/home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates.tab
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.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/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates
 Program version       	1.115
 Input files
	file2 	$RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf
	file1 	$RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf
 Output files
	alignments_1ton	$RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates_alignments_1ton.tab
	match_table_txt	$RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates.tab
	html_index   	$RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates_alignments_1ton.html
	output_prefix	$RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates
	match_table_html	$RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates.html
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.tf
	file2	130 matrices	$RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf
 Threshold values
	Parameter      	Lower	Upper
	w              	5	none
	offset_rank    	none	1
	wr             	0.3	none
	cor            	0.75	none
	Ncor           	0.4	none
	ncor           	0.4	none
 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_m1 MA0137.2 positions_7nt_m1 STAT1 0.945 0.675 7.824 0.676 0.979 0.6246 0.96275 21 15 15 21 0.7143 0.7143 1.0000 R 3 ...srTTTCCwGGAAats... GRYTTCYDGGAARTG 2 1 1 1 1 2 1 1.2857 1
positions_7nt_m1 MA0144.1 positions_7nt_m1 Stat3 0.948 0.451 7.793 0.447 0.973 0.5313 0.94846 21 10 10 21 0.4762 0.4762 1.0000 D 6 ......TTCCwGGAAa..... TTCCaGGAAr 1 2 2 2 2 1 2 1.7143 2
positions_7nt_m1 MA0062.2 positions_7nt_m1 GABPA 0.778 0.408 5.981 0.399 0.909 2.0038 0.90901 21 11 11 21 0.5238 0.5238 1.0000 D 9 .........CwGGAAatsAs. CCGGAAGygvc 3 3 3 3 3 3 3 3.0000 3
 Host name	rsat
 Job started	2013-01-11.111052
 Job done	2013-01-11.111055
 Seconds	1.72
	user	1.72
	system	0.02
	cuser	0.81
;	csystem	0.04