/var/www/html/rsat/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.214418_xIDv3W/compare-matrices.tab 
 compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.214418_xIDv3W/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -format2 tf -strand DR -lth cor 0.7 -lth Ncor 0.4 -uth match_rank 50 -return cor,Ncor,logoDP,NsEucl,NSW,match_rank,matrix_id,matrix_name,width,strand,offset,consensus,alignments_1ton -o $RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.214418_xIDv3W/compare-matrices.tab
 Program version       	1.118
 Slow mode 
 Input files
	file2 	$RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf
	file1 	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.214418_xIDv3W/compare-matrices_query_matrices.transfac
 Output files
	prefix       	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.214418_xIDv3W/compare-matrices
	alignments_1ton	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.214418_xIDv3W/compare-matrices_alignments_1ton.tab
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.214418_xIDv3W/compare-matrices_alignments_1ton.html
	match_table_html	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.214418_xIDv3W/compare-matrices.html
	html_index   	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.214418_xIDv3W/compare-matrices_index.html
	match_table_txt	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.214418_xIDv3W/compare-matrices.tab
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.214418_xIDv3W/compare-matrices_query_matrices.transfac
		file1	1	10	1112	wtAGGGCAtw
	file2	3463 matrices	$RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf
		file2		1		8		5		awmAGTTr
		file2		2		8		3		rkTAGTTr
		file2		3		8		5		wamaGTTr
		file2		4		8		1		GTTAGTTA
		file2		5		8		2		kwCwGTTr
		file2		6		8		2		GTTAGTTr
		file2		7		8		6		wwmaGTTr
		file2		8		8		2		rsTkGTTr
		file2		9		8		8		RkTwGKTr
		file2		10		8		1		TACTGTTG
		file2		11		8		4		WhhWGTTr
		...	3453 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	NSW          	Normalized Sandelin-Wasserman similarity. NSW = SW/w
	9	NsEucl       	relative Euclidian similarity. NsEucl = (max(dEucl) - dEucl)/max(dEucl)
	10	w1           	Width of the first matrix
	11	w2           	Width of the second matrix
	12	w            	Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset)
	13	W            	Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w
	14	Wr           	Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W
	15	wr1          	Alignment length relative to the width of the first matrix. wr1 = w/w1
	16	wr2          	Alignment length relative to the width of the second matrix. wr2 = w/w2
	17	strand       	"strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct;  R=reverse)
	18	offset       	shift of the second matrix relative to the first matrix (negative:left; positive: right)
	19	consensus1   	IUPAC consensus of matrix 1 (dots represent non-aligned columns)
	20	consensus2   	IUPAC consensus of matrix 2 (dots represent non-aligned columns)
	21	rcor         	Matching rank for cor
	22	rNcor        	Matching rank for Ncor
	23	rlogoDP      	Matching rank for logoDP
	24	rNsEucl      	Matching rank for NsEucl
	25	rNSW         	Matching rank for NSW
	26	rank_mean    	Mean of the matching ranks on all selected metrics
	27	match_rank   	Rank of the match (sorting by rank_mean)
id1 id2 name1 name2 cor Ncor logoDP NSW NsEucl w1 w2 w W Wr wr1 wr2 strand offset consensus1 consensus2 rcor rNcor rlogoDP rNsEucl rNSW rank_mean match_rank
oligos_6nt_mkv4_m4 TRFL5_M1316_1.02_CISBP oligos_6nt_mkv4_m4 TRFL5:M1316_1.02:CISBP 0.931 0.745 6.293 0.957 0.92626 10 8 8 10 0.8000 0.8000 1.0000 D 0 wtAGGGCA.. yTAGGGCa 2 1 2 3 4 2.4000 1
oligos_6nt_mkv4_m4 TRFL5_UN0839.1_JASPAR oligos_6nt_mkv4_m4 TRFL5:UN0839.1:JASPAR 0.943 0.660 0.800 0.958 0.92227 10 7 7 10 0.7000 0.7000 1.0000 R 1 .tAGGGCA.. TAGGGCA 1 3 9 6 1 4.0000 2
oligos_6nt_mkv4_m4 PK06103.1_M1304_1.02_CISBP oligos_6nt_mkv4_m4 PK06103.1:M1304_1.02:CISBP 0.902 0.722 6.487 0.932 0.90758 10 8 8 10 0.8000 0.8000 1.0000 D 0 wtAGGGCA.. CTAGGGCA 3 2 1 7 7 4.0000 3
oligos_6nt_mkv4_m4 ASR3_MA1733.1_JASPAR oligos_6nt_mkv4_m4 ASR3:MA1733.1:JASPAR 0.870 0.622 1.403 0.957 0.93444 10 14 10 14 0.7143 1.0000 0.7143 R -1 wtAGGGCAtw .TWAGGGYAHW... 5 9 7 1 2 4.8000 4
oligos_6nt_mkv4_m4 AT2G33550.ampDAP_M0774_AthalianaCistrome oligos_6nt_mkv4_m4 AT2G33550.ampDAP:M0774:AthalianaCistrome 0.870 0.622 1.403 0.957 0.93443 10 14 10 14 0.7143 1.0000 0.7143 R -1 wtAGGGCAtw .TWAGGGYAHW... 6 10 8 2 3 5.8000 5
oligos_6nt_mkv4_m4 ASR3_MA1733.2_JASPAR oligos_6nt_mkv4_m4 ASR3:MA1733.2:JASPAR 0.880 0.640 0.382 0.952 0.92239 10 9 8 11 0.7273 0.8000 0.8889 R -1 wtAGGGCA.. .TWAGGGYA 4 7 15 5 5 7.2000 6
oligos_6nt_mkv4_m4 TRB2_MA1073.1_JASPAR oligos_6nt_mkv4_m4 TRB2:MA1073.1:JASPAR 0.820 0.656 0.439 0.922 0.90111 10 8 8 10 0.8000 0.8000 1.0000 R 0 wtAGGGCA.. YTAGGKYW 8 4 14 8 8 8.4000 7
oligos_6nt_mkv4_m4 ATTRB2_M1346_1.02_CISBP oligos_6nt_mkv4_m4 ATTRB2:M1346_1.02:CISBP 0.819 0.655 0.441 0.921 0.90071 10 8 8 10 0.8000 0.8000 1.0000 R 0 wtAGGGCA.. YTAGGKYW 9 5 13 9 9 9.0000 8
oligos_6nt_mkv4_m4 AT2G33550.DAP_M0787_AthalianaCistrome oligos_6nt_mkv4_m4 AT2G33550.DAP:M0787:AthalianaCistrome 0.829 0.460 0.103 0.941 0.92314 10 18 10 18 0.5556 1.0000 0.5556 R -1 wtAGGGCAtw .TWAGGGYWWW....... 7 21 26 4 6 12.8000 9
oligos_6nt_mkv4_m4 estExt_fgenesh1_pg.C_Chr_13.00010057_M1396_1.02_CISBP oligos_6nt_mkv4_m4 estExt_fgenesh1_pg.C_Chr_13.00010057:M1396_1.02:CISBP 0.765 0.556 0.272 0.912 0.89498 10 9 8 11 0.7273 0.8000 0.8889 R -1 wtAGGGCA.. .YTAGGKYW 12 14 18 14 10 13.6000 10
oligos_6nt_mkv4_m4 0100010593_M1389_1.02_CISBP oligos_6nt_mkv4_m4 0100010593:M1389_1.02:CISBP 0.728 0.596 0.354 0.911 0.90037 10 10 9 11 0.8182 0.9000 0.9000 R -1 wtAGGGCAt. .YTAGGKTWW 20 11 16 11 11 13.8000 11
oligos_6nt_mkv4_m4 TBP3_MA1355.1_JASPAR oligos_6nt_mkv4_m4 TBP3:MA1355.1:JASPAR 0.751 0.500 2.056 0.892 0.89614 10 15 10 15 0.6667 1.0000 0.6667 R -2 wtAGGGCAtw ..TTAGGGYWWA... 15 20 4 13 18 14.0000 12
oligos_6nt_mkv4_m4 estExt_fgenesh1_pg.C_Chr_03.00010061_M1394_1.02_CISBP oligos_6nt_mkv4_m4 estExt_fgenesh1_pg.C_Chr_03.00010061:M1394_1.02:CISBP 0.701 0.631 0.508 0.907 0.89855 10 9 9 10 0.9000 0.9000 1.0000 R 0 wtAGGGCAt. YTRGGKYWW 26 8 12 12 12 14.0000 13
oligos_6nt_mkv4_m4 OsTRBF3_MA2404.1_JASPAR oligos_6nt_mkv4_m4 OsTRBF3:MA2404.1:JASPAR 0.776 0.543 0.583 0.902 0.88138 10 7 7 10 0.7000 0.7000 1.0000 R 1 .tAGGGCA.. TAGGKYW 10 15 10 20 16 14.2000 14
oligos_6nt_mkv4_m4 MYBR101_SMH1_B73_1_m1_EEAD0453_EEADannot oligos_6nt_mkv4_m4 MYBR101_SMH1_B73_1_m1:EEAD0453:EEADannot 0.711 0.647 1.977 0.884 0.89208 10 11 10 11 0.9091 1.0000 0.9091 R 0 wtAGGGCAtw YTAGGGYWWR. 24 6 5 15 21 14.2000 15
oligos_6nt_mkv4_m4 P0510F09.23_MA1030.2_JASPAR oligos_6nt_mkv4_m4 P0510F09.23:MA1030.2:JASPAR 0.776 0.543 0.581 0.902 0.88144 10 7 7 10 0.7000 0.7000 1.0000 R 1 .tAGGGCA.. TAGGKYW 11 16 11 19 15 14.4000 16
oligos_6nt_mkv4_m4 MYBR101_SMH1_Mo17_1_EEAD0454_EEADannot oligos_6nt_mkv4_m4 MYBR101_SMH1_Mo17_1:EEAD0454:EEADannot 0.749 0.576 0.246 0.901 0.90068 10 13 10 13 0.7692 1.0000 0.7692 R 0 wtAGGGCAtw YTAGGGYWAR... 16 12 19 10 17 14.8000 17
oligos_6nt_mkv4_m4 MYB1-like_MA1030.1_JASPAR oligos_6nt_mkv4_m4 MYB1-like:MA1030.1:JASPAR 0.760 0.507 0.234 0.907 0.89196 10 10 8 12 0.6667 0.8000 0.8000 R -2 wtAGGGCA.. ..YTAGGKYW 13 17 21 16 13 16.0000 18
oligos_6nt_mkv4_m4 LOC_Os01g51154_M1361_1.02_CISBP oligos_6nt_mkv4_m4 LOC_Os01g51154:M1361_1.02:CISBP 0.759 0.506 0.235 0.906 0.89137 10 10 8 12 0.6667 0.8000 0.8000 R -2 wtAGGGCA.. ..YTAGGKYW 14 18 20 17 14 16.6000 19
oligos_6nt_mkv4_m4 TRB2_MA1355.2_JASPAR oligos_6nt_mkv4_m4 TRB2:MA1355.2:JASPAR 0.748 0.561 0.331 0.881 0.88507 10 11 9 12 0.7500 0.9000 0.8182 R -2 wtAGGGCAt. ..TTAGGGYWW 17 13 17 18 22 17.4000 20
oligos_6nt_mkv4_m4 B3_6j9c_D_3D-footprint oligos_6nt_mkv4_m4 B3:6j9c_D:3D-footprint 0.747 0.448 3.668 0.879 0.85782 10 6 6 10 0.6000 0.6000 1.0000 D 4 ....GGCAtw tGCATG 19 23 3 23 23 18.2000 21
oligos_6nt_mkv4_m4 ONAC127_UN0428.2_JASPAR oligos_6nt_mkv4_m4 ONAC127:UN0428.2:JASPAR 0.719 0.503 1.710 0.840 0.84866 10 7 7 10 0.7000 0.7000 1.0000 R 3 ...GGGCAtw GGGCAGC 21 19 6 26 26 19.6000 22
oligos_6nt_mkv4_m4 B3_6j9a_A_3D-footprint oligos_6nt_mkv4_m4 B3:6j9a_A:3D-footprint 0.718 0.431 0.205 0.884 0.86107 10 6 6 10 0.6000 0.6000 1.0000 R 4 ....GGCAtw TGCATG 22 24 22 22 20 22.0000 23
oligos_6nt_mkv4_m4 B3_5yzy_C_3D-footprint oligos_6nt_mkv4_m4 B3:5yzy_C:3D-footprint 0.747 0.448 0.181 0.877 0.85706 10 6 6 10 0.6000 0.6000 1.0000 R 4 ....GGCAtw TGCATG 18 22 25 24 24 22.6000 24
oligos_6nt_mkv4_m4 B3_5yzz_C_3D-footprint oligos_6nt_mkv4_m4 B3:5yzz_C:3D-footprint 0.704 0.423 0.205 0.888 0.86363 10 6 6 10 0.6000 0.6000 1.0000 R 4 ....GGCAtw TGCATG 25 26 23 21 19 22.8000 25
oligos_6nt_mkv4_m4 B3_6j9b_A_3D-footprint oligos_6nt_mkv4_m4 B3:6j9b_A:3D-footprint 0.714 0.428 0.181 0.869 0.85224 10 6 6 10 0.6000 0.6000 1.0000 R 4 ....GGCAtw TGCATG 23 25 24 25 25 24.4000 26 
 Host name	rsat
 Job started	2026-03-29.214418
 Job done	2026-03-29.214433
 Seconds	9.77
	user	9.77
	system	0.74
	cuser	3.25
;	csystem	1.21