/var/www/html/rsat/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -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/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant
 Program version       	1.118
 Quick mode 
 Input files
	file1 	$RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf
	file2 	$RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt
 Output files
	html_index   	$RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant_index.html
	alignments_1ton	$RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant_alignments_1ton.tab
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant_alignments_1ton.html
	prefix       	$RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant
	match_table_html	$RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant.html
	match_table_txt	$RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant.tab
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf
		file1	1	10	27063
	file2	879 matrices	$RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt
		file2		1		6		20
		file2		2		14		43
		file2		3		10		25
		file2		4		15		10
		file2		5		10		17
		file2		6		10		18
		file2		7		17		25
		file2		8		15		33
		file2		9		14		16
		file2		10		6		16
		file2		11		15		1369
		...	869 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
positions_6nt_m3 MA0845.1 positions_6nt_m3 FOXB1 0.705 0.641 10 11 10 11 0.9091 1.0000 0.9091 R 0
positions_6nt_m3 MA0135.2 positions_6nt_m3 Lhx3 0.742 0.619 10 12 10 12 0.8333 1.0000 0.8333 R -1
positions_6nt_m3 MA0703.3 positions_6nt_m3 LMX1B 0.728 0.582 10 8 8 10 0.8000 0.8000 1.0000 R 0
positions_6nt_m3 MA0619.2 positions_6nt_m3 LIN54 0.798 0.558 10 7 7 10 0.7000 0.7000 1.0000 R 2
positions_6nt_m3 MA0601.2 positions_6nt_m3 Arid3b 0.738 0.517 10 7 7 10 0.7000 0.7000 1.0000 R 3
positions_6nt_m3 MA0621.2 positions_6nt_m3 mix-a 0.734 0.514 10 7 7 10 0.7000 0.7000 1.0000 R 1
positions_6nt_m3 MA0108.3 positions_6nt_m3 TBP 0.731 0.512 10 7 7 10 0.7000 0.7000 1.0000 D 3
positions_6nt_m3 MA0702.3 positions_6nt_m3 LMX1A 0.727 0.509 10 7 7 10 0.7000 0.7000 1.0000 R 1
positions_6nt_m3 MA0151.1 positions_6nt_m3 Arid3a 0.846 0.507 10 6 6 10 0.6000 0.6000 1.0000 R 3
positions_6nt_m3 MA0674.2 positions_6nt_m3 NKX6-1 0.872 0.476 10 7 6 11 0.5455 0.6000 0.8571 R 4
positions_6nt_m3 MA0683.2 positions_6nt_m3 POU4F2 0.713 0.475 10 15 10 15 0.6667 1.0000 0.6667 D -3
positions_6nt_m3 MA0635.2 positions_6nt_m3 BARHL2 0.756 0.454 10 6 6 10 0.6000 0.6000 1.0000 R 1
positions_6nt_m3 MA0650.4 positions_6nt_m3 Hoxa13 0.702 0.447 10 8 7 11 0.6364 0.7000 0.8750 R 3
positions_6nt_m3 MA0847.4 positions_6nt_m3 FOXD2 0.710 0.437 10 11 8 13 0.6154 0.8000 0.7273 R -3
positions_6nt_m3 MA1577.2 positions_6nt_m3 TLX2 0.720 0.432 10 6 6 10 0.6000 0.6000 1.0000 D 1
positions_6nt_m3 MA0654.2 positions_6nt_m3 ISX 0.714 0.429 10 6 6 10 0.6000 0.6000 1.0000 D 1
positions_6nt_m3 MA0718.2 positions_6nt_m3 RAX 0.711 0.427 10 6 6 10 0.6000 0.6000 1.0000 D 1
positions_6nt_m3 MA0894.2 positions_6nt_m3 HESX1 0.708 0.425 10 6 6 10 0.6000 0.6000 1.0000 R 1
positions_6nt_m3 MA0125.2 positions_6nt_m3 Nobox 0.708 0.425 10 6 6 10 0.6000 0.6000 1.0000 R 1
positions_6nt_m3 MA1487.3 positions_6nt_m3 FOXE1 0.742 0.424 10 12 8 14 0.5714 0.8000 0.6667 R -4
positions_6nt_m3 MA0628.2 positions_6nt_m3 POU6F1 0.703 0.422 10 6 6 10 0.6000 0.6000 1.0000 D 1
positions_6nt_m3 MA0899.2 positions_6nt_m3 HOXA10 0.722 0.421 10 9 7 12 0.5833 0.7000 0.7778 R 3
positions_6nt_m3 MA0612.3 positions_6nt_m3 EMX1 0.701 0.421 10 6 6 10 0.6000 0.6000 1.0000 D 1
positions_6nt_m3 MA0913.3 positions_6nt_m3 HOXD9 0.719 0.420 10 9 7 12 0.5833 0.7000 0.7778 R 3
positions_6nt_m3 MA0722.2 positions_6nt_m3 VAX1 0.753 0.411 10 7 6 11 0.5455 0.6000 0.8571 D 4
positions_6nt_m3 MA0876.2 positions_6nt_m3 BSX 0.889 0.404 10 6 5 11 0.4545 0.5000 0.8333 R 5
positions_6nt_m3 MA0892.2 positions_6nt_m3 GSX1 0.880 0.400 10 6 5 11 0.4545 0.5000 0.8333 R 5 
 Host name	rsat
 Job started	2026-01-05.130622
 Job done	2026-01-05.130631
 Seconds	1.51
	user	1.51
	system	0.49
	cuser	6.67
;	csystem	0.76