compare-matrices  -v 1 -mode matches -format1 transfac -file1 8/regulon8.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf -format2 transfac -file2 $RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o 8/regulon8.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab
 Program version       	1.118
 Slow mode 
 Input files
	file2 	$RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf
	file1 	8/regulon8.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf
 Output files
	alignments_1ton	8/regulon8.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_alignments_1ton.tab
	match_table_txt	8/regulon8.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab
	html_index   	8/regulon8.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_index.html
	alignments_1ton_html	8/regulon8.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_alignments_1ton.html
	match_table_html	8/regulon8.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.html
	prefix       	8/regulon8.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB
 Matrices
	file1	8 matrices	8/regulon8.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf
		file1	1	11	72	wkCTGTTGCdk
		file1	2	9	73	wrAGTATtw
		file1	3	9	79	grAGGGGmk
		file1	4	10	27	mhACTCTAmr
		file1	5	11	73	amATAACCCww
		file1	6	29	16	wmGCTdrhvymrgwymabrwkrhwGAAsm
		file1	7	27	19	ddAATrwycmwtkwymAkmwmwGATsw
		file1	8	28	24	vmCAAkawcymtwkwwmmkrwadGGAds
	file2	1055 matrices	$RSAT/_footprintDB/footprintDB.transfac.plants.motif.tf
		file2		1		16		5		TCATTCCACGTAGATr
		file2		2		8		5		awmAGTTr
		file2		3		8		3		rkTAGTTr
		file2		4		8		5		wamaGTTr
		file2		5		8		1		GTTAGTTA
		file2		6		8		2		kwCwGTTr
		file2		7		8		2		GTTAGTTr
		file2		8		8		6		wwmaGTTr
		file2		9		8		2		rsTkGTTr
		file2		10		8		8		RkTwGKTr
		file2		11		8		1		TACTGTTG
		...	1045 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	logoDP       	Dot product between the logo matrices.
	8	NIcor        	Normalized Pearson correlation between the information content matrices. NIcor = Icor * Wr
	9	NSW          	Normalized Sandelin-Wasserman similarity. NSW = SW/w
	10	SSD          	sum of squared distance.
	11	NsEucl       	relative Euclidian similarity. NsEucl = (max(dEucl) - dEucl)/max(dEucl)
	12	w1           	Width of the first matrix
	13	w2           	Width of the second matrix
	14	w            	Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset)
	15	W            	Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w
	16	Wr           	Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W
	17	wr1          	Alignment length relative to the width of the first matrix. wr1 = w/w1
	18	wr2          	Alignment length relative to the width of the second matrix. wr2 = w/w2
	19	strand       	"strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct;  R=reverse)
	20	offset       	shift of the second matrix relative to the first matrix (negative:left; positive: right)
	21	consensus1   	IUPAC consensus of matrix 1 (dots represent non-aligned columns)
	22	consensus2   	IUPAC consensus of matrix 2 (dots represent non-aligned columns)
	23	rcor         	Matching rank for cor
	24	rNcor        	Matching rank for Ncor
	25	rlogoDP      	Matching rank for logoDP
	26	rNIcor       	Matching rank for NIcor
	27	rNsEucl      	Matching rank for NsEucl
	28	rSSD         	Matching rank for SSD
	29	rNSW         	Matching rank for NSW
	30	rank_mean    	Mean of the matching ranks on all selected metrics
	31	match_rank   	Rank of the match (sorting by rank_mean)

 Host name	baobab.eead.csic.es
 Job started	2016-06-03.161202
 Job done	2016-06-03.161310
 Seconds	59.64
	user	59.64
	system	0.96
	cuser	6.56
;	csystem	1.2