/vh/rsat/rsat/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.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/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab
 Program version       	1.118
 Input files
	file2 	$RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf
	file1 	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_discovered.tf
 Output files
	alignments_1ton	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates_alignments_1ton.tab
	match_table_txt	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab
	html_index   	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates_alignments_1ton.html
	match_table_html	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.html
	prefix       	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates
 Matrices
	file1	17 matrices	$RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_discovered.tf
		file1	1	10	630	wwCTTTTCwh
		file1	2	10	792	wwAAATTAtw
		file1	3	12	1005	syCACTGCAmyc
		file1	4	13	849	ccAGGCTGGGCtc
		file1	5	11	1120	mkCCTCCCrms
		file1	6	10	6	CGCGCGCGCG
		file1	7	12	1277	dtATTTTTAdww
		file1	8	11	893	yyCTGCCTCmg
		file1	9	11	789	cyCTGTCTCwa
		file1	10	12	733	ccyCCACCTCss
		file1	11	12	730	wsaCTCTGTCtc
		...	7 more matrices
	file2	263 matrices	$RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.tf
		file2		1		11		26		wwyTGyGGTww
		file2		2		9		185		GCCcbrrGs
		file2		3		6		20		CACGTG
		file2		4		6		24		yGCGTG
		file2		5		22		24		hwwrGmACryyvtGTwCchrms
		file2		6		11		40		CTAGGTGTGAA
		file2		7		20		12		drvkcasygrwGcRkrrCsr
		file2		8		14		13		TGAmCTTTGmmCyt
		file2		9		12		16		bbkGrTGACGym
		file2		10		12		39		rrrTGCAATmcc
		file2		11		8		10		TTTsGCGC
		...	253 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
oligos_6nt_mkv4_m2 MA0075.1 oligos_6nt_mkv4_m2 Prrx2 0.998 0.499 8.498 0.498 0.998 0.0213 0.97938 10 5 5 10 0.5000 0.5000 1.0000 D 3 ...AATTA.. AATTA 1 15 4 7 1 1 1 4.2857 1
dyads_m4 MA0079.3 dyads_m4 SP1 0.865 0.560 8.778 0.561 0.933 1.4748 0.92193 17 11 11 17 0.6471 0.6471 1.0000 D 5 .....CCCCCRCCCCs. gCCCCkCCCCy 5 7 3 4 3 12 6 5.7143 2
dyads_m4 MA0079.2 dyads_m4 SP1 0.879 0.517 6.743 0.524 0.938 1.2343 0.92144 17 10 10 17 0.5882 0.5882 1.0000 D 6 ......CCCCRCCCCs. CCCCkCCCCC 4 12 10 6 4 7 3 6.5714 3
oligos_7nt_mkv5_m4 MA0130.1 oligos_7nt_mkv5_m4 ZNF354C 0.949 0.474 5.659 0.480 0.972 0.3357 0.93172 12 6 6 12 0.5000 0.5000 1.0000 D 1 .cyCCAC..... mTCCAC 2 20 14 10 2 2 2 7.4286 4
dyads_m4 MA0599.1 dyads_m4 KLF5 0.860 0.506 8.354 0.490 0.924 1.5115 0.91307 17 10 10 17 0.5882 0.5882 1.0000 D 5 .....CCCCCRCCCC.. gCCMCrCCCh 6 14 5 8 9 13 7 8.8571 5
dyads_m4 MA0162.2 dyads_m4 EGR1 0.816 0.515 6.724 0.489 0.917 1.9860 0.91696 17 14 12 19 0.6316 0.7059 0.8571 D 5 .....CCCCCRCCCCsv sccCCgCCCMCk.. 14 13 11 9 6 19 11 11.8571 6
oligos_6nt_mkv4_m2 MA0132.1 oligos_6nt_mkv4_m2 Pdx1 0.897 0.538 0.052 -0.147 0.937 0.7618 0.89714 10 6 6 10 0.6000 0.6000 1.0000 R 3 ...AATTAt. MATTAG 3 9 27 26 12 3 5 12.1429 7
oligos_6nt_mkv4_m5 MA0154.1 oligos_6nt_mkv4_m5 EBF1 0.859 0.430 2.370 0.268 0.937 0.8848 0.90498 11 10 7 14 0.5000 0.6364 0.7000 R 4 ....TCCCrms TCCCTKG... 7 24 20 18 11 4 4 12.5714 8
oligos_6nt_mkv4_m1 MA0152.1 oligos_6nt_mkv4_m1 NFATC2 0.811 0.568 6.389 0.551 0.896 1.4594 0.87797 10 7 7 10 0.7000 0.7000 1.0000 D 3 ...TTTTCwh TTTTCCA 15 6 12 5 23 11 17 12.7143 9
dyads_m1 MA0079.2 dyads_m1 SP1 0.822 0.483 5.411 0.472 0.918 1.6308 0.90970 17 10 10 17 0.5882 0.5882 1.0000 D 6 ......CCCAGCCCCs. CCCCkCCCCC 11 17 15 12 10 15 9 12.7143 10
oligos_7nt_mkv5_m1 MA0497.1 oligos_7nt_mkv5_m1 MEF2C 0.828 0.663 0.437 -0.188 0.924 1.8225 0.92045 12 15 12 15 0.8000 1.0000 0.8000 R -2 dtATTTTTAdww ..CTATTTTTRGMH. 10 2 25 27 5 16 8 13.2857 11
oligos_7nt_mkv5_m1 MA0052.1 oligos_7nt_mkv5_m1 MEF2A 0.782 0.652 9.521 0.612 0.877 2.4514 0.88929 12 10 10 12 0.8333 0.8333 1.0000 D 0 dtATTTTTAd.. CTATTTwTAG 21 4 2 3 16 25 23 13.4286 12
oligos_7nt_mkv5_m1 MA0052.2 oligos_7nt_mkv5_m1 MEF2A 0.816 0.653 2.905 0.033 0.916 2.0121 0.91641 12 15 12 15 0.8000 1.0000 0.8000 R -3 dtATTTTTAdww ...CTATTTTTRGMH 13 3 19 21 7 20 12 13.5714 13
dyads_m4 MA0516.1 dyads_m4 SP2 0.801 0.481 8.265 0.476 0.910 2.1643 0.91331 17 15 12 20 0.6000 0.7059 0.8000 D 5 .....CCCCCRCCCCsv gyCCCGCCyCyy... 17 18 6 11 8 21 14 13.5714 14
oligos_6nt_mkv4_m2 MA0158.1 oligos_6nt_mkv4_m2 HOXA5 0.833 0.530 2.201 0.105 0.914 1.2055 0.88909 10 8 7 11 0.6364 0.7000 0.8750 R 3 ...AATTAtw MATTWVH. 9 11 21 20 17 6 13 13.8571 15
oligos_6nt_mkv4_m5 MA0079.3 oligos_6nt_mkv4_m5 SP1 0.750 0.625 7.812 0.635 0.888 2.2487 0.89397 11 11 10 12 0.8333 0.9091 0.9091 D -1 mkCCTCCCrm. .CCCCkCCCCy 27 5 8 2 14 23 19 14.0000 16
positions_6nt MA0506.1 positions_6nt NRF1 0.760 0.691 10.568 0.669 0.840 3.1901 0.87371 10 11 10 11 0.9091 1.0000 0.9091 D -1 CGCGCGCGCG .CGCmTGCGCr 24 1 1 1 24 27 27 15.0000 17
oligos_6nt_mkv4_m5 MA0056.1 oligos_6nt_mkv4_m5 MZF1_1-4 0.839 0.458 0.098 -0.083 0.918 0.9880 0.88286 11 6 6 11 0.5455 0.5455 1.0000 R 4 ....TCCCrm. TCCCCR 8 22 26 24 19 5 10 16.2857 18
oligos_6nt_mkv4_m2 MA0151.1 oligos_6nt_mkv4_m2 ARID3A 0.795 0.477 6.375 0.451 0.883 1.3981 0.86065 10 6 6 10 0.6000 0.6000 1.0000 D 4 ....ATTAtw ATyAAA 19 19 13 14 26 9 22 17.4286 19
oligos_7nt_mkv5_m1 MA0465.1 oligos_7nt_mkv5_m1 CDX2 0.819 0.437 1.051 -0.020 0.904 1.5360 0.89045 12 11 8 15 0.5333 0.6667 0.7273 R 4 ....TTTTAdww TTTTATKR... 12 23 23 22 15 14 15 17.7143 20
oligos_6nt_mkv4_m2 MA0135.1 oligos_6nt_mkv4_m2 Lhx3 0.798 0.426 8.113 0.399 0.884 1.8507 0.87976 10 13 8 15 0.5333 0.8000 0.6154 D 2 ..AAATTAtw wAATTAAT..... 18 25 7 17 21 17 21 18.0000 21
oligos_7nt_mkv5_m4 MA0103.1 oligos_7nt_mkv5_m4 ZEB1 0.808 0.404 5.190 0.416 0.887 1.3505 0.86304 12 6 6 12 0.5000 0.5000 1.0000 D 4 ....CACCTC.. CACCTk 16 27 16 15 25 8 20 18.1429 22
oligos_7nt_mkv5_m2 MA0003.1 oligos_7nt_mkv5_m2 TFAP2A 0.773 0.416 5.145 0.401 0.896 1.4539 0.87820 11 9 7 13 0.5385 0.6364 0.7778 D 4 ....GCCTCmg GCCcbrr.. 22 26 17 16 22 10 16 18.4286 23
oligos_6nt_mkv4_m2 MA0485.1 oligos_6nt_mkv4_m2 Hoxc9 0.756 0.486 7.356 0.462 0.873 2.2790 0.88139 10 13 9 14 0.6429 0.9000 0.6923 D -4 wwAAATTAt. ....ATAAATCwy 26 16 9 13 20 24 25 19.0000 24
oligos_6nt_mkv4_m2 MA0063.1 oligos_6nt_mkv4_m2 Nkx2-5 0.765 0.536 2.977 0.115 0.864 1.9097 0.86040 10 7 7 10 0.7000 0.7000 1.0000 R 2 ..AAATTAt. CAMTTAW 23 10 18 19 27 18 26 20.1429 25
dyads_m4 MA0039.2 dyads_m4 Klf4 0.793 0.466 0.894 -0.092 0.889 2.2184 0.89468 17 10 10 17 0.5882 0.5882 1.0000 R 5 .....CCCCCRCCCC.. GCCMCRCCCW 20 21 24 25 13 22 18 20.4286 26
oligos_6nt_mkv4_m1 MA0029.1 oligos_6nt_mkv4_m1 Mecom 0.758 0.542 1.509 -0.029 0.875 2.5065 0.88805 10 14 10 14 0.7143 1.0000 0.7143 R -4 wwCTTTTCwh ....ATCTTRTCTT 25 8 22 23 18 26 24 20.8571 27 
 Host name	biow
 Job started	2014-10-08.084503
 Job done	2014-10-08.084539
 Seconds	26.69
	user	26.69
	system	0.42
	cuser	8.42
;	csystem	1.16