13/regulon13.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 13/regulon13.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 13/regulon13.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 	13/regulon13.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf
 Output files
	alignments_1ton	13/regulon13.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_alignments_1ton.tab
	match_table_txt	13/regulon13.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab
	html_index   	13/regulon13.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_index.html
	alignments_1ton_html	13/regulon13.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_alignments_1ton.html
	match_table_html	13/regulon13.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.html
	prefix       	13/regulon13.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB
 Matrices
	file1	5 matrices	13/regulon13.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf
		file1	1	9	36	wmAAGTGsa
		file1	2	9	28	ryGTCTArt
		file1	3	10	42	rkyCAAGAdr
		file1	4	11	24	bsATCCGGGws
		file1	5	22	22	khATTtwayhtwwwymmTCAwv
	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_m1 DAG2_DAG2_ArabidopsisPBM oligos_5-7nt_m1 DAG2_DAG2_ArabidopsisPBM 0.837 0.609 5.350 0.572 0.926 1.1810 0.90395 9 10 8 11 0.7273 0.8889 0.8000 D -2 wmAAGTGs. ..wAARGTgr 3 10 6 11 5 7 3 6.4286 1
oligos_5-7nt_m4 LBD16_LBD16_ArabidopsisPBM oligos_5-7nt_m4 LBD16_LBD16_ArabidopsisPBM 0.823 0.617 3.533 0.612 0.930 1.2662 0.91159 11 10 9 12 0.7500 0.8182 0.9000 D 2 ..ATCCGGGws wyCCGGrrw. 8 7 16 6 1 12 2 7.4286 2
oligos_5-7nt_m1 DOF2.5_MA0977.1_JASPAR oligos_5-7nt_m1 DOF2.5_MA0977.1_JASPAR 0.844 0.591 5.215 0.549 0.920 1.1250 0.89286 9 8 7 10 0.7000 0.7778 0.8750 D -1 wmAAGTG.. .wAARGTg 1 13 8 13 11 5 5 8.0000 3
oligos_5-7nt_m1 CDF3_MA0974.1_JASPAR oligos_5-7nt_m1 CDF3_MA0974.1_JASPAR 0.810 0.648 4.862 0.590 0.916 1.3474 0.89740 9 9 8 10 0.8000 0.8889 0.8889 D -1 wmAAGTGs. .wAAAGygm 11 4 9 9 8 15 6 8.8571 4
oligos_5-7nt_m1 cdf3_M0651_1.02_CISBP oligos_5-7nt_m1 cdf3_M0651_1.02_CISBP 0.810 0.648 4.820 0.589 0.916 1.3486 0.89735 9 9 8 10 0.8000 0.8889 0.8889 D -1 wmAAGTGs. .wAAAGygm 12 5 10 10 9 16 7 9.8571 5
oligos_5-7nt_m1 ZAT7_M0373_1.02_CISBP oligos_5-7nt_m1 ZAT7_M0373_1.02_CISBP 0.791 0.547 5.320 0.553 0.920 1.4452 0.90555 9 13 9 13 0.6923 1.0000 0.6923 D -1 wmAAGTGsa .hhbAGTGtr... 19 18 7 12 2 18 4 11.4286 6
oligos_5-7nt_m1 BHLH112_MA0961.1_JASPAR oligos_5-7nt_m1 BHLH112_MA0961.1_JASPAR 0.834 0.834 4.116 0.222 0.915 1.5212 0.90310 9 9 9 9 1.0000 1.0000 1.0000 R 0 wmAAGTGsa GCAAGTGGS 4 1 15 33 6 23 8 12.8571 7
oligos_5-7nt_m1 bhlh112_M0229_1.02_CISBP oligos_5-7nt_m1 bhlh112_M0229_1.02_CISBP 0.834 0.834 4.118 0.223 0.915 1.5249 0.90298 9 9 9 9 1.0000 1.0000 1.0000 R 0 wmAAGTGsa GCAAGTGGS 5 2 14 32 7 24 9 13.2857 8
oligos_5-7nt_m1 DOF2.4_MA0982.1_JASPAR oligos_5-7nt_m1 DOF2.4_MA0982.1_JASPAR 0.809 0.485 1.998 0.450 0.909 1.0885 0.87704 9 7 6 10 0.6000 0.6667 0.8571 D -1 wmAAGT... .wAAmGt 13 22 23 18 16 2 10 14.8571 9
oligos_5-7nt_m1 AZF2_M0372_1.02_CISBP oligos_5-7nt_m1 AZF2_M0372_1.02_CISBP 0.798 0.621 2.736 0.630 0.892 1.5057 0.87605 9 7 7 9 0.7778 0.7778 1.0000 D 2 ..AAGTGsa gAsTgwr 15 6 21 4 18 21 22 15.2857 10
oligos_5-7nt_m4 fgenesh1_pg.scaffold_70000111_M1388_1.02_CISBP oligos_5-7nt_m4 fgenesh1_pg.scaffold_70000111_M1388_1.02_CISBP 0.837 0.451 0.081 -0.056 0.936 0.9021 0.90406 11 9 7 13 0.5385 0.6364 0.7778 R -2 bsATCCG.... ..YTATCCR 2 28 38 35 4 1 1 15.5714 11
oligos_5-7nt_m1 ATDOF2.4_M0648_1.02_CISBP oligos_5-7nt_m1 ATDOF2.4_M0648_1.02_CISBP 0.808 0.485 1.969 0.449 0.909 1.0927 0.87681 9 7 6 10 0.6000 0.6667 0.8571 D -1 wmAAGT... .wAAaGt 14 23 24 19 17 3 11 15.8571 12
oligos_5-7nt_m1 CDF2_M0653_1.02_CISBP oligos_5-7nt_m1 CDF2_M0653_1.02_CISBP 0.781 0.568 4.741 0.515 0.903 1.5492 0.88998 9 10 8 11 0.7273 0.8889 0.8000 D -2 wmAAGTGs. ..WAAAGyrh 21 15 11 14 12 26 16 16.4286 13
oligos_5-7nt_m4 LBD4_M1274_1.02_CISBP oligos_5-7nt_m4 LBD4_M1274_1.02_CISBP 0.755 0.686 1.430 0.678 0.908 1.8363 0.90418 11 10 10 11 0.9091 0.9091 1.0000 D 1 .sATCCGGGws rahsCGgsrr 33 3 31 1 3 36 12 17.0000 14
oligos_5-7nt_m1 CDF2_MA0973.1_JASPAR oligos_5-7nt_m1 CDF2_MA0973.1_JASPAR 0.781 0.568 4.703 0.515 0.903 1.5515 0.88991 9 10 8 11 0.7273 0.8889 0.8000 D -2 wmAAGTGs. ..WAAAGyrh 23 16 12 15 13 27 17 17.5714 15
oligos_5-7nt_m1 e_gw1.149.93.1_M0658_1.02_CISBP oligos_5-7nt_m1 e_gw1.149.93.1_M0658_1.02_CISBP 0.828 0.452 1.414 0.430 0.905 1.1381 0.87428 9 8 6 11 0.5455 0.6667 0.7500 D -2 wmAAGT... ..waAmGy 7 27 32 22 21 6 15 18.5714 16
oligos_5-7nt_m1 fgenesh1_pg.C_Chr_08.0001000114_M0664_1.02_CISBP oligos_5-7nt_m1 fgenesh1_pg.C_Chr_08.0001000114_M0664_1.02_CISBP 0.833 0.454 1.156 0.437 0.901 1.1853 0.87170 9 8 6 11 0.5455 0.6667 0.7500 D -2 wmAAGT... ..waamGt 6 25 34 21 22 8 18 19.1429 17
oligos_5-7nt_m1 AZF1_M0378_1.02_CISBP oligos_5-7nt_m1 AZF1_M0378_1.02_CISBP 0.793 0.617 1.960 0.650 0.880 1.6751 0.86926 9 7 7 9 0.7778 0.7778 1.0000 D 2 ..AAGTGsa gasTgdr 17 8 25 2 26 30 28 19.4286 18
oligos_5-7nt_m1 PBF_M01829_TRANSFAC oligos_5-7nt_m1 PBF_M01829_TRANSFAC 0.822 0.548 0.174 -0.107 0.907 1.1148 0.87557 9 6 6 9 0.6667 0.6667 1.0000 R 0 wmAAGT... WAAAGK 9 17 36 37 20 4 14 19.5714 19
oligos_5-7nt_m1 PBF_M00355_TRANSFAC oligos_5-7nt_m1 PBF_M00355_TRANSFAC 0.761 0.507 6.085 0.470 0.890 1.7573 0.88283 9 11 8 12 0.6667 0.8889 0.7273 D -3 wmAAGTGs. ...wAAAGhgm 30 21 3 16 15 32 24 20.1429 20
oligos_5-7nt_m1 RHL41_M0377_1.02_CISBP oligos_5-7nt_m1 RHL41_M0377_1.02_CISBP 0.789 0.614 1.916 0.634 0.877 1.7243 0.86736 9 7 7 9 0.7778 0.7778 1.0000 D 2 ..AAGTGsa rwSTrwd 20 9 26 3 27 31 29 20.7143 21
oligos_5-7nt_m1 DOF5.6_M0657_1.02_CISBP oligos_5-7nt_m1 DOF5.6_M0657_1.02_CISBP 0.781 0.426 2.964 0.381 0.899 1.2086 0.87044 9 8 6 11 0.5455 0.6667 0.7500 D -2 wmAAGT... ..wAAmGy 22 33 19 28 23 9 19 21.8571 22
oligos_5-7nt_m1 PBF_MA0064.1_JASPAR oligos_5-7nt_m1 PBF_MA0064.1_JASPAR 0.797 0.443 5.972 0.405 0.874 1.2614 0.84117 9 5 5 9 0.5556 0.5556 1.0000 D 1 .mAAGT... AAAGy 16 30 4 26 37 11 31 22.1429 23
oligos_5-7nt_m1 AtMYB117_II_AthaMYB oligos_5-7nt_m1 AtMYB117_II_AthaMYB 0.813 0.443 7.706 0.422 0.873 1.5293 0.85426 9 8 6 11 0.5455 0.6667 0.7500 D 3 ...AGTGsa AGTGGT.. 10 29 1 24 35 25 32 22.2857 24
oligos_5-7nt_m1 ZAT18_ZAT18_ArabidopsisPBM oligos_5-7nt_m1 ZAT18_ZAT18_ArabidopsisPBM 0.775 0.452 3.025 0.421 0.892 1.5125 0.87577 9 10 7 12 0.5833 0.7778 0.7000 D 2 ..AAGTGsa dAGTGCA... 26 26 18 25 19 22 23 22.7143 25
oligos_5-7nt_m1 DOF5.6_MA0983.1_JASPAR oligos_5-7nt_m1 DOF5.6_MA0983.1_JASPAR 0.780 0.426 2.962 0.380 0.899 1.2108 0.87032 9 8 6 11 0.5455 0.6667 0.7500 D -2 wmAAGT... ..wAAmGt 24 34 20 29 24 10 20 23.0000 26
oligos_5-7nt_m1 Dof3_MA0021.1_JASPAR oligos_5-7nt_m1 Dof3_MA0021.1_JASPAR 0.777 0.518 6.206 0.462 0.868 1.5847 0.85164 9 6 6 9 0.6667 0.6667 1.0000 D 1 .mAAGTG.. AAAGyv 25 20 2 17 36 28 35 23.2857 27
oligos_5-7nt_m1 ZFP5_M0369_1.02_CISBP oligos_5-7nt_m1 ZFP5_M0369_1.02_CISBP 0.793 0.432 1.569 0.445 0.890 1.3190 0.86465 9 8 6 11 0.5455 0.6667 0.7500 D -2 wmAAGT... ..bdAwst 18 32 30 20 28 14 25 23.8571 28
oligos_5-7nt_m1 STZ_M0370_1.02_CISBP oligos_5-7nt_m1 STZ_M0370_1.02_CISBP 0.771 0.599 1.666 0.610 0.871 1.8081 0.86417 9 7 7 9 0.7778 0.7778 1.0000 D 2 ..AAGTGsa gAsTrwr 27 11 29 8 29 33 33 24.2857 29
oligos_5-7nt_m1 AT3G53600_M0374_1.02_CISBP oligos_5-7nt_m1 AT3G53600_M0374_1.02_CISBP 0.768 0.597 1.717 0.615 0.869 1.8355 0.86314 9 7 7 9 0.7778 0.7778 1.0000 D 2 ..AAGTGsa gwsTrwd 28 12 28 5 30 35 34 24.5714 30
oligos_5-7nt_m1 e_gw1.392.16.1_M0660_1.02_CISBP oligos_5-7nt_m1 e_gw1.392.16.1_M0660_1.02_CISBP 0.751 0.478 3.113 0.430 0.881 1.6678 0.86955 9 9 7 11 0.6364 0.7778 0.7778 D -2 wmAAGTG.. ..wAAaGyd 38 24 17 23 25 29 27 26.1429 31
oligos_5-7nt_m4 AT5G08520_M1339_1.02_CISBP oligos_5-7nt_m4 AT5G08520_M1339_1.02_CISBP 0.755 0.407 0.088 -0.076 0.908 1.2912 0.88522 11 9 7 13 0.5385 0.6364 0.7778 R -2 bsATCCG.... ..YTATCYD 32 38 37 36 14 13 13 26.1429 32
oligos_5-7nt_m4 AT1G74840_M1322_1.02_CISBP oligos_5-7nt_m4 AT1G74840_M1322_1.02_CISBP 0.766 0.530 0.371 -0.185 0.898 1.8340 0.89360 11 11 9 13 0.6923 0.8182 0.8182 R -2 bsATCCGGG.. ..WTATCCGGA 29 19 35 38 10 34 21 26.5714 33
oligos_5-7nt_m1 MNB1A_MA0053.1_JASPAR oligos_5-7nt_m1 MNB1A_MA0053.1_JASPAR 0.759 0.422 5.940 0.389 0.850 1.5045 0.82653 9 5 5 9 0.5556 0.5556 1.0000 D 1 .mAAGT... AAAGc 31 35 5 27 38 20 38 27.7143 34
oligos_5-7nt_m1 AT5G04390_M0375_1.02_CISBP oligos_5-7nt_m1 AT5G04390_M0375_1.02_CISBP 0.754 0.586 1.398 0.611 0.860 1.9628 0.85848 9 7 7 9 0.7778 0.7778 1.0000 D 2 ..AAGTGsa rasYrwm 34 14 33 7 33 38 37 28.0000 35
oligos_5-7nt_m1 AT1G29160_M0646_1.02_CISBP oligos_5-7nt_m1 AT1G29160_M0646_1.02_CISBP 0.754 0.411 4.210 0.368 0.875 1.4942 0.85594 9 8 6 11 0.5455 0.6667 0.7500 D -2 wmAAGT... ..WAAmGT 35 36 13 31 34 19 30 28.2857 36
oligos_5-7nt_m1 ADOF2_M0649_1.02_CISBP oligos_5-7nt_m1 ADOF2_M0649_1.02_CISBP 0.752 0.410 1.776 0.374 0.888 1.3493 0.86310 9 8 6 11 0.5455 0.6667 0.7500 D -2 wmAAGT... ..wAAmGy 36 37 27 30 31 17 26 29.1429 37
oligos_5-7nt_m4 PK23829.1_M1311_1.02_CISBP oligos_5-7nt_m4 PK23829.1_M1311_1.02_CISBP 0.751 0.438 2.598 0.157 0.867 1.8670 0.86197 11 8 7 12 0.5833 0.6364 0.8750 R -1 bsATCCG.... .TTATCCR 37 31 22 34 32 37 36 32.7143 38 
 Host name	baobab.eead.csic.es
 Job started	2016-06-03.165151
 Job done	2016-06-03.165239
 Seconds	35.01
	user	35.01
	system	1.3
	cuser	10.08
;	csystem	1.73