compare-matrices  -v 1 -format transfac -file Myogenin_Rep2_motifs50/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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 Myogenin_Rep2_motifs50/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
 Program version       	1.118
 Quick mode 
 Input files
	file2 	Myogenin_Rep2_motifs50/results/discovered_motifs/peak-motifs_motifs_discovered.tf
	file1 	Myogenin_Rep2_motifs50/results/discovered_motifs/peak-motifs_motifs_discovered.tf
 Output files
	alignments_1ton	Myogenin_Rep2_motifs50/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.tab
	match_table_txt	Myogenin_Rep2_motifs50/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
	html_index   	Myogenin_Rep2_motifs50/results/discovered_motifs/peak-motifs_motifs_disco_compa_index.html
	alignments_1ton_html	Myogenin_Rep2_motifs50/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.html
	match_table_html	Myogenin_Rep2_motifs50/results/discovered_motifs/peak-motifs_motifs_disco_compa.html
	prefix       	Myogenin_Rep2_motifs50/results/discovered_motifs/peak-motifs_motifs_disco_compa
 Matrices
	file1	275 matrices	Myogenin_Rep2_motifs50/results/discovered_motifs/peak-motifs_motifs_discovered.tf
		file1	1	16	1135
		file1	2	12	660
		file1	3	17	764
		file1	4	12	340
		file1	5	18	15
		file1	6	16	161
		file1	7	10	590
		file1	8	13	649
		file1	9	12	386
		file1	10	11	154
		file1	11	11	461
		...	265 more matrices
	file2	275 matrices	Myogenin_Rep2_motifs50/results/discovered_motifs/peak-motifs_motifs_discovered.tf
		file2		1		16		1135
		file2		2		12		660
		file2		3		17		764
		file2		4		12		340
		file2		5		18		15
		file2		6		16		161
		file2		7		10		590
		file2		8		13		649
		file2		9		12		386
		file2		10		11		154
		file2		11		11		461
		...	265 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)