/var/www/html/rsat/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163202_s4iGzw/compare-matrices.tab 
 compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163202_s4iGzw/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/2026/01/09/compare-matrices_2026-01-09.163202_s4iGzw/compare-matrices.tab
 Program version       	1.118
 Slow mode 
 Input files
	file1 	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163202_s4iGzw/compare-matrices_query_matrices.transfac
	file2 	$RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf
 Output files
	match_table_html	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163202_s4iGzw/compare-matrices.html
	html_index   	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163202_s4iGzw/compare-matrices_index.html
	prefix       	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163202_s4iGzw/compare-matrices
	alignments_1ton	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163202_s4iGzw/compare-matrices_alignments_1ton.tab
	match_table_txt	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163202_s4iGzw/compare-matrices.tab
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163202_s4iGzw/compare-matrices_alignments_1ton.html
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.163202_s4iGzw/compare-matrices_query_matrices.transfac
		file1	1	12	3939	wwTATAGwATww
	file2	3346 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
		...	3336 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
cluster_3 AT1G04880.DAP_M0148_AthalianaCistrome cluster_3 AT1G04880.DAP:M0148:AthalianaCistrome 0.826 0.534 4.964 0.928 0.91923 12 16 11 17 0.6471 0.9167 0.6875 D -5 wwTATAGwATw. .....TATAWaGTTTw 4 4 5 2 5 4.0000 1
cluster_3 HMGB15_UN0400.1_JASPAR cluster_3 HMGB15:UN0400.1:JASPAR 0.826 0.534 4.964 0.928 0.91921 12 16 11 17 0.6471 0.9167 0.6875 D -5 wwTATAGwATw. .....TATAWaGTTTw 5 5 6 3 6 5.0000 2
cluster_3 AT1G04880.ampDAP_M0144_AthalianaCistrome cluster_3 AT1G04880.ampDAP:M0144:AthalianaCistrome 0.801 0.551 5.009 0.917 0.91313 12 15 11 16 0.6875 0.9167 0.7333 D -4 wwTATAGwATw. ....yATATawTATA 8 2 4 4 9 5.4000 3
cluster_3 AGL3_AGL3_Athamap cluster_3 AGL3:AGL3:Athamap 0.790 0.458 2.513 0.932 0.92111 12 18 11 19 0.5789 0.9167 0.6111 D -7 wwTATAGwATw. .......wwwWwrGwwab 9 12 10 1 4 7.2000 4
cluster_3 TRANSCRIPTION_1qnb_B_3D-footprint cluster_3 TRANSCRIPTION:1qnb_B:3D-footprint 0.876 0.404 4.581 0.936 0.89683 12 7 6 13 0.4615 0.5000 0.8571 D -1 wwTATA...... .tTTATA 1 17 8 9 2 7.4000 5
cluster_3 AGL3_MA0001.3_JASPAR cluster_3 AGL3:MA0001.3:JASPAR 0.867 0.404 2.396 0.946 0.91188 12 10 7 15 0.4667 0.5833 0.7000 D -3 wwTATAG..... ...wwwWwrG 3 16 12 5 1 7.4000 6
cluster_3 PRH_M1167_1.02_CISBP cluster_3 PRH:M1167_1.02:CISBP 0.802 0.535 6.409 0.890 0.88273 12 8 8 12 0.6667 0.6667 1.0000 D 1 .wTATAGwA... ATATATwA 7 3 3 14 15 8.4000 7
cluster_3 TATA-box-binding_6njq_A_3D-footprint cluster_3 TATA-box-binding:6njq_A:3D-footprint 0.869 0.401 4.737 0.928 0.89018 12 7 6 13 0.4615 0.5000 0.8571 D -1 wwTATA...... .TTTATA 2 19 7 12 7 9.4000 8
cluster_3 FUL-3_EEAD0142_EEADannot cluster_3 FUL-3:EEAD0142:EEADannot 0.736 0.589 2.062 0.905 0.91101 12 15 12 15 0.8000 1.0000 0.8000 R -2 wwTATAGwATww ..TTTATRGTAWGT. 15 1 15 6 12 9.8000 9
cluster_3 AGL15_AGL15_Athamap cluster_3 AGL15:AGL15:Athamap 0.773 0.429 2.279 0.920 0.91057 12 16 10 18 0.5556 0.8333 0.6250 D -6 wwTATAGwAT.. ......wwwwwrGwAa 11 14 14 7 8 10.8000 10
cluster_3 KAN1_MA1027.2_JASPAR cluster_3 KAN1:MA1027.2:JASPAR 0.803 0.402 0.789 0.935 0.89583 12 6 6 12 0.5000 0.5000 1.0000 R 6 ......GwATww GAATAW 6 18 20 10 3 11.4000 11
cluster_3 TRANSCRIPTION_1qn6_B_3D-footprint cluster_3 TRANSCRIPTION:1qn6_B:3D-footprint 0.743 0.495 6.488 0.859 0.86742 12 8 8 12 0.6667 0.6667 1.0000 D 2 ..TATAGwAT.. TATAAtAg 14 7 1 18 18 11.6000 12
cluster_3 SEP1_MA0584.2_JASPAR cluster_3 SEP1:MA0584.2:JASPAR 0.704 0.469 2.417 0.895 0.89767 12 13 10 15 0.6667 0.8333 0.7692 D -3 wwTATAGwAT.. ...wWwwTrGwAa 20 11 11 8 14 12.8000 13
cluster_3 DcWRKY75_EEAD0058_EEADannot cluster_3 DcWRKY75:EEAD0058:EEADannot 0.747 0.436 2.396 0.900 0.88077 12 7 7 12 0.5833 0.5833 1.0000 D 5 .....AGwATww AGAAkbT 12 13 13 15 13 13.2000 14
cluster_3 AHL20_AHL20_ArabidopsisPBM cluster_3 AHL20:AHL20:ArabidopsisPBM 0.709 0.491 4.380 0.864 0.87703 12 10 9 13 0.6923 0.7500 0.9000 D -1 wwTATAGwA... .AATATATTw 17 8 9 16 17 13.4000 15
cluster_3 TRANSCRIPTION_1qn4_B_3D-footprint cluster_3 TRANSCRIPTION:1qn4_B:3D-footprint 0.779 0.520 0.886 0.879 0.87703 12 8 8 12 0.6667 0.6667 1.0000 R 2 ..TATAGwAT.. TATAAAAT 10 6 19 17 16 13.6000 16
cluster_3 AHL20_AHL20_3_ArabidopsisPBM cluster_3 AHL20:AHL20_3:ArabidopsisPBM 0.709 0.405 1.585 0.910 0.89379 12 10 8 14 0.5714 0.6667 0.8000 R 4 ....TAGwATww TAWWWWWW.. 18 15 16 11 10 14.0000 17
cluster_3 TATA_1vto_B_3D-footprint cluster_3 TATA:1vto_B:3D-footprint 0.706 0.470 6.472 0.839 0.85812 12 8 8 12 0.6667 0.6667 1.0000 D 2 ..TATAGwAT.. TATAAaAg 19 10 2 20 20 14.2000 18
cluster_3 AT1G14600_MA1706.2_JASPAR cluster_3 AT1G14600:MA1706.2:JASPAR 0.743 0.400 1.303 0.908 0.88512 12 8 7 13 0.5385 0.5833 0.8750 R 5 .....AGwATww RGAATRT. 13 20 17 13 11 14.8000 19
cluster_3 TRANSCRIPTION_1qne_B_3D-footprint cluster_3 TRANSCRIPTION:1qne_B:3D-footprint 0.710 0.473 0.890 0.841 0.85919 12 8 8 12 0.6667 0.6667 1.0000 R 2 ..TATAGwAT.. TATAAAAG 16 9 18 19 19 16.2000 20 
 Host name	rsat
 Job started	2026-01-09.163202
 Job done	2026-01-09.163217
 Seconds	10.54
	user	10.54
	system	0.58
	cuser	2.73
;	csystem	0.86