/vh/rsat/rsat/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_vs_db_jaspar_core_vertebrates.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.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/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_vs_db_jaspar_core_vertebrates
 Program version       	1.118
 Input files
	file2 	$RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf
	file1 	$RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4.tf
 Output files
	alignments_1ton	$RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_vs_db_jaspar_core_vertebrates_alignments_1ton.tab
	match_table_txt	$RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_vs_db_jaspar_core_vertebrates.tab
	html_index   	$RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_vs_db_jaspar_core_vertebrates_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_vs_db_jaspar_core_vertebrates_alignments_1ton.html
	match_table_html	$RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_vs_db_jaspar_core_vertebrates.html
	prefix       	$RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_vs_db_jaspar_core_vertebrates
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4.tf
		file1	1	11	977	cvAGGTCAGsg
	file2	263 matrices	$RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf
		file2		1		11		26		wwyTGyGGTww
		file2		2		9		185		GCCcbrrGs
		file2		3		6		20		CACGTG
		file2		4		6		24		yGCGTG
		file2		5		22		24		hwwrGmACryyvtGTwCchrms
		file2		6		11		40		CTAGGTGTGAA
		file2		7		20		12		drvkcasygrwGcRkrrCsr
		file2		8		14		13		TGAmCTTTGmmCyt
		file2		9		12		16		bbkGrTGACGym
		file2		10		12		39		rrrTGCAATmcc
		file2		11		8		10		TTTsGCGC
		...	253 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_mkv4_m4 MA0071.1 oligos_6nt_mkv4_m4 RORA_1 0.977 0.601 10.345 0.606 0.987 0.2059 0.95989 11 10 8 13 0.6154 0.7273 0.8000 D -2 cvAGGTCA... ..cwAGGTCA 1 4 2 4 1 1 1 2.0000 1
oligos_6nt_mkv4_m4 MA0512.1 oligos_6nt_mkv4_m4 Rxra 0.887 0.739 8.345 0.734 0.947 1.0601 0.92720 11 11 10 12 0.8333 0.9091 0.9091 D -1 cvAGGTCAGs. .ArAGKTCAgd 5 1 8 1 4 5 6 4.2857 2
oligos_6nt_mkv4_m4 MA0258.2 oligos_6nt_mkv4_m4 ESR2 0.923 0.489 7.461 0.484 0.958 0.7585 0.93157 11 15 9 17 0.5294 0.8182 0.6000 D 2 ..AGGTCAGsg rGGTCAsms...... 2 8 11 7 3 2 2 5.0000 3
oligos_6nt_mkv4_m4 MA0141.1 oligos_6nt_mkv4_m4 Esrrb 0.910 0.485 8.828 0.476 0.948 0.8391 0.91904 11 12 8 15 0.5333 0.7273 0.6667 D -4 cvAGGTCA... ....CAAGGTCA 3 9 6 9 6 3 4 5.7143 4
oligos_6nt_mkv4_m4 MA0258.1 oligos_6nt_mkv4_m4 ESR2 0.885 0.541 6.407 0.539 0.950 1.1049 0.93243 11 18 11 18 0.6111 1.0000 0.6111 D 0 cvAGGTCAGsg cwrGGTCAsgk....... 6 6 14 5 2 6 3 6.0000 5
oligos_6nt_mkv4_m4 MA0141.2 oligos_6nt_mkv4_m4 Esrrb 0.910 0.485 8.936 0.475 0.947 0.8455 0.91873 11 12 8 15 0.5333 0.7273 0.6667 D -4 cvAGGTCA... ....CAAGGTCA 4 10 5 10 7 4 5 6.4286 6
oligos_6nt_mkv4_m4 MA0592.1 oligos_6nt_mkv4_m4 ESRRA 0.833 0.695 9.293 0.672 0.915 1.6962 0.90791 11 11 10 12 0.8333 0.9091 0.9091 D -1 cvAGGTCAGs. .CAAGGTCAcm 10 2 4 2 9 11 9 6.7143 7
oligos_6nt_mkv4_m4 MA0160.1 oligos_6nt_mkv4_m4 NR4A2 0.870 0.633 7.532 0.627 0.925 1.1940 0.90342 11 8 8 11 0.7273 0.7273 1.0000 D 1 .vAGGTCAG.. aAGGTCAc 7 3 10 3 12 7 8 7.1429 8
oligos_6nt_mkv4_m4 MA0112.2 oligos_6nt_mkv4_m4 ESR1 0.840 0.462 4.366 0.459 0.933 1.4838 0.92170 11 20 11 20 0.5500 1.0000 0.5500 D -3 cvAGGTCAGsg ...cmaGGtCAccc...... 8 13 16 13 5 9 7 10.1429 9
oligos_6nt_mkv4_m4 MA0072.1 oligos_6nt_mkv4_m4 RORA_2 0.835 0.469 10.206 0.465 0.909 1.6402 0.89938 11 14 9 16 0.5625 0.8182 0.6429 D -5 cvAGGTCAG.. .....bTAGGTCAr 9 12 3 12 15 10 11 10.2857 10
oligos_6nt_mkv4_m4 MA0112.1 oligos_6nt_mkv4_m4 ESR1 0.793 0.485 6.878 0.482 0.915 1.8699 0.91210 11 18 11 18 0.6111 1.0000 0.6111 D 0 cvAGGTCAGsg ccAGGTCaCcr....... 12 11 12 8 8 12 10 10.4286 11
oligos_6nt_mkv4_m4 MA0505.1 oligos_6nt_mkv4_m4 Nr5a2 0.805 0.503 7.773 0.467 0.904 1.9155 0.90214 11 15 10 16 0.6250 0.9091 0.6667 D -5 cvAGGTCAGs. .....CAAGGyCAgs 11 7 9 11 14 13 13 11.1429 12
oligos_6nt_mkv4_m4 MA0504.1 oligos_6nt_mkv4_m4 NR2C2 0.771 0.565 5.902 0.534 0.903 2.1349 0.90608 11 15 11 15 0.7333 1.0000 0.7333 D 0 cvAGGTCAGsg mgrGGTCArAG.... 16 5 15 6 11 15 14 11.7143 13
oligos_6nt_mkv4_m4 MA0066.1 oligos_6nt_mkv4_m4 PPARG 0.776 0.427 6.761 0.428 0.907 2.0524 0.90791 11 20 11 20 0.5500 1.0000 0.5500 D 0 cvAGGTCAGsg sTrGGTCAcsg......... 15 16 13 14 10 14 12 13.4286 14
oligos_6nt_mkv4_m4 MA0065.1 oligos_6nt_mkv4_m4 PPARG::RXRA 0.778 0.428 8.775 0.416 0.895 2.3160 0.90217 11 20 11 20 0.5500 1.0000 0.5500 D -9 cvAGGTCAGsg .........AAAGGTCAymk 14 15 7 16 13 16 15 13.7143 15
oligos_6nt_mkv4_m4 MA0115.1 oligos_6nt_mkv4_m4 NR1H2::RXRA 0.762 0.424 11.168 0.418 0.860 2.8044 0.88158 11 17 10 18 0.5556 0.9091 0.5882 D -7 cvAGGTCAGs. .......AAAGGTCAAc 17 17 1 15 16 17 17 14.2857 16
oligos_6nt_mkv4_m4 MA0089.1 oligos_6nt_mkv4_m4 NFE2L1::MafG 0.791 0.431 0.095 -0.131 0.887 1.3618 0.86247 11 6 6 11 0.5455 0.5455 1.0000 R 4 ....GTCAGs. GTCATS 13 14 17 17 17 8 16 14.5714 17 
 Host name	biow
 Job started	2014-10-07.093552
 Job done	2014-10-07.093558
 Seconds	2.32
	user	2.32
	system	0.14
	cuser	3.98
;	csystem	0.51