/var/www/html/rsat/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.101952_AsEjLa/compare-matrices.tab 
 compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.101952_AsEjLa/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_2026-04-09.101952_AsEjLa/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_2026-04-09.101952_AsEjLa/compare-matrices_query_matrices.transfac
 Output files
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.101952_AsEjLa/compare-matrices_alignments_1ton.html
	alignments_1ton	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.101952_AsEjLa/compare-matrices_alignments_1ton.tab
	match_table_html	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.101952_AsEjLa/compare-matrices.html
	prefix       	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.101952_AsEjLa/compare-matrices
	html_index   	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.101952_AsEjLa/compare-matrices_index.html
	match_table_txt	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.101952_AsEjLa/compare-matrices.tab
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.101952_AsEjLa/compare-matrices_query_matrices.transfac
		file1	1	15	2777	wwAAAATTAAAATww
	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_7nt_m4 SOL1_MA1379.1_JASPAR positions_7nt_m4 SOL1:MA1379.1:JASPAR 0.832 0.636 5.755 0.928 0.92547 15 15 13 17 0.7647 0.8667 0.8667 D -2 wwAAAATTAAAAT.. ..wwAAAATTYAAAw 6 7 6 2 4 5.0000 1
positions_7nt_m4 AT2G17410.DAP_M0147_AthalianaCistrome positions_7nt_m4 AT2G17410.DAP:M0147:AthalianaCistrome 0.833 0.555 5.204 0.933 0.92517 15 15 12 18 0.6667 0.8000 0.8000 D -3 wwAAAATTAAAA... ...wtrAAATYAAwW 3 14 10 3 1 6.2000 2
positions_7nt_m4 ARID3_UN0388.1_JASPAR positions_7nt_m4 ARID3:UN0388.1:JASPAR 0.833 0.555 5.204 0.933 0.92517 15 15 12 18 0.6667 0.8000 0.8000 D -3 wwAAAATTAAAA... ...wtrAAATYAAwW 4 15 9 4 2 6.8000 3
positions_7nt_m4 TCX3_MA1682.1_JASPAR positions_7nt_m4 TCX3:MA1682.1:JASPAR 0.803 0.750 5.343 0.920 0.92456 15 14 14 15 0.9333 0.9333 1.0000 D 1 .wAAAATTAAAATww wwAAATTCAAATww 13 1 7 5 10 7.2000 4
positions_7nt_m4 TSO1_MA1161.1_JASPAR positions_7nt_m4 TSO1:MA1161.1:JASPAR 0.832 0.555 6.071 0.922 0.91947 15 15 12 18 0.6667 0.8000 0.8000 D -3 wwAAAATTAAAA... ...TwaAAATTYAAA 5 16 2 9 8 8.0000 5
positions_7nt_m4 TCX2.ampDAP_M0355_AthalianaCistrome positions_7nt_m4 TCX2.ampDAP:M0355:AthalianaCistrome 0.806 0.655 5.882 0.917 0.91990 15 14 13 16 0.8125 0.8667 0.9286 D -1 wwAAAATTAAAAT.. .TyaAAATTyRAAw 12 5 5 8 11 8.2000 6
positions_7nt_m4 AT1G20910.DAP_M0143_AthalianaCistrome positions_7nt_m4 AT1G20910.DAP:M0143:AthalianaCistrome 0.842 0.617 3.907 0.932 0.92120 15 11 11 15 0.7333 0.7333 1.0000 R 3 ...AAATTAAAATw. AAATTRAWTTW 2 11 18 7 3 8.2000 7
positions_7nt_m4 TCX2_MA1162.1_JASPAR positions_7nt_m4 TCX2:MA1162.1:JASPAR 0.807 0.617 6.096 0.915 0.91937 15 15 13 17 0.7647 0.8667 0.8667 D -2 wwAAAATTAAAAT.. ..TyaAAATTyRAAw 10 10 1 11 12 8.8000 8
positions_7nt_m4 AT2G20110.ampDAP_M0354_AthalianaCistrome positions_7nt_m4 AT2G20110.ampDAP:M0354:AthalianaCistrome 0.809 0.708 2.221 0.927 0.92800 15 15 14 16 0.8750 0.9333 0.9333 R -1 wwAAAATTAAAATw. .TTMAAATTYAAAWT 9 2 29 1 6 9.4000 9
positions_7nt_m4 AT2G20110_MA1380.1_JASPAR positions_7nt_m4 AT2G20110:MA1380.1:JASPAR 0.814 0.623 3.834 0.923 0.92280 15 15 13 17 0.7647 0.8667 0.8667 R -2 wwAAAATTAAAAT.. ..WAAAWATTYAAAW 7 9 19 6 7 9.6000 10
positions_7nt_m4 TCX3_MA1682.2_JASPAR positions_7nt_m4 TCX3:MA1682.2:JASPAR 0.813 0.650 5.292 0.915 0.91581 15 12 12 15 0.8000 0.8000 1.0000 D 3 ...AAATTAAAATww AAATTCAAATww 8 6 8 14 13 9.8000 11
positions_7nt_m4 ATHB-23_MA1327.3_JASPAR positions_7nt_m4 ATHB-23:MA1327.3:JASPAR 0.888 0.414 5.901 0.928 0.89837 15 7 7 15 0.4667 0.4667 1.0000 D 3 ...AAATTAA..... tAATTAA 1 42 4 31 5 16.6000 12
positions_7nt_m4 SOL1.ampDAP_M0356_AthalianaCistrome positions_7nt_m4 SOL1.ampDAP:M0356:AthalianaCistrome 0.748 0.655 2.398 0.901 0.91577 15 15 14 16 0.8750 0.9333 0.9333 R -1 wwAAAATTAAAATw. .TTVAAATTYRAAWT 25 4 26 15 24 18.8000 13
positions_7nt_m4 BBX31.DAP_M0718_AthalianaCistrome positions_7nt_m4 BBX31.DAP:M0718:AthalianaCistrome 0.721 0.631 4.541 0.896 0.91386 15 15 14 16 0.8750 0.9333 0.9333 D 1 .wAAAATTAAAATww AAAAAGtaAAAaaw. 35 8 14 18 30 21.0000 14
positions_7nt_m4 At1g76110.DAP_M0146_AthalianaCistrome positions_7nt_m4 At1g76110.DAP:M0146:AthalianaCistrome 0.772 0.566 1.627 0.901 0.90507 15 11 11 15 0.7333 0.7333 1.0000 R 4 ....AATTAAAATww AATTAAWTWWW 19 12 37 22 22 22.4000 15
positions_7nt_m4 HMGB9_UN0401.1_JASPAR positions_7nt_m4 HMGB9:UN0401.1:JASPAR 0.771 0.566 1.626 0.901 0.90506 15 11 11 15 0.7333 0.7333 1.0000 R 4 ....AATTAAAATww AATTAAWTWWW 20 13 38 23 23 23.4000 16
positions_7nt_m4 TCX5_UN0411.1_JASPAR positions_7nt_m4 TCX5:UN0411.1:JASPAR 0.757 0.504 4.560 0.896 0.89780 15 10 10 15 0.6667 0.6667 1.0000 D 4 ....AATTAAAATw. aaTTCAAAyt 21 19 13 32 33 23.6000 17
positions_7nt_m4 dof24.DAP_M0252_AthalianaCistrome positions_7nt_m4 dof24.DAP:M0252:AthalianaCistrome 0.707 0.707 0.875 0.899 0.91812 15 15 15 15 1.0000 1.0000 1.0000 R 0 wwAAAATTAAAATww MAAAAAGTWAAAWWW 41 3 42 13 27 25.2000 18
positions_7nt_m4 DOF1.7_MA1277.2_JASPAR positions_7nt_m4 DOF1.7:MA1277.2:JASPAR 0.737 0.540 4.048 0.890 0.90011 15 11 11 15 0.7333 0.7333 1.0000 D 1 .wAAAATTAAAA... aAAAAGtaraa 28 17 16 27 38 25.2000 19
positions_7nt_m4 AT4G29000_M0591_1.02_CISBP positions_7nt_m4 AT4G29000:M0591_1.02:CISBP 0.756 0.504 4.007 0.895 0.89758 15 10 10 15 0.6667 0.6667 1.0000 R 4 ....AATTAAAATw. AATTCAAAYT 22 20 17 33 35 25.4000 20
positions_7nt_m4 ATHB23_MA1327.2_JASPAR positions_7nt_m4 ATHB23:MA1327.2:JASPAR 0.752 0.501 5.979 0.879 0.89011 15 10 10 15 0.6667 0.6667 1.0000 D 2 ..AAAATTAAAA... wtAATTAAww 24 21 3 37 43 25.6000 21
positions_7nt_m4 AT3G04850_M0589_1.02_CISBP positions_7nt_m4 AT3G04850:M0589_1.02:CISBP 0.736 0.491 1.977 0.904 0.90205 15 10 10 15 0.6667 0.6667 1.0000 R 4 ....AATTAAAATw. AWTTYRAAWT 30 23 32 25 18 25.6000 22
positions_7nt_m4 PK22848.1_M0587_1.02_CISBP positions_7nt_m4 PK22848.1:M0587_1.02:CISBP 0.738 0.478 0.876 0.906 0.90773 15 13 11 17 0.6471 0.7333 0.8462 R 4 ....AATTAAAATww TWTTWAAATTT.. 27 26 41 20 15 25.8000 23
positions_7nt_m4 AT5G02460_MA1281.1_JASPAR positions_7nt_m4 AT5G02460:MA1281.1:JASPAR 0.709 0.451 1.690 0.909 0.91942 15 21 14 22 0.6364 0.9333 0.6667 D -7 wwAAAATTAAAATw. .......waAAaaraaaaara 39 31 35 10 14 25.8000 24
positions_7nt_m4 AHL20_MA0933.1_JASPAR positions_7nt_m4 AHL20:MA0933.1:JASPAR 0.791 0.422 3.126 0.905 0.89090 15 8 8 15 0.5333 0.5333 1.0000 D 4 ....AATTAAAA... AATWAAwT 15 39 23 36 16 25.8000 25
positions_7nt_m4 At1g76110.ampDAP_M0145_AthalianaCistrome positions_7nt_m4 At1g76110.ampDAP:M0145:AthalianaCistrome 0.748 0.433 2.339 0.902 0.90537 15 15 11 19 0.5789 0.7333 0.7333 R 4 ....AATTAAAATww AATTWAATTWT.... 26 35 27 21 21 26.0000 26
positions_7nt_m4 YAB5_UN0416.2_JASPAR positions_7nt_m4 YAB5:UN0416.2:JASPAR 0.781 0.416 3.043 0.903 0.88977 15 8 8 15 0.5333 0.5333 1.0000 D 2 ..AAAATTAA..... ATaATTAw 16 40 24 38 19 27.4000 27
positions_7nt_m4 AT5G66940.ampDAP_M0257_AthalianaCistrome positions_7nt_m4 AT5G66940.ampDAP:M0257:AthalianaCistrome 0.700 0.500 1.087 0.902 0.91907 15 21 15 21 0.7143 1.0000 0.7143 R -6 wwAAAATTAAAATww ......SAAAAAGTARAAAAA 46 22 39 12 20 27.8000 28
positions_7nt_m4 DOF5.1_MA1281.2_JASPAR positions_7nt_m4 DOF5.1:MA1281.2:JASPAR 0.716 0.444 1.687 0.904 0.91421 15 19 13 21 0.6190 0.8667 0.6842 D -6 wwAAAATTAAAAT.. ......waAAaaraaaaar 36 33 36 17 17 27.8000 29
positions_7nt_m4 DOF5.8_MA1267.2_JASPAR positions_7nt_m4 DOF5.8:MA1267.2:JASPAR 0.723 0.506 0.594 0.900 0.91535 15 19 14 20 0.7000 0.9333 0.7368 R 1 .wAAAATTAAAATww AAAAAGTAAAAARA..... 34 18 45 16 26 27.8000 30
positions_7nt_m4 TCX5_UN0411.2_JASPAR positions_7nt_m4 TCX5:UN0411.2:JASPAR 0.795 0.424 4.563 0.895 0.88561 15 8 8 15 0.5333 0.5333 1.0000 D 5 .....ATTAAAAT.. aTTCAAAy 14 38 12 43 34 28.2000 31
positions_7nt_m4 AHL25_AHL25_3_ArabidopsisPBM positions_7nt_m4 AHL25:AHL25_3:ArabidopsisPBM 0.727 0.485 2.002 0.900 0.90011 15 10 10 15 0.6667 0.6667 1.0000 R 4 ....AATTAAAATw. WAWTWWWWTW 33 25 31 28 25 28.4000 32
positions_7nt_m4 LOC_Os02g57820_M0137_1.02_CISBP positions_7nt_m4 LOC_Os02g57820:M0137_1.02:CISBP 0.756 0.403 0.936 0.920 0.90030 15 8 8 15 0.5333 0.5333 1.0000 D 0 wwAAAATT....... awwwAwww 23 45 40 26 9 28.6000 33
positions_7nt_m4 WOX13_WOX13_2_ArabidopsisPBM positions_7nt_m4 WOX13:WOX13_2:ArabidopsisPBM 0.730 0.486 1.958 0.898 0.89919 15 10 10 15 0.6667 0.6667 1.0000 R 1 .wAAAATTAAA.... KTTAATTAAA 32 24 33 30 29 29.6000 34
positions_7nt_m4 DOF1.5_MA1279.2_JASPAR positions_7nt_m4 DOF1.5:MA1279.2:JASPAR 0.709 0.448 4.109 0.886 0.90263 15 16 12 19 0.6316 0.8000 0.7500 D -4 wwAAAATTAAAA... ....rAAAAAGtraaa 38 32 15 24 41 30.0000 35
positions_7nt_m4 Medtr8g106590.1_M0145_1.02_CISBP positions_7nt_m4 Medtr8g106590.1:M0145_1.02:CISBP 0.777 0.414 3.644 0.896 0.88584 15 8 8 15 0.5333 0.5333 1.0000 D 3 ...AAATTAAA.... AAAWTAAT 17 41 20 42 32 30.4000 36
positions_7nt_m4 SOL1_M0590_1.02_CISBP positions_7nt_m4 SOL1:M0590_1.02:CISBP 0.772 0.412 3.419 0.896 0.88599 15 8 8 15 0.5333 0.5333 1.0000 R 5 .....ATTAAAAT.. WTTYAAAY 18 43 21 41 31 30.8000 37
positions_7nt_m4 OBP3.ampDAP_M0274_AthalianaCistrome positions_7nt_m4 OBP3.ampDAP:M0274:AthalianaCistrome 0.736 0.402 1.918 0.899 0.90823 15 19 12 22 0.5455 0.8000 0.6316 R -7 wwAAAATTAAAA... .......TWAAARAAWAAA 29 46 34 19 28 31.2000 38
positions_7nt_m4 ATGRP2B_M0583_1.02_CISBP positions_7nt_m4 ATGRP2B:M0583_1.02:CISBP 0.806 0.430 2.296 0.889 0.88226 15 8 8 15 0.5333 0.5333 1.0000 R 4 ....AATTAAAA... AAWAAAAM 11 36 28 45 40 32.0000 39
positions_7nt_m4 AHL20_AHL20_3_ArabidopsisPBM positions_7nt_m4 AHL20:AHL20_3:ArabidopsisPBM 0.708 0.472 2.483 0.893 0.89649 15 10 10 15 0.6667 0.6667 1.0000 D 4 ....AATTAAAATw. tAwwWWwwTa 40 27 25 34 36 32.4000 40
positions_7nt_m4 ZHD1_MA1329.3_JASPAR positions_7nt_m4 ZHD1:MA1329.3:JASPAR 0.730 0.438 4.913 0.862 0.87598 15 9 9 15 0.6000 0.6000 1.0000 D 1 .wAAAATTAA..... AyTAATTAA 31 34 11 46 46 33.6000 41
positions_7nt_m4 AHL12_AHL12_3_ArabidopsisPBM positions_7nt_m4 AHL12:AHL12_3:ArabidopsisPBM 0.700 0.467 2.188 0.892 0.89598 15 10 10 15 0.6667 0.6667 1.0000 R 4 ....AATTAAAATw. WAWWWWWWTW 45 30 30 35 37 35.4000 42
positions_7nt_m4 AHL20_AHL20_2_ArabidopsisPBM positions_7nt_m4 AHL20:AHL20_2:ArabidopsisPBM 0.701 0.467 3.212 0.874 0.88791 15 10 10 15 0.6667 0.6667 1.0000 D 3 ...AAATTAAAAT.. hAATWAAwTa 44 29 22 40 45 36.0000 43
positions_7nt_m4 EMB1789.DAP_M0345_AthalianaCistrome positions_7nt_m4 EMB1789.DAP:M0345:AthalianaCistrome 0.702 0.406 0.654 0.889 0.89968 15 15 11 19 0.5789 0.7333 0.7333 R -4 wwAAAATTAAA.... ....TAAAAAAWDWW 42 44 43 29 39 39.4000 44
positions_7nt_m4 fgeneshCV_pg.C_scaffold_18000164_M0599_1.02_CISBP positions_7nt_m4 fgeneshCV_pg.C_scaffold_18000164:M0599_1.02:CISBP 0.701 0.467 0.633 0.876 0.88857 15 10 10 15 0.6667 0.6667 1.0000 R 3 ...AAATTAAAAT.. WWWTTYAAAH 43 28 44 39 44 39.6000 45
positions_7nt_m4 BRADI5G22430_M0121_1.02_CISBP positions_7nt_m4 BRADI5G22430:M0121_1.02:CISBP 0.715 0.429 0.531 0.880 0.88432 15 9 9 15 0.6000 0.6000 1.0000 D 1 .wAAAATTAA..... rsawwwwar 37 37 46 44 42 41.2000 46 
 Host name	rsat
 Job started	2026-04-09.101952
 Job done	2026-04-09.102015
 Seconds	13.28
	user	13.28
	system	1.26
	cuser	6.45
;	csystem	1.97