/vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_footprintDB.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_footprintDB
 Program version       	1.118
 Input files
	file2 	$RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf
	file1 	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf
 Output files
	alignments_1ton	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_footprintDB_alignments_1ton.tab
	match_table_txt	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_footprintDB.tab
	html_index   	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_footprintDB_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_footprintDB_alignments_1ton.html
	match_table_html	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_footprintDB.html
	prefix       	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_footprintDB
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2.tf
		file1	1	11	7	wwATATAAGkb
	file2	4196 matrices	$RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf
		file2		1		17		100		yyaymCATCAAwmwwmm
		file2		2		10		7		ACCGGAAGws
		file2		3		16		100		wwtksgTAATTACsdy
		file2		4		17		100		twrttaATTAwtaawwr
		file2		5		18		100		TCCGynnnnnnnnnCGGA
		file2		6		20		100		gwrastTTCCGGAAyrywrr
		file2		7		20		100		yrawygGyGCCGyrysackh
		file2		8		21		100		wmrmraAtmGAAGaaawawww
		file2		9		20		100		rkmkkakCACGTGmyyrvwy
		file2		10		6		1		CTATCA
		file2		11		18		66		hTTwCCwWAwwdGGhAat
		...	4186 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	NIcor        	Normalized Pearson correlation between the information content matrices. NIcor = Icor * Wr
	9	NSW          	Normalized Sandelin-Wasserman similarity. NSW = SW/w
	10	SSD          	sum of squared distance.
	11	NsEucl       	relative Euclidian similarity. NsEucl = (max(dEucl) - dEucl)/max(dEucl)
	12	w1           	Width of the first matrix
	13	w2           	Width of the second matrix
	14	w            	Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset)
	15	W            	Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w
	16	Wr           	Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W
	17	wr1          	Alignment length relative to the width of the first matrix. wr1 = w/w1
	18	wr2          	Alignment length relative to the width of the second matrix. wr2 = w/w2
	19	strand       	"strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct;  R=reverse)
	20	offset       	shift of the second matrix relative to the first matrix (negative:left; positive: right)
	21	consensus1   	IUPAC consensus of matrix 1 (dots represent non-aligned columns)
	22	consensus2   	IUPAC consensus of matrix 2 (dots represent non-aligned columns)
	23	rcor         	Matching rank for cor
	24	rNcor        	Matching rank for Ncor
	25	rlogoDP      	Matching rank for logoDP
	26	rNIcor       	Matching rank for NIcor
	27	rNsEucl      	Matching rank for NsEucl
	28	rSSD         	Matching rank for SSD
	29	rNSW         	Matching rank for NSW
	30	rank_mean    	Mean of the matching ranks on all selected metrics
	31	match_rank   	Rank of the match (sorting by rank_mean)
id1 id2 name1 name2 cor Ncor logoDP NIcor NSW SSD NsEucl w1 w2 w W Wr wr1 wr2 strand offset consensus1 consensus2 rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank
positions_7nt_m2 2613_MA0379.1_JASPAR_CORE_2009_ positions_7nt_m2 2613_MA0379.1_JASPAR_CORE_2009_ 0.999 0.454 9.094 0.454 0.999 0.0078 0.98751 11 5 5 11 0.4545 0.4545 1.0000 D 2 ..ATATA.... ATATA 1 11 2 6 1 1 1 3.2857 1
positions_7nt_m2 6327_1tgh_A_3D-footprint_20130124_ positions_7nt_m2 6327_1tgh_A_3D-footprint_20130124_ 0.890 0.519 8.646 0.505 0.936 0.8900 0.90470 11 8 7 12 0.5833 0.6364 0.8750 D -1 wwATATA.... .AtATATA 3 7 5 4 3 3 3 4.0000 2
positions_7nt_m2 6272_1qn7_A_3D-footprint_20130124_ positions_7nt_m2 6272_1qn7_A_3D-footprint_20130124_ 0.947 0.689 5.800 0.285 0.966 0.5452 0.93474 11 8 8 11 0.7273 0.7273 1.0000 R 1 .wATATAAG.. TATATAAG 2 1 10 11 2 2 2 4.2857 3
positions_7nt_m2 2427_MA0033.1_JASPAR_CORE_2009_ positions_7nt_m2 2427_MA0033.1_JASPAR_CORE_2009_ 0.854 0.498 4.621 0.481 0.922 1.0897 0.89455 11 8 7 12 0.5833 0.6364 0.8750 D -1 wwATATA.... .wdayATA 4 8 11 5 4 4 4 5.7143 4
positions_7nt_m2 6359_1ytf_A_3D-footprint_20130124_ positions_7nt_m2 6359_1ytf_A_3D-footprint_20130124_ 0.853 0.427 8.224 0.397 0.907 1.3056 0.88458 11 10 7 14 0.5000 0.6364 0.7000 D -3 wwATATA.... ...TTATATA 5 12 6 8 9 6 6 7.4286 5
positions_7nt_m2 6360_1ytf_AC_3D-footprint_20130124_ positions_7nt_m2 6360_1ytf_AC_3D-footprint_20130124_ 0.853 0.427 8.224 0.397 0.907 1.3056 0.88458 11 10 7 14 0.5000 0.6364 0.7000 D -3 wwATATA.... ...TTATATA 5 12 6 8 9 6 6 7.4286 6
positions_7nt_m2 6725_4aik_A_3D-footprint_20130124_ positions_7nt_m2 6725_4aik_A_3D-footprint_20130124_ 0.829 0.528 6.685 0.509 0.898 1.4234 0.87948 11 7 7 11 0.6364 0.6364 1.0000 D 1 .wATATAA... CATAnAA 8 6 9 3 11 10 8 7.8571 7
positions_7nt_m2 2713_PF0026.1_JASPAR_CORE_2009_ positions_7nt_m2 2713_PF0026.1_JASPAR_CORE_2009_ 0.799 0.581 8.896 0.530 0.879 1.9398 0.87689 11 8 8 11 0.7273 0.7273 1.0000 D 0 wwATATAA... TTAyrTAA 12 3 4 1 14 16 14 9.1429 8
positions_7nt_m2 6276_1qnb_A_3D-footprint_20130124_ positions_7nt_m2 6276_1qnb_A_3D-footprint_20130124_ 0.818 0.595 2.306 0.010 0.894 1.6977 0.88483 11 8 8 11 0.7273 0.7273 1.0000 R 3 ...TATAAGkb TATAAMTS 9 2 14 16 7 13 10 10.1429 9
positions_7nt_m2 6246_1osl_A_3D-footprint_20130124_ positions_7nt_m2 6246_1osl_A_3D-footprint_20130124_ 0.839 0.489 0.367 -0.142 0.907 1.3021 0.88473 11 8 7 12 0.5833 0.6364 0.8750 R 4 ....ATAAGkb ATAAGAT. 7 9 20 20 8 5 5 10.5714 10
positions_7nt_m2 2814_PF0127.1_JASPAR_CORE_2009_ positions_7nt_m2 2814_PF0127.1_JASPAR_CORE_2009_ 0.783 0.570 9.022 0.518 0.868 2.1093 0.87163 11 8 8 11 0.7273 0.7273 1.0000 D 3 ...TATAAGkb wwTAAGGC 14 5 3 2 15 18 17 10.5714 11
positions_7nt_m2 6724_4aij_AB_3D-footprint_20130124_ positions_7nt_m2 6724_4aij_AB_3D-footprint_20130124_ 0.803 0.401 1.286 0.138 0.897 1.6531 0.88636 11 13 8 16 0.5000 0.7273 0.6154 R 3 ...TATAAGkb TATANNNN..... 11 21 17 14 6 12 9 12.8571 12
positions_7nt_m2 2595_MA0356.1_JASPAR_CORE_2009_ positions_7nt_m2 2595_MA0356.1_JASPAR_CORE_2009_ 0.769 0.419 3.043 0.146 0.891 1.3114 0.86504 11 6 6 11 0.5455 0.5455 1.0000 R 0 wwATAT..... WAWTAW 17 16 13 13 17 8 11 13.5714 13
positions_7nt_m2 6270_1qn5_A_3D-footprint_20130124_ positions_7nt_m2 6270_1qn5_A_3D-footprint_20130124_ 0.797 0.580 0.345 -0.179 0.883 1.8701 0.87913 11 8 8 11 0.7273 0.7273 1.0000 R 3 ...TATAAGkb TATAAGAG 13 4 21 21 12 14 12 13.8571 14
positions_7nt_m2 2738_PF0051.1_JASPAR_CORE_2009_ positions_7nt_m2 2738_PF0051.1_JASPAR_CORE_2009_ 0.778 0.424 9.609 0.424 0.833 2.0000 0.83333 11 6 6 11 0.5455 0.5455 1.0000 D 3 ...TATAAG.. TATAAA 16 15 1 7 21 17 21 14.0000 15
positions_7nt_m2 2509_MA0124.1_JASPAR_CORE_2009_ positions_7nt_m2 2509_MA0124.1_JASPAR_CORE_2009_ 0.808 0.404 2.199 0.041 0.882 1.4209 0.85952 11 7 6 12 0.5000 0.5455 0.8571 R 5 .....TAAGkb TAAGTA. 10 20 15 15 19 9 13 14.4286 16
positions_7nt_m2 6236_1nvp_AC_3D-footprint_20130124_ positions_7nt_m2 6236_1nvp_AC_3D-footprint_20130124_ 0.761 0.489 4.213 0.209 0.867 2.3979 0.87834 11 12 9 14 0.6429 0.8182 0.7500 R -3 wwATATAAG.. ...NTATAAAAG 19 10 12 12 13 20 19 15.0000 17
positions_7nt_m2 6637_3jxb_CD_3D-footprint_20130124_ positions_7nt_m2 6637_3jxb_CD_3D-footprint_20130124_ 0.752 0.418 2.027 0.002 0.874 2.5231 0.88768 11 17 10 18 0.5556 0.9091 0.5882 R 1 .wATATAAGkb TATTTAAGNN....... 20 17 16 17 5 21 15 15.8571 18
positions_7nt_m2 2715_PF0028.1_JASPAR_CORE_2009_ positions_7nt_m2 2715_PF0028.1_JASPAR_CORE_2009_ 0.751 0.404 6.877 0.370 0.863 1.9221 0.85995 11 9 7 13 0.5385 0.6364 0.7778 D -2 wwATATA.... ..AwwwATA 21 19 8 10 18 15 20 15.8571 19
positions_7nt_m2 6434_2h7h_A_3D-footprint_20130124_ positions_7nt_m2 6434_2h7h_A_3D-footprint_20130124_ 0.779 0.425 0.553 -0.053 0.869 1.5764 0.85203 11 6 6 11 0.5455 0.5455 1.0000 R 4 ....ATAAGk. ATGAGT 15 14 19 19 20 11 16 16.2857 20
positions_7nt_m2 6358_1ytb_A_3D-footprint_20130124_ positions_7nt_m2 6358_1ytb_A_3D-footprint_20130124_ 0.766 0.409 0.658 -0.044 0.868 2.1103 0.87160 11 12 8 15 0.5333 0.7273 0.6667 R -4 wwATATAA... ....TTATATAC 18 18 18 18 16 19 18 17.8571 21 
 Host name	biow
 Job started	2014-09-05.203302
 Job done	2014-09-05.203336
 Seconds	29.83
	user	29.83
	system	0.47
	cuser	3.84
;	csystem	0.82