/vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_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/dyads_m4/peak-motifs_dyads_m4.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/dyads_m4/peak-motifs_dyads_m4_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/dyads_m4/peak-motifs_dyads_m4.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/dyads_m4/peak-motifs_dyads_m4_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/dyads_m4/peak-motifs_dyads_m4_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/dyads_m4/peak-motifs_dyads_m4_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/dyads_m4/peak-motifs_dyads_m4_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/dyads_m4/peak-motifs_dyads_m4_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/dyads_m4/peak-motifs_dyads_m4_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/dyads_m4/peak-motifs_dyads_m4.tf
		file1	1	11	37	ymTCCAGAccr
	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
dyads_m4 1921_PB0060.1_JASPAR_CORE_2009_ dyads_m4 1921_PB0060.1_JASPAR_CORE_2009_ 0.832 0.538 6.936 0.529 0.931 1.5076 0.92107 11 17 11 17 0.6471 1.0000 0.6471 D -2 ymTCCAGAccr ..watCCAGACrk.... 7 5 4 2 1 10 5 4.8571 1
dyads_m4 3697_UP00000_UniPROBE_20120919_ dyads_m4 3697_UP00000_UniPROBE_20120919_ 0.832 0.538 6.960 0.529 0.931 1.5090 0.92103 11 17 11 17 0.6471 1.0000 0.6471 D -2 ymTCCAGAccr ..wawCCAGACrk.... 8 6 3 1 2 11 6 5.2857 2
dyads_m4 2481_MA0092.1_JASPAR_CORE_2009_ dyads_m4 2481_MA0092.1_JASPAR_CORE_2009_ 0.846 0.769 3.725 0.338 0.932 1.3589 0.91757 11 10 10 11 0.9091 0.9091 1.0000 R 0 ymTCCAGAcc. AWKCCAGAYS 4 1 10 9 4 9 4 5.8571 3
dyads_m4 7423_HAND1_si_HOCOMOCO_v9_ dyads_m4 7423_HAND1_si_HOCOMOCO_v9_ 0.860 0.717 0.284 -0.134 0.938 1.2487 0.92098 11 11 10 12 0.8333 0.9091 0.9091 R -1 ymTCCAGAcc. .AWKCCAGAYV 3 2 15 15 3 6 3 6.7143 4
dyads_m4 1711_MA0152.1_JASPAR_CORE_2009_ dyads_m4 1711_MA0152.1_JASPAR_CORE_2009_ 0.840 0.420 5.947 0.398 0.913 1.0500 0.87924 11 7 6 12 0.5000 0.5455 0.8571 D -1 ymTCCA..... .TTTCCA 5 12 5 8 10 3 7 7.1429 5
dyads_m4 6130_1imh_C_3D-footprint_20130124_ dyads_m4 6130_1imh_C_3D-footprint_20130124_ 0.918 0.417 0.358 -0.024 0.952 0.4771 0.90232 11 5 5 11 0.4545 0.4545 1.0000 R 1 .mTCCA..... TTCCA 1 13 14 13 6 2 2 7.2857 6
dyads_m4 6074_1gji_A_3D-footprint_20130124_ dyads_m4 6074_1gji_A_3D-footprint_20130124_ 0.918 0.417 0.121 -0.063 0.952 0.4768 0.90235 11 5 5 11 0.4545 0.4545 1.0000 R 1 .mTCCA..... KTCCR 2 14 16 14 5 1 1 7.5714 7
dyads_m4 7686_UBIP1_f1_HOCOMOCO_v9_ dyads_m4 7686_UBIP1_f1_HOCOMOCO_v9_ 0.809 0.441 5.844 0.468 0.902 1.1757 0.87221 11 6 6 11 0.5455 0.5455 1.0000 D 4 ....CAGAcc. CAGArA 9 10 6 5 12 5 9 8.0000 8
dyads_m4 6322_1svc_P_3D-footprint_20130124_ dyads_m4 6322_1svc_P_3D-footprint_20130124_ 0.805 0.402 5.817 0.403 0.909 1.0924 0.87682 11 7 6 12 0.5000 0.5455 0.8571 D -1 ymTCCA..... .nnTCCc 10 16 7 7 11 4 8 9.0000 9
dyads_m4 7623_SMAD4_si_HOCOMOCO_v9_ dyads_m4 7623_SMAD4_si_HOCOMOCO_v9_ 0.801 0.582 4.026 0.195 0.894 1.7021 0.88469 11 8 8 11 0.7273 0.7273 1.0000 R 1 .mTCCAGAc.. RKMCAGAC 11 4 9 10 9 12 11 9.4286 10
dyads_m4 7622_SMAD3_f1_HOCOMOCO_v9_ dyads_m4 7622_SMAD3_f1_HOCOMOCO_v9_ 0.782 0.640 2.851 0.185 0.897 1.8482 0.89319 11 9 9 11 0.8182 0.8182 1.0000 R 1 .mTCCAGAcc. RGCCAGACA 12 3 11 11 8 13 10 9.7143 11
dyads_m4 2553_MA0292.1_JASPAR_CORE_2009_ dyads_m4 2553_MA0292.1_JASPAR_CORE_2009_ 0.765 0.487 6.968 0.500 0.862 1.9327 0.85957 11 7 7 11 0.6364 0.6364 1.0000 D 1 .mTCCAGA... hTCCGGA 14 7 2 3 15 14 15 10.0000 12
dyads_m4 2742_PF0055.1_JASPAR_CORE_2009_ dyads_m4 2742_PF0055.1_JASPAR_CORE_2009_ 0.836 0.456 1.961 0.003 0.887 1.3557 0.86278 11 6 6 11 0.5455 0.5455 1.0000 R 0 ymTCCA..... TTTCCA 6 9 12 12 14 8 14 10.7143 13
dyads_m4 2532_MA0266.1_JASPAR_CORE_2009_ dyads_m4 2532_MA0266.1_JASPAR_CORE_2009_ 0.757 0.482 7.967 0.486 0.850 2.0954 0.85378 11 7 7 11 0.6364 0.6364 1.0000 D 1 .mTCCAGA... sTCTAGA 16 8 1 4 16 15 16 10.8571 14
dyads_m4 2487_MA0098.1_JASPAR_CORE_2009_ dyads_m4 2487_MA0098.1_JASPAR_CORE_2009_ 0.761 0.415 5.191 0.426 0.887 1.3546 0.86284 11 6 6 11 0.5455 0.5455 1.0000 D 0 ymTCCA..... ywTCCk 15 15 8 6 13 7 13 11.0000 15
dyads_m4 2362_CN0199.1_JASPAR_CORE_2009_ dyads_m4 2362_CN0199.1_JASPAR_CORE_2009_ 0.775 0.431 0.369 -0.146 0.891 2.1725 0.89578 11 17 10 18 0.5556 0.9091 0.5882 R -7 ymTCCAGAcc. .......TTTCCAGAGC 13 11 13 16 7 16 12 12.5714 16 
 Host name	biow
 Job started	2014-09-05.204103
 Job done	2014-09-05.204137
 Seconds	29.73
	user	29.73
	system	0.39
	cuser	3.02
;	csystem	0.62