/var/www/html/rsat/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.120806_R1Lva7/compare-matrices.tab 
 compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.120806_R1Lva7/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/2026/04/09/compare-matrices_2026-04-09.120806_R1Lva7/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/2026/04/09/compare-matrices_2026-04-09.120806_R1Lva7/compare-matrices_query_matrices.transfac
 Output files
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.120806_R1Lva7/compare-matrices_alignments_1ton.html
	alignments_1ton	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.120806_R1Lva7/compare-matrices_alignments_1ton.tab
	html_index   	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.120806_R1Lva7/compare-matrices_index.html
	prefix       	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.120806_R1Lva7/compare-matrices
	match_table_html	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.120806_R1Lva7/compare-matrices.html
	match_table_txt	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.120806_R1Lva7/compare-matrices.tab
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.120806_R1Lva7/compare-matrices_query_matrices.transfac
		file1	1	12	3750	haAAACCCTAaw
	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_7nt_mkv5_m3 TRB1_MA2032.1_JASPAR oligos_7nt_mkv5_m3 TRB1:MA2032.1:JASPAR 0.989 0.907 6.852 0.995 0.97869 12 11 11 12 0.9167 0.9167 1.0000 D 1 .aAAACCCTAaw aaAACCCTArw 2 1 4 1 1 1.8000 1
oligos_7nt_mkv5_m3 TRB1_MA2032.2_JASPAR oligos_7nt_mkv5_m3 TRB1:MA2032.2:JASPAR 0.990 0.742 6.850 0.994 0.97469 12 9 9 12 0.7500 0.7500 1.0000 D 2 ..AAACCCTAa. aAACCCTAr 1 6 5 2 2 3.2000 2
oligos_7nt_mkv5_m3 PNRC2_UN0276.1_JASPAR oligos_7nt_mkv5_m3 PNRC2:UN0276.1:JASPAR 0.961 0.641 6.381 0.979 0.94846 12 8 8 12 0.6667 0.6667 1.0000 D 2 ..AAACCCTA.. AAWMCCTA 7 11 9 7 6 8.0000 3
oligos_7nt_mkv5_m3 TBP3_MA1355.1_JASPAR oligos_7nt_mkv5_m3 TBP3:MA1355.1:JASPAR 0.901 0.721 6.712 0.960 0.94217 12 15 12 15 0.8000 1.0000 0.8000 D -2 haAAACCCTAaw ..wtwwrCCCTAAw. 14 8 6 8 9 9.0000 4
oligos_7nt_mkv5_m3 TRB2_MA1355.2_JASPAR oligos_7nt_mkv5_m3 TRB2:MA1355.2:JASPAR 0.913 0.702 6.710 0.958 0.93544 12 11 10 13 0.7692 0.8333 0.9091 D 2 ..AAACCCTAaw wwrCCCTAAw. 13 9 7 9 10 9.6000 5
oligos_7nt_mkv5_m3 AT1G72740_MA1353.1_JASPAR oligos_7nt_mkv5_m3 AT1G72740:MA1353.1:JASPAR 0.973 0.779 0.479 0.984 0.96357 12 15 12 15 0.8000 1.0000 0.8000 R 0 haAAACCCTAaw MWAAACCCTAAW... 5 3 38 4 5 11.0000 6
oligos_7nt_mkv5_m3 AT1G72740_MA1353.2_JASPAR oligos_7nt_mkv5_m3 AT1G72740:MA1353.2:JASPAR 0.982 0.756 0.478 0.986 0.96293 12 11 10 13 0.7692 0.8333 0.9091 R 2 ..AAACCCTAaw AAACCCTAAW. 3 5 39 5 4 11.2000 7
oligos_7nt_mkv5_m3 AL2G32420.t2_MYBRELATED_1_AT1G72740_EEAD0583_EEADannot oligos_7nt_mkv5_m3 AL2G32420.t2_MYBRELATED_1_AT1G72740:EEAD0583:EEADannot 0.928 0.596 6.386 0.956 0.93026 12 11 9 14 0.6429 0.7500 0.8182 D 3 ...AACCCTAaw AACCCTAAA.. 9 19 8 10 11 11.4000 8
oligos_7nt_mkv5_m3 MYBR101_SMH1_B73_1_m1_EEAD0453_EEADannot oligos_7nt_mkv5_m3 MYBR101_SMH1_B73_1_m1:EEAD0453:EEADannot 0.857 0.785 6.236 0.939 0.92564 12 11 11 12 0.9167 0.9167 1.0000 D 0 haAAACCCTAa. cywWrCCCTAr 29 2 10 14 19 14.8000 9
oligos_7nt_mkv5_m3 AT1G72740.ampDAP_M0588_AthalianaCistrome oligos_7nt_mkv5_m3 AT1G72740.ampDAP:M0588:AthalianaCistrome 0.979 0.560 0.246 0.988 0.96889 12 21 12 21 0.5714 1.0000 0.5714 R 0 haAAACCCTAaw MWAAACCCTAAW......... 4 23 42 3 3 15.0000 10
oligos_7nt_mkv5_m3 TBP3.ampDAP_M0621_AthalianaCistrome oligos_7nt_mkv5_m3 TBP3.ampDAP:M0621:AthalianaCistrome 0.937 0.592 0.317 0.975 0.95403 12 19 12 19 0.6316 1.0000 0.6316 R -5 haAAACCCTAaw .....HTAARCCCTAAW.. 8 21 41 6 7 16.6000 11
oligos_7nt_mkv5_m3 0100010593_M1389_1.02_CISBP oligos_7nt_mkv5_m3 0100010593:M1389_1.02:CISBP 0.887 0.739 3.200 0.949 0.92827 12 10 10 12 0.8333 0.8333 1.0000 D 2 ..AAACCCTAaw wwAMCCTarw 18 7 32 12 15 16.8000 12
oligos_7nt_mkv5_m3 TRP2_MA1356.1_JASPAR oligos_7nt_mkv5_m3 TRP2:MA1356.1:JASPAR 0.895 0.512 8.589 0.930 0.92368 12 21 12 21 0.5714 1.0000 0.5714 D -4 haAAACCCTAaw ....cTAAACCCTAAA..... 16 29 2 15 22 16.8000 13
oligos_7nt_mkv5_m3 1200010153_M1391_1.02_CISBP oligos_7nt_mkv5_m3 1200010153:M1391_1.02:CISBP 0.871 0.603 5.019 0.944 0.92082 12 10 9 13 0.6923 0.7500 0.9000 D 3 ...AACCCTAaw amCCCTAry. 21 16 18 17 16 17.6000 14
oligos_7nt_mkv5_m3 TRP2.ampDAP_M0612_AthalianaCistrome oligos_7nt_mkv5_m3 TRP2.ampDAP:M0612:AthalianaCistrome 0.890 0.509 8.596 0.928 0.92276 12 21 12 21 0.5714 1.0000 0.5714 D -5 haAAACCCTAaw .....CTAAACCCTAAA.... 17 30 1 16 25 17.8000 15
oligos_7nt_mkv5_m3 TRP5_MA1802.2_JASPAR oligos_7nt_mkv5_m3 TRP5:MA1802.2:JASPAR 0.924 0.539 3.017 0.964 0.92861 12 7 7 12 0.5833 0.5833 1.0000 D 1 .aAAACCC.... wAAACCy 10 26 35 11 8 18.0000 16
oligos_7nt_mkv5_m3 TRP5_MA1802.1_JASPAR oligos_7nt_mkv5_m3 TRP5:MA1802.1:JASPAR 0.884 0.612 3.044 0.952 0.92724 12 10 9 13 0.6923 0.7500 0.9000 D -1 haAAACCCT... .wwAAACCyy 19 13 34 13 12 18.2000 17
oligos_7nt_mkv5_m3 Solyc07g040920.2.1_MYBRELATED_1_AT1G72740_EEAD0654_EEADannot oligos_7nt_mkv5_m3 Solyc07g040920.2.1_MYBRELATED_1_AT1G72740:EEAD0654:EEADannot 0.914 0.487 4.945 0.950 0.92056 12 11 8 15 0.5333 0.6667 0.7273 D 4 ....ACCCTAaw ACCCTAAA... 11 35 19 18 13 19.2000 18
oligos_7nt_mkv5_m3 LOC_Os01g51154.1_MYBRELATED_1_AT1G72740_EEAD0624_EEADannot oligos_7nt_mkv5_m3 LOC_Os01g51154.1_MYBRELATED_1_AT1G72740:EEAD0624:EEADannot 0.865 0.595 6.046 0.930 0.92048 12 15 11 16 0.6875 0.9167 0.7333 D -4 haAAACCCTAa. ....CTAAACCCTAA 25 20 12 20 21 19.6000 19
oligos_7nt_mkv5_m3 XP_013589913.1_MYBRELATED_1_AT1G72740_EEAD0665_EEADannot oligos_7nt_mkv5_m3 XP_013589913.1_MYBRELATED_1_AT1G72740:EEAD0665:EEADannot 0.913 0.487 4.856 0.949 0.92054 12 11 8 15 0.5333 0.6667 0.7273 D 4 ....ACCCTAaw ACCCTAAA... 12 36 20 19 14 20.2000 20
oligos_7nt_mkv5_m3 TRP1_MA1352.1_JASPAR oligos_7nt_mkv5_m3 TRP1:MA1352.1:JASPAR 0.881 0.503 8.450 0.921 0.91904 12 21 12 21 0.5714 1.0000 0.5714 D -3 haAAACCCTAaw ...CTAAACCCTAAA...... 20 33 3 22 27 21.0000 21
oligos_7nt_mkv5_m3 MYBR101_SMH1_Mo17_1_EEAD0454_EEADannot oligos_7nt_mkv5_m3 MYBR101_SMH1_Mo17_1:EEAD0454:EEADannot 0.826 0.649 5.850 0.927 0.91872 12 13 11 14 0.7857 0.9167 0.8462 D -2 haAAACCCTAa. ..CytwrCCCTAr 32 10 14 24 26 21.2000 22
oligos_7nt_mkv5_m3 LOC_Os01g51154_M1361_1.02_CISBP oligos_7nt_mkv5_m3 LOC_Os01g51154:M1361_1.02:CISBP 0.863 0.597 4.111 0.941 0.91917 12 10 9 13 0.6923 0.7500 0.9000 D 3 ...AACCCTAaw wrmCCTArh. 27 17 25 21 17 21.4000 23
oligos_7nt_mkv5_m3 MYB1-like_MA1030.1_JASPAR oligos_7nt_mkv5_m3 MYB1-like:MA1030.1:JASPAR 0.862 0.597 4.052 0.941 0.91894 12 10 9 13 0.6923 0.7500 0.9000 D 3 ...AACCCTAaw wrmCCTArh. 28 18 27 23 18 22.8000 24
oligos_7nt_mkv5_m3 estExt_fgenesh1_pg.C_Chr_13.00010057_M1396_1.02_CISBP oligos_7nt_mkv5_m3 estExt_fgenesh1_pg.C_Chr_13.00010057:M1396_1.02:CISBP 0.838 0.628 3.828 0.931 0.91275 12 9 9 12 0.7500 0.7500 1.0000 D 3 ...AACCCTAaw wrmCCTArh 30 12 30 27 20 23.8000 25
oligos_7nt_mkv5_m3 AT1G72740_MA1353.1_JASPAR oligos_7nt_mkv5_m3 AT1G72740:MA1353.1:JASPAR 0.963 0.770 8.378 0.978 0.95767 12 15 12 15 0.8000 1.0000 0.8000 D -1 haAAACCCTAaw .ctAAACCCTAAw.. 6 4 40 42 42 26.8000 26
oligos_7nt_mkv5_m3 P0510F09.23_MA1030.2_JASPAR oligos_7nt_mkv5_m3 P0510F09.23:MA1030.2:JASPAR 0.868 0.506 4.047 0.929 0.89906 12 7 7 12 0.5833 0.5833 1.0000 D 3 ...AACCCTA.. wrmCCTA 22 31 28 30 23 26.8000 27
oligos_7nt_mkv5_m3 SRS7.DAP_M0745_AthalianaCistrome oligos_7nt_mkv5_m3 SRS7.DAP:M0745:AthalianaCistrome 0.836 0.436 6.139 0.916 0.91621 12 23 12 23 0.5217 1.0000 0.5217 D -5 haAAACCCTAaw .....CTAAACCCTAAA...... 31 40 11 25 29 27.2000 28
oligos_7nt_mkv5_m3 OsTRBF3_MA2404.1_JASPAR oligos_7nt_mkv5_m3 OsTRBF3:MA2404.1:JASPAR 0.868 0.506 4.079 0.929 0.89900 12 7 7 12 0.5833 0.5833 1.0000 D 3 ...AACCCTA.. wrmCCTA 23 32 26 31 24 27.2000 29
oligos_7nt_mkv5_m3 ATTRB2_M1346_1.02_CISBP oligos_7nt_mkv5_m3 ATTRB2:M1346_1.02:CISBP 0.815 0.544 5.265 0.909 0.89360 12 8 8 12 0.6667 0.6667 1.0000 D 3 ...AACCCTAa. wrmCCTAr 33 24 17 32 32 27.6000 30
oligos_7nt_mkv5_m3 TRB2_MA1073.1_JASPAR oligos_7nt_mkv5_m3 TRB2:MA1073.1:JASPAR 0.814 0.543 5.283 0.909 0.89320 12 8 8 12 0.6667 0.6667 1.0000 D 3 ...AACCCTAa. wrmCCTAr 34 25 16 33 33 28.2000 31
oligos_7nt_mkv5_m3 TRP2_MA1356.1_JASPAR oligos_7nt_mkv5_m3 TRP2:MA1356.1:JASPAR 0.867 0.520 8.258 0.915 0.91606 12 20 12 20 0.6000 1.0000 0.6000 D -5 haAAACCCTAaw .....CTAAACCCTAAA... 24 28 15 39 39 29.0000 32
oligos_7nt_mkv5_m3 estExt_fgenesh1_pg.C_Chr_03.00010061_M1394_1.02_CISBP oligos_7nt_mkv5_m3 estExt_fgenesh1_pg.C_Chr_03.00010061:M1394_1.02:CISBP 0.810 0.607 2.786 0.911 0.90037 12 9 9 12 0.7500 0.7500 1.0000 D 2 ..AAACCCTAa. wwrmCCYar 35 15 36 29 31 29.2000 33
oligos_7nt_mkv5_m3 TOE1_TOE1_3_ArabidopsisPBM oligos_7nt_mkv5_m3 TOE1:TOE1_3:ArabidopsisPBM 0.731 0.609 4.383 0.880 0.89045 12 10 10 12 0.8333 0.8333 1.0000 D 2 ..AAACCCTAaw wAACCTTAAm 40 14 23 35 35 29.4000 34
oligos_7nt_mkv5_m3 AT4G12670.ampDAP_M0623_AthalianaCistrome oligos_7nt_mkv5_m3 AT4G12670.ampDAP:M0623:AthalianaCistrome 0.804 0.459 6.021 0.908 0.91238 12 21 12 21 0.5714 1.0000 0.5714 D -8 haAAACCCTAaw ........mTAMACmYKAAA. 36 37 13 28 34 29.6000 35
oligos_7nt_mkv5_m3 AT2G33550.DAP_M0787_AthalianaCistrome oligos_7nt_mkv5_m3 AT2G33550.DAP:M0787:AthalianaCistrome 0.753 0.502 4.331 0.912 0.91437 12 18 12 18 0.6667 1.0000 0.6667 D -6 haAAACCCTAaw ......awwwrCCCTwAa 38 34 24 26 30 30.4000 36
oligos_7nt_mkv5_m3 TBP3_MA1355.1_JASPAR oligos_7nt_mkv5_m3 TBP3:MA1355.1:JASPAR 0.898 0.567 6.701 0.959 0.94131 12 19 12 19 0.6316 1.0000 0.6316 D -4 haAAACCCTAaw ....htwwrCCCTAAw... 15 22 37 41 40 31.0000 37
oligos_7nt_mkv5_m3 ASR3_MA1733.2_JASPAR oligos_7nt_mkv5_m3 ASR3:MA1733.2:JASPAR 0.712 0.534 3.919 0.877 0.88317 12 9 9 12 0.7500 0.7500 1.0000 D 3 ...AACCCTAaw TrCCCTwaa 41 27 29 36 36 33.8000 38
oligos_7nt_mkv5_m3 OsWRKY45_6ir8_A_3D-footprint oligos_7nt_mkv5_m3 OsWRKY45:6ir8_A:3D-footprint 0.770 0.449 3.104 0.918 0.89175 12 7 7 12 0.5833 0.5833 1.0000 D 0 haAAACC..... tnnnACC 37 39 33 34 28 34.2000 39
oligos_7nt_mkv5_m3 STY1_STY1_ArabidopsisPBM oligos_7nt_mkv5_m3 STY1:STY1:ArabidopsisPBM 0.751 0.429 4.442 0.875 0.87501 12 10 8 14 0.5714 0.6667 0.8000 R 4 ....ACCCTAaw RCCCTAGG.. 39 41 22 37 37 35.2000 40
oligos_7nt_mkv5_m3 TRP1_MA1352.1_JASPAR oligos_7nt_mkv5_m3 TRP1:MA1352.1:JASPAR 0.863 0.450 8.129 0.915 0.91574 12 23 12 23 0.5217 1.0000 0.5217 D -5 haAAACCCTAaw .....CTAAACCCTAAA...... 26 38 31 40 41 35.2000 41
oligos_7nt_mkv5_m3 MYB92_MA1780.2_JASPAR oligos_7nt_mkv5_m3 MYB92:MA1780.2:JASPAR 0.705 0.411 4.519 0.849 0.85333 12 7 7 12 0.5833 0.5833 1.0000 D 5 .....CCCTAaw ACCTAMc 42 42 21 38 38 36.2000 42 
 Host name	rsat
 Job started	2026-04-09.120806
 Job done	2026-04-09.120826
 Seconds	11.19
	user	11.2
	system	1.03
	cuser	5.63
;	csystem	1.58