/var/www/html/rsat/public_html/tmp/www-data/2025/03/15/compare-matrices_2025-03-15.183841_2Q1EjC/compare-matrices.tab 
 compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/03/15/compare-matrices_2025-03-15.183841_2Q1EjC/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/ENCODE/encode-motifs_Kheradpour_Kellis_NAR2013.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/2025/03/15/compare-matrices_2025-03-15.183841_2Q1EjC/compare-matrices.tab
 Program version       	1.118
 Slow mode 
 Input files
	file2 	$RSAT/public_html/motif_databases/ENCODE/encode-motifs_Kheradpour_Kellis_NAR2013.tf
	file1 	$RSAT/public_html/tmp/www-data/2025/03/15/compare-matrices_2025-03-15.183841_2Q1EjC/compare-matrices_query_matrices.transfac
 Output files
	match_table_html	$RSAT/public_html/tmp/www-data/2025/03/15/compare-matrices_2025-03-15.183841_2Q1EjC/compare-matrices.html
	html_index   	$RSAT/public_html/tmp/www-data/2025/03/15/compare-matrices_2025-03-15.183841_2Q1EjC/compare-matrices_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2025/03/15/compare-matrices_2025-03-15.183841_2Q1EjC/compare-matrices_alignments_1ton.html
	match_table_txt	$RSAT/public_html/tmp/www-data/2025/03/15/compare-matrices_2025-03-15.183841_2Q1EjC/compare-matrices.tab
	prefix       	$RSAT/public_html/tmp/www-data/2025/03/15/compare-matrices_2025-03-15.183841_2Q1EjC/compare-matrices
	alignments_1ton	$RSAT/public_html/tmp/www-data/2025/03/15/compare-matrices_2025-03-15.183841_2Q1EjC/compare-matrices_alignments_1ton.tab
 Matrices
	file1	11 matrices	$RSAT/public_html/tmp/www-data/2025/03/15/compare-matrices_2025-03-15.183841_2Q1EjC/compare-matrices_query_matrices.transfac
		file1	1	13	225	srkCyGAGATsws
		file1	2	10	14	aaATATATtt
		file1	3	11	1474	aaAArAATtaw
		file1	4	13	6709	ysCCTCTsCCysg
		file1	5	19	6705	AAAAAAAAAAAAAAwwwwa
		file1	6	13	6706	sGCtCCTCMCTyC
		file1	7	11	138	AgAATTATsaa
		file1	8	12	750	yGgGAGGCyGsa
		file1	9	11	695	gaCACTGCAvm
		file1	10	10	465	mkCACATCyy
		file1	11	10	173	GTAGACATGG
		...	1 more matrices
	file2	2065 matrices	$RSAT/public_html/motif_databases/ENCODE/encode-motifs_Kheradpour_Kellis_NAR2013.tf
		file2		1		11		1000000		ATTAAyTrCAC
		file2		2		18		1000000		cyyCsrrs-wGCG-Gasw
		file2		3		11		1000000		cTtGCG-Gmsm
		file2		4		16		1000001		kddkrktyGCG-Gcms
		file2		5		19		1000000		GrgkATyGCG-GmswrsCC
		file2		6		6		1000000		yGCG-G
		file2		7		9		1000001		krCG-Gmgs
		file2		8		26		1000000		wwwkkwmhtGGwwwwwwwGGwywwww
		file2		9		25		1000001		Sg--A-TAAKTGGTTATAT-GGkTd
		file2		10		18		1000001		mvc-AATTmmhATTAbyd
		file2		11		17		1000001		cgmryTAATTArtymcy
		...	2055 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
cluster_7 ZBTB3_1 cluster_7 ZBTB3_1 0.905 0.585 6.886 0.961 0.94041 11 17 11 17 0.6471 1.0000 0.6471 D -3 gaCACTGCAvm ...bsCACTGCAyt... 1 11 16 1 1 6.0000 1
cluster_1 HDAC2_disc6 cluster_1 HDAC2_disc6 0.783 0.618 5.843 0.903 0.91971 19 15 15 19 0.7895 0.7895 1.0000 D 0 AAAAAAAAAAAAAAw.... arrrrAArAAArrmA 26 6 39 3 26 20.0000 2
cluster_2 LHX3_2 cluster_2 LHX3_2 0.786 0.665 4.947 0.911 0.91013 11 13 11 13 0.8462 1.0000 0.8462 D 0 aaAArAATtaw wAA--AATTAw.. 24 3 66 12 18 24.6000 3
cluster_5 DLX1_2 cluster_5 DLX1_2 0.828 0.621 4.254 0.924 0.90804 11 10 9 12 0.7500 0.8182 0.9000 D -1 AgAATTATs.. .myAATTAkc 7 5 105 15 5 27.4000 4
cluster_2 PAX4_2 cluster_2 PAX4_2 0.832 0.694 3.580 0.940 0.92264 11 11 10 12 0.8333 0.9091 0.9091 D 1 .aAArAATtaw rAmwAATTav. 6 1 134 2 2 29.0000 5
cluster_2 ZNF384_1 cluster_2 ZNF384_1 0.765 0.626 6.674 0.896 0.89265 11 9 9 11 0.8182 0.8182 1.0000 D 1 .aAArAATta. sAAAAAvyc 41 4 22 43 38 29.6000 6
cluster_2 SOX17_3 cluster_2 SOX17_3 0.781 0.573 4.373 0.921 0.91521 11 15 11 15 0.7333 1.0000 0.7333 D -1 aaAArAATtaw .waAACAATTrA... 29 17 99 5 7 31.4000 7
cluster_10 TATA_known6 cluster_10 TATA_known6 0.815 0.509 5.648 0.918 0.90963 10 16 10 16 0.6250 1.0000 0.6250 D -3 aaATATATtt ...wwwTATAwww... 11 99 44 13 11 35.6000 8
cluster_5 DLX5_2 cluster_5 DLX5_2 0.816 0.594 4.209 0.912 0.89510 11 8 8 11 0.7273 0.7273 1.0000 D 0 AgAATTAT... vyAATTAh 9 10 107 38 17 36.2000 9
cluster_5 DLX1_3 cluster_5 DLX1_3 0.795 0.578 4.741 0.902 0.88932 11 8 8 11 0.7273 0.7273 1.0000 D 0 AgAATTAT... syAATTAm 17 14 78 57 27 38.6000 10
cluster_5 DLX6_1 cluster_5 DLX6_1 0.787 0.572 5.026 0.898 0.88698 11 8 8 11 0.7273 0.7273 1.0000 D 0 AgAATTAT... syAATTAm 23 18 61 72 36 42.0000 11
cluster_10 FOXL1_2 cluster_10 FOXL1_2 0.843 0.537 4.621 0.916 0.89028 10 8 7 11 0.6364 0.7000 0.8750 D -1 aaATATA... .wdayATA 2 63 84 50 12 42.2000 12
cluster_2 SOX13_1 cluster_2 SOX13_1 0.765 0.526 5.011 0.912 0.91067 11 16 11 16 0.6875 1.0000 0.6875 D -3 aaAArAATtaw ...rgAACAATwww.. 43 79 62 11 16 42.2000 13
cluster_5 HESX1_1 cluster_5 HESX1_1 0.760 0.570 5.938 0.889 0.88895 11 10 9 12 0.7500 0.8182 0.9000 R -1 AgAATTATs.. .YYAATTARC 47 21 34 62 54 43.6000 14
cluster_5 EN2_2 cluster_5 EN2_2 0.753 0.565 5.537 0.891 0.89008 11 10 9 12 0.7500 0.8182 0.9000 D -1 AgAATTATs.. .yyAATTAac 61 23 49 51 45 45.8000 15
cluster_2 SOX5_3 cluster_2 SOX5_3 0.757 0.521 5.470 0.907 0.90803 11 16 11 16 0.6875 1.0000 0.6875 D -3 aaAArAATtaw ...rgAACAATwaa.. 52 87 54 16 21 46.0000 16
cluster_2 NKX6-2_1 cluster_2 NKX6-2_1 0.744 0.682 3.809 0.916 0.91241 11 12 11 12 0.9167 1.0000 0.9167 D 0 aaAArAATtaw rwrd-AAwTab. 78 2 129 8 14 46.2000 17
cluster_2 SOX18_1 cluster_2 SOX18_1 0.790 0.543 0.531 0.926 0.91811 11 16 11 16 0.6875 1.0000 0.6875 R -4 aaAArAATtaw ....ARAACAATDRW. 20 50 167 4 4 49.0000 18
cluster_5 DLX3_2 cluster_5 DLX3_2 0.788 0.573 4.048 0.900 0.88819 11 8 8 11 0.7273 0.7273 1.0000 D 0 AgAATTAT... syAATTAm 22 16 118 65 29 50.0000 19
cluster_5 DLX4_2 cluster_5 DLX4_2 0.784 0.570 4.398 0.898 0.88697 11 8 8 11 0.7273 0.7273 1.0000 D 0 AgAATTAT... syAATTAm 25 20 97 73 37 50.4000 20
cluster_5 GBX2_2 cluster_5 GBX2_2 0.750 0.563 6.209 0.887 0.88779 11 10 9 12 0.7500 0.8182 0.9000 D -1 AgAATTATs.. .syAATTArs 64 25 31 68 66 50.8000 21
cluster_6 GTF2I_1 cluster_6 GTF2I_1 0.837 0.418 6.388 0.919 0.89226 12 9 7 14 0.5000 0.5833 0.7778 D -2 yGgGAGG..... ..AgGkAGG 5 171 27 45 10 51.6000 22
cluster_7 SOX8_2 cluster_7 SOX8_2 0.801 0.551 4.424 0.883 0.89682 11 16 11 16 0.6875 1.0000 0.6875 R 0 gaCACTGCAvm AACACTGCAYA..... 14 39 96 34 77 52.0000 23
cluster_5 RAX_2 cluster_5 RAX_2 0.747 0.561 5.893 0.887 0.88802 11 10 9 12 0.7500 0.8182 0.9000 D -1 AgAATTATs.. .yyAATTAry 68 26 37 66 64 52.2000 24
cluster_7 KLF12_1 cluster_7 KLF12_1 0.839 0.534 0.300 0.938 0.90614 11 7 7 11 0.6364 0.6364 1.0000 R 0 gaCACTG.... CCCACTG 4 67 176 18 3 53.6000 25
cluster_7 GFI1B_1 cluster_7 GFI1B_1 0.783 0.503 4.668 0.905 0.89724 11 12 9 14 0.6429 0.8182 0.7500 D -3 gaCACTGCA.. ...A-CAstGCw 27 106 81 33 24 54.2000 26
cluster_5 NKX6-2_1 cluster_5 NKX6-2_1 0.790 0.508 4.178 0.908 0.89870 11 12 9 14 0.6429 0.8182 0.7500 D -3 AgAATTATs.. ...d-AAwTabb 21 100 108 32 20 56.2000 27
cluster_5 EVX1_2 cluster_5 EVX1_2 0.747 0.561 4.480 0.892 0.89053 11 10 9 12 0.7500 0.8182 0.9000 D -1 AgAATTATs.. .vtaATTAsc 70 27 93 49 44 56.6000 28
cluster_4 ZNF263_disc1 cluster_4 ZNF263_disc1 0.793 0.610 0.929 0.889 0.89450 13 10 10 13 0.7692 0.7692 1.0000 R 1 .GCtCCTCMCT.. CCTCCTCCCY 18 7 162 39 58 56.8000 29
cluster_5 ALX3_2 cluster_5 ALX3_2 0.745 0.559 4.905 0.889 0.88898 11 10 9 12 0.7500 0.8182 0.9000 D -1 AgAATTATs.. .cyAATTArc 75 28 68 61 53 57.0000 30
cluster_9 FOXO3_4 cluster_9 FOXO3_4 0.782 0.558 10.933 0.860 0.88174 10 14 10 14 0.7143 1.0000 0.7143 D 0 GTAGACATGG GTAAACATG-.... 28 29 1 93 135 57.2000 31
cluster_5 PRRX1_2 cluster_5 PRRX1_2 0.765 0.557 5.087 0.888 0.88157 11 8 8 11 0.7273 0.7273 1.0000 D 0 AgAATTAT... yyAATTAr 42 31 58 95 61 57.4000 32
cluster_2 SOX12_1 cluster_2 SOX12_1 0.791 0.527 0.367 0.916 0.90818 11 14 10 15 0.6667 0.9091 0.7143 R -4 aaAArAATta. ....AGAACAATWA 19 74 173 14 13 58.6000 33
cluster_2 ZNF35_1 cluster_2 ZNF35_1 0.778 0.486 3.498 0.923 0.91213 11 15 10 16 0.6250 0.9091 0.6667 D -5 aaAArAATta. .....whAAmAAkar 31 117 136 9 6 59.8000 34
cluster_2 SOX8_1 cluster_2 SOX8_1 0.773 0.500 2.181 0.920 0.91481 11 17 11 17 0.6471 1.0000 0.6471 R -3 aaAArAATtaw ...WKAACAATWRA... 35 108 148 6 8 61.0000 35
cluster_5 GBX1_3 cluster_5 GBX1_3 0.741 0.556 5.518 0.886 0.88727 11 10 9 12 0.7500 0.8182 0.9000 D -1 AgAATTATs.. .cyAATTArs 85 33 50 71 71 62.0000 36
cluster_9 FOXO1_4 cluster_9 FOXO1_4 0.767 0.548 9.506 0.860 0.88184 10 14 10 14 0.7143 1.0000 0.7143 D 0 GTAGACATGG rTAAACATG-.... 39 46 3 92 134 62.8000 37
cluster_1 ZNF35_1 cluster_1 ZNF35_1 0.724 0.571 4.386 0.885 0.91252 19 15 15 19 0.7895 0.7895 1.0000 D 1 .AAAAAAAAAAAAAww... wayAAwhAAmAAkar 126 19 98 7 72 64.4000 38
cluster_5 LHX3_2 cluster_5 LHX3_2 0.740 0.529 5.471 0.886 0.89330 11 13 10 14 0.7143 0.9091 0.7692 D -3 AgAATTATsa. ...--AATTAwyy 88 72 53 42 69 64.8000 39
cluster_2 SOX15_1 cluster_2 SOX15_1 0.740 0.479 4.808 0.906 0.90746 11 17 11 17 0.6471 1.0000 0.6471 D -3 aaAArAATtaw ...wgAACAATwrr... 89 128 73 17 23 66.0000 40
cluster_5 GBX2_4 cluster_5 GBX2_4 0.742 0.557 3.903 0.891 0.88986 11 10 9 12 0.7500 0.8182 0.9000 D -1 AgAATTATs.. .cyAATTArc 81 30 126 52 47 67.2000 41
cluster_5 ESX1_2 cluster_5 ESX1_2 0.741 0.556 4.021 0.890 0.88953 11 10 9 12 0.7500 0.8182 0.9000 D -1 AgAATTATs.. .cyAATTAvc 84 32 119 55 49 67.8000 42
cluster_5 SHOX_1 cluster_5 SHOX_1 0.755 0.549 5.662 0.880 0.87775 11 8 8 11 0.7273 0.7273 1.0000 D 0 AgAATTAT... yyAATTAr 58 44 43 107 89 68.2000 43
cluster_5 ESX1_3 cluster_5 ESX1_3 0.741 0.556 4.078 0.890 0.88940 11 10 9 12 0.7500 0.8182 0.9000 D -1 AgAATTATs.. .cyAATTArc 86 34 115 56 50 68.2000 44
cluster_5 PAX4_2 cluster_5 PAX4_2 0.755 0.523 3.842 0.896 0.89248 11 11 9 13 0.6923 0.8182 0.8182 D -2 AgAATTATs.. ..mwAATTavs 56 86 128 44 39 70.6000 45
cluster_5 DLX2_1 cluster_5 DLX2_1 0.722 0.496 5.810 0.891 0.90047 11 16 11 16 0.6875 1.0000 0.6875 D -3 AgAATTATsaa ...rYAATTRbhym.. 131 110 40 27 46 70.8000 46
cluster_6 AP1_disc10 cluster_6 AP1_disc10 0.726 0.605 3.929 0.887 0.89364 12 10 10 12 0.8333 0.8333 1.0000 D 1 .GgGAGGCyGs. GssgrGssGs 117 8 124 41 65 71.0000 47
cluster_5 DLX3_1 cluster_5 DLX3_1 0.756 0.489 3.386 0.899 0.90407 11 17 11 17 0.6471 1.0000 0.6471 R -4 AgAATTATsaa ....GTAATTATHKY.. 53 114 138 19 33 71.4000 48
cluster_2 TATA_known1 cluster_2 TATA_known1 0.810 0.405 4.995 0.907 0.88470 11 10 7 14 0.5000 0.6364 0.7000 D -3 aaAArAA.... ...W-AAAAr 12 178 63 83 22 71.6000 49
cluster_1 FOXC1_3 cluster_1 FOXC1_3 0.738 0.505 7.772 0.870 0.90003 19 13 13 19 0.6842 0.6842 1.0000 D 0 AAAAAAAAAAAAA...... AarTAAAyAAAcA 96 104 9 28 121 71.6000 50 
 Host name	rsat
 Job started	2025-03-15.183841
 Job done	2025-03-15.194633
 Seconds	741.08
	user	741.08
	system	130.42
	cuser	3068.08
;	csystem	136.32