/home/rsat/rsa-tools/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/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/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.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/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab
 Program version       	1.115
 Input files
	file2 	$RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.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_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates_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_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab
	html_index   	$RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates_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_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates_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_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates
	match_table_html	$RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.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	130 matrices	$RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.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
positions_7nt_m3 MA0137.2 positions_7nt_m3 STAT1 0.975 0.914 8.663 0.878 0.990 0.3072 0.97387 16 15 15 16 0.9375 0.9375 1.0000 R 0 srTTTCYwGGAArts. GRYTTCYDGGAARTG 1 1 5 2 1 1 1 1.7143 1
oligos_7nt_mkv4_m3 MA0137.2 oligos_7nt_mkv4_m3 STAT1 0.972 0.842 9.634 0.851 0.987 0.3293 0.96879 13 15 13 15 0.8667 1.0000 0.8667 D -1 ryTTCCmrGAAry .ayTTCChrGAAry. 2 3 1 3 3 2 2 2.2857 2
oligos_7nt_mkv4_m1 MA0137.2 oligos_7nt_mkv4_m1 STAT1 0.967 0.903 9.138 0.901 0.987 0.3723 0.96918 14 15 14 15 0.9333 1.0000 0.9333 D 0 srTTTCCwGGAAay cayTTCChrGAAry. 3 2 3 1 2 4 3 2.5714 3
positions_7nt_m3 MA0144.1 positions_7nt_m3 Stat3 0.963 0.602 9.169 0.595 0.980 0.3905 0.95581 16 10 10 16 0.6250 0.6250 1.0000 D 3 ...TTCYwGGAAr... TTCCaGGAAr 4 8 2 7 5 5 4 5.0000 4
positions_7nt_m1 MA0137.2 positions_7nt_m1 STAT1 0.945 0.675 7.824 0.676 0.979 0.6246 0.96275 21 15 15 21 0.7143 0.7143 1.0000 R 3 ...srTTTCCwGGAAats... GRYTTCYDGGAARTG 8 6 6 4 4 9 5 6.0000 5
oligos_7nt_mkv4_m1 MA0144.1 oligos_7nt_mkv4_m1 Stat3 0.948 0.677 8.999 0.673 0.973 0.5409 0.94800 14 10 10 14 0.7143 0.7143 1.0000 D 3 ...TTCCwGGAAa. TTCCaGGAAr 6 5 4 5 8 8 7 6.1429 6
oligos_7nt_mkv4_m2 MA0099.2 oligos_7nt_mkv4_m2 AP1 0.951 0.512 6.533 0.518 0.969 0.4408 0.93293 13 7 7 13 0.5385 0.5385 1.0000 R 3 ...TGAsTCA... TGAKTCA 5 12 13 8 10 6 9 9.0000 7
positions_7nt_m2 MA0137.2 positions_7nt_m2 STAT1 0.916 0.654 7.464 0.646 0.968 0.9732 0.95350 21 15 15 21 0.7143 0.7143 1.0000 D 3 ...satTTCCcrGAAATs... cayTTCChrGAAryc 12 7 8 6 6 16 10 9.2857 8
positions_7nt_m1 MA0144.1 positions_7nt_m1 Stat3 0.948 0.451 7.793 0.447 0.973 0.5313 0.94846 21 10 10 21 0.4762 0.4762 1.0000 D 6 ......TTCCwGGAAa..... TTCCaGGAAr 7 22 7 18 7 7 6 10.5714 9
positions_7nt_m3 MA0156.1 positions_7nt_m3 FEV 0.925 0.462 6.770 0.460 0.960 0.6460 0.92896 16 8 8 16 0.5000 0.5000 1.0000 D 6 ......YwGGAArt.. CAGGAArT 10 19 11 16 13 11 11 13.0000 10
oligos_7nt_mkv4_m3 MA0144.1 oligos_7nt_mkv4_m3 Stat3 0.922 0.709 4.339 0.204 0.957 0.8612 0.93438 13 10 10 13 0.7692 0.7692 1.0000 R 1 .yTTCCmrGAA.. YTTCCTGGAA 11 4 24 24 9 13 12 13.8571 11
oligos_7nt_mkv4_m1 MA0152.1 oligos_7nt_mkv4_m1 NFATC2 0.913 0.456 6.329 0.454 0.954 0.6387 0.91927 14 7 7 14 0.5000 0.5000 1.0000 D 1 .rTTTCCw...... TTTTCCA 13 20 14 17 16 10 13 14.7143 12
oligos_7nt_mkv4_m2 MA0089.1 oligos_7nt_mkv4_m2 NFE2L1::MafG 0.942 0.435 0.077 -0.104 0.972 0.3401 0.93127 13 6 6 13 0.4615 0.4615 1.0000 R 6 ......sTCATt. GTCATS 9 23 30 27 12 3 8 16.0000 13
oligos_7nt_mkv4_m3 MA0152.1 oligos_7nt_mkv4_m3 NFATC2 0.875 0.471 6.581 0.469 0.936 0.9009 0.90412 13 7 7 13 0.5385 0.5385 1.0000 D 0 ryTTCCm...... TTTTCCA 16 17 12 14 22 14 17 16.0000 14
oligos_7nt_mkv4_m1 MA0156.1 oligos_7nt_mkv4_m1 FEV 0.858 0.491 5.956 0.468 0.927 1.1611 0.90476 14 8 8 14 0.5714 0.5714 1.0000 D 6 ......CwGGAAay CAGGAArT 18 13 17 15 21 20 20 17.7143 15
oligos_7nt_mkv4_m3 MA0156.1 oligos_7nt_mkv4_m3 FEV 0.846 0.521 6.282 0.484 0.921 1.2635 0.90064 13 8 8 13 0.6154 0.6154 1.0000 D 5 .....CmrGAAry CAGGAArT 20 11 15 13 24 21 22 18.0000 16
positions_7nt_m2 MA0144.1 positions_7nt_m2 Stat3 0.906 0.432 2.935 0.118 0.953 0.9386 0.93149 21 10 10 21 0.4762 0.4762 1.0000 R 5 .....tTTCCcrGAA...... YTTCCTGGAA 14 25 25 25 11 15 14 18.4286 17
local_words_7nt_m3 MA0137.2 local_words_7nt_m3 STAT1 0.783 0.559 4.929 0.508 0.921 2.3817 0.92725 21 15 15 21 0.7143 0.7143 1.0000 D 3 ...CATTTyCmrgaAATG... cayTTCChrGAAryc 25 9 21 9 14 29 23 18.5714 18
positions_7nt_m3 MA0062.2 positions_7nt_m3 GABPA 0.822 0.483 7.163 0.488 0.919 1.6209 0.90997 16 11 10 17 0.5882 0.6250 0.9091 D 6 ......YwGGAArtsr CCGGAAGygv. 24 15 10 12 19 26 24 18.5714 19
local_words_7nt_m1 MA0137.2 local_words_7nt_m1 STAT1 0.778 0.556 4.892 0.505 0.917 2.5010 0.92545 21 15 15 21 0.7143 0.7143 1.0000 D 3 ...CATTTcchgkAAATG... cayTTCChrGAAryc 27 10 22 10 15 30 25 19.8571 20
oligos_7nt_mkv4_m1 MA0080.2 oligos_7nt_mkv4_m1 SPI1 0.855 0.427 5.088 0.423 0.929 0.9997 0.89900 14 7 7 14 0.5000 0.5000 1.0000 D 7 .......wGGAAay AGGAAGT 19 26 20 20 26 17 19 21.0000 21
positions_7nt_m3 MA0136.1 positions_7nt_m3 ELF5 0.834 0.469 0.177 -0.102 0.938 1.1110 0.91718 16 9 9 16 0.5625 0.5625 1.0000 R 6 ......YwGGAArts. MMGGAWRTW 23 18 28 26 17 19 16 21.0000 22
oligos_7nt_mkv4_m3 MA0080.2 oligos_7nt_mkv4_m3 SPI1 0.842 0.453 5.422 0.442 0.923 1.0815 0.89495 13 7 7 13 0.5385 0.5385 1.0000 D 6 ......mrGAAry AGGAAGT 22 21 18 19 29 18 21 21.1429 23
local_words_7nt_m1 MA0144.1 local_words_7nt_m1 Stat3 0.860 0.410 4.350 0.385 0.931 1.3745 0.91710 21 10 10 21 0.4762 0.4762 1.0000 D 6 ......TTcchgkAAA..... TTCCaGGAAr 17 28 23 23 18 23 18 21.4286 24
oligos_7nt_mkv4_m3 MA0098.1 oligos_7nt_mkv4_m3 ETS1 0.876 0.404 0.152 -0.109 0.945 0.6624 0.90408 13 6 6 13 0.4615 0.4615 1.0000 R 6 ......mrGAAr. MGGAWR 15 30 29 28 23 12 15 21.7143 25
oligos_7nt_mkv4_m3 MA0062.2 oligos_7nt_mkv4_m3 GABPA 0.845 0.422 7.243 0.402 0.915 1.3604 0.89691 13 11 8 16 0.5000 0.6154 0.7273 D 5 .....CmrGAAry CCGGAAGy... 21 27 9 21 27 22 26 21.8571 26
oligos_7nt_mkv4_m1 MA0136.1 oligos_7nt_mkv4_m1 ELF5 0.760 0.488 5.328 0.495 0.908 1.6506 0.89906 14 9 9 14 0.6429 0.6429 1.0000 D 0 srTTTCCwG..... waywTCCkk 29 14 19 11 25 27 29 22.0000 27
positions_7nt_m1 MA0062.2 positions_7nt_m1 GABPA 0.778 0.408 5.981 0.399 0.909 2.0038 0.90901 21 11 11 21 0.5238 0.5238 1.0000 D 9 .........CwGGAAatsAs. CCGGAAGygvc 26 29 16 22 20 28 28 24.1429 28
oligos_7nt_mkv4_m2 MA0067.1 oligos_7nt_mkv4_m2 Pax2 0.767 0.472 0.370 -0.142 0.914 1.3786 0.89622 13 8 8 13 0.6154 0.6154 1.0000 R 0 rwrTGAsT..... VMRTGACW 28 16 26 30 28 24 27 25.5714 29
oligos_7nt_mkv4_m3 MA0136.1 oligos_7nt_mkv4_m3 ELF5 0.758 0.433 0.210 -0.127 0.899 1.6080 0.88792 13 9 8 14 0.5714 0.6154 0.8889 R 5 .....CmrGAAry MMGGAWRT. 30 24 27 29 30 25 30 27.8571 30
 Host name	rsat
 Job started	2013-01-11.111101
 Job done	2013-01-11.111119
 Seconds	11.17
	user	11.17
	system	0.16
	cuser	6.87
;	csystem	0.37