/var/www/html/rsat/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.164230_oAljwC/compare-matrices.tab 
 compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.164230_oAljwC/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/2025/09/15/compare-matrices_2025-09-15.164230_oAljwC/compare-matrices.tab
 Program version       	1.118
 Slow mode 
 Input files
	file1 	$RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.164230_oAljwC/compare-matrices_query_matrices.transfac
	file2 	$RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf
 Output files
	match_table_html	$RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.164230_oAljwC/compare-matrices.html
	html_index   	$RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.164230_oAljwC/compare-matrices_index.html
	prefix       	$RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.164230_oAljwC/compare-matrices
	match_table_txt	$RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.164230_oAljwC/compare-matrices.tab
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.164230_oAljwC/compare-matrices_alignments_1ton.html
	alignments_1ton	$RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.164230_oAljwC/compare-matrices_alignments_1ton.tab
 Matrices
	file1	13 matrices	$RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.164230_oAljwC/compare-matrices_query_matrices.transfac
		file1	1	14	497	wdGcAGAGAGAcww
		file1	2	17	544	dwtGAAGAAGArGArra
		file1	3	11	412	hdCCGGCGAww
		file1	4	12	394	daAGCAGCAGmw
		file1	5	13	105	wwTGAGCTTCCww
		file1	6	11	3312	waACCACAAww
		file1	7	12	422	wwTGAGCTGAww
		file1	8	10	951	waAGAAAGww
		file1	9	10	1043	wwCAAAAGww
		file1	10	10	263	waAGGACAwd
		file1	11	11	2159	wwTCTGAGAww
		...	3 more matrices
	file2	3346 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
		...	3336 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
tcp4_c1_m6_assembly_6 AtNLP4.DAP_M0717_AthalianaCistrome assembly_6 AtNLP4.DAP:M0717:AthalianaCistrome 0.950 0.760 6.320 0.983 0.96183 12 15 12 15 0.8000 1.0000 0.8000 D 0 daAGCAGCAGmw dhwgCAGCAgcr... 5 6 131 2 2 29.2000 1
tcp4_c1_m16_assembly_16 TRANSCRIPTION_1qn9_B_3D-footprint assembly_16 TRANSCRIPTION:1qn9_B:3D-footprint 0.879 0.703 8.570 0.931 0.90701 10 8 8 10 0.8000 0.8000 1.0000 D 0 wwCAAAAG.. TACAAaAG 39 20 31 59 45 38.8000 2
tcp4_c1_m14_assembly_14 ChFLCrsat_EEAD0164_EEADannot assembly_14 ChFLCrsat:EEAD0164:EEADannot 0.875 0.729 7.241 0.943 0.92445 10 12 10 12 0.8333 1.0000 0.8333 D -2 waAGAAAGww ..ATAGAAAGww 40 15 98 22 36 42.2000 3
tcp4_c1_m5_assembly_5 AT3G11100_UN0353.1_JASPAR assembly_5 AT3G11100:UN0353.1:JASPAR 0.902 0.827 5.014 0.965 0.94372 11 12 11 12 0.9167 1.0000 0.9167 D 0 hdCCGGCGAww ygmCGGCGAsr. 26 1 164 7 13 42.2000 4
tcp4_c1_m5_assembly_5 AT5G05550.DAP_M0772_AthalianaCistrome assembly_5 AT5G05550.DAP:M0772:AthalianaCistrome 0.918 0.673 5.090 0.968 0.94610 11 15 11 15 0.7333 1.0000 0.7333 D -3 hdCCGGCGAww ...ytCCGGCGayr. 17 29 159 4 8 43.4000 5
tcp4_c1_m5_assembly_5 AT5G05550.ampDAP_M0775_AthalianaCistrome assembly_5 AT5G05550.ampDAP:M0775:AthalianaCistrome 0.916 0.671 5.292 0.965 0.94397 11 15 11 15 0.7333 1.0000 0.7333 D -3 hdCCGGCGAww ...yTCCGGCGayr. 21 32 157 6 12 45.6000 6
tcp4_c1_m5_assembly_5 AT3G58630.DAP_M0782_AthalianaCistrome assembly_5 AT3G58630.DAP:M0782:AthalianaCistrome 0.911 0.668 5.397 0.962 0.94132 11 15 11 15 0.7333 1.0000 0.7333 D -4 hdCCGGCGAww ....CTCCGGCGAcr 22 36 155 8 15 47.2000 7
tcp4_c1_m5_assembly_5 AT5G05550_UN0356.1_JASPAR assembly_5 AT5G05550:UN0356.1:JASPAR 0.896 0.758 5.015 0.957 0.93728 11 13 11 13 0.8462 1.0000 0.8462 D -2 hdCCGGCGAww ..CTCCGGCGahr 31 8 163 13 24 47.8000 8
tcp4_c1_m5_assembly_5 ASIL2_UN0352.1_JASPAR assembly_5 ASIL2:UN0352.1:JASPAR 0.895 0.758 4.992 0.957 0.93712 11 13 11 13 0.8462 1.0000 0.8462 D -2 hdCCGGCGAww ..CTCCGGCGamd 33 9 169 14 27 50.4000 9
tcp4_c1_m5_assembly_5 ENAP2_MA2040.2_JASPAR assembly_5 ENAP2:MA2040.2:JASPAR 0.898 0.735 5.014 0.949 0.92454 11 9 9 11 0.8182 0.8182 1.0000 D 0 hdCCGGCGA.. CTCCGGCGa 27 10 165 21 30 50.6000 10
tcp4_c1_m6_assembly_6 GRF4_MA1815.1_JASPAR assembly_6 GRF4:MA1815.1:JASPAR 0.896 0.704 4.884 0.959 0.93875 12 13 11 14 0.7857 0.9167 0.8462 D 1 .aAGCAGCAGmw mwGCAGCAGCw.. 32 19 178 11 21 52.2000 11
tcp4_c1_m5_assembly_5 ASIL2_MA2039.2_JASPAR assembly_5 ASIL2:MA2039.2:JASPAR 0.898 0.734 4.991 0.948 0.92410 11 9 9 11 0.8182 0.8182 1.0000 D 0 hdCCGGCGA.. CTCCGGCGa 29 11 170 23 31 52.8000 12
tcp4_c1_m5_assembly_5 AT3G58630.ampDAP_M0783_AthalianaCistrome assembly_5 AT3G58630.ampDAP:M0783:AthalianaCistrome 0.898 0.659 5.194 0.958 0.93837 11 15 11 15 0.7333 1.0000 0.7333 D -4 hdCCGGCGAww ....YTCCGGCGacr 28 48 158 12 22 53.6000 13
tcp4_c1_m5_assembly_5 AT3G58630_UN0391.2_JASPAR assembly_5 AT3G58630:UN0391.2:JASPAR 0.918 0.688 4.771 0.958 0.93128 11 10 9 12 0.7500 0.8182 0.9000 R -1 hdCCGGCGA.. .CTCCGGCGA 20 22 189 16 23 54.0000 14
tcp4_c1_m16_assembly_16 Dof2_MA0020.1_JASPAR assembly_16 Dof2:MA0020.1:JASPAR 0.936 0.561 7.694 0.966 0.92460 10 6 6 10 0.6000 0.6000 1.0000 D 4 ....AAAGww AAAGcm 11 148 84 19 11 54.6000 15
tcp4_c1_m14_assembly_14 Dof2_MA0020.1_JASPAR assembly_14 Dof2:MA0020.1:JASPAR 0.926 0.556 7.700 0.961 0.91915 10 6 6 10 0.6000 0.6000 1.0000 D 4 ....AAAGww AAAGcm 13 161 79 29 18 60.0000 16
tcp4_c1_m16_assembly_16 Dof3_MA0021.1_JASPAR assembly_16 Dof3:MA0021.1:JASPAR 0.925 0.555 7.699 0.961 0.91897 10 6 6 10 0.6000 0.6000 1.0000 D 4 ....AAAGww AAAGyv 14 162 81 30 19 61.2000 17
tcp4_c1_m6_assembly_6 GRF4_MA1815.2_JASPAR assembly_6 GRF4:MA1815.2:JASPAR 0.925 0.616 4.870 0.960 0.92964 12 8 8 12 0.6667 0.6667 1.0000 D 3 ...GCAGCAGm. GCAGCAGC 15 77 183 17 20 62.4000 18
tcp4_c1_m14_assembly_14 Dof3_MA0021.1_JASPAR assembly_14 Dof3:MA0021.1:JASPAR 0.918 0.551 7.704 0.956 0.91467 10 6 6 10 0.6000 0.6000 1.0000 D 4 ....AAAGww AAAGyv 19 165 77 37 28 65.2000 19
tcp4_c1_m5_assembly_5 AT3G11100_UN0353.2_JASPAR assembly_5 AT3G11100:UN0353.2:JASPAR 0.920 0.586 5.012 0.957 0.92132 11 7 7 11 0.6364 0.6364 1.0000 D 2 ..CCGGCGA.. mCGGCGA 16 109 166 26 26 68.6000 20
tcp4_c1_m5_assembly_5 VFP5_UN0412.1_JASPAR assembly_5 VFP5:UN0412.1:JASPAR 0.918 0.673 1.773 0.968 0.94609 11 15 11 15 0.7333 1.0000 0.7333 R -3 hdCCGGCGAww ...YTCCGGCGAYR. 18 30 325 5 9 77.4000 21
tcp4_c1_m5_assembly_5 AT3G58630_UN0391.1_JASPAR assembly_5 AT3G58630:UN0391.1:JASPAR 0.911 0.668 2.305 0.962 0.94129 11 15 11 15 0.7333 1.0000 0.7333 R -4 hdCCGGCGAww ....CTCCGGCGACR 23 37 305 9 16 78.0000 22
tcp4_c1_m16_assembly_16 MNB1A_MA0053.1_JASPAR assembly_16 MNB1A:MA0053.1:JASPAR 0.955 0.477 7.695 0.972 0.92458 10 5 5 10 0.5000 0.5000 1.0000 D 4 ....AAAGw. AAAGc 3 279 83 20 6 78.2000 23
tcp4_c1_m5_assembly_5 ERF105_MA1000.1_JASPAR assembly_5 ERF105:MA1000.1:JASPAR 0.871 0.633 4.693 0.930 0.90663 11 8 8 11 0.7273 0.7273 1.0000 D 0 hdCCGGCG... kGCCGGCG 42 60 194 62 47 81.0000 24
tcp4_c1_m5_assembly_5 AT5G51190_M0040_1.02_CISBP assembly_5 AT5G51190:M0040_1.02:CISBP 0.872 0.634 4.793 0.930 0.90642 11 8 8 11 0.7273 0.7273 1.0000 D 0 hdCCGGCG... kGCCGGCG 41 59 188 67 50 81.0000 25
tcp4_c1_m16_assembly_16 PBF_MA0064.1_JASPAR assembly_16 PBF:MA0064.1:JASPAR 0.952 0.476 7.693 0.970 0.92267 10 5 5 10 0.5000 0.5000 1.0000 D 4 ....AAAGw. AAAGy 4 285 88 25 7 81.8000 26
tcp4_c1_m14_assembly_14 MNB1A_MA0053.1_JASPAR assembly_14 MNB1A:MA0053.1:JASPAR 0.949 0.474 7.703 0.968 0.91968 10 5 5 10 0.5000 0.5000 1.0000 D 4 ....AAAGw. AAAGc 7 289 78 28 10 82.4000 27
tcp4_c1_m16_assembly_16 AT3G12130.ampDAP_M0341_AthalianaCistrome assembly_16 AT3G12130.ampDAP:M0341:AthalianaCistrome 0.798 0.570 8.434 0.913 0.90659 10 14 10 14 0.7143 1.0000 0.7143 D -2 wwCAAAAGww ..wsAAAAAGkw.. 111 136 48 65 78 87.6000 28
tcp4_c1_m14_assembly_14 PBF_MA0064.1_JASPAR assembly_14 PBF:MA0064.1:JASPAR 0.940 0.470 7.698 0.963 0.91357 10 5 5 10 0.5000 0.5000 1.0000 D 4 ....AAAGw. AAAGy 9 295 82 38 14 87.6000 29
tcp4_c1_m5_assembly_5 At3g14180.DAP_M0777_AthalianaCistrome assembly_5 At3g14180.DAP:M0777:AthalianaCistrome 0.906 0.627 2.378 0.953 0.92749 11 11 9 13 0.6923 0.8182 0.8182 R -2 hdCCGGCGA.. ..YTCCGGYGA 25 68 300 18 29 88.0000 30
tcp4_c1_m16_assembly_16 KHZ1_UN0404.1_JASPAR assembly_16 KHZ1:UN0404.1:JASPAR 0.798 0.570 8.433 0.913 0.90656 10 14 10 14 0.7143 1.0000 0.7143 D -2 wwCAAAAGww ..wsAAAAAGkw.. 113 137 49 66 79 88.8000 31
tcp4_c1_m16_assembly_16 Dof2_MA0020.2_JASPAR assembly_16 Dof2:MA0020.2:JASPAR 0.939 0.470 7.693 0.962 0.91251 10 5 5 10 0.5000 0.5000 1.0000 D 4 ....AAAGw. AAAGc 10 299 86 41 17 90.6000 32
tcp4_c1_m6_assembly_6 NLP4_UN0406.1_JASPAR assembly_6 NLP4:UN0406.1:JASPAR 0.950 0.760 0.240 0.983 0.96183 12 15 12 15 0.8000 1.0000 0.8000 R 0 daAGCAGCAGmw DHWGCAGCAGCR... 6 7 436 3 3 91.0000 33
tcp4_c1_m16_assembly_16 DOF2.2_MA1272.2_JASPAR assembly_16 DOF2.2:MA1272.2:JASPAR 0.772 0.772 9.512 0.894 0.89723 10 10 10 10 1.0000 1.0000 1.0000 D 0 wwCAAAAGww wyAAAAAGtw 169 2 5 124 167 93.4000 34
tcp4_c1_m16_assembly_16 CDF5_UN0360.1_JASPAR assembly_16 CDF5:UN0360.1:JASPAR 0.772 0.772 9.555 0.894 0.89717 10 10 10 10 1.0000 1.0000 1.0000 D 0 wwCAAAAGww wtAAAAAGtr 170 3 4 125 168 94.0000 35
tcp4_c1_m14_assembly_14 Dof2_MA0020.2_JASPAR assembly_14 Dof2:MA0020.2:JASPAR 0.932 0.466 7.699 0.957 0.90696 10 5 5 10 0.5000 0.5000 1.0000 D 4 ....AAAGw. AAAGc 12 310 80 61 25 97.6000 36
tcp4_c1_m5_assembly_5 ERF6_MA1006.2_JASPAR assembly_5 ERF6:MA1006.2:JASPAR 0.894 0.569 4.981 0.931 0.90049 11 7 7 11 0.6364 0.6364 1.0000 D 0 hdCCGGC.... tGCCGGC 35 139 172 97 46 97.8000 37
tcp4_c1_m8_assembly_8 NF_CO_EEAD0014_EEADannot assembly_8 NF_CO:EEAD0014:EEADannot 0.910 0.661 1.184 0.943 0.91566 11 8 8 11 0.7273 0.7273 1.0000 D 1 .aACCACAA.. aaCCAcaa 24 43 356 34 35 98.4000 38
tcp4_c1_m18_assembly_18 GRF6_MA2016.1_JASPAR assembly_18 GRF6:MA2016.1:JASPAR 0.782 0.711 5.516 0.905 0.90243 11 10 10 11 0.9091 0.9091 1.0000 D 1 .wTCTGAGAww ttCTGACAma 148 16 146 79 104 98.6000 39
tcp4_c1_m16_assembly_16 PHYPADRAFT_153324_MA0989.1_JASPAR assembly_16 PHYPADRAFT_153324:MA0989.1:JASPAR 0.816 0.734 4.156 0.909 0.89937 10 9 9 10 0.9000 0.9000 1.0000 D 1 .wCAAAAGww vrwAAaGyd 74 12 227 105 90 101.6000 40
tcp4_c1_m16_assembly_16 e_gw1.392.16.1_M0660_1.02_CISBP assembly_16 e_gw1.392.16.1:M0660_1.02:CISBP 0.814 0.733 4.140 0.908 0.89906 10 9 9 10 0.9000 0.9000 1.0000 D 1 .wCAAAAGww vrwAAaGyd 79 14 228 107 92 104.0000 41
tcp4_c1_m14_assembly_14 Zm00001d027846_MA1823.1_JASPAR assembly_14 Zm00001d027846:MA1823.1:JASPAR 0.786 0.655 6.650 0.902 0.90100 10 12 10 12 0.8333 1.0000 0.8333 D -2 waAGAAAGww ..AAAGAAAAar 137 52 117 94 122 104.4000 42
tcp4_c1_m14_assembly_14 CDF5_UN0360.1_JASPAR assembly_14 CDF5:UN0360.1:JASPAR 0.766 0.766 9.610 0.890 0.89531 10 10 10 10 1.0000 1.0000 1.0000 D 0 waAGAAAGww wtAAAAAGtr 188 4 1 144 186 104.6000 43
tcp4_c1_m16_assembly_16 CDF2_MA0973.1_JASPAR assembly_16 CDF2:MA0973.1:JASPAR 0.793 0.648 6.752 0.904 0.89671 10 10 9 11 0.8182 0.9000 0.9000 D 1 .wCAAAAGww maWAAAGyr. 127 54 110 131 109 106.2000 44
tcp4_c1_m16_assembly_16 CDF2_M0653_1.02_CISBP assembly_16 CDF2:M0653_1.02:CISBP 0.792 0.648 6.778 0.904 0.89654 10 10 9 11 0.8182 0.9000 0.9000 D 1 .wCAAAAGww maWAAAGyr. 128 55 108 133 111 107.0000 45
tcp4_c1_m16_assembly_16 e_gw1.170.52.1_M0659_1.02_CISBP assembly_16 e_gw1.170.52.1:M0659_1.02:CISBP 0.820 0.671 3.904 0.909 0.89921 10 10 9 11 0.8182 0.9000 0.9000 D 1 .wCAAAAGww srwAAAGyd. 67 33 245 106 91 108.4000 46
tcp4_c1_m14_assembly_14 DOF2.2_MA1272.2_JASPAR assembly_14 DOF2.2:MA1272.2:JASPAR 0.764 0.764 9.596 0.889 0.89483 10 10 10 10 1.0000 1.0000 1.0000 D 0 waAGAAAGww wyAAAAAGtw 200 5 2 147 188 108.4000 47
tcp4_c1_m16_assembly_16 PHYPADRAFT_140773_MA0987.1_JASPAR assembly_16 PHYPADRAFT_140773:MA0987.1:JASPAR 0.817 0.668 3.875 0.907 0.89857 10 10 9 11 0.8182 0.9000 0.9000 D 1 .wCAAAAGww srwAAAGyd. 72 34 247 109 94 111.2000 48
tcp4_c1_m8_assembly_8 CO-NF-trimer_EEAD0156_EEADannot assembly_8 CO-NF-trimer:EEAD0156:EEADannot 0.978 0.444 4.607 0.980 0.93609 11 5 5 11 0.4545 0.4545 1.0000 D 3 ...CCACA... YCACA 2 346 200 15 4 113.4000 49
tcp4_c1_m16_assembly_16 DOF1_PBF1_Mo17_1_EEAD0326_EEADannot assembly_16 DOF1_PBF1_Mo17_1:EEAD0326:EEADannot 0.787 0.524 8.204 0.907 0.90365 10 15 10 15 0.6667 1.0000 0.6667 D -3 wwCAAAAGww ...syaAAAAGkw.. 136 208 56 77 95 114.4000 50 
 Host name	rsat
 Job started	2025-09-15.164230
 Job done	2025-09-15.164650
 Seconds	103.43
	user	103.43
	system	42.88
	cuser	59.85
;	csystem	53.86