/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/peak-motifs_motifs_disco_compa.tab 
 compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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/peak-motifs_motifs_disco_compa.tab
 Program version       	1.115
 Input files
	file2 	$RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_discovered.tf
	file1 	$RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_discovered.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/peak-motifs_motifs_disco_compa_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/peak-motifs_motifs_disco_compa.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/peak-motifs_motifs_disco_compa_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/peak-motifs_motifs_disco_compa_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/peak-motifs_motifs_disco_compa
	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/peak-motifs_motifs_disco_compa.html
 Matrices
	file1	9 matrices	$RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_discovered.tf
	file2	9 matrices	$RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_discovered.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
local_words_7nt_m1 local_words_7nt_m3 local_words_7nt_m1 local_words_7nt_m3 0.969 0.969 7.137 0.970 0.991 0.3817 0.97920 21 21 21 21 1.0000 1.0000 1.0000 D 0 wbwCATTTcchgkAAATGtat kdaCATTTyCmrgaAATGtmw 1 1 8 1 1 1 1 2.0000 1
local_words_7nt_m1 local_words_7nt_m2 local_words_7nt_m1 local_words_7nt_m2 0.963 0.963 6.461 0.954 0.989 0.4568 0.97724 21 21 21 21 1.0000 1.0000 1.0000 D 0 wbwCATTTcchgkAAATGtat awaCATTTcybgkaaATGtaw 4 2 9 2 2 4 2 3.5714 2
oligos_7nt_mkv4_m1 positions_7nt_m3 oligos_7nt_mkv4_m1 positions_7nt_m3 0.966 0.846 10.644 0.844 0.986 0.3896 0.96847 14 16 14 16 0.8750 1.0000 0.8750 D 0 srTTTCCwGGAAay srTTTCYwGGAArt.. 2 6 2 6 5 2 3 3.7143 3
oligos_7nt_mkv4_m1 oligos_7nt_mkv4_m3 oligos_7nt_mkv4_m1 oligos_7nt_mkv4_m3 0.947 0.879 11.578 0.881 0.977 0.6084 0.95757 14 13 13 14 0.9286 0.9286 1.0000 D 1 .rTTTCCwGGAAay ryTTCCmrGAAry 6 5 1 5 9 6 9 5.8571 4
positions_7nt_m1 positions_7nt_m2 positions_7nt_m1 positions_7nt_m2 0.941 0.941 8.066 0.934 0.982 0.7676 0.97050 21 21 21 21 1.0000 1.0000 1.0000 D 0 wsTsrTTTCCwGGAAatsAsa dsTsatTTCCcrGAAATsAsr 9 4 7 3 4 9 6 6.0000 5
local_words_7nt_m2 local_words_7nt_m3 local_words_7nt_m2 local_words_7nt_m3 0.942 0.942 5.912 0.929 0.983 0.6934 0.97196 21 21 21 21 1.0000 1.0000 1.0000 D 0 awaCATTTcybgkaaATGtaw kdaCATTTyCmrgaAATGtmw 8 3 14 4 3 8 5 6.4286 6
oligos_7nt_mkv4_m1 positions_7nt_m1 oligos_7nt_mkv4_m1 positions_7nt_m1 0.963 0.642 9.650 0.644 0.985 0.4212 0.96722 14 21 14 21 0.6667 1.0000 0.6667 D -3 srTTTCCwGGAAay ...srTTTCCwGGAAat.... 3 15 4 12 6 3 4 6.7143 7
local_words_7nt_m3 positions_7nt_m2 local_words_7nt_m3 positions_7nt_m2 0.842 0.842 6.437 0.812 0.952 2.0195 0.95215 21 21 21 21 1.0000 1.0000 1.0000 D 0 kdaCATTTyCmrgaAATGtmw dsTsatTTCCcrGAAATsAsr 14 7 10 7 11 14 14 11.0000 8
oligos_7nt_mkv4_m3 positions_7nt_m1 oligos_7nt_mkv4_m3 positions_7nt_m1 0.927 0.574 9.770 0.577 0.968 0.8193 0.95077 13 21 13 21 0.6190 1.0000 0.6190 D -4 ryTTCCmrGAAry ....rTTTCCwGGAAat.... 10 19 3 14 12 10 10 11.1429 9
oligos_7nt_mkv4_m3 positions_7nt_m3 oligos_7nt_mkv4_m3 positions_7nt_m3 0.956 0.777 5.037 0.262 0.980 0.5091 0.96119 13 16 13 16 0.8125 1.0000 0.8125 R -2 ryTTCCmrGAAry ..AYTTCCWRGAAAY. 5 10 22 22 8 5 7 11.2857 10
positions_7nt_m1 positions_7nt_m3 positions_7nt_m1 positions_7nt_m3 0.945 0.720 5.359 0.294 0.979 0.6620 0.96404 21 16 16 21 0.7619 0.7619 1.0000 R 2 ..TsrTTTCCwGGAAats... YSAYTTCCWRGAAAYS 7 13 20 21 7 7 8 11.8571 11
local_words_7nt_m1 positions_7nt_m2 local_words_7nt_m1 positions_7nt_m2 0.824 0.824 6.141 0.786 0.946 2.2708 0.94926 21 21 21 21 1.0000 1.0000 1.0000 R 0 wbwCATTTcchgkAAATGtat YSTSATTTCYGGGAAATSASH 15 8 11 8 13 16 15 12.2857 12
oligos_7nt_mkv4_m1 positions_7nt_m2 oligos_7nt_mkv4_m1 positions_7nt_m2 0.898 0.599 8.852 0.587 0.958 1.1781 0.94518 14 21 14 21 0.6667 1.0000 0.6667 D -3 srTTTCCwGGAAay ...satTTCCcrGAAAT.... 13 18 6 13 15 13 13 13.0000 13
oligos_7nt_mkv4_m3 positions_7nt_m2 oligos_7nt_mkv4_m3 positions_7nt_m2 0.907 0.561 9.364 0.549 0.959 1.0633 0.94391 13 21 13 21 0.6190 1.0000 0.6190 D -4 ryTTCCmrGAAry ....atTTCCcrGAAAT.... 12 20 5 16 16 11 12 13.1429 14
local_words_7nt_m1 positions_7nt_m1 local_words_7nt_m1 positions_7nt_m1 0.814 0.814 5.915 0.768 0.944 2.3409 0.94848 21 21 21 21 1.0000 1.0000 1.0000 R 0 wbwCATTTcchgkAAATGtat TSTSATTTCCWGGAAAYSASW 16 9 13 9 14 17 16 13.4286 15
positions_7nt_m2 positions_7nt_m3 positions_7nt_m2 positions_7nt_m3 0.913 0.696 3.888 0.201 0.967 1.0715 0.95425 21 16 16 21 0.7619 0.7619 1.0000 R 2 ..TsatTTCCcrGAAATs... YSAYTTCCWRGAAAYS 11 14 23 23 10 12 11 14.8571 16
local_words_7nt_m3 positions_7nt_m1 local_words_7nt_m3 positions_7nt_m1 0.774 0.774 5.740 0.734 0.933 2.8217 0.94344 21 21 21 21 1.0000 1.0000 1.0000 R 0 kdaCATTTyCmrgaAATGtmw TSTSATTTCCWGGAAAYSASW 21 11 17 10 17 23 17 16.5714 17
local_words_7nt_m1 positions_7nt_m3 local_words_7nt_m1 positions_7nt_m3 0.805 0.613 5.774 0.554 0.927 2.3452 0.93232 21 16 16 21 0.7619 0.7619 1.0000 D 3 ...CATTTcchgkAAATGt.. srTTTCYwGGAArtsr 18 16 16 15 19 18 19 17.2857 18
local_words_7nt_m1 oligos_7nt_mkv4_m1 local_words_7nt_m1 oligos_7nt_mkv4_m1 0.813 0.542 6.083 0.495 0.925 2.1078 0.92667 21 14 14 21 0.6667 0.6667 1.0000 D 3 ...CATTTcchgkAAAT.... srTTTCCwGGAAay 17 21 12 17 21 15 21 17.7143 19
local_words_7nt_m2 positions_7nt_m2 local_words_7nt_m2 positions_7nt_m2 0.758 0.758 5.275 0.702 0.928 3.0222 0.94146 21 21 21 21 1.0000 1.0000 1.0000 R 0 awaCATTTcybgkaaATGtaw YSTSATTTCYGGGAAATSASH 23 12 21 11 18 24 18 18.1429 20
local_words_7nt_m3 oligos_7nt_mkv4_m1 local_words_7nt_m3 oligos_7nt_mkv4_m1 0.785 0.524 5.874 0.471 0.914 2.3996 0.92176 21 14 14 21 0.6667 0.6667 1.0000 D 3 ...CATTTyCmrgaAAT.... srTTTCCwGGAAay 20 22 15 18 22 20 22 19.8571 21
local_words_7nt_m3 positions_7nt_m3 local_words_7nt_m3 positions_7nt_m3 0.797 0.607 3.470 0.166 0.925 2.3938 0.93162 21 16 16 21 0.7619 0.7619 1.0000 R 2 ..aCATTTyCmrgaAATG... YSAYTTCCWRGAAAYS 19 17 24 24 20 19 20 20.4286 22
local_words_7nt_m3 oligos_7nt_mkv4_m3 local_words_7nt_m3 oligos_7nt_mkv4_m3 0.770 0.477 5.615 0.420 0.904 2.4838 0.91428 21 13 13 21 0.6190 0.6190 1.0000 D 4 ....ATTTyCmrgaAAT.... ryTTCCmrGAAry 22 23 18 19 23 21 23 21.2857 23
local_words_7nt_m1 oligos_7nt_mkv4_m3 local_words_7nt_m1 oligos_7nt_mkv4_m3 0.755 0.467 5.502 0.418 0.898 2.6592 0.91130 21 13 13 21 0.6190 0.6190 1.0000 R 4 ....ATTTcchgkAAAT.... RYTTCYKGGAARY 24 24 19 20 24 22 24 22.4286 24 
 Host name	rsat
 Job started	2013-01-11.111029
 Job done	2013-01-11.111036
 Seconds	0.99
	user	0.99
	system	0.09
	cuser	5.83
;	csystem	0.3