/var/www/html/rsat/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.112629_Ehould/compare-matrices.tab 
 compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.112629_Ehould/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_2026-04-09.112629_Ehould/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_2026-04-09.112629_Ehould/compare-matrices_query_matrices.transfac
 Output files
	prefix       	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.112629_Ehould/compare-matrices
	match_table_txt	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.112629_Ehould/compare-matrices.tab
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.112629_Ehould/compare-matrices_alignments_1ton.html
	match_table_html	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.112629_Ehould/compare-matrices.html
	html_index   	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.112629_Ehould/compare-matrices_index.html
	alignments_1ton	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.112629_Ehould/compare-matrices_alignments_1ton.tab
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.112629_Ehould/compare-matrices_query_matrices.transfac
		file1	1	11	3112	wwTAAAAAGyw
	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_m2 DOF2.2_MA1272.2_JASPAR oligos_6nt_mkv4_m2 DOF2.2:MA1272.2:JASPAR 0.966 0.878 8.564 0.984 0.96033 11 10 10 11 0.9091 0.9091 1.0000 D 1 .wTAAAAAGyw wyAAAAAGtw 6 1 3 2 2 2.8000 1
oligos_6nt_mkv4_m2 CDF5_UN0360.1_JASPAR oligos_6nt_mkv4_m2 CDF5:UN0360.1:JASPAR 0.962 0.875 8.587 0.982 0.95814 11 10 10 11 0.9091 0.9091 1.0000 D 1 .wTAAAAAGyw wtAAAAAGtr 11 2 2 3 8 5.2000 2
oligos_6nt_mkv4_m2 C3H36_UN0844.1_JASPAR oligos_6nt_mkv4_m2 C3H36:UN0844.1:JASPAR 0.965 0.643 6.540 0.984 0.95464 11 9 8 12 0.6667 0.7273 0.8889 D 3 ...AAAAAGyw AAAAAGkw. 8 22 30 4 3 13.4000 3
oligos_6nt_mkv4_m2 DOF2.2_MA1272.3_JASPAR oligos_6nt_mkv4_m2 DOF2.2:MA1272.3:JASPAR 0.996 0.543 8.559 0.995 0.96979 11 6 6 11 0.5455 0.5455 1.0000 D 3 ...AAAAAG.. AAAAAG 1 63 4 1 1 14.0000 4
oligos_6nt_mkv4_m2 KHZ1_UN0404.2_JASPAR oligos_6nt_mkv4_m2 KHZ1:UN0404.2:JASPAR 0.965 0.643 6.536 0.983 0.95458 11 9 8 12 0.6667 0.7273 0.8889 D 3 ...AAAAAGyw AAAAAGkw. 9 23 31 5 4 14.4000 5
oligos_6nt_mkv4_m2 DOF5.4_MA1280.2_JASPAR oligos_6nt_mkv4_m2 DOF5.4:MA1280.2:JASPAR 0.971 0.618 7.238 0.983 0.95132 11 7 7 11 0.6364 0.6364 1.0000 D 3 ...AAAAAGy. AAAAAGk 3 40 15 11 5 14.8000 6
oligos_6nt_mkv4_m2 C3H67_UN0851.1_JASPAR oligos_6nt_mkv4_m2 C3H67:UN0851.1:JASPAR 0.966 0.595 7.410 0.982 0.95201 11 10 8 13 0.6154 0.7273 0.8000 D 3 ...AAAAAGyw AAAAAGTd.. 5 51 7 9 10 16.4000 7
oligos_6nt_mkv4_m2 At1g64620.ampDAP_M0251_AthalianaCistrome oligos_6nt_mkv4_m2 At1g64620.ampDAP:M0251:AthalianaCistrome 0.939 0.650 7.618 0.971 0.94349 11 11 9 13 0.6923 0.8182 0.8182 D 2 ..TAAAAAGyw sAAAAAGkw.. 19 17 5 24 23 17.6000 8
oligos_6nt_mkv4_m2 dof24.ampDAP_M0269_AthalianaCistrome oligos_6nt_mkv4_m2 dof24.ampDAP:M0269:AthalianaCistrome 0.923 0.677 7.308 0.971 0.94835 11 15 11 15 0.7333 1.0000 0.7333 D -3 wwTAAAAAGyw ...aacAWAAAGTd. 28 13 11 16 26 18.8000 9
oligos_6nt_mkv4_m2 AT3G12130.ampDAP_M0341_AthalianaCistrome oligos_6nt_mkv4_m2 AT3G12130.ampDAP:M0341:AthalianaCistrome 0.915 0.719 6.543 0.969 0.94717 11 14 11 14 0.7857 1.0000 0.7857 D -1 wwTAAAAAGyw .awsAAAAAGkw.. 37 4 29 17 27 22.8000 10
oligos_6nt_mkv4_m2 KHZ1_UN0404.1_JASPAR oligos_6nt_mkv4_m2 KHZ1:UN0404.1:JASPAR 0.915 0.719 6.544 0.969 0.94715 11 14 11 14 0.7857 1.0000 0.7857 D -1 wwTAAAAAGyw .awsAAAAAGkw.. 38 5 28 18 28 23.4000 11
oligos_6nt_mkv4_m2 At1g64620.DAP_M0263_AthalianaCistrome oligos_6nt_mkv4_m2 At1g64620.DAP:M0263:AthalianaCistrome 0.935 0.541 7.261 0.975 0.95259 11 19 11 19 0.5789 1.0000 0.5789 D -4 wwTAAAAAGyw ....aamAAAAAGkw.... 20 66 13 8 16 24.6000 12
oligos_6nt_mkv4_m2 AT5G63260.ampDAP_M0343_AthalianaCistrome oligos_6nt_mkv4_m2 AT5G63260.ampDAP:M0343:AthalianaCistrome 0.927 0.642 7.409 0.965 0.93808 11 11 9 13 0.6923 0.8182 0.8182 D 2 ..TAAAAAGyw sAAAAAGTd.. 24 24 8 37 33 25.2000 13
oligos_6nt_mkv4_m2 OBP4.ampDAP_M0261_AthalianaCistrome oligos_6nt_mkv4_m2 OBP4.ampDAP:M0261:AthalianaCistrome 0.932 0.540 7.166 0.975 0.95185 11 19 11 19 0.5789 1.0000 0.5789 D -4 wwTAAAAAGyw ....aacAAAAAGtw.... 21 67 17 10 18 26.6000 14
oligos_6nt_mkv4_m2 DAG2_MA1271.1_JASPAR oligos_6nt_mkv4_m2 DAG2:MA1271.1:JASPAR 0.921 0.638 7.004 0.964 0.93705 11 11 9 13 0.6923 0.8182 0.8182 D 2 ..TAAAAAGyw sAAAAAGkd.. 32 25 18 39 36 30.0000 15
oligos_6nt_mkv4_m2 DOF1.7_MA1277.2_JASPAR oligos_6nt_mkv4_m2 DOF1.7:MA1277.2:JASPAR 0.949 0.542 6.373 0.976 0.94473 11 11 8 14 0.5714 0.7273 0.7273 D 3 ...AAAAAGyw aAAAAGta... 17 65 37 22 14 31.0000 16
oligos_6nt_mkv4_m2 BBX31.DAP_M0718_AthalianaCistrome oligos_6nt_mkv4_m2 BBX31.DAP:M0718:AthalianaCistrome 0.965 0.429 6.573 0.983 0.95417 11 15 8 18 0.4444 0.7273 0.5333 D 3 ...AAAAAGyw AAAAAGta....... 7 115 27 6 6 32.2000 17
oligos_6nt_mkv4_m2 DOF1_PBF1_Mo17_1_EEAD0326_EEADannot oligos_6nt_mkv4_m2 DOF1_PBF1_Mo17_1:EEAD0326:EEADannot 0.903 0.662 6.271 0.964 0.94300 11 15 11 15 0.7333 1.0000 0.7333 D -2 wwTAAAAAGyw ..rsyaAAAAGkw.. 43 16 40 25 37 32.2000 18
oligos_6nt_mkv4_m2 CDF2_MA0973.2_JASPAR oligos_6nt_mkv4_m2 CDF2:MA0973.2:JASPAR 0.953 0.607 5.106 0.975 0.94066 11 7 7 11 0.6364 0.6364 1.0000 D 3 ...AAAAAGy. aWAAAGy 16 46 57 32 15 33.2000 19
oligos_6nt_mkv4_m2 RIN_EEAD0575_EEADannot oligos_6nt_mkv4_m2 RIN:EEAD0575:EEADannot 0.898 0.817 8.765 0.947 0.92687 11 10 10 11 0.9091 0.9091 1.0000 D 0 wwTAAAAAGy. mmyAAAAAGr 46 3 1 58 61 33.8000 20
oligos_6nt_mkv4_m2 DAG2.ampDAP_M0266_AthalianaCistrome oligos_6nt_mkv4_m2 DAG2.ampDAP:M0266:AthalianaCistrome 0.923 0.554 7.298 0.965 0.93740 11 13 9 15 0.6000 0.8182 0.6923 D 2 ..TAAAAAGyw cAAAAAGkk.... 29 60 12 38 35 34.8000 21
oligos_6nt_mkv4_m2 AT2G28810.ampDAP_M0245_AthalianaCistrome oligos_6nt_mkv4_m2 AT2G28810.ampDAP:M0245:AthalianaCistrome 0.923 0.677 0.604 0.972 0.94956 11 15 11 15 0.7333 1.0000 0.7333 R -2 wwTAAAAAGyw ..ARSAWAAAGTR.. 27 12 114 13 22 37.6000 22
oligos_6nt_mkv4_m2 DOF1.5_MA1279.2_JASPAR oligos_6nt_mkv4_m2 DOF1.5:MA1279.2:JASPAR 0.897 0.617 6.645 0.961 0.94071 11 16 11 16 0.6875 1.0000 0.6875 D -2 wwTAAAAAGyw ..aarAAAAAGtr... 48 43 25 30 43 37.8000 23
oligos_6nt_mkv4_m2 DOF4.7_MA2380.1_JASPAR oligos_6nt_mkv4_m2 DOF4.7:MA2380.1:JASPAR 0.955 0.637 0.579 0.977 0.94582 11 9 8 12 0.6667 0.7273 0.8889 R 3 ...AAAAAGyw AWAAAGTW. 14 26 118 20 12 38.0000 24
oligos_6nt_mkv4_m2 AT5G63260.DAP_M0340_AthalianaCistrome oligos_6nt_mkv4_m2 AT5G63260.DAP:M0340:AthalianaCistrome 0.908 0.628 6.740 0.959 0.93214 11 11 9 13 0.6923 0.8182 0.8182 D 2 ..TAAAAAGyw sAWAAAGKd.. 41 31 24 47 48 38.2000 25
oligos_6nt_mkv4_m2 Dof2_MA0020.1_JASPAR oligos_6nt_mkv4_m2 Dof2:MA0020.1:JASPAR 0.957 0.522 5.707 0.976 0.93643 11 6 6 11 0.5455 0.5455 1.0000 D 5 .....AAAGyw AAAGcm 13 75 49 42 13 38.4000 26
oligos_6nt_mkv4_m2 DOF3.5_MA1276.2_JASPAR oligos_6nt_mkv4_m2 DOF3.5:MA1276.2:JASPAR 0.932 0.593 6.800 0.963 0.92700 11 7 7 11 0.6364 0.6364 1.0000 D 3 ...AAAAAGy. AwAAAGk 22 52 21 57 41 38.6000 27
oligos_6nt_mkv4_m2 At5g62940.DAP_M0244_AthalianaCistrome oligos_6nt_mkv4_m2 At5g62940.DAP:M0244:AthalianaCistrome 0.915 0.479 6.741 0.969 0.94663 11 21 11 21 0.5238 1.0000 0.5238 D -6 wwTAAAAAGyw ......arrAAAAAGtw.... 36 92 23 19 29 39.8000 28
oligos_6nt_mkv4_m2 PBF_MA0064.1_JASPAR oligos_6nt_mkv4_m2 PBF:MA0064.1:JASPAR 0.976 0.444 5.707 0.983 0.94106 11 5 5 11 0.4545 0.4545 1.0000 D 5 .....AAAGy. AAAGy 2 111 51 29 7 40.0000 29
oligos_6nt_mkv4_m2 Dof3_MA0021.1_JASPAR oligos_6nt_mkv4_m2 Dof3:MA0021.1:JASPAR 0.955 0.521 5.709 0.975 0.93499 11 6 6 11 0.5455 0.5455 1.0000 D 5 .....AAAGyw AAAGyv 15 78 47 44 17 40.2000 30
oligos_6nt_mkv4_m2 Adof1.ampDAP_M0277_AthalianaCistrome oligos_6nt_mkv4_m2 Adof1.ampDAP:M0277:AthalianaCistrome 0.914 0.479 6.817 0.968 0.94574 11 21 11 21 0.5238 1.0000 0.5238 D -4 wwTAAAAAGyw ....aasAAAAAGtw...... 39 93 19 21 30 40.4000 31
oligos_6nt_mkv4_m2 DOF4.5_MA1269.2_JASPAR oligos_6nt_mkv4_m2 DOF4.5:MA1269.2:JASPAR 0.940 0.470 6.309 0.972 0.94124 11 13 8 16 0.5000 0.7273 0.6154 D 3 ...AAAAAGyw awAAAGtw..... 18 99 39 28 20 40.8000 32
oligos_6nt_mkv4_m2 CDF3.DAP_M0268_AthalianaCistrome oligos_6nt_mkv4_m2 CDF3.DAP:M0268:AthalianaCistrome 0.904 0.523 6.785 0.964 0.94251 11 19 11 19 0.5789 1.0000 0.5789 D -4 wwTAAAAAGyw ....argAAAAAGtr.... 42 74 22 27 40 41.0000 33
oligos_6nt_mkv4_m2 At4g38000.ampDAP_M0275_AthalianaCistrome oligos_6nt_mkv4_m2 At4g38000.ampDAP:M0275:AthalianaCistrome 0.901 0.624 7.173 0.954 0.92854 11 11 9 13 0.6923 0.8182 0.8182 D 2 ..TAAAAAGyw sAWAAAGTw.. 44 35 16 55 56 41.2000 34
oligos_6nt_mkv4_m2 DOF3.2_MA1270.2_JASPAR oligos_6nt_mkv4_m2 DOF3.2:MA1270.2:JASPAR 0.923 0.634 0.902 0.971 0.94879 11 16 11 16 0.6875 1.0000 0.6875 R -4 wwTAAAAAGyw ....RRSAAAAAGTW. 30 27 111 14 24 41.2000 35
oligos_6nt_mkv4_m2 OBP4_MA1280.1_JASPAR oligos_6nt_mkv4_m2 OBP4:MA1280.1:JASPAR 0.918 0.516 7.243 0.962 0.93524 11 14 9 16 0.5625 0.8182 0.6429 D 2 ..TAAAAAGyw sAAAAAGkw..... 35 81 14 43 42 43.0000 36
oligos_6nt_mkv4_m2 MNB1A_MA0053.1_JASPAR oligos_6nt_mkv4_m2 MNB1A:MA0053.1:JASPAR 0.970 0.441 5.707 0.979 0.93480 11 5 5 11 0.4545 0.4545 1.0000 D 5 .....AAAGy. AAAGc 4 112 48 45 11 44.0000 37
oligos_6nt_mkv4_m2 DOF4.2_MA1273.2_JASPAR oligos_6nt_mkv4_m2 DOF4.2:MA1273.2:JASPAR 0.920 0.526 7.361 0.956 0.92600 11 11 8 14 0.5714 0.7273 0.7273 D 3 ...AAAAAGyw AAAAAGGy... 33 72 10 59 49 44.6000 38
oligos_6nt_mkv4_m2 CDF2_M0653_1.02_CISBP oligos_6nt_mkv4_m2 CDF2:M0653_1.02:CISBP 0.893 0.670 5.137 0.955 0.92898 11 10 9 12 0.7500 0.8182 0.9000 D 2 ..TAAAAAGyw maWAAAGyr. 53 14 55 53 52 45.4000 39
oligos_6nt_mkv4_m2 DOF24_B73_2_m1_EEAD0327_EEADannot oligos_6nt_mkv4_m2 DOF24_B73_2_m1:EEAD0327:EEADannot 0.964 0.428 2.174 0.982 0.95300 11 15 8 18 0.4444 0.7273 0.5333 R 3 ...AAAAAGyw AAAAAGBW....... 10 116 91 7 9 46.6000 40
oligos_6nt_mkv4_m2 CDF2_MA0973.1_JASPAR oligos_6nt_mkv4_m2 CDF2:MA0973.1:JASPAR 0.891 0.669 5.110 0.954 0.92855 11 10 9 12 0.7500 0.8182 0.9000 D 2 ..TAAAAAGyw maWAAAGyr. 56 15 56 54 55 47.2000 41
oligos_6nt_mkv4_m2 TAGL1_UN0426.1_JASPAR oligos_6nt_mkv4_m2 TAGL1:UN0426.1:JASPAR 0.849 0.719 6.402 0.939 0.92543 11 13 11 13 0.8462 1.0000 0.8462 D -1 wwTAAAAAGyw .aagAAAAAGGa. 73 6 34 60 66 47.8000 42
oligos_6nt_mkv4_m2 COG1_MA1279.1_JASPAR oligos_6nt_mkv4_m2 COG1:MA1279.1:JASPAR 0.897 0.470 6.645 0.961 0.94071 11 21 11 21 0.5238 1.0000 0.5238 D -6 wwTAAAAAGyw ......aarAAAAAGtr.... 48 100 25 30 43 49.2000 43
oligos_6nt_mkv4_m2 DOF2.5_MA0977.1_JASPAR oligos_6nt_mkv4_m2 DOF2.5:MA0977.1:JASPAR 0.892 0.649 5.498 0.950 0.92102 11 8 8 11 0.7273 0.7273 1.0000 D 3 ...AAAAAGyw AwAARGTg 55 19 53 66 58 50.2000 44
oligos_6nt_mkv4_m2 AT3G52440_MA1276.1_JASPAR oligos_6nt_mkv4_m2 AT3G52440:MA1276.1:JASPAR 0.880 0.609 6.806 0.946 0.92281 11 11 9 13 0.6923 0.8182 0.8182 D 2 ..TAAAAAGyw sAwAAAGkd.. 61 45 20 65 62 50.6000 45
oligos_6nt_mkv4_m2 AT3G45610_MA1270.1_JASPAR oligos_6nt_mkv4_m2 AT3G45610:MA1270.1:JASPAR 0.923 0.534 0.461 0.971 0.94879 11 19 11 19 0.5789 1.0000 0.5789 R -6 wwTAAAAAGyw ......RRSAAAAAGTW.. 30 70 120 14 24 51.6000 46
oligos_6nt_mkv4_m2 Dof2_MA0020.2_JASPAR oligos_6nt_mkv4_m2 Dof2:MA0020.2:JASPAR 0.959 0.436 5.707 0.972 0.92525 11 5 5 11 0.4545 0.4545 1.0000 D 5 .....AAAGy. AAAGc 12 114 50 61 21 51.6000 47
oligos_6nt_mkv4_m2 AT3G52440.ampDAP_M0247_AthalianaCistrome oligos_6nt_mkv4_m2 AT3G52440.ampDAP:M0247:AthalianaCistrome 0.927 0.485 0.590 0.973 0.95026 11 21 11 21 0.5238 1.0000 0.5238 R -5 wwTAAAAAGyw .....RRVAAAAAGKW..... 23 91 116 12 19 52.2000 48
oligos_6nt_mkv4_m2 dof4.2_MA1273.1_JASPAR oligos_6nt_mkv4_m2 dof4.2:MA1273.1:JASPAR 0.875 0.506 7.368 0.949 0.93187 11 19 11 19 0.5789 1.0000 0.5789 D -2 wwTAAAAAGyw ..aarAAAAAGGy...... 63 83 9 48 59 52.4000 49
oligos_6nt_mkv4_m2 cdf3_M0651_1.02_CISBP oligos_6nt_mkv4_m2 cdf3:M0651_1.02:CISBP 0.897 0.598 5.001 0.954 0.92440 11 9 8 12 0.6667 0.7273 0.8889 D 3 ...AAAAAGyw awAAAGyg. 47 47 58 62 53 53.4000 50 
 Host name	rsat
 Job started	2026-04-09.112629
 Job done	2026-04-09.112706
 Seconds	11.35
	user	11.35
	system	3.11
	cuser	17.12
;	csystem	5.03