/vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_footprintDB.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.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/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_footprintDB
 Program version       	1.118
 Input files
	file2 	$RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf
	file1 	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf
 Output files
	alignments_1ton	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_footprintDB_alignments_1ton.tab
	match_table_txt	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_footprintDB.tab
	html_index   	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_footprintDB_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_footprintDB_alignments_1ton.html
	match_table_html	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_footprintDB.html
	prefix       	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_footprintDB
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf
		file1	1	11	1	TCCCCTAGCGC
	file2	4196 matrices	$RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf
		file2		1		17		100		yyaymCATCAAwmwwmm
		file2		2		10		7		ACCGGAAGws
		file2		3		16		100		wwtksgTAATTACsdy
		file2		4		17		100		twrttaATTAwtaawwr
		file2		5		18		100		TCCGynnnnnnnnnCGGA
		file2		6		20		100		gwrastTTCCGGAAyrywrr
		file2		7		20		100		yrawygGyGCCGyrysackh
		file2		8		21		100		wmrmraAtmGAAGaaawawww
		file2		9		20		100		rkmkkakCACGTGmyyrvwy
		file2		10		6		1		CTATCA
		file2		11		18		66		hTTwCCwWAwwdGGhAat
		...	4186 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
positions_6nt_m2 2623_MA0396.1_JASPAR_CORE_2009_ positions_6nt_m2 2623_MA0396.1_JASPAR_CORE_2009_ 0.837 0.558 10.099 0.542 0.888 1.7968 0.88152 11 9 8 12 0.6667 0.7273 0.8889 D 3 ...CCTAGCGC rcTAGCGc. 7 2 4 2 7 9 7 5.4286 1
positions_6nt_m2 3076_HipB_RegulonDB_7.5_ positions_6nt_m2 3076_HipB_RegulonDB_7.5_ 0.850 0.492 11.098 0.472 0.892 2.3750 0.90093 11 19 11 19 0.5789 1.0000 0.5789 D -2 TCCCCTAGCGC ..TCCbbKWdhGM...... 6 5 1 5 5 13 6 5.8571 2
positions_6nt_m2 2588_MA0342.1_JASPAR_CORE_2009_ positions_6nt_m2 2588_MA0342.1_JASPAR_CORE_2009_ 0.994 0.452 0.018 -0.150 0.995 0.0524 0.96761 11 5 5 11 0.4545 0.4545 1.0000 R 1 .CCCCT..... CCCCT 1 9 15 14 1 1 1 6.0000 3
positions_6nt_m2 2604_MA0366.1_JASPAR_CORE_2009_ positions_6nt_m2 2604_MA0366.1_JASPAR_CORE_2009_ 0.990 0.450 0.000 -0.143 0.992 0.0794 0.96015 11 5 5 11 0.4545 0.4545 1.0000 R 1 .CCCCT..... CCCCT 2 10 16 13 2 2 2 6.7143 4
positions_6nt_m2 5966_1a3q_A_3D-footprint_20130124_ positions_6nt_m2 5966_1a3q_A_3D-footprint_20130124_ 0.967 0.403 0.084 -0.125 0.974 0.2559 0.92847 11 6 5 12 0.4167 0.4545 0.8333 R -1 TCCCC...... .TCCCC 3 15 12 9 3 3 3 6.8571 5
positions_6nt_m2 2624_MA0397.1_JASPAR_CORE_2009_ positions_6nt_m2 2624_MA0397.1_JASPAR_CORE_2009_ 0.816 0.544 10.327 0.529 0.874 2.0121 0.87462 11 9 8 12 0.6667 0.7273 0.8889 D 3 ...CCTAGCGC gmTAGCGC. 10 4 2 4 10 10 9 7.0000 6
positions_6nt_m2 2447_MA0056.1_JASPAR_CORE_2009_ positions_6nt_m2 2447_MA0056.1_JASPAR_CORE_2009_ 0.878 0.479 0.037 -0.132 0.914 1.0350 0.88010 11 6 6 11 0.5455 0.5455 1.0000 R 0 TCCCCT..... TCCCCR 5 6 14 11 8 5 5 7.7143 7
positions_6nt_m2 2587_MA0341.1_JASPAR_CORE_2009_ positions_6nt_m2 2587_MA0341.1_JASPAR_CORE_2009_ 0.965 0.439 0.052 -0.152 0.974 0.2647 0.92724 11 5 5 11 0.4545 0.4545 1.0000 R 1 .CCCCT..... CCCCY 4 12 13 15 4 4 4 8.0000 8
positions_6nt_m2 5080_Mta_DBTBS_1.0_ positions_6nt_m2 5080_Mta_DBTBS_1.0_ 0.818 0.460 8.656 0.449 0.874 2.2640 0.88178 11 14 9 16 0.5625 0.8182 0.6429 D -5 TCCCCTAGC.. .....TmCssTWGs 9 8 6 6 6 12 10 8.1429 9
positions_6nt_m2 7264_STY1_ArabidopsisPBM_20140210_ positions_6nt_m2 7264_STY1_ArabidopsisPBM_20140210_ 0.773 0.702 9.744 0.689 0.848 3.0358 0.87680 11 10 10 11 0.9091 0.9091 1.0000 D 1 .CCCCTAGCGC cCCCTAGGGy 13 1 5 1 9 16 13 8.2857 10
positions_6nt_m2 2609_MA0372.1_JASPAR_CORE_2009_ positions_6nt_m2 2609_MA0372.1_JASPAR_CORE_2009_ 0.757 0.551 10.156 0.538 0.836 2.6179 0.85699 11 8 8 11 0.7273 0.7273 1.0000 D 0 TCCCCTAG... aCCCCTwA 15 3 3 3 13 15 16 9.7143 11
positions_6nt_m2 6016_1cf7_A_3D-footprint_20130124_ positions_6nt_m2 6016_1cf7_A_3D-footprint_20130124_ 0.834 0.417 0.108 -0.155 0.885 1.3750 0.86181 11 7 6 12 0.5000 0.5455 0.8571 R 5 .....TAGCGC TCGCGC. 8 14 11 16 11 6 8 10.5714 12
positions_6nt_m2 6459_2isz_B_3D-footprint_20130124_ positions_6nt_m2 6459_2isz_B_3D-footprint_20130124_ 0.788 0.430 1.714 -0.040 0.858 1.7031 0.84620 11 6 6 11 0.5455 0.5455 1.0000 R 2 ..CCCTAG... CCCTAA 12 13 7 7 16 8 12 10.7143 13
positions_6nt_m2 2448_MA0057.1_JASPAR_CORE_2009_ positions_6nt_m2 2448_MA0057.1_JASPAR_CORE_2009_ 0.755 0.465 0.728 -0.108 0.838 2.5938 0.85765 11 10 8 13 0.6154 0.7273 0.8000 R -2 TCCCCTAG... ..MCCCMTMV 16 7 8 8 12 14 15 11.4286 14
positions_6nt_m2 2471_MA0081.1_JASPAR_CORE_2009_ positions_6nt_m2 2471_MA0081.1_JASPAR_CORE_2009_ 0.801 0.401 0.209 -0.140 0.865 1.6160 0.85019 11 7 6 12 0.5000 0.5455 0.8571 R -1 TCCCCT..... .TCCKSW 11 16 10 12 14 7 11 11.5714 15
positions_6nt_m2 7511_MZF1_f1_HOCOMOCO_v9_ positions_6nt_m2 7511_MZF1_f1_HOCOMOCO_v9_ 0.766 0.447 0.267 -0.129 0.841 2.2282 0.84921 11 8 7 12 0.5833 0.6364 0.8750 R -1 TCCCCTA.... .TCCCCMY 14 11 9 10 15 11 14 12.0000 16 
 Host name	biow
 Job started	2014-09-05.203152
 Job done	2014-09-05.203225
 Seconds	30.04
	user	30.04
	system	0.38
	cuser	2.73
;	csystem	0.64