/var/www/html/rsat/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3_vs_db_footprintDB-plants.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3_vs_db_footprintDB-plants
 Program version       	1.118
 Quick mode 
 Input files
	file1 	$RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3.tf
	file2 	$RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf
 Output files
	alignments_1ton	$RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3_vs_db_footprintDB-plants_alignments_1ton.tab
	html_index   	$RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3_vs_db_footprintDB-plants_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3_vs_db_footprintDB-plants_alignments_1ton.html
	match_table_html	$RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3_vs_db_footprintDB-plants.html
	prefix       	$RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3_vs_db_footprintDB-plants
	match_table_txt	$RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3_vs_db_footprintDB-plants.tab
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3.tf
		file1	1	12	628
	file2	2958 matrices	$RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf
		file2		1		8		5
		file2		2		8		3
		file2		3		8		5
		file2		4		8		1
		file2		5		8		2
		file2		6		8		2
		file2		7		8		6
		file2		8		8		2
		file2		9		8		8
		file2		10		8		1
		file2		11		8		4
		...	2948 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	w1           	Width of the first matrix
	8	w2           	Width of the second matrix
	9	w            	Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset)
	10	W            	Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w
	11	Wr           	Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W
	12	wr1          	Alignment length relative to the width of the first matrix. wr1 = w/w1
	13	wr2          	Alignment length relative to the width of the second matrix. wr2 = w/w2
	14	strand       	"strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct;  R=reverse)
	15	offset       	shift of the second matrix relative to the first matrix (negative:left; positive: right)
id1 id2 name1 name2 cor Ncor w1 w2 w W Wr wr1 wr2 strand offset
oligos_6-8nt_m3 AtLEC2/AtLEC2/Athamap oligos_6-8nt_m3 AtLEC2:AtLEC2:Athamap 0.811 0.676 12 10 10 12 0.8333 0.8333 1.0000 D 2
oligos_6-8nt_m3 LEC2/MA0581.1/JASPAR oligos_6-8nt_m3 LEC2:MA0581.1:JASPAR 0.840 0.646 12 11 10 13 0.7692 0.8333 0.9091 D 2
oligos_6-8nt_m3 FUS3/MA0565.2/JASPAR oligos_6-8nt_m3 FUS3:MA0565.2:JASPAR 0.751 0.626 12 10 10 12 0.8333 0.8333 1.0000 D 1
oligos_6-8nt_m3 FUS3.DAP/M0003/AthalianaCistrome oligos_6-8nt_m3 FUS3.DAP:M0003:AthalianaCistrome 0.760 0.608 12 15 12 15 0.8000 1.0000 0.8000 D -1
oligos_6-8nt_m3 ABI3/ABI3/Athamap oligos_6-8nt_m3 ABI3:ABI3:Athamap 0.797 0.598 12 9 9 12 0.7500 0.7500 1.0000 D 1
oligos_6-8nt_m3 FUS3/FUS3/Athamap oligos_6-8nt_m3 FUS3:FUS3:Athamap 0.862 0.575 12 8 8 12 0.6667 0.6667 1.0000 D 3
oligos_6-8nt_m3 FUS3/MA0565.1/JASPAR oligos_6-8nt_m3 FUS3:MA0565.1:JASPAR 0.750 0.562 12 9 9 12 0.7500 0.7500 1.0000 D 2
oligos_6-8nt_m3 ABI3/MA0564.1/JASPAR oligos_6-8nt_m3 ABI3:MA0564.1:JASPAR 0.734 0.551 12 9 9 12 0.7500 0.7500 1.0000 R 2
oligos_6-8nt_m3 LEC2/M0146_1.02/CISBP oligos_6-8nt_m3 LEC2:M0146_1.02:CISBP 0.807 0.538 12 8 8 12 0.6667 0.6667 1.0000 R 3
oligos_6-8nt_m3 LEC2/MA0581.2/JASPAR oligos_6-8nt_m3 LEC2:MA0581.2:JASPAR 0.977 0.488 12 6 6 12 0.5000 0.5000 1.0000 D 4
oligos_6-8nt_m3 B3/5yzz_C/3D-footprint oligos_6-8nt_m3 B3:5yzz_C:3D-footprint 0.970 0.485 12 6 6 12 0.5000 0.5000 1.0000 D 4
oligos_6-8nt_m3 B3/6j9b_A/3D-footprint oligos_6-8nt_m3 B3:6j9b_A:3D-footprint 0.966 0.483 12 6 6 12 0.5000 0.5000 1.0000 D 4
oligos_6-8nt_m3 B3/6j9c_D/3D-footprint oligos_6-8nt_m3 B3:6j9c_D:3D-footprint 0.963 0.482 12 6 6 12 0.5000 0.5000 1.0000 R 4
oligos_6-8nt_m3 FUS3/MA0565.3/JASPAR oligos_6-8nt_m3 FUS3:MA0565.3:JASPAR 0.824 0.481 12 7 7 12 0.5833 0.5833 1.0000 D 3
oligos_6-8nt_m3 B3/6j9a_A/3D-footprint oligos_6-8nt_m3 B3:6j9a_A:3D-footprint 0.961 0.480 12 6 6 12 0.5000 0.5000 1.0000 D 4
oligos_6-8nt_m3 B3/5yzy_C/3D-footprint oligos_6-8nt_m3 B3:5yzy_C:3D-footprint 0.960 0.480 12 6 6 12 0.5000 0.5000 1.0000 D 4
oligos_6-8nt_m3 NAC/3swm_B/3D-footprint oligos_6-8nt_m3 NAC:3swm_B:3D-footprint 0.910 0.455 12 6 6 12 0.5000 0.5000 1.0000 D 4
oligos_6-8nt_m3 NAC037/MA2047.2/JASPAR oligos_6-8nt_m3 NAC037:MA2047.2:JASPAR 0.720 0.420 12 7 7 12 0.5833 0.5833 1.0000 D 4
oligos_6-8nt_m3 ABI3/MA0564.2/JASPAR oligos_6-8nt_m3 ABI3:MA0564.2:JASPAR 0.833 0.416 12 6 6 12 0.5000 0.5000 1.0000 R 3
oligos_6-8nt_m3 NAC/3swm_ABD/3D-footprint oligos_6-8nt_m3 NAC:3swm_ABD:3D-footprint 0.806 0.403 12 18 10 20 0.5000 0.8333 0.5556 R -8 
 Host name	rsat
 Job started	2025-06-19.085551
 Job done	2025-06-19.085553
 Seconds	1.28
	user	1.28
	system	0.07
	cuser	0.24
;	csystem	0.03