/vh/rsat/rsat/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_discovered.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/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab
 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/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_discovered.tf
 Output files
	alignments_1ton	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates_alignments_1ton.tab
	match_table_txt	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab
	html_index   	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates_alignments_1ton.html
	match_table_html	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.html
	prefix       	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates
 Matrices
	file1	15 matrices	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_discovered.tf
		file1	1	24	121	aaTgAGATAAAaAttaaAaTcTww
		file1	2	24	212	watAgAGATAAAaAttaaaawhww
		file1	3	24	128	wwaaTtTTTATCAGATAAAwAwww
		file1	4	24	151	wwTTAGATGATAAAaattAAaaww
		file1	5	24	150	wwcAAGATAAAaattaaaATcTww
		file1	6	16	452	wwcTTTATCTGATAww
		file1	7	12	474	wwTAGATGATaw
		file1	8	15	613	wwcTTTATCTCTAww
		file1	9	12	200	wwGATTAATCww
		file1	10	15	559	wwtaATGATAAAgww
		file1	11	20	417	wwTATCwwwwhwdwyATCww
		...	5 more matrices
	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_7nt_test_vs_ctrl_m3 MA0035.3 oligos_7nt_test_vs_ctrl_m3 Gata1 0.803 0.589 5.942 0.568 0.913 1.9069 0.91123 15 11 11 15 0.7333 0.7333 1.0000 D 1 .wcTTTATCTCT... tyCTTATCTsy 4 1 1 1 9 8 8 4.5714 1
oligos_7nt_test_vs_ctrl_m1 MA0037.2 oligos_7nt_test_vs_ctrl_m1 GATA3 0.877 0.438 2.500 0.052 0.926 1.1782 0.90406 16 8 8 16 0.5000 0.5000 1.0000 R 2 ..cTTTATCT...... TYTTATCT 1 10 5 6 10 1 2 5.0000 2
oligos_7nt_test_vs_ctrl_m3 MA0037.2 oligos_7nt_test_vs_ctrl_m3 GATA3 0.858 0.458 2.390 0.043 0.917 1.3273 0.89817 15 8 8 15 0.5333 0.5333 1.0000 R 2 ..cTTTATCT..... TYTTATCT 2 7 6 7 11 3 7 6.1429 3
oligos_7nt_test_vs_ctrl_m1 MA0035.2 oligos_7nt_test_vs_ctrl_m1 Gata1 0.797 0.548 0.468 -0.135 0.922 1.7178 0.91575 16 11 11 16 0.6875 0.6875 1.0000 R 1 .wcTTTATCTGA.... YYCTTATCWSY 6 3 12 13 4 6 3 6.7143 4
oligos_7nt_test_vs_ctrl_m3 MA0035.2 oligos_7nt_test_vs_ctrl_m3 Gata1 0.798 0.585 0.537 -0.176 0.920 1.7538 0.91487 15 11 11 15 0.7333 0.7333 1.0000 R 1 .wcTTTATCTCT... YYCTTATCWSY 5 2 11 14 5 7 5 7.0000 5
oligos_6nt_test_vs_ctrl_m3 MA0036.2 oligos_6nt_test_vs_ctrl_m3 GATA2 0.784 0.457 1.090 -0.022 0.928 2.0028 0.92852 24 14 14 24 0.5833 0.5833 1.0000 R 10 ..........TCAGATAAAwAwww DSWGATAAGAAYYW 9 8 10 11 1 9 1 7.0000 6
oligos_7nt_test_vs_ctrl_m1 MA0036.2 oligos_7nt_test_vs_ctrl_m1 GATA2 0.765 0.510 5.523 0.505 0.910 2.1617 0.91336 16 14 12 18 0.6667 0.7500 0.8571 D -2 wwcTTTATCTGA.... ..rttCTTATCWsh 11 5 4 3 7 11 10 7.2857 7
oligos_6nt_test_vs_ctrl_m2 MA0036.2 oligos_6nt_test_vs_ctrl_m2 GATA2 0.785 0.458 1.215 -0.018 0.921 2.2088 0.92494 24 14 14 24 0.5833 0.5833 1.0000 R 3 ...AgAGATAAAaAtta....... DSWGATAAGAAYYW 8 6 9 10 2 12 4 7.2857 8
oligos_7nt_test_vs_ctrl_m4 MA0151.1 oligos_7nt_test_vs_ctrl_m4 ARID3A 0.834 0.417 5.853 0.398 0.900 1.2031 0.87074 12 6 6 12 0.5000 0.5000 1.0000 R 3 ...ATTAAT... TTTRAT 3 13 2 4 14 2 13 7.2857 9
oligos_7nt_test_vs_ctrl_m3 MA0036.2 oligos_7nt_test_vs_ctrl_m3 GATA2 0.764 0.539 5.531 0.527 0.908 2.2159 0.91228 15 14 12 17 0.7059 0.8000 0.8571 D -2 wwcTTTATCTCT... ..rttCTTATCWsh 12 4 3 2 8 13 11 7.5714 10
oligos_6nt_test_vs_ctrl_m1 MA0036.2 oligos_6nt_test_vs_ctrl_m1 GATA2 0.769 0.448 1.262 -0.016 0.919 2.2710 0.92389 24 14 14 24 0.5833 0.5833 1.0000 R 2 ..TgAGATAAAaAtta........ DSWGATAAGAAYYW 10 9 8 9 3 14 6 8.4286 11
oligos_7nt_test_vs_ctrl_m3 MA0140.1 oligos_7nt_test_vs_ctrl_m3 Tal1::Gata1 0.760 0.434 0.233 0.012 0.913 2.0949 0.91471 15 18 12 21 0.5714 0.8000 0.6667 R 3 ...TTTATCTCTAww CTTATCWSYCCS...... 13 11 14 8 6 10 9 10.1429 12
oligos_7nt_test_vs_ctrl_m4 MA0467.1 oligos_7nt_test_vs_ctrl_m4 Crx 0.792 0.422 0.344 -0.094 0.902 1.5702 0.88924 12 11 8 15 0.5333 0.6667 0.7273 R 4 ....TTAATCww YTAATCCY... 7 12 13 12 12 4 12 10.2857 13
oligos_7nt_test_vs_ctrl_m3 MA0033.1 oligos_7nt_test_vs_ctrl_m3 FOXL1 0.751 0.400 1.587 0.205 0.895 1.6757 0.88558 15 8 8 15 0.5333 0.5333 1.0000 R 5 .....TATCTCTA.. TATRTHWW 14 14 7 5 13 5 14 10.2857 14 
 Host name	biow
 Job started	2014-10-08.083039
 Job done	2014-10-08.083121
 Seconds	34.82
	user	34.82
	system	0.38
	cuser	6.15
;	csystem	0.7