/var/www/html/rsat/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.111959_ecHkIx/compare-matrices.tab 
 compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.111959_ecHkIx/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_2026-04-09.111959_ecHkIx/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_2026-04-09.111959_ecHkIx/compare-matrices_query_matrices.transfac
 Output files
	match_table_txt	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.111959_ecHkIx/compare-matrices.tab
	alignments_1ton	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.111959_ecHkIx/compare-matrices_alignments_1ton.tab
	prefix       	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.111959_ecHkIx/compare-matrices
	html_index   	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.111959_ecHkIx/compare-matrices_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.111959_ecHkIx/compare-matrices_alignments_1ton.html
	match_table_html	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.111959_ecHkIx/compare-matrices.html
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.111959_ecHkIx/compare-matrices_query_matrices.transfac
		file1	1	14	2524	hhwAAACCCTArww
	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_m1 TRB1_MA2032.1_JASPAR oligos_6nt_mkv4_m1 TRB1:MA2032.1:JASPAR 0.979 0.769 7.108 0.991 0.97100 14 11 11 14 0.7857 0.7857 1.0000 D 2 ..wAAACCCTArw. aaAACCCTArw 2 4 4 1 2 2.6000 1
oligos_6nt_mkv4_m1 TRB1_MA2032.2_JASPAR oligos_6nt_mkv4_m1 TRB1:MA2032.2:JASPAR 0.985 0.633 7.105 0.992 0.96987 14 9 9 14 0.6429 0.6429 1.0000 D 3 ...AAACCCTAr.. aAACCCTAr 1 13 5 2 1 4.4000 2
oligos_6nt_mkv4_m1 TBP3_MA1355.1_JASPAR oligos_6nt_mkv4_m1 TBP3:MA1355.1:JASPAR 0.894 0.835 7.074 0.961 0.94751 14 15 14 15 0.9333 1.0000 0.9333 D -1 hhwAAACCCTArww .wwtwwrCCCTAAwt 11 2 6 8 9 7.2000 3
oligos_6nt_mkv4_m1 TRB2_MA1355.2_JASPAR oligos_6nt_mkv4_m1 TRB2:MA1355.2:JASPAR 0.897 0.705 7.068 0.954 0.93507 14 11 11 14 0.7857 0.7857 1.0000 D 3 ...AAACCCTArww wwrCCCTAAwt 10 6 7 10 11 8.8000 4
oligos_6nt_mkv4_m1 AT1G72740_MA1353.1_JASPAR oligos_6nt_mkv4_m1 AT1G72740:MA1353.1:JASPAR 0.962 0.781 0.490 0.981 0.96153 14 15 13 16 0.8125 0.9286 0.8667 R 1 .hwAAACCCTArww MWAAACCCTAAWY.. 5 3 35 4 4 10.2000 5
oligos_6nt_mkv4_m1 PNRC2_UN0276.1_JASPAR oligos_6nt_mkv4_m1 PNRC2:UN0276.1:JASPAR 0.961 0.549 6.584 0.978 0.94785 14 8 8 14 0.5714 0.5714 1.0000 D 3 ...AAACCCTA... AAWMCCTA 6 24 9 7 6 10.4000 6
oligos_6nt_mkv4_m1 AT1G72740_MA1353.2_JASPAR oligos_6nt_mkv4_m1 AT1G72740:MA1353.2:JASPAR 0.967 0.760 0.487 0.980 0.95788 14 11 11 14 0.7857 0.7857 1.0000 R 3 ...AAACCCTArww AAACCCTAAWY 3 5 36 5 5 10.8000 7
oligos_6nt_mkv4_m1 TBP3.ampDAP_M0621_AthalianaCistrome oligos_6nt_mkv4_m1 TBP3.ampDAP:M0621:AthalianaCistrome 0.922 0.680 0.366 0.972 0.95530 14 19 14 19 0.7368 1.0000 0.7368 R -4 hhwAAACCCTArww ....HHTAARCCCTAAWY. 9 7 40 6 8 14.0000 8
oligos_6nt_mkv4_m1 AT1G72740.ampDAP_M0588_AthalianaCistrome oligos_6nt_mkv4_m1 AT1G72740.ampDAP:M0588:AthalianaCistrome 0.965 0.570 0.278 0.984 0.96491 14 21 13 22 0.5909 0.9286 0.6190 R 1 .hwAAACCCTArww MWAAACCCTAAWY........ 4 20 41 3 3 14.2000 9
oligos_6nt_mkv4_m1 1200010153_M1391_1.02_CISBP oligos_6nt_mkv4_m1 1200010153:M1391_1.02:CISBP 0.882 0.630 5.269 0.952 0.93044 14 10 10 14 0.7143 0.7143 1.0000 D 4 ....AACCCTArww amCCCTAryy 15 14 18 12 12 14.2000 10
oligos_6nt_mkv4_m1 MYBR101_SMH1_B73_1_m1_EEAD0453_EEADannot oligos_6nt_mkv4_m1 MYBR101_SMH1_B73_1_m1:EEAD0453:EEADannot 0.854 0.671 6.560 0.937 0.92424 14 11 11 14 0.7857 0.7857 1.0000 D 1 .hwAAACCCTAr.. cywWrCCCTAr 21 8 10 16 16 14.2000 11
oligos_6nt_mkv4_m1 TRP5_MA1802.1_JASPAR oligos_6nt_mkv4_m1 TRP5:MA1802.1:JASPAR 0.892 0.637 3.124 0.958 0.93483 14 10 10 14 0.7143 0.7143 1.0000 D 0 hhwAAACCCT.... swwAAACCyy 13 11 31 11 10 15.2000 12
oligos_6nt_mkv4_m1 LOC_Os01g51154_M1361_1.02_CISBP oligos_6nt_mkv4_m1 LOC_Os01g51154:M1361_1.02:CISBP 0.872 0.623 4.354 0.948 0.92810 14 10 10 14 0.7143 0.7143 1.0000 D 4 ....AACCCTArww wrmCCTArhy 18 15 24 13 13 16.6000 13
oligos_6nt_mkv4_m1 0100010593_M1389_1.02_CISBP oligos_6nt_mkv4_m1 0100010593:M1389_1.02:CISBP 0.887 0.633 3.399 0.945 0.92614 14 10 10 14 0.7143 0.7143 1.0000 D 3 ...AAACCCTArw. wwAMCCTarw 14 12 30 15 15 17.2000 14
oligos_6nt_mkv4_m1 TRP5_MA1802.2_JASPAR oligos_6nt_mkv4_m1 TRP5:MA1802.2:JASPAR 0.945 0.472 3.093 0.972 0.93689 14 7 7 14 0.5000 0.5000 1.0000 D 2 ..wAAACCC..... wAAACCy 7 34 32 9 7 17.8000 15
oligos_6nt_mkv4_m1 MYB1-like_MA1030.1_JASPAR oligos_6nt_mkv4_m1 MYB1-like:MA1030.1:JASPAR 0.872 0.623 4.293 0.948 0.92790 14 10 10 14 0.7143 0.7143 1.0000 D 4 ....AACCCTArww wrmCCTArhy 19 16 26 14 14 17.8000 16
oligos_6nt_mkv4_m1 TRP2_MA1356.1_JASPAR oligos_6nt_mkv4_m1 TRP2:MA1356.1:JASPAR 0.851 0.568 9.042 0.912 0.92051 14 21 14 21 0.6667 1.0000 0.6667 D -3 hhwAAACCCTArww ...CcTAAACCCTAAAC.... 22 21 1 19 29 18.4000 17
oligos_6nt_mkv4_m1 TRP2.ampDAP_M0612_AthalianaCistrome oligos_6nt_mkv4_m1 TRP2.ampDAP:M0612:AthalianaCistrome 0.851 0.567 9.009 0.912 0.92086 14 21 14 21 0.6667 1.0000 0.6667 D -4 hhwAAACCCTArww ....CCTAAACCCTAAAC... 24 22 2 18 27 18.6000 18
oligos_6nt_mkv4_m1 MYBR101_SMH1_Mo17_1_EEAD0454_EEADannot oligos_6nt_mkv4_m1 MYBR101_SMH1_Mo17_1:EEAD0454:EEADannot 0.821 0.657 6.160 0.929 0.92321 14 13 12 15 0.8000 0.8571 0.9231 D -1 hhwAAACCCTAr.. .cCytwrCCCTAr 32 10 14 17 20 18.6000 19
oligos_6nt_mkv4_m1 AL2G32420.t2_MYBRELATED_1_AT1G72740_EEAD0583_EEADannot oligos_6nt_mkv4_m1 AL2G32420.t2_MYBRELATED_1_AT1G72740:EEAD0583:EEADannot 0.863 0.575 6.594 0.923 0.91229 14 11 10 15 0.6667 0.7143 0.9091 D 4 ....AACCCTArww AACCCTAAAC. 20 18 8 26 21 18.6000 20
oligos_6nt_mkv4_m1 LOC_Os01g51154.1_MYBRELATED_1_AT1G72740_EEAD0624_EEADannot oligos_6nt_mkv4_m1 LOC_Os01g51154.1_MYBRELATED_1_AT1G72740:EEAD0624:EEADannot 0.840 0.593 6.315 0.918 0.91749 14 15 12 17 0.7059 0.8571 0.8000 D -3 hhwAAACCCTAr.. ...CCTAAACCCTAA 27 17 13 21 24 20.4000 21
oligos_6nt_mkv4_m1 TRP1_MA1352.1_JASPAR oligos_6nt_mkv4_m1 TRP1:MA1352.1:JASPAR 0.828 0.552 8.896 0.895 0.91360 14 21 14 21 0.6667 1.0000 0.6667 D -2 hhwAAACCCTArww ..CCTAAACCCTAAAC..... 28 23 3 24 33 22.2000 22
oligos_6nt_mkv4_m1 estExt_fgenesh1_pg.C_Chr_13.00010057_M1396_1.02_CISBP oligos_6nt_mkv4_m1 estExt_fgenesh1_pg.C_Chr_13.00010057:M1396_1.02:CISBP 0.843 0.542 4.030 0.931 0.91234 14 9 9 14 0.6429 0.6429 1.0000 D 4 ....AACCCTArw. wrmCCTArh 26 25 28 25 17 24.2000 23
oligos_6nt_mkv4_m1 Solyc07g040920.2.1_MYBRELATED_1_AT1G72740_EEAD0654_EEADannot oligos_6nt_mkv4_m1 Solyc07g040920.2.1_MYBRELATED_1_AT1G72740:EEAD0654:EEADannot 0.851 0.479 5.238 0.921 0.90629 14 11 9 16 0.5625 0.6429 0.8182 D 5 .....ACCCTArww ACCCTAAAC.. 23 32 19 28 23 25.0000 24
oligos_6nt_mkv4_m1 XP_013589913.1_MYBRELATED_1_AT1G72740_EEAD0665_EEADannot oligos_6nt_mkv4_m1 XP_013589913.1_MYBRELATED_1_AT1G72740:EEAD0665:EEADannot 0.851 0.478 5.176 0.921 0.90634 14 11 9 16 0.5625 0.6429 0.8182 D 5 .....ACCCTArww ACCCTAAAC.. 25 33 20 27 22 25.4000 25
oligos_6nt_mkv4_m1 P0510F09.23_MA1030.2_JASPAR oligos_6nt_mkv4_m1 P0510F09.23:MA1030.2:JASPAR 0.873 0.436 4.281 0.929 0.89953 14 7 7 14 0.5000 0.5000 1.0000 D 4 ....AACCCTA... wrmCCTA 16 38 27 29 18 25.6000 26
oligos_6nt_mkv4_m1 AT4G12670.ampDAP_M0623_AthalianaCistrome oligos_6nt_mkv4_m1 AT4G12670.ampDAP:M0623:AthalianaCistrome 0.774 0.516 6.418 0.898 0.91454 14 21 14 21 0.6667 1.0000 0.6667 D -7 hhwAAACCCTArww .......CmTAMACmYKAAAy 36 27 12 22 31 25.6000 27
oligos_6nt_mkv4_m1 OsTRBF3_MA2404.1_JASPAR oligos_6nt_mkv4_m1 OsTRBF3:MA2404.1:JASPAR 0.872 0.436 4.315 0.929 0.89948 14 7 7 14 0.5000 0.5000 1.0000 D 4 ....AACCCTA... wrmCCTA 17 39 25 30 19 26.0000 28
oligos_6nt_mkv4_m1 AT1G72740_MA1353.1_JASPAR oligos_6nt_mkv4_m1 AT1G72740:MA1353.1:JASPAR 0.944 0.881 8.741 0.973 0.95638 14 15 14 15 0.9333 1.0000 0.9333 D 0 hhwAAACCCTArww cctAAACCCTAAwy. 8 1 39 42 42 26.4000 29
oligos_6nt_mkv4_m1 SRS7.DAP_M0745_AthalianaCistrome oligos_6nt_mkv4_m1 SRS7.DAP:M0745:AthalianaCistrome 0.793 0.482 6.559 0.896 0.91366 14 23 14 23 0.6087 1.0000 0.6087 D -4 hhwAAACCCTArww ....CCTAAACCCTAAAC..... 35 31 11 23 32 26.4000 30
oligos_6nt_mkv4_m1 AT2G33550.DAP_M0787_AthalianaCistrome oligos_6nt_mkv4_m1 AT2G33550.DAP:M0787:AthalianaCistrome 0.748 0.512 4.600 0.914 0.91867 14 18 13 19 0.6842 0.9286 0.7222 D -5 hhwAAACCCTArw. .....wawwwrCCCTwAa 38 28 23 20 25 26.8000 31
oligos_6nt_mkv4_m1 TBP3_MA1355.1_JASPAR oligos_6nt_mkv4_m1 TBP3:MA1355.1:JASPAR 0.893 0.658 7.064 0.961 0.94713 14 19 14 19 0.7368 1.0000 0.7368 D -3 hhwAAACCCTArww ...whtwwrCCCTAAwt.. 12 9 34 41 40 27.2000 32
oligos_6nt_mkv4_m1 ATTRB2_M1346_1.02_CISBP oligos_6nt_mkv4_m1 ATTRB2:M1346_1.02:CISBP 0.826 0.472 5.535 0.913 0.89563 14 8 8 14 0.5714 0.5714 1.0000 D 4 ....AACCCTAr.. wrmCCTAr 29 35 17 32 26 27.8000 33
oligos_6nt_mkv4_m1 TRB2_MA1073.1_JASPAR oligos_6nt_mkv4_m1 TRB2:MA1073.1:JASPAR 0.825 0.471 5.555 0.912 0.89520 14 8 8 14 0.5714 0.5714 1.0000 D 4 ....AACCCTAr.. wrmCCTAr 30 36 16 33 28 28.6000 34
oligos_6nt_mkv4_m1 TRP2_MA1356.1_JASPAR oligos_6nt_mkv4_m1 TRP2:MA1356.1:JASPAR 0.821 0.575 8.648 0.895 0.91330 14 20 14 20 0.7000 1.0000 0.7000 D -4 hhwAAACCCTArww ....CCTAAACCCTAAAC.. 33 19 15 39 39 29.0000 35
oligos_6nt_mkv4_m1 estExt_fgenesh1_pg.C_Chr_03.00010061_M1394_1.02_CISBP oligos_6nt_mkv4_m1 estExt_fgenesh1_pg.C_Chr_03.00010061:M1394_1.02:CISBP 0.811 0.521 2.886 0.906 0.89802 14 9 9 14 0.6429 0.6429 1.0000 D 3 ...AAACCCTAr.. wwrmCCYar 34 26 33 31 30 30.8000 36
oligos_6nt_mkv4_m1 TOE1_TOE1_3_ArabidopsisPBM oligos_6nt_mkv4_m1 TOE1:TOE1_3:ArabidopsisPBM 0.715 0.511 4.640 0.870 0.88601 14 10 10 14 0.7143 0.7143 1.0000 D 3 ...AAACCCTArw. wAACCTTAAm 40 29 22 35 36 32.4000 37
oligos_6nt_mkv4_m1 TRP1_MA1352.1_JASPAR oligos_6nt_mkv4_m1 TRP1:MA1352.1:JASPAR 0.822 0.500 8.551 0.897 0.91424 14 23 14 23 0.6087 1.0000 0.6087 D -4 hhwAAACCCTArww ....CCTAAACCCTAAAC..... 31 30 29 40 41 34.2000 38
oligos_6nt_mkv4_m1 STY1_STY1_ArabidopsisPBM oligos_6nt_mkv4_m1 STY1:STY1:ArabidopsisPBM 0.731 0.439 4.797 0.868 0.87892 14 10 9 15 0.6000 0.6429 0.9000 R 5 .....ACCCTArww RCCCTAGGG. 39 37 21 37 37 34.2000 39
oligos_6nt_mkv4_m1 NAC25_B73_1_m1_EEAD0471_EEADannot oligos_6nt_mkv4_m1 NAC25_B73_1_m1:EEAD0471:EEADannot 0.764 0.402 0.486 0.890 0.89494 14 15 10 19 0.5263 0.7143 0.6667 R -5 hhwAAACCCT.... .....CAAAAACTCT 37 42 37 34 35 37.0000 40
oligos_6nt_mkv4_m1 Probable_6j4f_F_3D-footprint oligos_6nt_mkv4_m1 Probable:6j4f_F:3D-footprint 0.713 0.408 0.461 0.893 0.88451 14 8 8 14 0.5714 0.5714 1.0000 R 0 hhwAAACC...... CTTNNACC 41 40 38 36 34 37.8000 41
oligos_6nt_mkv4_m1 TRFL5_M1316_1.02_CISBP oligos_6nt_mkv4_m1 TRFL5:M1316_1.02:CISBP 0.705 0.403 0.266 0.833 0.85555 14 8 8 14 0.5714 0.5714 1.0000 R 4 ....AACCCTAr.. TGCCCTAR 42 41 42 38 38 40.2000 42 
 Host name	rsat
 Job started	2026-04-09.112000
 Job done	2026-04-09.112021
 Seconds	12.53
	user	12.54
	system	1.21
	cuser	5.92
;	csystem	1.73