4/regulon4.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 4/regulon4.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 4/regulon4.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 	4/regulon4.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf
 Output files
	alignments_1ton	4/regulon4.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_alignments_1ton.tab
	match_table_txt	4/regulon4.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab
	html_index   	4/regulon4.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_index.html
	alignments_1ton_html	4/regulon4.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_alignments_1ton.html
	match_table_html	4/regulon4.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.html
	prefix       	4/regulon4.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB
 Matrices
	file1	7 matrices	4/regulon4.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf
		file1	1	11	133	wwcGTTTTAtr
		file1	2	9	100	hsATTCGdt
		file1	3	10	51	kwCGATGAwv
		file1	4	9	159	mdGCACAwk
		file1	5	11	193	srTCGACGAss
		file1	6	10	65	wyGTTTTAwr
		file1	7	29	116	wwatGTwwwACwwwwhhwwwwwawatgwd
	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)
id1 id2 name1 name2 cor Ncor logoDP NIcor NSW SSD NsEucl w1 w2 w W Wr wr1 wr2 strand offset consensus1 consensus2 rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank
oligos_5-7nt_m3 Opaque-2_M00374_TRANSFAC oligos_5-7nt_m3 Opaque-2_M00374_TRANSFAC 0.911 0.490 9.625 0.507 0.946 0.7494 0.91255 10 10 7 13 0.5385 0.7000 0.7000 D 3 ...GATGAwv GATGAyR... 1 15 1 10 1 4 2 4.8571 1
oligos_5-7nt_m2 AT3G04030_M1325_1.02_CISBP oligos_5-7nt_m2 AT3G04030_M1325_1.02_CISBP 0.804 0.804 3.925 0.784 0.925 1.3584 0.90843 9 9 9 9 1.0000 1.0000 1.0000 D 0 hsATTCGdt wkATtCbsy 10 1 9 1 4 10 8 6.1429 2
oligos_5-7nt_m2 AT3G24120_M1328_1.02_CISBP oligos_5-7nt_m2 AT3G24120_M1328_1.02_CISBP 0.814 0.733 3.524 0.714 0.926 1.3340 0.90926 9 10 9 10 0.9000 1.0000 0.9000 D -1 hsATTCGdt .wkATtCbby 9 2 12 2 3 9 7 6.2857 3
oligos_5-7nt_m2 KAN1_MA1027.1_JASPAR oligos_5-7nt_m2 KAN1_MA1027.1_JASPAR 0.878 0.479 3.573 0.479 0.942 0.6909 0.90204 9 8 6 11 0.5455 0.6667 0.7500 D -2 hsATTC... ..wtATtC 6 16 11 12 7 2 4 8.2857 4
oligos_5-7nt_m4 CONS_ARATH_CONS2_EEADannot oligos_5-7nt_m4 CONS_ARATH_CONS2_EEADannot 0.892 0.520 1.930 0.036 0.945 0.7721 0.91124 9 10 7 12 0.5833 0.7778 0.7000 R -3 mdGCACA.. ...NNNCACA 3 12 18 18 2 6 3 8.8571 5
oligos_5-7nt_m4 NAC_domain-containing_protein_19_3swm_B_3D-footprint oligos_5-7nt_m4 NAC_domain-containing_protein_19_3swm_B_3D-footprint 0.898 0.449 0.080 -0.107 0.953 0.4679 0.90327 9 6 5 10 0.5000 0.5556 0.8333 R -1 mdGCA.... .ANGCA 2 17 22 20 6 1 1 9.8571 6
oligos_5-7nt_m2 LOC_Os02g22020_M1363_1.02_CISBP oligos_5-7nt_m2 LOC_Os02g22020_M1363_1.02_CISBP 0.757 0.681 3.368 0.672 0.910 1.6138 0.90019 9 10 9 10 0.9000 1.0000 0.9000 D -1 hsATTCGdt .agATtCysy 17 5 13 3 9 14 12 10.4286 7
oligos_5-7nt_m2 KAN1_KAN1_ArabidopsisPBM oligos_5-7nt_m2 KAN1_KAN1_ArabidopsisPBM 0.846 0.493 3.756 0.485 0.922 1.0874 0.89466 9 10 7 12 0.5833 0.7778 0.7000 D -3 hsATTCG.. ...wtATtCk 7 14 10 11 17 7 10 10.8571 8
dyads_test_vs_ctrl_m1 TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint dyads_test_vs_ctrl_m1 TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint 0.887 0.443 2.596 0.139 0.938 0.7415 0.89852 10 8 6 12 0.5000 0.6000 0.7500 R 4 ....TTTAwr TTTAAA.. 4 20 16 14 14 3 5 10.8571 9
oligos_5-7nt_m2 AT1G25550_M1320_1.02_CISBP oligos_5-7nt_m2 AT1G25550_M1320_1.02_CISBP 0.756 0.681 5.282 0.669 0.908 1.6646 0.89863 9 10 9 10 0.9000 1.0000 0.9000 D -1 hsATTCGdt .aGATtCysy 18 6 4 4 13 19 16 11.4286 10
oligos_5-7nt_m2 AtPHR1_M1334_1.02_CISBP oligos_5-7nt_m2 AtPHR1_M1334_1.02_CISBP 0.754 0.679 4.575 0.666 0.909 1.6302 0.89969 9 10 9 10 0.9000 1.0000 0.9000 D -1 hsATTCGdt .akATkCbsy 21 8 6 6 10 16 13 11.4286 11
oligos_5-7nt_m2 ATMYR1_M1341_1.02_CISBP oligos_5-7nt_m2 ATMYR1_M1341_1.02_CISBP 0.804 0.724 0.118 -0.162 0.924 1.3606 0.90836 9 10 9 10 0.9000 1.0000 0.9000 R 0 hsATTCGdt AKATTCSSS. 11 3 21 21 5 11 9 11.5714 12
oligos_5-7nt_m2 LOC_Os03g21240_M1364_1.02_CISBP oligos_5-7nt_m2 LOC_Os03g21240_M1364_1.02_CISBP 0.753 0.678 4.600 0.667 0.909 1.6366 0.89949 9 10 9 10 0.9000 1.0000 0.9000 D -1 hsATTCGdt .akATkCbyy 22 9 5 5 11 17 14 11.8571 13
oligos_5-7nt_m1 TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint oligos_5-7nt_m1 TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qna_B_3D-footprint 0.883 0.408 1.732 0.135 0.937 0.7594 0.89730 11 8 6 13 0.4615 0.5455 0.7500 R 5 .....TTTAtr TTTAAA.. 5 21 19 15 15 5 6 12.2857 14
oligos_5-7nt_m2 PK14402.1_M1308_1.02_CISBP oligos_5-7nt_m2 PK14402.1_M1308_1.02_CISBP 0.769 0.629 7.297 0.618 0.902 1.7616 0.89572 9 11 9 11 0.8182 1.0000 0.8182 D -2 hsATTCGdt ..aGATTCsgy 15 10 2 8 16 20 17 12.5714 15
oligos_5-7nt_m2 KAN4_MA1028.1_JASPAR oligos_5-7nt_m2 KAN4_MA1028.1_JASPAR 0.817 0.445 5.628 0.427 0.897 1.2302 0.86928 9 8 6 11 0.5455 0.6667 0.7500 D -2 hsATTC... ..ATATTC 8 19 3 13 22 8 19 13.1429 16
oligos_5-7nt_m2 PK19779.1_M1310_1.02_CISBP oligos_5-7nt_m2 PK19779.1_M1310_1.02_CISBP 0.756 0.681 3.020 0.656 0.908 1.6634 0.89867 9 10 9 10 0.9000 1.0000 0.9000 D -1 hsATTCGdt .wkATwCyvy 19 7 15 7 12 18 15 13.2857 17
oligos_5-7nt_m2 AT1G68670_M1321_1.02_CISBP oligos_5-7nt_m2 AT1G68670_M1321_1.02_CISBP 0.768 0.691 0.251 -0.175 0.913 1.5650 0.90171 9 10 9 10 0.9000 1.0000 0.9000 R -1 hsATTCGdt .AGATTCYMY 16 4 20 22 8 12 11 13.2857 18
oligos_5-7nt_m2 AT3G13040_M1326_1.02_CISBP oligos_5-7nt_m2 AT3G13040_M1326_1.02_CISBP 0.754 0.549 4.500 0.536 0.898 1.6266 0.88727 9 10 8 11 0.7273 0.8889 0.8000 D -2 hsATTCGd. ..akATtCbc 20 11 7 9 18 15 18 14.0000 19
oligos_5-7nt_m4 CONS_ARATH_CONS1_EEADannot oligos_5-7nt_m4 CONS_ARATH_CONS1_EEADannot 0.791 0.504 1.937 0.016 0.888 1.5693 0.87346 9 9 7 11 0.6364 0.7778 0.7778 R -2 mdGCACA.. ..TNNCACA 14 13 17 19 21 13 20 16.7143 20
dyads_test_vs_ctrl_m1 SR1_SR1_Athamap dyads_test_vs_ctrl_m1 SR1_SR1_Athamap 0.801 0.400 3.965 0.053 0.872 2.0436 0.87365 10 14 8 16 0.5000 0.8000 0.5714 R -6 wyGTTTTA.. ......GCGKTTTA 12 22 8 17 20 21 21 17.2857 21
oligos_5-7nt_m1 SR1_SR1_Athamap oligos_5-7nt_m1 SR1_SR1_Athamap 0.796 0.448 3.081 0.097 0.872 2.3019 0.88080 11 14 9 16 0.5625 0.8182 0.6429 R -5 wwcGTTTTA.. .....CGCGKTTTA 13 18 14 16 19 22 22 17.7143 22 
 Host name	baobab.eead.csic.es
 Job started	2016-06-03.161033
 Job done	2016-06-03.161128
 Seconds	46.4
	user	46.4
	system	0.85
	cuser	6.56
;	csystem	1.26