/var/www/html/rsat/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151903_RSnfAu/compare-matrices.tab 
 compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151903_RSnfAu/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.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/2026/05/29/compare-matrices_2026-05-29.151903_RSnfAu/compare-matrices.tab
 Program version       	1.118
 Slow mode 
 Input files
	file1 	$RSAT/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151903_RSnfAu/compare-matrices_query_matrices.transfac
	file2 	$RSAT/public_html/motif_databases/footprintDB/footprintDB.motif.tf
 Output files
	prefix       	$RSAT/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151903_RSnfAu/compare-matrices
	html_index   	$RSAT/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151903_RSnfAu/compare-matrices_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151903_RSnfAu/compare-matrices_alignments_1ton.html
	match_table_txt	$RSAT/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151903_RSnfAu/compare-matrices.tab
	match_table_html	$RSAT/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151903_RSnfAu/compare-matrices.html
	alignments_1ton	$RSAT/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151903_RSnfAu/compare-matrices_alignments_1ton.tab
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/www-data/2026/05/29/compare-matrices_2026-05-29.151903_RSnfAu/compare-matrices_query_matrices.transfac
		file1	1	19	21	gmkGCATGwrwcakGCCkw
	file2	14372 matrices	$RSAT/public_html/motif_databases/footprintDB/footprintDB.motif.tf
		file2		1		17		1.01		yyaymCATCAAwmwwmm
		file2		2		7		96		tGTCnaA
		file2		3		8		5		awmAGTTr
		file2		4		8		3		rkTAGTTr
		file2		5		8		5		wamaGTTr
		file2		6		8		1		GTTAGTTA
		file2		7		8		2		kwCwGTTr
		file2		8		8		2		GTTAGTTr
		file2		9		8		6		wwmaGTTr
		file2		10		8		2		rsTkGTTr
		file2		11		8		8		RkTwGKTr
		...	14362 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
dyads_test_vs_ctrl_m1 M03D4.4_M0460_1.02_CISBP dyads_test_vs_ctrl_m1 M03D4.4:M0460_1.02:CISBP 0.879 0.509 5.477 0.947 0.93036 19 11 11 19 0.5789 0.5789 1.0000 D 0 gmkGCATGwrw........ caTGCATGAwc 1 1 1 2 3 1.6000 1
dyads_test_vs_ctrl_m1 LEC2_MA0581.1_JASPAR dyads_test_vs_ctrl_m1 LEC2:MA0581.1:JASPAR 0.878 0.439 0.350 0.952 0.93072 19 11 10 20 0.5000 0.5263 0.9091 R -1 gmkGCATGwr......... .WGYGCATGSA 2 8 10 1 1 4.4000 2
dyads_test_vs_ctrl_m1 stuA_M0087_1.02_CISBP dyads_test_vs_ctrl_m1 stuA:M0087_1.02:CISBP 0.799 0.421 0.369 0.950 0.92947 19 10 10 19 0.5263 0.5263 1.0000 R 0 gmkGCATGwr......... CMTGCAKRWR 5 11 9 3 2 6.0000 3
dyads_test_vs_ctrl_m1 hbx7_M0876_1.02_CISBP dyads_test_vs_ctrl_m1 hbx7:M0876_1.02:CISBP 0.755 0.453 0.240 0.938 0.92815 19 13 12 20 0.6000 0.6316 0.9231 R -1 gmkGCATGwrwc....... .WGKGCATKTTHT 7 5 11 4 4 6.2000 4
dyads_test_vs_ctrl_m1 FUS3_MA0565.2_JASPAR dyads_test_vs_ctrl_m1 FUS3:MA0565.2:JASPAR 0.849 0.447 3.776 0.923 0.91217 19 10 10 19 0.5263 0.5263 1.0000 R 1 .mkGCATGwrw........ WTGCATGTDW 4 7 6 9 6 6.4000 5
dyads_test_vs_ctrl_m1 AtLEC2_AtLEC2_Athamap dyads_test_vs_ctrl_m1 AtLEC2:AtLEC2:Athamap 0.851 0.448 0.235 0.926 0.91408 19 10 10 19 0.5263 0.5263 1.0000 R 0 gmkGCATGwr......... TTTGCATGRM 3 6 12 6 5 6.4000 6
dyads_test_vs_ctrl_m1 Cgd2_3490_UP00395A_1_UniPROBE dyads_test_vs_ctrl_m1 Cgd2_3490:UP00395A_1:UniPROBE 0.714 0.464 5.376 0.901 0.91261 19 14 13 20 0.6500 0.6842 0.9286 R -1 gmkGCATGwrwca...... .SRYGCATGCRKKK 11 2 2 8 10 6.6000 7
dyads_test_vs_ctrl_m1 FUS3.DAP_M0003_AthalianaCistrome dyads_test_vs_ctrl_m1 FUS3.DAP:M0003:AthalianaCistrome 0.741 0.459 0.378 0.907 0.91557 19 15 13 21 0.6190 0.6842 0.8667 R -2 gmkGCATGwrwca...... ..YWTGCATGYATDT 9 4 8 5 7 6.6000 8
dyads_test_vs_ctrl_m1 PF14_0633_UP00394A_1_UniPROBE dyads_test_vs_ctrl_m1 PF14_0633:UP00394A_1:UniPROBE 0.708 0.460 4.823 0.903 0.91347 19 14 13 20 0.6500 0.6842 0.9286 R -1 gmkGCATGwrwca...... .MYYGCATGCRWWH 13 3 5 7 8 7.2000 9
dyads_test_vs_ctrl_m1 p53-a_UN0461.2_JASPAR dyads_test_vs_ctrl_m1 p53-a:UN0461.2:JASPAR 0.761 0.401 5.127 0.902 0.90103 19 10 10 19 0.5263 0.5263 1.0000 D 8 ........wrwcakGCCk. rGRCwTGCCC 6 13 4 10 9 8.4000 10
dyads_test_vs_ctrl_m1 BACH2_MA1101.3_JASPAR dyads_test_vs_ctrl_m1 BACH2:MA1101.3:JASPAR 0.747 0.433 3.509 0.880 0.89534 19 11 11 19 0.5789 0.5789 1.0000 R 4 ....CATGwrwcakG.... SATGASTCATG 8 9 7 12 12 9.6000 11
dyads_test_vs_ctrl_m1 ABI19_B73_1_m1_EEAD0171_EEADannot dyads_test_vs_ctrl_m1 ABI19_B73_1_m1:EEAD0171:EEADannot 0.728 0.421 5.243 0.872 0.89234 19 11 11 19 0.5789 0.5789 1.0000 D 0 gmkGCATGwrw........ CwTGCATGCry 10 10 3 13 13 9.8000 12
dyads_test_vs_ctrl_m1 at_AC_acceptor_SD0002.1_JASPAR dyads_test_vs_ctrl_m1 at_AC_acceptor:SD0002.1:JASPAR 0.711 0.411 0.225 0.890 0.89978 19 11 11 19 0.5789 0.5789 1.0000 R 8 ........wrwcakGCCkw RYACTTGCCTK 12 12 13 11 11 11.8000 13 
 Host name	rsat
 Job started	2026-05-29.151904
 Job done	2026-05-29.152018
 Seconds	67.3
	user	67.3
	system	2.09
	cuser	3.69
;	csystem	1.72