/home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_FlyFactorSurvey.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf -format2 tf -file2 data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.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 tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_FlyFactorSurvey
 Program version       	1.114
 Input files
	file2 	data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.tf
	file1 	tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf
 Output files
	alignments_1ton	tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_FlyFactorSurvey_alignments_1ton.tab
	match_table_txt	tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_FlyFactorSurvey.tab
	html_index   	tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_FlyFactorSurvey_index.html
	alignments_1ton_html	tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_FlyFactorSurvey_alignments_1ton.html
	output_prefix	tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_FlyFactorSurvey
	match_table_html	tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_FlyFactorSurvey.html
 Matrices
	file1	1 matrices	tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3.tf
	file2	470 matrices	data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.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
oligos_7nt_mkv5_m3 CG12029_SOLEXA_5_FBgn0035454 oligos_7nt_mkv5_m3 CG12029_SOLEXA_5_FBgn0035454 0.896 0.716 0.880 -0.075 0.956 1.0644 0.93921 12 15 12 15 0.8000 1.0000 0.8000 R -2 wsCCACdCmCac ..RRCCACACCCAY. 1 7 5 2 1 1 1 2.5714 1
oligos_7nt_mkv5_m3 CG9895_SOLEXA_5_FBgn0034810 oligos_7nt_mkv5_m3 CG9895_SOLEXA_5_FBgn0034810 0.876 0.803 0.412 -0.142 0.946 1.1782 0.93022 12 11 11 12 0.9167 0.9167 1.0000 R 0 wsCCACdCmCa. RRCCACRCCCA 3 1 6 6 3 3 3 3.5714 2
oligos_7nt_mkv5_m3 CG9895_SANGER_10_FBgn0034810 oligos_7nt_mkv5_m3 CG9895_SANGER_10_FBgn0034810 0.881 0.746 1.008 -0.170 0.948 1.1493 0.93109 12 12 11 13 0.8462 0.9167 0.9167 R 1 .sCCACdCmCac RCCACRCCCWH. 2 4 4 9 2 2 2 3.5714 3
oligos_7nt_mkv5_m3 CG3065_F1-5_SOLEXA_2.5_FBgn0034946 oligos_7nt_mkv5_m3 CG3065_F1-5_SOLEXA_2.5_FBgn0034946 0.850 0.728 1.503 -0.035 0.936 1.5433 0.92680 12 14 12 14 0.8571 1.0000 0.8571 R -1 wsCCACdCmCac .RRCCACGCCCMC. 6 5 1 1 4 5 4 3.7143 4
oligos_7nt_mkv5_m3 luna_SOLEXA_5_FBgn0040765 oligos_7nt_mkv5_m3 luna_SOLEXA_5_FBgn0040765 0.837 0.717 1.085 -0.079 0.935 1.5626 0.92634 12 14 12 14 0.8571 1.0000 0.8571 R 0 wsCCACdCmCac GRCCACGCCCWT.. 8 6 3 3 5 6 5 5.1429 5
oligos_7nt_mkv5_m3 CG12029_SANGER_10_FBgn0035454 oligos_7nt_mkv5_m3 CG12029_SANGER_10_FBgn0035454 0.865 0.793 0.144 -0.192 0.933 1.4648 0.92220 12 11 11 12 0.9167 0.9167 1.0000 R 1 .sCCACdCmCac RCCACACCCAC 4 2 9 10 7 4 6 6.0000 6
oligos_7nt_mkv5_m3 CG3065_F1-3_SOLEXA_2.5_FBgn0034946 oligos_7nt_mkv5_m3 CG3065_F1-3_SOLEXA_2.5_FBgn0034946 0.844 0.675 0.051 -0.153 0.930 1.6803 0.92362 12 15 12 15 0.8000 1.0000 0.8000 R -1 wsCCACdCmCac .ARCCACGCCCMC.. 7 8 12 7 6 7 7 7.7143 7
oligos_7nt_mkv5_m3 CG3065_F1-3_SANGER_2.5_FBgn0034946 oligos_7nt_mkv5_m3 CG3065_F1-3_SANGER_2.5_FBgn0034946 0.855 0.784 0.079 -0.218 0.922 1.7136 0.91585 12 11 11 12 0.9167 0.9167 1.0000 R 1 .sCCACdCmCac RCCACGCCCMC 5 3 11 11 8 8 8 7.7143 8
oligos_7nt_mkv5_m3 CG5669_SANGER_10_FBgn0039169 oligos_7nt_mkv5_m3 CG5669_SANGER_10_FBgn0039169 0.768 0.614 1.132 -0.092 0.899 2.4280 0.90818 12 15 12 15 0.8000 1.0000 0.8000 R -2 wsCCACdCmCac ..GRCCMCGCCCMY. 12 10 2 4 10 12 11 8.7143 9
oligos_7nt_mkv5_m3 sr_SOLEXA_5_FBgn0003499 oligos_7nt_mkv5_m3 sr_SOLEXA_5_FBgn0003499 0.782 0.489 0.322 -0.101 0.905 1.9056 0.90239 12 14 10 16 0.6250 0.8333 0.7143 R -4 wsCCACdCmC.. ....RCCCMCRCMM 11 12 7 5 11 9 10 9.2857 10
oligos_7nt_mkv5_m3 klu_SOLEXA_5_FBgn0013469 oligos_7nt_mkv5_m3 klu_SOLEXA_5_FBgn0013469 0.793 0.634 0.139 -0.165 0.915 2.0465 0.91570 12 15 12 15 0.8000 1.0000 0.8000 R -2 wsCCACdCmCac ..MMMCACCCMCRC. 10 9 10 8 9 10 9 9.2857 11
oligos_7nt_mkv5_m3 klu_SANGER_10_FBgn0013469 oligos_7nt_mkv5_m3 klu_SANGER_10_FBgn0013469 0.793 0.610 0.211 -0.227 0.892 2.1509 0.89630 12 11 10 13 0.7692 0.8333 0.9091 R 2 ..CCACdCmCac MCACCCMCRC. 9 11 8 12 12 11 12 10.7143 12 
 Host name	rsat
 Job started	2012_03_11.083931
 Job done	2012_03_11.083936
 Seconds	3.7
	user	3.7
	system	0.07
	cuser	1.71
;	csystem	0.19