/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_vs_db_jaspar_core_vertebrates.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5.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/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_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/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5.tf
 Output files
	alignments_1ton	$RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_vs_db_jaspar_core_vertebrates_alignments_1ton.tab
	match_table_txt	$RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_vs_db_jaspar_core_vertebrates.tab
	html_index   	$RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_vs_db_jaspar_core_vertebrates_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_vs_db_jaspar_core_vertebrates_alignments_1ton.html
	match_table_html	$RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_vs_db_jaspar_core_vertebrates.html
	prefix       	$RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5_vs_db_jaspar_core_vertebrates
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m5/peak-motifs_oligos_6nt_test_vs_ctrl_m5.tf
		file1	1	12	715	cmAAGGTCAGrr
	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_test_vs_ctrl_m5 MA0141.2 oligos_6nt_test_vs_ctrl_m5 Esrrb 0.957 0.574 10.632 0.573 0.975 0.4527 0.94714 12 12 9 15 0.6000 0.7500 0.7500 D -3 cmAAGGTCA... ...yCAAGGTCA 1 4 5 4 1 1 1 2.4286 1
oligos_6nt_test_vs_ctrl_m5 MA0071.1 oligos_6nt_test_vs_ctrl_m5 RORA_1 0.913 0.632 10.808 0.628 0.951 0.8863 0.92604 12 10 9 13 0.6923 0.7500 0.9000 D -1 cmAAGGTCA... .wcwAGGTCA 3 3 4 3 3 3 3 3.1429 2
oligos_6nt_test_vs_ctrl_m5 MA0141.1 oligos_6nt_test_vs_ctrl_m5 Esrrb 0.956 0.574 10.474 0.573 0.975 0.4555 0.94698 12 12 9 15 0.6000 0.7500 0.7500 D -3 cmAAGGTCA... ...yCAAGGTCA 2 5 6 5 2 2 2 3.4286 3
oligos_6nt_test_vs_ctrl_m5 MA0592.1 oligos_6nt_test_vs_ctrl_m5 ESRRA 0.870 0.797 11.273 0.783 0.931 1.5109 0.92098 12 11 11 12 0.9167 0.9167 1.0000 D 0 cmAAGGTCAGr. yCAAGGTCAcm 5 1 2 1 4 7 5 3.5714 4
oligos_6nt_test_vs_ctrl_m5 MA0512.1 oligos_6nt_test_vs_ctrl_m5 Rxra 0.853 0.782 9.135 0.742 0.925 1.6602 0.91717 12 11 11 12 0.9167 0.9167 1.0000 D 0 cmAAGGTCAGr. CArAGKTCAgd 9 2 8 2 6 10 7 6.2857 5
oligos_6nt_test_vs_ctrl_m5 MA0258.2 oligos_6nt_test_vs_ctrl_m5 ESR2 0.896 0.448 7.773 0.442 0.940 1.0748 0.91855 12 15 9 18 0.5000 0.7500 0.6000 D 3 ...AGGTCAGrr rGGTCAsms...... 4 14 10 12 5 4 4 7.5714 6
oligos_6nt_test_vs_ctrl_m5 MA0065.1 oligos_6nt_test_vs_ctrl_m5 PPARG::RXRA 0.831 0.498 11.103 0.484 0.915 2.0482 0.91567 12 20 12 20 0.6000 1.0000 0.6000 D -8 cmAAGGTCAGrr ........CAAAGGTCAymk 13 8 3 8 7 14 11 9.1429 7
oligos_6nt_test_vs_ctrl_m5 MA0505.1 oligos_6nt_test_vs_ctrl_m5 Nr5a2 0.833 0.573 9.942 0.545 0.913 1.9094 0.91117 12 15 11 16 0.6875 0.9167 0.7333 D -4 cmAAGGTCAGr. ....TCAAGGyCAgs 12 6 7 7 9 13 12 9.4286 8
oligos_6nt_test_vs_ctrl_m5 MA0160.1 oligos_6nt_test_vs_ctrl_m5 NR4A2 0.859 0.573 8.211 0.562 0.900 1.6058 0.88799 12 8 8 12 0.6667 0.6667 1.0000 D 2 ..AAGGTCAG.. aAGGTCAc 7 7 9 6 16 9 14 9.7143 9
oligos_6nt_test_vs_ctrl_m5 MA0258.1 oligos_6nt_test_vs_ctrl_m5 ESR2 0.849 0.491 6.707 0.476 0.919 1.7856 0.91410 12 18 11 19 0.5789 0.9167 0.6111 D 1 .mAAGGTCAGrr cwrGGTCAsgk....... 10 9 11 9 8 12 9 9.7143 10
oligos_6nt_test_vs_ctrl_m5 MA0017.1 oligos_6nt_test_vs_ctrl_m5 NR2F1 0.868 0.460 0.751 -0.135 0.926 1.3389 0.90909 12 14 9 17 0.5294 0.7500 0.6429 R -5 cmAAGGTCA... .....CAAAGKTCA 6 12 16 16 10 5 6 10.1429 11
oligos_6nt_test_vs_ctrl_m5 MA0065.2 oligos_6nt_test_vs_ctrl_m5 PPARG::RXRA 0.858 0.429 4.750 0.402 0.920 1.4319 0.90599 12 15 9 18 0.5000 0.7500 0.6000 D -6 cmAAGGTCA... ......cArAGGkcA 8 15 13 15 11 6 8 10.8571 12
oligos_6nt_test_vs_ctrl_m5 MA0115.1 oligos_6nt_test_vs_ctrl_m5 NR1H2::RXRA 0.797 0.487 13.304 0.469 0.875 2.7537 0.89333 12 17 11 18 0.6111 0.9167 0.6471 D -6 cmAAGGTCAGr. ......CAAAGGTCAAc 15 10 1 10 15 16 16 11.8571 13
oligos_6nt_test_vs_ctrl_m5 MA0504.1 oligos_6nt_test_vs_ctrl_m5 NR2C2 0.845 0.423 6.396 0.402 0.916 1.5170 0.90323 12 15 9 18 0.5000 0.7500 0.6000 D -6 cmAAGGTCA... ......CArAGGTCA 11 16 12 14 13 8 10 12.0000 14
oligos_6nt_test_vs_ctrl_m5 MA0114.1 oligos_6nt_test_vs_ctrl_m5 HNF4A 0.818 0.460 3.992 0.424 0.901 1.7817 0.89513 12 13 9 16 0.5625 0.7500 0.6923 D -4 cmAAGGTCA... ....CAAAGkyCa 14 11 15 13 14 11 13 13.0000 15
oligos_6nt_test_vs_ctrl_m5 MA0112.2 oligos_6nt_test_vs_ctrl_m5 ESR1 0.751 0.451 4.613 0.445 0.889 2.6723 0.90367 12 20 12 20 0.6000 1.0000 0.6000 D -2 cmAAGGTCAGrr ..scmaGGtCAccc...... 16 13 14 11 12 15 15 13.7143 16 
 Host name	rsat
 Job started	2014-09-06.124829
 Job done	2014-09-06.124835
 Seconds	2.83
	user	2.83
	system	0.09
	cuser	3.7
;	csystem	0.2