Myogenin_Rep2_motifs50/results/discovered_motifs/dyads_m39/peak-motifs_dyads_m39_vs_db_jaspar_core_nonredundant_vertebrates.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/dyads_m39/peak-motifs_dyads_m39.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/dyads_m39/peak-motifs_dyads_m39_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/dyads_m39/peak-motifs_dyads_m39.tf
 Output files
	alignments_1ton	Myogenin_Rep2_motifs50/results/discovered_motifs/dyads_m39/peak-motifs_dyads_m39_vs_db_jaspar_core_nonredundant_vertebrates_alignments_1ton.tab
	match_table_txt	Myogenin_Rep2_motifs50/results/discovered_motifs/dyads_m39/peak-motifs_dyads_m39_vs_db_jaspar_core_nonredundant_vertebrates.tab
	html_index   	Myogenin_Rep2_motifs50/results/discovered_motifs/dyads_m39/peak-motifs_dyads_m39_vs_db_jaspar_core_nonredundant_vertebrates_index.html
	alignments_1ton_html	Myogenin_Rep2_motifs50/results/discovered_motifs/dyads_m39/peak-motifs_dyads_m39_vs_db_jaspar_core_nonredundant_vertebrates_alignments_1ton.html
	match_table_html	Myogenin_Rep2_motifs50/results/discovered_motifs/dyads_m39/peak-motifs_dyads_m39_vs_db_jaspar_core_nonredundant_vertebrates.html
	prefix       	Myogenin_Rep2_motifs50/results/discovered_motifs/dyads_m39/peak-motifs_dyads_m39_vs_db_jaspar_core_nonredundant_vertebrates
 Matrices
	file1	1 matrices	Myogenin_Rep2_motifs50/results/discovered_motifs/dyads_m39/peak-motifs_dyads_m39.tf
		file1	1	11	135
	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)
id1 id2 name1 name2 cor Ncor w1 w2 w W Wr wr1 wr2 strand offset
dyads_m39 MA0513.1 dyads_m39dyads_m39 SMAD2::SMAD3::SMAD4 0.760 0.643 11 13 11 13 0.8462 1.0000 0.8462 R -1
dyads_m39 MA0774.1 dyads_m39dyads_m39 MEIS2 0.833 0.606 11 8 8 11 0.7273 0.7273 1.0000 D 1
dyads_m39 MA0775.1 dyads_m39dyads_m39 MEIS3 0.824 0.600 11 8 8 11 0.7273 0.7273 1.0000 D 1
dyads_m39 MA0498.2 dyads_m39dyads_m39 MEIS1 0.923 0.587 11 7 7 11 0.6364 0.6364 1.0000 D 1
dyads_m39 MA0782.2 dyads_m39dyads_m39 PKNOX1 0.793 0.581 11 15 11 15 0.7333 1.0000 0.7333 D -4
dyads_m39 MA1642.1 dyads_m39dyads_m39 NEUROG2(var.2) 0.707 0.505 11 13 10 14 0.7143 0.9091 0.7692 D 1
dyads_m39 MA0797.1 dyads_m39dyads_m39 TGIF2 0.777 0.499 11 12 9 14 0.6429 0.8182 0.7500 D 2
dyads_m39 MA1114.1 dyads_m39dyads_m39 PBX3 0.768 0.497 11 17 11 17 0.6471 1.0000 0.6471 D -5
dyads_m39 MA0783.1 dyads_m39dyads_m39 PKNOX2 0.766 0.492 11 12 9 14 0.6429 0.8182 0.7500 D 2
dyads_m39 MA0796.1 dyads_m39dyads_m39 TGIF1 0.763 0.490 11 12 9 14 0.6429 0.8182 0.7500 D 2
dyads_m39 MA1572.1 dyads_m39dyads_m39 TGIF2LY 0.748 0.481 11 12 9 14 0.6429 0.8182 0.7500 R 2
dyads_m39 MA1571.1 dyads_m39dyads_m39 TGIF2LX 0.745 0.479 11 12 9 14 0.6429 0.8182 0.7500 D 2
dyads_m39 MA0067.1 dyads_m39dyads_m39 Pax2 0.781 0.456 11 8 7 12 0.5833 0.6364 0.8750 R -1
dyads_m39 MA1638.1 dyads_m39dyads_m39 HAND2 0.723 0.445 11 10 8 13 0.6154 0.7273 0.8000 D 3
dyads_m39 MA1109.1 dyads_m39dyads_m39 NEUROD1 0.736 0.442 11 13 9 15 0.6000 0.8182 0.6923 D 2
dyads_m39 MA1618.1 dyads_m39dyads_m39 Ptf1a 0.708 0.425 11 13 9 15 0.6000 0.8182 0.6923 D 2 
 Host name	pedagogix
 Job started	2020-04-14.000747
 Job done	2020-04-14.000805
 Seconds	2.72
	user	2.72
	system	0.42
	cuser	13.5
;	csystem	0.83