/var/www/html/rsat/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.153903_sHLRXa/compare-matrices.tab 
 compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.153903_sHLRXa/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -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/2026/03/29/compare-matrices_2026-03-29.153903_sHLRXa/compare-matrices.tab
 Program version       	1.118
 Slow mode 
 Input files
	file1 	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.153903_sHLRXa/compare-matrices_query_matrices.transfac
	file2 	$RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt
 Output files
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.153903_sHLRXa/compare-matrices_alignments_1ton.html
	match_table_txt	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.153903_sHLRXa/compare-matrices.tab
	alignments_1ton	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.153903_sHLRXa/compare-matrices_alignments_1ton.tab
	html_index   	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.153903_sHLRXa/compare-matrices_index.html
	match_table_html	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.153903_sHLRXa/compare-matrices.html
	prefix       	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.153903_sHLRXa/compare-matrices
 Matrices
	file1	5 matrices	$RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.153903_sHLRXa/compare-matrices_query_matrices.transfac
		file1	1	12	15	kyCCTGGGCCmd
		file1	2	12	26	rwAATTAAAcyy
		file1	3	11	42	wcCCCAGCChy
		file1	4	12	15	wvAGTGAGTCaa
		file1	5	12	17	wrAGTCAAGAar
	file2	879 matrices	$RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt
		file2		1		6		20		CACGTG
		file2		2		14		43		TTyACGCwTsAvTk
		file2		3		10		25		wwcwAGGTCA
		file2		4		15		10		RGGTCAwcGrGTTCA
		file2		5		10		17		sGGrmwTTCC
		file2		6		10		18		gGGraTTTCC
		file2		7		17		25		AAAGGTCAAAGGTCAAc
		file2		8		15		33		gsmmCCyWrGGkkkm
		file2		9		14		16		TGGCAssrwGCCAA
		file2		10		6		16		mTCCAC
		file2		11		15		1369		ywTTswyATGCAaAt
		...	869 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
assembly_2 MA0151.1 assembly_2 Arid3a 0.966 0.483 7.361 0.979 0.94027 12 6 6 12 0.5000 0.5000 1.0000 D 3 ...ATTAAA... ATyAAA 2 88 5 2 2 19.8000 1
assembly_2 MA1577.2 assembly_2 TLX2 0.967 0.483 7.093 0.977 0.93864 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 1 87 7 4 4 20.6000 2
assembly_5 MA0676.1 assembly_5 Nr2e1 0.930 0.572 5.991 0.964 0.93319 12 9 8 13 0.6154 0.6667 0.8889 D -1 wrAGTCAA.... .aAAGTCAA 30 20 35 15 26 25.2000 3
assembly_2 MA0718.2 assembly_2 RAX 0.961 0.481 5.908 0.978 0.93934 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 3 90 40 3 3 27.8000 4
assembly_2 MA1519.2 assembly_2 LHX5 0.926 0.540 6.723 0.958 0.92281 12 7 7 12 0.5833 0.5833 1.0000 D 0 rwAATTA..... sYAATTA 33 42 11 30 34 30.0000 5
assembly_4 MA0835.3 assembly_4 BATF3 0.952 0.555 4.935 0.970 0.93480 12 7 7 12 0.5833 0.5833 1.0000 R 4 ....TGAGTCa. TGAGTCA 9 31 96 8 14 31.6000 6
assembly_2 MA1481.2 assembly_2 DRGX 0.954 0.477 5.640 0.975 0.93524 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 5 93 56 7 7 33.6000 7
assembly_2 MA0889.2 assembly_2 GBX1 0.920 0.536 6.393 0.957 0.92146 12 7 7 12 0.5833 0.5833 1.0000 D 0 rwAATTA..... syAATTA 35 45 19 33 37 33.8000 8
assembly_4 MA1928.2 assembly_4 BNC2 0.945 0.551 5.252 0.968 0.93248 12 7 7 12 0.5833 0.5833 1.0000 D 4 ....TGAGTCa. TGAGTCA 19 38 77 17 22 34.6000 9
assembly_2 MA0027.3 assembly_2 EN1 0.952 0.476 5.834 0.973 0.93331 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 8 96 44 14 12 34.8000 10
assembly_2 MA0720.2 assembly_2 Shox2 0.954 0.477 5.656 0.974 0.93438 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 6 94 55 10 9 34.8000 11
assembly_3 MA2341.1 assembly_3 FEZF2 0.916 0.666 5.165 0.957 0.92664 11 8 8 11 0.7273 0.7273 1.0000 D 2 ..CCCAGCCh. CCCAGCCT 37 2 81 27 36 36.6000 12
assembly_2 MA0075.4 assembly_2 PRRX2 0.908 0.530 6.754 0.948 0.91412 12 7 7 12 0.5833 0.5833 1.0000 D 0 rwAATTA..... cyAATTA 40 49 9 42 45 37.0000 13
assembly_2 MA0890.2 assembly_2 GBX2 0.949 0.474 6.115 0.969 0.92840 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 13 103 28 24 17 37.0000 14
assembly_2 MA0654.2 assembly_2 ISX 0.949 0.474 6.536 0.967 0.92611 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 14 104 16 28 24 37.2000 15
assembly_4 MA0462.3 assembly_4 BATF::JUN 0.946 0.552 4.945 0.968 0.93266 12 7 7 12 0.5833 0.5833 1.0000 R 4 ....TGAGTCa. TGAGTCA 18 36 95 16 21 37.2000 16
assembly_2 MA0716.2 assembly_2 PRRX1 0.959 0.480 5.029 0.979 0.94048 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 4 91 90 1 1 37.4000 17
assembly_4 MA1988.2 assembly_4 Atf3 0.947 0.552 4.839 0.969 0.93356 12 7 7 12 0.5833 0.5833 1.0000 R 4 ....TGAGTCa. TGAGTCA 17 35 106 13 19 38.0000 18
assembly_4 MA1634.2 assembly_4 BATF 0.944 0.551 4.891 0.968 0.93198 12 7 7 12 0.5833 0.5833 1.0000 R 4 ....TGAGTCa. TGAGTCA 20 39 99 18 23 39.8000 19
assembly_2 MA0703.3 assembly_2 LMX1B 0.888 0.592 7.383 0.933 0.90833 12 8 8 12 0.6667 0.6667 1.0000 R 0 rwAATTAA.... TTAATTAA 53 12 4 55 79 40.6000 20
assembly_2 MA0644.3 assembly_2 ESX1 0.908 0.530 5.860 0.953 0.91824 12 7 7 12 0.5833 0.5833 1.0000 D 0 rwAATTA..... yyAATTA 41 50 42 35 41 41.8000 21
assembly_2 MA0666.3 assembly_2 MSX1 0.941 0.470 6.330 0.964 0.92223 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 23 110 21 31 28 42.6000 22
assembly_2 MA0894.2 assembly_2 HESX1 0.952 0.476 5.364 0.969 0.92839 12 6 6 12 0.5000 0.5000 1.0000 R 1 .wAATTA..... YAATTA 10 97 72 25 18 44.4000 23
assembly_3 MA2125.1 assembly_3 Zfp809 0.874 0.715 5.494 0.938 0.91724 11 9 9 11 0.8182 0.8182 1.0000 D 0 wcCCCAGCC.. wTCCCAGCc 65 1 66 36 59 45.4000 24
assembly_2 MA0709.2 assembly_2 Msx3 0.940 0.470 6.073 0.964 0.92212 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 25 112 30 32 29 45.6000 25
assembly_2 MA0708.3 assembly_2 MSX2 0.936 0.468 6.056 0.962 0.92063 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... YAATTA 27 114 31 34 30 47.2000 26
assembly_2 MA0612.3 assembly_2 EMX1 0.933 0.466 6.324 0.959 0.91715 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... TAATTA 29 117 22 37 32 47.4000 27
assembly_2 MA0701.3 assembly_2 LHX9 0.888 0.518 6.245 0.939 0.90692 12 7 7 12 0.5833 0.5833 1.0000 D 0 rwAATTA..... CyAATTA 52 56 23 59 55 49.0000 28
assembly_2 MA0898.2 assembly_2 Hmx3 0.877 0.540 6.052 0.937 0.91102 12 9 8 13 0.6154 0.6667 0.8889 D -1 rwAATTAA.... .gCAATTAA 59 43 32 48 68 50.0000 29
assembly_1 MA1986.2 assembly_1 ZNF692 0.930 0.620 2.948 0.960 0.92941 12 8 8 12 0.6667 0.6667 1.0000 R 3 ...CTGGGCCm. STGGGCCC 31 5 162 21 31 50.0000 30
assembly_2 MA0886.2 assembly_2 EMX2 0.930 0.465 6.021 0.958 0.91662 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... TAATTA 32 119 33 38 33 51.0000 31
assembly_2 MA0630.2 assembly_2 SHOX 0.953 0.476 3.637 0.976 0.93686 12 6 6 12 0.5000 0.5000 1.0000 R 1 .wAATTA..... YAATTA 7 95 154 5 5 53.2000 32
assembly_2 MA0721.2 assembly_2 UNCX 0.952 0.476 3.949 0.976 0.93619 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 11 98 147 6 6 53.6000 33
assembly_2 MA0896.2 assembly_2 Hmx1 0.873 0.537 6.440 0.931 0.90738 12 9 8 13 0.6154 0.6667 0.8889 D -1 rwAATTAA.... .GCAATTAA 68 44 18 56 84 54.0000 34
assembly_2 MA0662.2 assembly_2 MIXL1 0.949 0.474 4.051 0.974 0.93458 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 12 102 143 9 8 54.8000 35
assembly_2 MA0882.2 assembly_2 DLX6 0.942 0.471 4.784 0.970 0.92871 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 22 109 108 22 16 55.4000 36
assembly_2 MA0634.2 assembly_2 ALX3 0.948 0.474 3.985 0.974 0.93388 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 15 105 146 11 10 57.4000 37
assembly_2 MA0717.2 assembly_2 RAX2 0.948 0.474 3.948 0.974 0.93371 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 16 106 148 12 11 58.6000 38
assembly_2 MA0699.2 assembly_2 LBX2 0.943 0.471 3.997 0.971 0.93096 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 21 107 145 19 13 61.0000 39
assembly_2 MA0132.3 assembly_2 PDX1 0.912 0.456 5.768 0.951 0.90930 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... ymATTA 39 123 47 53 44 61.2000 40
assembly_2 MA0897.2 assembly_2 Hmx2 0.760 0.608 6.202 0.905 0.91120 12 15 12 15 0.8000 1.0000 0.8000 D -2 rwAATTAAAcyy ..gCAATTAAwgvr. 129 7 26 47 104 62.6000 41
assembly_2 MA0125.2 assembly_2 Nobox 0.935 0.467 4.511 0.964 0.92294 12 6 6 12 0.5000 0.5000 1.0000 R 1 .wAATTA..... YAATTA 28 115 122 29 25 63.8000 42
assembly_2 MA0880.2 assembly_2 Dlx3 0.941 0.470 3.900 0.970 0.92955 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 24 111 150 20 15 64.0000 43
assembly_2 MA0881.2 assembly_2 Dlx4 0.938 0.469 4.208 0.969 0.92785 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... yAATTA 26 113 137 26 20 64.4000 44
assembly_2 MA0902.3 assembly_2 HOXB2 0.907 0.453 5.506 0.951 0.90955 12 6 6 12 0.5000 0.5000 1.0000 D 1 .wAATTA..... ymATTA 43 125 63 50 43 64.8000 45
assembly_2 MA1463.2 assembly_2 ARGFX 0.836 0.557 6.524 0.913 0.89578 12 8 8 12 0.6667 0.6667 1.0000 D 0 rwAATTAA.... cTAATTAr 95 30 17 92 97 66.2000 46
assembly_2 MA0854.2 assembly_2 Alx1 0.832 0.555 6.606 0.911 0.89478 12 8 8 12 0.6667 0.6667 1.0000 D 0 rwAATTAA.... yTAATTAr 98 32 14 96 99 67.8000 47
assembly_2 MA0642.3 assembly_2 EN2 0.876 0.511 4.652 0.943 0.90953 12 7 7 12 0.5833 0.5833 1.0000 D 0 rwAATTA..... syAATTA 61 61 118 51 49 68.0000 48
assembly_2 MA1502.2 assembly_2 HOXB8 0.868 0.506 5.418 0.938 0.90569 12 7 7 12 0.5833 0.5833 1.0000 D 0 rwAATTA..... gymATTA 80 68 68 63 62 68.2000 49
assembly_2 MA0913.3 assembly_2 HOXD9 0.793 0.595 7.151 0.894 0.89159 12 9 9 12 0.7500 0.7500 1.0000 D 0 rwAATTAAA... GymATAAAA 113 10 6 103 113 69.0000 50 
 Host name	rsat
 Job started	2026-03-29.153904
 Job done	2026-03-29.154051
 Seconds	24.21
	user	24.21
	system	6.74
	cuser	68.05
;	csystem	8.31