/vh/rsat/rsat/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab 
 compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/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/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
 Program version       	1.118
 Input files
	file2 	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_discovered.tf
	file1 	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_discovered.tf
 Output files
	alignments_1ton	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.tab
	match_table_txt	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
	html_index   	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_disco_compa_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_disco_compa_alignments_1ton.html
	match_table_html	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_disco_compa.html
	prefix       	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_disco_compa
 Matrices
	file1	15 matrices	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_discovered.tf
		file1	1	24	121	aaTgAGATAAAaAttaaAaTcTww
		file1	2	24	212	watAgAGATAAAaAttaaaawhww
		file1	3	24	128	wwaaTtTTTATCAGATAAAwAwww
		file1	4	24	151	wwTTAGATGATAAAaattAAaaww
		file1	5	24	150	wwcAAGATAAAaattaaaATcTww
		file1	6	16	452	wwcTTTATCTGATAww
		file1	7	12	474	wwTAGATGATaw
		file1	8	15	613	wwcTTTATCTCTAww
		file1	9	12	200	wwGATTAATCww
		file1	10	15	559	wwtaATGATAAAgww
		file1	11	20	417	wwTATCwwwwhwdwyATCww
		...	5 more matrices
	file2	15 matrices	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/peak-motifs_motifs_discovered.tf
		file2		1		24		121		aaTgAGATAAAaAttaaAaTcTww
		file2		2		24		212		watAgAGATAAAaAttaaaawhww
		file2		3		24		128		wwaaTtTTTATCAGATAAAwAwww
		file2		4		24		151		wwTTAGATGATAAAaattAAaaww
		file2		5		24		150		wwcAAGATAAAaattaaaATcTww
		file2		6		16		452		wwcTTTATCTGATAww
		file2		7		12		474		wwTAGATGATaw
		file2		8		15		613		wwcTTTATCTCTAww
		file2		9		12		200		wwGATTAATCww
		file2		10		15		559		wwtaATGATAAAgww
		file2		11		20		417		wwTATCwwwwhwdwyATCww
		...	5 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_test_vs_ctrl_m3 dyads_test_vs_ctrl_m5 dyads_test_vs_ctrl_m3 dyads_test_vs_ctrl_m5 0.931 0.899 4.038 0.877 0.986 0.8042 0.97735 28 29 28 29 0.9655 1.0000 0.9655 D 0 wwGATawwawwwTAGrwwmwwwwAAAww awGATaawwwamTAGrwwmwwwwwAAAw. 1 1 6 1 1 1 1 1.7143 1
oligos_6nt_test_vs_ctrl_m1 oligos_6nt_test_vs_ctrl_m5 oligos_6nt_test_vs_ctrl_m1 oligos_6nt_test_vs_ctrl_m5 0.859 0.859 4.769 0.853 0.961 1.8914 0.95948 24 24 24 24 1.0000 1.0000 1.0000 D 0 aaTgAGATAAAaAttaaAaTcTww wwcAAGATAAAaattaaaATcTww 5 2 2 2 4 8 6 4.1429 2
dyads_test_vs_ctrl_m2 dyads_test_vs_ctrl_m3 dyads_test_vs_ctrl_m2 dyads_test_vs_ctrl_m3 0.837 0.777 4.096 0.742 0.967 1.7368 0.96416 26 28 26 28 0.9286 1.0000 0.9286 D 0 wwGATwwwwwwwwwkawhmwwAAAww wwGATawwawwwTAGrwwmwwwwAAA.. 7 4 4 5 2 5 3 4.2857 3
oligos_6nt_test_vs_ctrl_m1 oligos_6nt_test_vs_ctrl_m2 oligos_6nt_test_vs_ctrl_m1 oligos_6nt_test_vs_ctrl_m2 0.853 0.784 4.594 0.770 0.958 1.9257 0.95734 24 24 23 25 0.9200 0.9583 0.9583 D -1 aaTgAGATAAAaAttaaAaTcTw. .atAgAGATAAAaAttaaaawhww 6 3 3 3 5 10 8 5.4286 4
oligos_6nt_test_vs_ctrl_m2 oligos_6nt_test_vs_ctrl_m5 oligos_6nt_test_vs_ctrl_m2 oligos_6nt_test_vs_ctrl_m5 0.835 0.768 4.827 0.760 0.953 2.1512 0.95491 24 24 23 25 0.9200 0.9583 0.9583 D 1 .atAgAGATAAAaAttaaaawhww wwcAAGATAAAaattaaaATcTw. 8 5 1 4 6 12 9 6.4286 5
dyads_test_vs_ctrl_m2 dyads_test_vs_ctrl_m5 dyads_test_vs_ctrl_m2 dyads_test_vs_ctrl_m5 0.810 0.726 3.714 0.685 0.962 1.9784 0.96175 26 29 26 29 0.8966 1.0000 0.8966 D 0 wwGATwwwwwwwwwkawhmwwAAAww awGATaawwwamTAGrwwmwwwwwAA... 10 6 9 6 3 11 4 7.0000 6
oligos_6nt_test_vs_ctrl_m4 oligos_7nt_test_vs_ctrl_m2 oligos_6nt_test_vs_ctrl_m4 oligos_7nt_test_vs_ctrl_m2 0.890 0.445 3.895 0.427 0.959 0.9858 0.94149 24 12 12 24 0.5000 0.5000 1.0000 D 1 .wTTAGATGATAA........... wwTAGATGATaw 3 13 8 9 12 3 7 7.8571 7
oligos_6nt_test_vs_ctrl_m2 oligos_7nt_test_vs_ctrl_m3 oligos_6nt_test_vs_ctrl_m2 oligos_7nt_test_vs_ctrl_m3 0.904 0.565 0.770 -0.123 0.968 0.9711 0.95354 24 15 15 24 0.6250 0.6250 1.0000 R 0 watAgAGATAAAaAt......... WWTAGAGATAAAGWW 2 10 16 16 7 2 2 7.8571 8
oligos_6nt_test_vs_ctrl_m3 oligos_7nt_test_vs_ctrl_m1 oligos_6nt_test_vs_ctrl_m3 oligos_7nt_test_vs_ctrl_m1 0.889 0.592 2.493 0.168 0.961 1.2433 0.95072 24 16 16 24 0.6667 0.6667 1.0000 R 6 ......TTTATCAGATAAAwAw.. WWTATCAGATAAAGWW 4 9 12 12 9 4 5 7.8571 9
oligos_6nt_test_vs_ctrl_m1 oligos_6nt_test_vs_ctrl_m3 oligos_6nt_test_vs_ctrl_m1 oligos_6nt_test_vs_ctrl_m3 0.829 0.414 3.658 0.413 0.946 1.7428 0.94166 24 24 16 32 0.5000 0.6667 0.6667 D -8 aaTgAGATAAAaAtta........ ........TATCAGATAAAwAwww 9 14 10 10 11 6 11 10.1429 10
oligos_6nt_test_vs_ctrl_m4 oligos_6nt_test_vs_ctrl_m5 oligos_6nt_test_vs_ctrl_m4 oligos_6nt_test_vs_ctrl_m5 0.777 0.604 3.915 0.590 0.933 2.8169 0.94349 24 24 21 27 0.7778 0.8750 0.8750 D 3 ...TAGATGATAAAaattAAaaww wwcAAGATAAAaattaaaATc... 13 7 7 7 10 16 12 10.2857 11
dyads_test_vs_ctrl_m1 dyads_test_vs_ctrl_m2 dyads_test_vs_ctrl_m1 dyads_test_vs_ctrl_m2 0.778 0.599 1.410 0.137 0.952 1.9190 0.95102 20 26 20 26 0.7692 1.0000 0.7692 R -6 wwTATCwwwwhwdwyATCww ......WKDWTMWWWWWWWWWATCWW 12 8 14 13 8 9 10 10.5714 12
oligos_6nt_test_vs_ctrl_m4 oligos_7nt_test_vs_ctrl_m5 oligos_6nt_test_vs_ctrl_m4 oligos_7nt_test_vs_ctrl_m5 0.763 0.477 4.051 0.466 0.919 2.4209 0.92665 24 15 15 24 0.6250 0.6250 1.0000 D 2 ..TTAGATGATAAAaat....... wwtaATGATAAAgww 16 12 5 8 14 14 15 12.0000 13
oligos_6nt_test_vs_ctrl_m3 oligos_6nt_test_vs_ctrl_m4 oligos_6nt_test_vs_ctrl_m3 oligos_6nt_test_vs_ctrl_m4 0.772 0.551 1.794 0.125 0.930 2.7999 0.94084 24 24 20 28 0.7143 0.8333 0.8333 R -4 wwaaTtTTTATCAGATAAAw.... ....TTAATTTTTATCATCTAAWW 14 11 13 14 13 15 13 13.2857 14
dyads_test_vs_ctrl_m1 oligos_7nt_test_vs_ctrl_m5 dyads_test_vs_ctrl_m1 oligos_7nt_test_vs_ctrl_m5 0.788 0.411 0.859 0.013 0.927 1.7593 0.92184 20 15 12 23 0.5217 0.6000 0.8000 R -3 wwTATCwwwwhw........ ...TTTATCATTAWW 11 16 15 15 16 7 14 13.4286 15
oligos_6nt_test_vs_ctrl_m1 oligos_7nt_test_vs_ctrl_m1 oligos_6nt_test_vs_ctrl_m1 oligos_7nt_test_vs_ctrl_m1 0.767 0.413 2.680 0.184 0.918 2.3088 0.92326 24 16 14 26 0.5385 0.5833 0.8750 R -2 aaTgAGATAAAaAt.......... ..TATCAGATAAAGWW 15 15 11 11 15 13 16 13.7143 16 
 Host name	biow
 Job started	2014-10-08.082933
 Job done	2014-10-08.082940
 Seconds	1.98
	user	1.98
	system	0.11
	cuser	4.35
;	csystem	0.71