/var/www/html/rsat/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.173131_9JJg0K/compare-matrices.tab 
 compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.173131_9JJg0K/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_2026-01-09.173131_9JJg0K/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/2026/01/09/compare-matrices_2026-01-09.173131_9JJg0K/compare-matrices_query_matrices.transfac
 Output files
	html_index   	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.173131_9JJg0K/compare-matrices_index.html
	match_table_txt	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.173131_9JJg0K/compare-matrices.tab
	prefix       	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.173131_9JJg0K/compare-matrices
	match_table_html	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.173131_9JJg0K/compare-matrices.html
	alignments_1ton	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.173131_9JJg0K/compare-matrices_alignments_1ton.tab
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.173131_9JJg0K/compare-matrices_alignments_1ton.html
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/www-data/2026/01/09/compare-matrices_2026-01-09.173131_9JJg0K/compare-matrices_query_matrices.transfac
		file1	1	11	290	wwGTGGGGAwa
	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_4 TCP24.ampDAP_M0768_AthalianaCistrome cluster_4 TCP24.ampDAP:M0768:AthalianaCistrome 0.808 0.560 4.972 0.897 0.89321 11 11 9 13 0.6923 0.8182 0.8182 D 2 ..GTGGGGAwa GTGGGGACC.. 12 1 4 3 7 5.4000 1
cluster_4 ARF39_EEAD0041_EEADannot cluster_4 ARF39:EEAD0041:EEADannot 0.848 0.539 4.575 0.897 0.87897 11 7 7 11 0.6364 0.6364 1.0000 D 4 ....GGGGAwa GGGGACA 3 5 5 12 6 6.2000 2
cluster_4 TCP17_MA1290.1_JASPAR cluster_4 TCP17:MA1290.1:JASPAR 0.805 0.557 3.522 0.900 0.89460 11 11 9 13 0.6923 0.8182 0.8182 R 2 ..GTGGGGAwa GTGGGGACC.. 17 2 11 2 5 7.4000 3
cluster_4 StCONSTANSlike1_EEAD0013_EEADannot cluster_4 StCONSTANSlike1:EEAD0013:EEADannot 0.810 0.515 4.364 0.903 0.88243 11 7 7 11 0.6364 0.6364 1.0000 D 1 .wGTGGGG... TGTGGTG 10 7 10 9 4 8.0000 4
cluster_4 TCP13_MA1282.2_JASPAR cluster_4 TCP13:MA1282.2:JASPAR 0.797 0.552 4.446 0.895 0.89209 11 11 9 13 0.6923 0.8182 0.8182 D 2 ..GTGGGGAwa GTGGGGACC.. 18 3 8 4 8 8.2000 5
cluster_4 PTF1_MA1282.1_JASPAR cluster_4 PTF1:MA1282.1:JASPAR 0.797 0.478 4.446 0.895 0.89209 11 13 9 15 0.6000 0.8182 0.6923 D 2 ..GTGGGGAwa GTGGGGACC.... 18 9 8 4 8 9.4000 6
cluster_4 TCP17.ampDAP_M0766_AthalianaCistrome cluster_4 TCP17.ampDAP:M0766:AthalianaCistrome 0.793 0.549 4.481 0.894 0.89126 11 11 9 13 0.6923 0.8182 0.8182 D 2 ..GTGGGGAwa gTGGGGACC.. 20 4 7 6 11 9.6000 7
cluster_4 O2DREME_EEAD0018_EEADannot cluster_4 O2DREME:EEAD0018:EEADannot 0.886 0.409 1.820 0.920 0.88480 11 8 6 13 0.4615 0.5455 0.7500 R -2 wwGTGG..... ..AYGTGG 2 24 19 7 2 10.8000 8
cluster_4 CO-NF-trimer_EEAD0156_EEADannot cluster_4 CO-NF-trimer:EEAD0156:EEADannot 0.902 0.410 0.176 0.933 0.88435 11 5 5 11 0.4545 0.4545 1.0000 R 1 .wGTGG..... TGTGR 1 21 27 8 1 11.6000 9
cluster_4 ASHR1.DAP_M0716_AthalianaCistrome cluster_4 ASHR1.DAP:M0716:AthalianaCistrome 0.726 0.533 1.475 0.895 0.90219 11 15 11 15 0.7333 1.0000 0.7333 R 0 wwGTGGGGAwa TGATGGTGAWG.... 24 6 20 1 10 12.2000 10
cluster_4 Zm00001d034298_MA1834.2_JASPAR cluster_4 Zm00001d034298:MA1834.2:JASPAR 0.825 0.413 0.664 0.915 0.88074 11 7 6 12 0.5000 0.5455 0.8571 R -1 wwGTGG..... .GCGTGG 6 20 24 11 3 12.8000 11
cluster_4 DEP_UN0855.1_JASPAR cluster_4 DEP:UN0855.1:JASPAR 0.814 0.444 5.956 0.873 0.85474 11 6 6 11 0.5455 0.5455 1.0000 D 3 ...TGGGGA.. TGGTGA 7 10 1 24 22 12.8000 12
cluster_4 FEM111.DAP_M0491_AthalianaCistrome cluster_4 FEM111.DAP:M0491:AthalianaCistrome 0.814 0.444 5.956 0.873 0.85474 11 6 6 11 0.5455 0.5455 1.0000 D 3 ...TGGGGA.. TGGTGA 7 10 1 24 22 12.8000 13
cluster_4 bHLH112_MA0961.2_JASPAR cluster_4 bHLH112:MA0961.2:JASPAR 0.836 0.418 2.498 0.889 0.86424 11 7 6 12 0.5000 0.5455 0.8571 R -1 wwGTGG..... .AAGTGG 4 16 15 17 13 13.0000 14
cluster_4 OsFBH1_MA2350.1_JASPAR cluster_4 OsFBH1:MA2350.1:JASPAR 0.836 0.418 2.498 0.889 0.86424 11 7 6 12 0.5000 0.5455 0.8571 R -1 wwGTGG..... .AAGTGG 5 17 16 18 14 14.0000 15
cluster_4 At1g70910.DAP_M0349_AthalianaCistrome cluster_4 At1g70910.DAP:M0349:AthalianaCistrome 0.809 0.515 0.288 0.887 0.87302 11 7 7 11 0.6364 0.6364 1.0000 R 3 ...TGGGGAw. TGGTGAK 11 8 25 13 16 14.6000 16
cluster_4 AT2G48100_UN0843.1_JASPAR cluster_4 AT2G48100:UN0843.1:JASPAR 0.807 0.440 5.546 0.874 0.85490 11 6 6 11 0.5455 0.5455 1.0000 D 3 ...TGGGGA.. TGGTGA 15 14 3 22 20 14.8000 17
cluster_4 AGL80_UN0852.1_JASPAR cluster_4 AGL80:UN0852.1:JASPAR 0.814 0.444 2.866 0.873 0.85474 11 6 6 11 0.5455 0.5455 1.0000 R 3 ...TGGGGA.. TGGTGA 7 10 12 24 22 15.0000 18
cluster_4 BHLH112_MA0961.1_JASPAR cluster_4 BHLH112:MA0961.1:JASPAR 0.770 0.414 2.501 0.877 0.86761 11 9 7 13 0.5385 0.6364 0.7778 R -2 wwGTGGG.... ..AAGTGGS 21 18 13 14 17 16.6000 19
cluster_4 AGL55_MA1202.1_JASPAR cluster_4 AGL55:MA1202.1:JASPAR 0.807 0.440 2.368 0.874 0.85503 11 6 6 11 0.5455 0.5455 1.0000 R 3 ...TGGGGA.. TGGTGA 14 13 18 21 19 17.0000 20
cluster_4 bhlh112_M0229_1.02_CISBP cluster_4 bhlh112:M0229_1.02:CISBP 0.769 0.414 2.501 0.877 0.86752 11 9 7 13 0.5385 0.6364 0.7778 R -2 wwGTGGG.... ..AAGTGGS 22 19 14 15 18 17.6000 21
cluster_4 At2g48100.DAP_M0339_AthalianaCistrome cluster_4 At2g48100.DAP:M0339:AthalianaCistrome 0.807 0.440 2.417 0.874 0.85490 11 6 6 11 0.5455 0.5455 1.0000 R 3 ...TGGGGA.. TGGTGA 16 15 17 23 21 18.4000 22
cluster_4 ABF4_MA1659.2_JASPAR cluster_4 ABF4:MA1659.2:JASPAR 0.808 0.404 0.268 0.891 0.86525 11 7 6 12 0.5000 0.5455 0.8571 R -1 wwGTGG..... .ACGTGG 13 26 26 16 12 18.6000 23
cluster_4 Zm00001d034298_MA1834.1_JASPAR cluster_4 Zm00001d034298:MA1834.1:JASPAR 0.716 0.409 0.675 0.888 0.88158 11 11 8 14 0.5714 0.7273 0.7273 R -3 wwGTGGGG... ...GCGTGGGS 25 22 23 10 15 19.0000 24
cluster_4 BHLH168_ZmSPT2_Mo17_1_EEAD0221_EEADannot cluster_4 BHLH168_ZmSPT2_Mo17_1:EEAD0221:EEADannot 0.715 0.409 4.510 0.850 0.86328 11 11 8 14 0.5714 0.7273 0.7273 D -3 wwGTGGGG... ...ACGTGGGc 27 25 6 19 25 20.4000 25
cluster_4 BHLH168_ZmSPT2_B73_3_m1_EEAD0220_EEADannot cluster_4 BHLH168_ZmSPT2_B73_3_m1:EEAD0220:EEADannot 0.716 0.409 1.237 0.848 0.86238 11 11 8 14 0.5714 0.7273 0.7273 R -3 wwGTGGGG... ...ACGTGGGC 26 23 22 20 26 23.4000 26
cluster_4 bZIP44:bZIP63_2_EEAD0123_EEADannot cluster_4 bZIP44:bZIP63_2:EEAD0123:EEADannot 0.737 0.402 1.264 0.848 0.84059 11 6 6 11 0.5455 0.5455 1.0000 R 0 wwGTGG..... ACGTGK 23 27 21 27 27 25.0000 27 
 Host name	rsat
 Job started	2026-01-09.173131
 Job done	2026-01-09.173147
 Seconds	10.09
	user	10.09
	system	0.71
	cuser	3.73
;	csystem	1.13