compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_8nt_mkv5_m5/peak-motifs_oligos_8nt_mkv5_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.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 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_8nt_mkv5_m5/peak-motifs_oligos_8nt_mkv5_m5_vs_db_jaspar_core_nonredundant_vertebrates
 Program version       	1.118
 Quick mode 
 Input files
	file2 	$RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf
	file1 	Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_8nt_mkv5_m5/peak-motifs_oligos_8nt_mkv5_m5.tf
 Output files
	alignments_1ton	Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_8nt_mkv5_m5/peak-motifs_oligos_8nt_mkv5_m5_vs_db_jaspar_core_nonredundant_vertebrates_alignments_1ton.tab
	match_table_txt	Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_8nt_mkv5_m5/peak-motifs_oligos_8nt_mkv5_m5_vs_db_jaspar_core_nonredundant_vertebrates.tab
	html_index   	Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_8nt_mkv5_m5/peak-motifs_oligos_8nt_mkv5_m5_vs_db_jaspar_core_nonredundant_vertebrates_index.html
	alignments_1ton_html	Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_8nt_mkv5_m5/peak-motifs_oligos_8nt_mkv5_m5_vs_db_jaspar_core_nonredundant_vertebrates_alignments_1ton.html
	match_table_html	Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_8nt_mkv5_m5/peak-motifs_oligos_8nt_mkv5_m5_vs_db_jaspar_core_nonredundant_vertebrates.html
	prefix       	Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_8nt_mkv5_m5/peak-motifs_oligos_8nt_mkv5_m5_vs_db_jaspar_core_nonredundant_vertebrates
 Matrices
	file1	1 matrices	Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_8nt_mkv5_m5/peak-motifs_oligos_8nt_mkv5_m5.tf
		file1	1	16	210
	file2	746 matrices	$RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf
		file2		1		6		24
		file2		2		17		100
		file2		3		10		9897
		file2		4		17		101
		file2		5		17		3851
		file2		6		10		25318
		file2		7		6		27
		file2		8		11		1001
		file2		9		14		101
		file2		10		6		20
		file2		11		8		104
		...	736 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)

 Host name	pedagogix
 Job started	2020-04-13.233137
 Job done	2020-04-13.233204
 Seconds	3.99
	user	3.99
	system	0.52
	cuser	20.73
;	csystem	1.24