 3 1 5.6000 5
positions_6nt_m2 TCX3_MA1682.1_JASPAR positions_6nt_m2 TCX3:MA1682.1:JASPAR 0.756 0.504 4.345 0.902 0.91641 21 14 14 21 0.6667 0.6667 1.0000 D 6 ......ATAAATTAAAATTw. wwAAATTCAAATww 10 3 1 7 10 6.2000 6
positions_6nt_m2 PK22848.1_M0587_1.02_CISBP positions_6nt_m2 PK22848.1:M0587_1.02:CISBP 0.783 0.427 0.884 0.932 0.92469 21 13 12 22 0.5455 0.5714 0.9231 R 9 .........AATTAAAATTww TWTTWAAATTTT. 6 10 13 4 5 7.6000 7
positions_6nt_m2 TSO1_MA1161.1_JASPAR positions_6nt_m2 TSO1:MA1161.1:JASPAR 0.761 0.430 3.041 0.913 0.91839 21 15 13 23 0.5652 0.6190 0.8667 D 8 ........AAATTAAAATTww wwwTwaAAATTYA.. 9 9 7 6 7 7.6000 8
positions_6nt_m2 ARID6_UN0351.1_JASPAR positions_6nt_m2 ARID6:UN0351.1:JASPAR 0.727 0.519 2.697 0.893 0.91554 21 15 15 21 0.7143 0.7143 1.0000 R 4 ....AAATAAATTAAAATT.. WWTTCAATTAAWWWW 12 1 9 9 11 8.4000 9
positions_6nt_m2 ARID6_UN0351.2_JASPAR positions_6nt_m2 ARID6:UN0351.2:JASPAR 0.731 0.487 4.075 0.890 0.91147 21 14 14 21 0.6667 0.6667 1.0000 R 4 ....AAATAAATTAAAAT... WWTTCAATTAAWWW 11 4 3 11 13 8.4000 10
positions_6nt_m2 AT2G20110.ampDAP_M0354_AthalianaCistrome positions_6nt_m2 AT2G20110.ampDAP:M0354:AthalianaCistrome 0.712 0.509 2.812 0.891 0.91489 21 15 15 21 0.7143 0.7143 1.0000 R 4 ....AAATAAATTAAAATT.. WTTMAAATTYAAAWT 13 2 8 10 12 9.0000 11
positions_6nt_m2 At1g76110.DAP_M0146_AthalianaCistrome positions_6nt_m2 At1g76110.DAP:M0146:AthalianaCistrome 0.771 0.404 1.547 0.904 0.90671 21 11 11 21 0.5238 0.5238 1.0000 R 0 wwtTAAATAAA.......... AATTAAWTWWW 7 11 11 12 8 9.8000 12
positions_6nt_m2 HMGB9_UN0401.1_JASPAR positions_6nt_m2 HMGB9:UN0401.1:JASPAR 0.771 0.404 1.547 0.904 0.90671 21 11 11 21 0.5238 0.5238 1.0000 R 0 wwtTAAATAAA.......... AATTAAWTWWW 8 12 12 13 9 10.8000 13 
 Host name	rsat
 Job started	2026-04-09.105353
 Job done	2026-04-09.105413
 Seconds	16.91
	user	16.91
	system	0.51
	cuser	1.82
;	csystem	0.54