6/regulon6.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 6/regulon6.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 6/regulon6.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 	6/regulon6.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf
 Output files
	alignments_1ton	6/regulon6.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_alignments_1ton.tab
	match_table_txt	6/regulon6.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.tab
	html_index   	6/regulon6.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_index.html
	alignments_1ton_html	6/regulon6.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB_alignments_1ton.html
	match_table_html	6/regulon6.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB.html
	prefix       	6/regulon6.rm.fna.peaks-rm/results/discovered_vs_db/peaks_motifs_vs_db_footDB
 Matrices
	file1	6 matrices	6/regulon6.rm.fna.peaks-rm/results/discovered_motifs/peaks_motifs_discovered.tf
		file1	1	10	163	waaAAATAtw
		file1	2	12	74	waAAAATATCww
		file1	3	11	68	mtAGTCCCTry
		file1	4	9	83	ggCGGGCss
		file1	5	9	140	ybCCTCCty
		file1	6	30	31	ssgCGrgwCyCsscgscsbgccbCsTCCsy
	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_m2 RVE1_RVE1_ArabidopsisPBM oligos_5-7nt_m2 RVE1_RVE1_ArabidopsisPBM 0.946 0.788 7.322 0.778 0.971 0.5771 0.94628 12 10 10 12 0.8333 0.8333 1.0000 D 2 ..AAAATATCww wAAATATCTk 2 1 8 1 1 3 1 2.4286 1
oligos_5-7nt_m2 CCA1_CCA1_ArabidopsisPBM oligos_5-7nt_m2 CCA1_CCA1_ArabidopsisPBM 0.943 0.786 7.931 0.771 0.968 0.6450 0.94321 12 10 10 12 0.8333 0.8333 1.0000 D 2 ..AAAATATCww aAAATATCTt 3 2 5 2 2 5 3 3.1429 2
oligos_5-7nt_m2 CCA1_MA0972.1_JASPAR oligos_5-7nt_m2 CCA1_MA0972.1_JASPAR 0.960 0.640 7.692 0.631 0.971 0.4703 0.93938 12 8 8 12 0.6667 0.6667 1.0000 D 3 ...AAATATCw. AAATATCT 1 8 6 5 3 1 2 3.7143 3
oligos_5-7nt_m2 CCA1_M01819_TRANSFAC oligos_5-7nt_m2 CCA1_M01819_TRANSFAC 0.901 0.636 8.811 0.624 0.946 1.2948 0.93295 12 17 12 17 0.7059 1.0000 0.7059 D -3 waAAAATATCww ...arAAAAwATCTA.. 5 9 1 6 4 17 6 6.8571 4
oligos_5-7nt_m1 CCA1_CCA1_ArabidopsisPBM oligos_5-7nt_m1 CCA1_CCA1_ArabidopsisPBM 0.851 0.567 8.375 0.540 0.912 1.4035 0.89529 10 10 8 12 0.6667 0.8000 0.8000 D 2 ..aAAATAtw aAAATATC.. 12 10 2 7 12 21 16 11.4286 5
oligos_5-7nt_m1 Medtr8g106590.1_M0145_1.02_CISBP oligos_5-7nt_m1 Medtr8g106590.1_M0145_1.02_CISBP 0.825 0.660 5.248 0.635 0.919 1.2890 0.89965 10 8 8 10 0.8000 0.8000 1.0000 D 2 ..aAAATAtw AAAWTAAT 18 6 16 4 11 16 12 11.8571 6
oligos_5-7nt_m1 RVE1_RVE1_ArabidopsisPBM oligos_5-7nt_m1 RVE1_RVE1_ArabidopsisPBM 0.843 0.562 7.524 0.532 0.911 1.4195 0.89469 10 10 8 12 0.6667 0.8000 0.8000 D 2 ..aAAATAtw wAAATATC.. 15 11 7 8 13 22 17 13.2857 7
oligos_5-7nt_m2 EPR1_M1317_1.02_CISBP oligos_5-7nt_m2 EPR1_M1317_1.02_CISBP 0.886 0.665 2.039 0.120 0.945 0.9871 0.92194 12 9 9 12 0.7500 0.7500 1.0000 R 2 ..AAAATATCw. WAAATATCT 7 5 29 33 6 8 7 13.5714 8
oligos_5-7nt_m1 CCA1_MA0972.1_JASPAR oligos_5-7nt_m1 CCA1_MA0972.1_JASPAR 0.851 0.542 8.273 0.514 0.904 1.3464 0.88279 10 8 7 11 0.6364 0.7000 0.8750 D 3 ...AAATAtw AAATATC. 11 13 4 10 20 19 20 13.8571 9
oligos_5-7nt_m2 PK08316.1_M1306_1.02_CISBP oligos_5-7nt_m2 PK08316.1_M1306_1.02_CISBP 0.846 0.705 1.861 0.662 0.926 1.4861 0.91380 12 10 10 12 0.8333 0.8333 1.0000 D 2 ..AAAATATCww wwaawATCtw 14 3 35 3 9 26 11 14.4286 10
oligos_5-7nt_m4 E2L_M01839_TRANSFAC oligos_5-7nt_m4 E2L_M01839_TRANSFAC 0.848 0.509 6.206 0.467 0.906 1.1314 0.87464 9 7 6 10 0.6000 0.6667 0.8571 D -1 ggCGGG... .GGCGGG 13 14 9 13 25 10 19 14.7143 11
oligos_5-7nt_m2 PK02532.1_M1303_1.02_CISBP oligos_5-7nt_m2 PK02532.1_M1303_1.02_CISBP 0.898 0.673 1.947 -0.037 0.940 1.0765 0.91848 12 9 9 12 0.7500 0.7500 1.0000 R 3 ...AAATATCww WAATATCTN 6 4 31 39 7 9 8 14.8571 12
oligos_5-7nt_m2 LOC_Os08g06110_M1365_1.02_CISBP oligos_5-7nt_m2 LOC_Os08g06110_M1365_1.02_CISBP 0.878 0.659 0.509 -0.090 0.949 0.9243 0.92446 12 9 9 12 0.7500 0.7500 1.0000 R 3 ...AAATATCww AAATATCTW 8 7 39 40 5 7 5 15.8571 13
oligos_5-7nt_m1 TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qnc_B_3D-footprint oligos_5-7nt_m1 TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qnc_B_3D-footprint 0.923 0.462 0.203 -0.034 0.957 0.5169 0.91527 10 8 6 12 0.5000 0.6000 0.7500 R 4 ....AATAtw AATAAA.. 4 21 40 38 8 2 4 16.7143 14
oligos_5-7nt_m1 HMGA_M0118_1.02_CISBP oligos_5-7nt_m1 HMGA_M0118_1.02_CISBP 0.810 0.472 2.283 0.476 0.917 1.1605 0.89118 10 9 7 12 0.5833 0.7000 0.7778 D -2 waaAAAT... ..rrwAAwt 22 19 28 12 15 11 13 17.1429 15
oligos_5-7nt_m2 RVE1_RVE1_2_ArabidopsisPBM oligos_5-7nt_m2 RVE1_RVE1_2_ArabidopsisPBM 0.787 0.545 2.522 0.520 0.915 1.5383 0.90255 12 10 9 13 0.6923 0.7500 0.9000 D 3 ...AAATATCww smatATCwa. 28 12 26 9 10 28 14 18.1429 16
oligos_5-7nt_m4 TCP23_MA1066.1_JASPAR oligos_5-7nt_m4 TCP23_MA1066.1_JASPAR 0.835 0.455 5.923 0.422 0.899 1.2120 0.87026 9 8 6 11 0.5455 0.6667 0.7500 D 3 ...GGGCss GGGCCC.. 17 25 11 16 28 14 22 19.0000 17
oligos_5-7nt_m1 AHL20_AHL20_ArabidopsisPBM oligos_5-7nt_m1 AHL20_AHL20_ArabidopsisPBM 0.820 0.441 5.335 0.405 0.906 1.3116 0.88431 10 10 7 13 0.5385 0.7000 0.7000 D 3 ...AAATAtw wAATATA... 20 30 14 20 19 18 18 19.8571 18
oligos_5-7nt_m2 HMGIY_M01800_TRANSFAC oligos_5-7nt_m2 HMGIY_M01800_TRANSFAC 0.878 0.439 2.003 0.049 0.927 0.8755 0.88973 12 6 6 12 0.5000 0.5000 1.0000 R 2 ..AAAATA.... AAAWWW 9 32 30 35 17 6 10 19.8571 19
oligos_5-7nt_m4 DREB1B_M01700_TRANSFAC oligos_5-7nt_m4 DREB1B_M01700_TRANSFAC 0.859 0.477 0.147 -0.147 0.940 0.6021 0.89027 9 5 5 9 0.5556 0.5556 1.0000 R 0 ggCGG.... GTCGG 10 18 41 41 16 4 9 19.8571 20
oligos_5-7nt_m4 TCP15_MA1062.1_JASPAR oligos_5-7nt_m4 TCP15_MA1062.1_JASPAR 0.823 0.449 5.750 0.412 0.894 1.2751 0.86692 9 8 6 11 0.5455 0.6667 0.7500 D 3 ...GGGCss GGGCCC.. 19 27 12 18 30 15 26 21.0000 21
oligos_5-7nt_m1 CCA1_M01819_TRANSFAC oligos_5-7nt_m1 CCA1_M01819_TRANSFAC 0.780 0.459 8.358 0.427 0.887 2.2547 0.89382 10 17 10 17 0.5882 1.0000 0.5882 D -3 waaAAATAtw ...arAAAAwATC.... 31 22 3 14 14 41 27 21.7143 22
oligos_5-7nt_m1 HMGIY_M01800_TRANSFAC oligos_5-7nt_m1 HMGIY_M01800_TRANSFAC 0.840 0.504 2.388 0.072 0.903 1.1621 0.87295 10 6 6 10 0.6000 0.6000 1.0000 R 2 ..aAAATA.. AAAWWW 16 16 27 34 26 12 21 21.7143 23
oligos_5-7nt_m4 ERF13_M03170_TRANSFAC oligos_5-7nt_m4 ERF13_M03170_TRANSFAC 0.820 0.478 4.286 0.228 0.894 1.4868 0.87683 9 10 7 12 0.5833 0.7778 0.7000 R 2 ..CGGGCss CGGGCGG... 21 17 18 25 24 27 25 22.4286 24
oligos_5-7nt_m2 HMGA_M0118_1.02_CISBP oligos_5-7nt_m2 HMGA_M0118_1.02_CISBP 0.802 0.401 1.878 0.399 0.914 1.2002 0.88934 12 9 7 14 0.5000 0.5833 0.7778 D -2 waAAAAT..... ..rrwAAwt 23 41 33 21 18 13 15 23.4286 25
oligos_5-7nt_m1 AHL25_AHL25_2_ArabidopsisPBM oligos_5-7nt_m1 AHL25_AHL25_2_ArabidopsisPBM 0.790 0.425 3.008 0.422 0.898 1.4289 0.87925 10 10 7 13 0.5385 0.7000 0.7000 D 3 ...AAATAtw aAwwWWw... 27 36 25 15 22 23 23 24.4286 26
oligos_5-7nt_m4 ESR1_M03213_TRANSFAC oligos_5-7nt_m4 ESR1_M03213_TRANSFAC 0.795 0.464 5.633 0.278 0.881 1.6714 0.86941 9 10 7 12 0.5833 0.7778 0.7000 R 2 ..CGGGCss CGGGCGG... 25 20 13 24 29 30 31 24.5714 27
oligos_5-7nt_m4 OsI_08196_M1658_1.02_CISBP oligos_5-7nt_m4 OsI_08196_M1658_1.02_CISBP 0.797 0.435 4.736 0.387 0.886 1.3736 0.86188 9 8 6 11 0.5455 0.6667 0.7500 D 3 ...GGGCss GGGCCC.. 24 34 17 23 35 20 29 26.0000 28
oligos_5-7nt_m1 KAN_M1340_1.02_CISBP oligos_5-7nt_m1 KAN_M1340_1.02_CISBP 0.760 0.507 1.468 0.491 0.886 1.8221 0.88069 10 10 8 12 0.6667 0.8000 0.8000 D 2 ..aAAATAtw rrwaTAtw.. 36 15 37 11 21 35 28 26.1429 29
oligos_5-7nt_m4 LjSGA_053525.1_M1662_1.02_CISBP oligos_5-7nt_m4 LjSGA_053525.1_M1662_1.02_CISBP 0.794 0.433 5.996 0.388 0.877 1.4714 0.85705 9 8 6 11 0.5455 0.6667 0.7500 D 3 ...GGGCss GGgCCC.. 26 35 10 22 41 24 32 27.1429 30
oligos_5-7nt_m4 CRF1_M03193_TRANSFAC oligos_5-7nt_m4 CRF1_M03193_TRANSFAC 0.781 0.455 4.176 0.213 0.875 1.7540 0.86622 9 10 7 12 0.5833 0.7778 0.7000 R 2 ..CGGGCss SGGGCGG... 30 24 19 27 32 32 34 28.2857 31
oligos_5-7nt_m1 gw1.20.00.89.1_M0601_1.02_CISBP oligos_5-7nt_m1 gw1.20.00.89.1_M0601_1.02_CISBP 0.773 0.416 0.697 0.405 0.894 1.4841 0.87694 10 10 7 13 0.5385 0.7000 0.7000 D -3 waaAAAT... ...tyraawt 33 37 38 19 23 25 24 28.4286 32
oligos_5-7nt_m4 AT5G07580_M03194_TRANSFAC oligos_5-7nt_m4 AT5G07580_M03194_TRANSFAC 0.778 0.454 4.005 0.183 0.875 1.7478 0.86645 9 10 7 12 0.5833 0.7778 0.7000 R 2 ..CGGGCss CGGKCGG... 32 26 24 32 31 31 33 29.8571 33
oligos_5-7nt_m4 ERF6_M03208_TRANSFAC oligos_5-7nt_m4 ERF6_M03208_TRANSFAC 0.763 0.445 4.031 0.190 0.871 1.8060 0.86425 9 10 7 12 0.5833 0.7778 0.7000 R 2 ..CGGGCss SGGGCGG... 34 28 22 29 34 34 36 31.0000 34
oligos_5-7nt_m1 AHL25_AHL25_3_ArabidopsisPBM oligos_5-7nt_m1 AHL25_AHL25_3_ArabidopsisPBM 0.755 0.407 1.867 0.224 0.884 1.6229 0.87131 10 10 7 13 0.5385 0.7000 0.7000 R 3 ...AAATAtw WAWTWWW... 38 39 34 26 27 29 30 31.8571 35
oligos_5-7nt_m4 RAP2.11_M03202_TRANSFAC oligos_5-7nt_m4 RAP2.11_M03202_TRANSFAC 0.762 0.444 4.156 0.200 0.862 1.9300 0.85967 9 10 7 12 0.5833 0.7778 0.7000 R 2 ..CGGGCss SGGGCGG... 35 29 20 28 38 38 39 32.4286 36
oligos_5-7nt_m1 PK02532.1_M1303_1.02_CISBP oligos_5-7nt_m1 PK02532.1_M1303_1.02_CISBP 0.785 0.458 1.941 -0.011 0.866 1.8756 0.86166 10 9 7 12 0.5833 0.7000 0.7778 R 3 ...AAATAtw WAATATC.. 29 23 32 37 36 36 37 32.8571 37
oligos_5-7nt_m2 PRH_M1167_1.02_CISBP oligos_5-7nt_m2 PRH_M1167_1.02_CISBP 0.755 0.406 5.334 0.412 0.861 1.9443 0.85915 12 8 7 13 0.5385 0.5833 0.8750 D 5 .....ATATCww ATATATw. 40 40 15 17 39 39 40 32.8571 38
oligos_5-7nt_m4 CRF3_M03190_TRANSFAC oligos_5-7nt_m4 CRF3_M03190_TRANSFAC 0.755 0.440 4.031 0.190 0.864 1.8982 0.86083 9 10 7 12 0.5833 0.7778 0.7000 R 2 ..CGGGCss CKGGCGG... 39 31 23 31 37 37 38 33.7143 39
oligos_5-7nt_m4 ERF-1_M03189_TRANSFAC oligos_5-7nt_m4 ERF-1_M03189_TRANSFAC 0.752 0.439 4.040 0.190 0.861 1.9510 0.85891 9 10 7 12 0.5833 0.7778 0.7000 R 2 ..CGGGCss CGGKCGG... 41 33 21 30 40 40 41 35.1429 40
oligos_5-7nt_m2 TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qn4_B_3D-footprint oligos_5-7nt_m2 TRANSCRIPTION_INITIATION_FACTOR_TFIID-1_1qn4_B_3D-footprint 0.756 0.407 1.807 -0.009 0.873 1.7827 0.86513 12 8 7 13 0.5385 0.5833 0.8750 R -1 waAAAAT..... .ATAAAAT 37 38 36 36 33 33 35 35.4286 41 
 Host name	baobab.eead.csic.es
 Job started	2016-06-03.161110
 Job done	2016-06-03.161207
 Seconds	41.14
	user	41.14
	system	1.4
	cuser	11.3
;	csystem	1.84