/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_7nt_m3/peak-motifs_positions_7nt_m3_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_7nt_m3/peak-motifs_positions_7nt_m3.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_7nt_m3/peak-motifs_positions_7nt_m3_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_7nt_m3/peak-motifs_positions_7nt_m3.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_7nt_m3/peak-motifs_positions_7nt_m3_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_7nt_m3/peak-motifs_positions_7nt_m3_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_7nt_m3/peak-motifs_positions_7nt_m3_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_7nt_m3/peak-motifs_positions_7nt_m3_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_7nt_m3/peak-motifs_positions_7nt_m3_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_7nt_m3/peak-motifs_positions_7nt_m3_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_7nt_m3/peak-motifs_positions_7nt_m3.tf
		file1	1	11	10	sgCTCAGGCgr
	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_7nt_m3 5875_TFAP2B_DBD_2_HumanTF_1.0_ positions_7nt_m3 5875_TFAP2B_DBD_2_HumanTF_1.0_ 0.785 0.654 7.834 0.607 0.888 2.2404 0.89416 11 11 10 12 0.8333 0.9091 0.9091 D -1 sgCTCAGGCg. .GCCysAGGCd 6 1 1 1 6 9 9 4.7143 1
positions_7nt_m3 5902_Tcfap2a_DBD_2_HumanTF_1.0_ positions_7nt_m3 5902_Tcfap2a_DBD_2_HumanTF_1.0_ 0.785 0.654 7.151 0.606 0.890 2.2086 0.89492 11 11 10 12 0.8333 0.9091 0.9091 D -1 sgCTCAGGCg. .GCCysAGGCd 7 2 2 2 5 8 8 4.8571 2
positions_7nt_m3 6491_2pe5_C_3D-footprint_20130124_ positions_7nt_m3 6491_2pe5_C_3D-footprint_20130124_ 0.951 0.432 4.678 0.421 0.964 0.3622 0.91489 11 5 5 11 0.4545 0.4545 1.0000 D 1 .gCTCA..... gcTCA 1 11 10 9 1 1 1 4.8571 3
positions_7nt_m3 5872_TFAP2A_DBD_2_HumanTF_1.0_ positions_7nt_m3 5872_TFAP2A_DBD_2_HumanTF_1.0_ 0.783 0.652 6.662 0.600 0.890 2.2014 0.89509 11 11 10 12 0.8333 0.9091 0.9091 D -1 sgCTCAGGCg. .GCCysAGGCw 8 3 5 3 4 7 7 5.2857 4
positions_7nt_m3 7566_PAX5_si_HOCOMOCO_v9_ positions_7nt_m3 7566_PAX5_si_HOCOMOCO_v9_ 0.843 0.537 6.019 0.430 0.903 1.3554 0.88240 11 7 7 11 0.6364 0.6364 1.0000 R 1 .gCTCAGG... CCTCAGC 3 10 7 8 11 3 3 6.4286 5
positions_7nt_m3 3725_UP00028_UniPROBE_20120919_ positions_7nt_m3 3725_UP00028_UniPROBE_20120919_ 0.765 0.561 6.752 0.492 0.890 2.4155 0.90009 11 15 11 15 0.7333 1.0000 0.7333 R -3 sgCTCAGGCgr ...SCCYSRGGSDW. 10 8 3 7 2 11 5 6.5714 6
positions_7nt_m3 6022_1cjg_A_3D-footprint_20130124_ positions_7nt_m3 6022_1cjg_A_3D-footprint_20130124_ 0.900 0.409 3.648 0.375 0.939 0.6115 0.88941 11 5 5 11 0.4545 0.4545 1.0000 D 1 .gCTCA..... GCTcA 2 13 11 11 9 2 2 7.1429 7
positions_7nt_m3 1944_PB0088.1_JASPAR_CORE_2009_ positions_7nt_m3 1944_PB0088.1_JASPAR_CORE_2009_ 0.764 0.561 6.657 0.495 0.890 2.4195 0.90001 11 15 11 15 0.7333 1.0000 0.7333 R -3 sgCTCAGGCgr ...SCCYSRGGSDW. 11 9 6 6 3 12 6 7.5714 8
positions_7nt_m3 7295_AP2A_f2_HOCOMOCO_v9_ positions_7nt_m3 7295_AP2A_f2_HOCOMOCO_v9_ 0.802 0.584 2.399 -0.007 0.893 1.7176 0.88416 11 8 8 11 0.7273 0.7273 1.0000 R 0 sgCTCAGG... SCCYCAGG 4 6 13 13 10 5 4 7.8571 9
positions_7nt_m3 5878_TFAP2C_DBD_2_HumanTF_1.0_ positions_7nt_m3 5878_TFAP2C_DBD_2_HumanTF_1.0_ 0.762 0.635 6.738 0.583 0.879 2.4212 0.88997 11 11 10 12 0.8333 0.9091 0.9091 D -1 sgCTCAGGCg. .GCCtsAGGCw 12 4 4 4 8 13 12 8.1429 10
positions_7nt_m3 5882_TFAP2C_full_3_HumanTF_1.0_ positions_7nt_m3 5882_TFAP2C_full_3_HumanTF_1.0_ 0.757 0.631 5.039 0.573 0.880 2.4054 0.89033 11 11 10 12 0.8333 0.9091 0.9091 D -1 sgCTCAGGCg. .GCCysAGGCw 13 5 9 5 7 10 11 8.5714 11
positions_7nt_m3 7297_AP2C_f1_HOCOMOCO_v9_ positions_7nt_m3 7297_AP2C_f1_HOCOMOCO_v9_ 0.785 0.571 2.819 -0.001 0.883 1.8768 0.87891 11 8 8 11 0.7273 0.7273 1.0000 R 0 sgCTCAGG... SCCYCAGG 5 7 12 12 12 6 10 9.1429 12
positions_7nt_m3 6517_2wbs_A_3D-footprint_20130124_ positions_7nt_m3 6517_2wbs_A_3D-footprint_20130124_ 0.766 0.418 5.958 0.398 0.870 1.5602 0.85279 11 6 6 11 0.5455 0.5455 1.0000 D 5 .....AGGCgr aGGCGC 9 12 8 10 13 4 13 9.8571 13 
 Host name	biow
 Job started	2014-09-05.203338
 Job done	2014-09-05.203412
 Seconds	30.29
	user	30.29
	system	0.39
	cuser	3.37
;	csystem	0.53