/workspace/rsat/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_vs_db_jaspar_core_vertebrates.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.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/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_vs_db_jaspar_core_vertebrates
 Program version       	1.118
 Slow mode 
 Input files
	file2 	$RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf
	file1 	$RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2.tf
 Output files
	html_index   	$RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_vs_db_jaspar_core_vertebrates_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_vs_db_jaspar_core_vertebrates_alignments_1ton.html
	alignments_1ton	$RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_vs_db_jaspar_core_vertebrates_alignments_1ton.tab
	match_table_html	$RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_vs_db_jaspar_core_vertebrates.html
	match_table_txt	$RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_vs_db_jaspar_core_vertebrates.tab
	prefix       	$RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_vs_db_jaspar_core_vertebrates
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/www-data/2015/11/03/peak-motifs.2015-11-03.065540_2015-11-03.065540_cr9ytx/results/discovered_motifs/oligos_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2.tf
		file1	1	11	86	yrAGGTCAGar
	file2	205 matrices	$RSAT/public_html/motif_databases/JASPAR/jaspar_core_vertebrates_2015_03.tf
		file2		1		6		20		CACGTG
		file2		2		6		24		yGCGTG
		file2		3		11		40		CTAGGTGTGAA
		file2		4		14		13		TGAmCTTTGmmCyt
		file2		5		12		39		rrrTGCAATmcc
		file2		6		11		23		TTAyGTAAyrt
		file2		7		11		10		waRTdRWkbyc
		file2		8		10		28		varcCGGAAr
		file2		9		14		27		aAGAyAAGATAAba
		file2		10		14		28		bmaasRTAAACAaw
		file2		11		8		20		GTAAACAw
		...	195 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
oligos_6nt_mkv3_m2 MA0071.1 oligos_6nt_mkv3_m2 RORA_1 0.977 0.601 10.437 0.605 0.987 0.2017 0.96030 11 10 8 13 0.6154 0.7273 0.8000 D -2 yrAGGTCA... ..cwAGGTCA 1 4 1 4 1 1 1 1.8571 1
oligos_6nt_mkv3_m2 MA0512.1 oligos_6nt_mkv3_m2 Rxra 0.889 0.741 8.430 0.732 0.947 1.0558 0.92734 11 11 10 12 0.8333 0.9091 0.9091 D -1 yrAGGTCAGa. .ArAGKTCAgd 4 1 5 1 2 4 3 2.8571 2
oligos_6nt_mkv3_m2 MA0258.2 oligos_6nt_mkv3_m2 ESR2 0.909 0.481 7.498 0.480 0.950 0.8981 0.92554 11 15 9 17 0.5294 0.8182 0.6000 D 2 ..AGGTCAGar rGGTCAsms...... 2 8 8 6 3 2 2 4.4286 3
oligos_6nt_mkv3_m2 MA0141.2 oligos_6nt_mkv3_m2 Esrrb 0.902 0.481 9.026 0.473 0.943 0.9177 0.91533 11 12 8 15 0.5333 0.7273 0.6667 D -4 yrAGGTCA... ....CAAGGTCA 3 7 4 7 4 3 4 4.5714 4
oligos_6nt_mkv3_m2 MA0592.1 oligos_6nt_mkv3_m2 ESRRA 0.822 0.685 9.380 0.666 0.909 1.8281 0.90439 11 11 10 12 0.8333 0.9091 0.9091 D -1 yrAGGTCAGa. .CAAGGTCAcm 7 2 3 2 8 9 9 5.7143 5
oligos_6nt_mkv3_m2 MA0160.1 oligos_6nt_mkv3_m2 NR4A2 0.854 0.621 7.578 0.622 0.916 1.3416 0.89762 11 8 8 11 0.7273 0.7273 1.0000 D 1 .rAGGTCAG.. aAGGTCAc 5 3 7 3 11 5 6 5.7143 6
oligos_6nt_mkv3_m2 MA0072.1 oligos_6nt_mkv3_m2 RORA_2 0.838 0.471 10.296 0.463 0.910 1.6216 0.89995 11 14 9 16 0.5625 0.8182 0.6429 D -5 yrAGGTCAG.. .....bTAGGTCAr 6 9 2 8 9 7 8 7.0000 7
oligos_6nt_mkv3_m2 MA0504.1 oligos_6nt_mkv3_m2 NR2C2 0.797 0.585 6.029 0.552 0.913 1.9156 0.91103 11 15 11 15 0.7333 1.0000 0.7333 D 0 yrAGGTCAGar mgrGGTCArAG.... 9 5 10 5 6 10 7 7.4286 8
oligos_6nt_mkv3_m2 MA0112.2 oligos_6nt_mkv3_m2 ESR1 0.809 0.445 4.397 0.450 0.920 1.7543 0.91486 11 20 11 20 0.5500 1.0000 0.5500 D -3 yrAGGTCAGar ...cmaGGtCAccc...... 8 10 11 10 5 8 5 8.1429 9
oligos_6nt_mkv3_m2 MA0505.1 oligos_6nt_mkv3_m2 Nr5a2 0.790 0.494 7.874 0.460 0.896 2.0772 0.89809 11 15 10 16 0.6250 0.9091 0.6667 D -5 yrAGGTCAGa. .....CAAGGyCAgs 10 6 6 9 10 11 11 9.0000 10
oligos_6nt_mkv3_m2 MA0066.1 oligos_6nt_mkv3_m2 PPARG 0.766 0.421 6.837 0.424 0.901 2.1765 0.90517 11 20 11 20 0.5500 1.0000 0.5500 D 0 yrAGGTCAGar sTrGGTCAcsg......... 12 12 9 11 7 12 10 10.4286 11
oligos_6nt_mkv3_m2 MA0089.1 oligos_6nt_mkv3_m2 NFE2L1::MafG 0.787 0.429 0.090 -0.133 0.883 1.4034 0.86039 11 6 6 11 0.5455 0.5455 1.0000 R 4 ....GTCAGa. GTCATS 11 11 12 12 12 6 12 10.8571 12 
 Host name	rsat-tagc
 Job started	2015-11-03.065845
 Job done	2015-11-03.065853
 Seconds	2.58
	user	2.58
	system	0.21
	cuser	5.49
;	csystem	0.47