/vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_footprintDB.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.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/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_footprintDB
 Program version       	1.118
 Input files
	file2 	$RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf
	file1 	$RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2.tf
 Output files
	alignments_1ton	$RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_footprintDB_alignments_1ton.tab
	match_table_txt	$RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_footprintDB.tab
	html_index   	$RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_footprintDB_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_footprintDB_alignments_1ton.html
	match_table_html	$RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_footprintDB.html
	prefix       	$RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2_vs_db_footprintDB
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/oligos_6nt_mkv2/peak-motifs_oligos_6nt_mkv2.tf
		file1	1	11	5	taGATCAATrw
	file2	4196 matrices	$RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.tf
		file2		1		17		100		yyaymCATCAAwmwwmm
		file2		2		10		7		ACCGGAAGws
		file2		3		16		100		wwtksgTAATTACsdy
		file2		4		17		100		twrttaATTAwtaawwr
		file2		5		18		100		TCCGynnnnnnnnnCGGA
		file2		6		20		100		gwrastTTCCGGAAyrywrr
		file2		7		20		100		yrawygGyGCCGyrysackh
		file2		8		21		100		wmrmraAtmGAAGaaawawww
		file2		9		20		100		rkmkkakCACGTGmyyrvwy
		file2		10		6		1		CTATCA
		file2		11		18		66		hTTwCCwWAwwdGGhAat
		...	4186 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_mkv2 7424_HBP1_f1_HOCOMOCO_v9_ oligos_6nt_mkv2 7424_HBP1_f1_HOCOMOCO_v9_ 0.939 0.433 6.895 0.434 0.967 0.4000 0.92546 11 8 6 13 0.4615 0.5455 0.7500 D 5 .....CAATrw CAATgr.. 1 20 19 13 2 1 1 8.1429 1
oligos_6nt_mkv2 6530_3a01_E_3D-footprint_20130124_ oligos_6nt_mkv2 6530_3a01_E_3D-footprint_20130124_ 0.896 0.489 7.801 0.504 0.941 0.7118 0.90057 11 6 6 11 0.5455 0.5455 1.0000 D 5 .....CAATrw CAATtA 6 13 11 10 15 3 6 9.1429 2
oligos_6nt_mkv2 5763_SOX15_full_2_HumanTF_1.0_ oligos_6nt_mkv2 5763_SOX15_full_2_HumanTF_1.0_ 0.925 0.411 10.378 0.414 0.954 0.7301 0.92448 11 15 8 18 0.4444 0.7273 0.5333 D 3 ...ATCAATrw ATCAATAm....... 3 29 2 21 3 4 3 9.2857 3
oligos_6nt_mkv2 2784_PF0097.1_JASPAR_CORE_2009_ oligos_6nt_mkv2 2784_PF0097.1_JASPAR_CORE_2009_ 0.916 0.666 7.697 0.346 0.945 0.8854 0.91683 11 8 8 11 0.7273 0.7273 1.0000 R 2 ..GATCAATr. GATRAATR 5 4 14 28 5 6 5 9.5714 4
oligos_6nt_mkv2 5766_SOX18_full_2_HumanTF_1.0_ oligos_6nt_mkv2 5766_SOX18_full_2_HumanTF_1.0_ 0.921 0.410 10.470 0.424 0.954 0.7428 0.92382 11 15 8 18 0.4444 0.7273 0.5333 D 3 ...ATCAATrw ATCAATwk....... 4 32 1 17 4 5 4 9.5714 5
oligos_6nt_mkv2 5774_SOX2_DBD_3_HumanTF_1.0_ oligos_6nt_mkv2 5774_SOX2_DBD_3_HumanTF_1.0_ 0.886 0.420 10.258 0.408 0.933 1.2123 0.91350 11 17 9 19 0.4737 0.8182 0.5294 D 2 ..GATCAATrw rATCAATGk........ 7 23 3 22 6 9 7 11.0000 6
oligos_6nt_mkv2 1999_PB0144.1_JASPAR_CORE_2009_ oligos_6nt_mkv2 1999_PB0144.1_JASPAR_CORE_2009_ 0.818 0.562 7.711 0.585 0.914 1.8973 0.91146 11 16 11 16 0.6875 1.0000 0.6875 D -1 taGATCAATrw .wrsATCAATCr.... 15 6 13 4 8 20 12 11.1429 7
oligos_6nt_mkv2 5829_Sox3_DBD_2_HumanTF_1.0_ oligos_6nt_mkv2 5829_Sox3_DBD_2_HumanTF_1.0_ 0.884 0.419 10.178 0.419 0.931 1.2360 0.91265 11 17 9 19 0.4737 0.8182 0.5294 D 2 ..GATCAATrw sATCAATGt........ 8 24 4 18 7 10 8 11.2857 8
oligos_6nt_mkv2 5048_ZmHOX2a_2__Athamap_20091028_ oligos_6nt_mkv2 5048_ZmHOX2a_2__Athamap_20091028_ 0.926 0.589 0.139 -0.157 0.961 0.5430 0.92556 11 7 7 11 0.6364 0.6364 1.0000 R 0 taGATCA.... CMGATCA 2 5 34 33 1 2 2 11.2857 9
oligos_6nt_mkv2 2042_PB0188.1_JASPAR_CORE_2009_ oligos_6nt_mkv2 2042_PB0188.1_JASPAR_CORE_2009_ 0.814 0.559 7.045 0.586 0.913 1.9228 0.91086 11 16 11 16 0.6875 1.0000 0.6875 D -1 taGATCAATrw .drsWTCAATCr.... 16 7 18 3 9 21 13 12.4286 10
oligos_6nt_mkv2 5197_CUX1_DBD_3_HumanTF_1.0_ oligos_6nt_mkv2 5197_CUX1_DBD_3_HumanTF_1.0_ 0.792 0.720 9.238 0.710 0.893 2.1482 0.89636 11 10 10 11 0.9091 0.9091 1.0000 D 1 .aGATCAATrw TrATCrATam 20 1 6 1 18 28 21 13.5714 11
oligos_6nt_mkv2 5776_SOX2_full_2_HumanTF_1.0_ oligos_6nt_mkv2 5776_SOX2_full_2_HumanTF_1.0_ 0.870 0.412 9.016 0.406 0.922 1.3993 0.90706 11 17 9 19 0.4737 0.8182 0.5294 R 2 ..GATCAATrw KATCAATGK........ 9 28 7 23 10 13 9 14.1429 12
oligos_6nt_mkv2 2653_MA0434.1_JASPAR_CORE_2009_ oligos_6nt_mkv2 2653_MA0434.1_JASPAR_CORE_2009_ 0.845 0.455 6.405 0.438 0.921 1.1002 0.89404 11 9 7 13 0.5385 0.6364 0.7778 D -2 taGATCA.... ..ymrATCm 13 16 22 12 19 8 10 14.2857 13
oligos_6nt_mkv2 5199_CUX2_DBD_2_HumanTF_1.0_ oligos_6nt_mkv2 5199_CUX2_DBD_2_HumanTF_1.0_ 0.768 0.698 8.936 0.681 0.880 2.4073 0.89029 11 10 10 11 0.9091 0.9091 1.0000 D 1 .aGATCAATrw TrATCRATaa 26 2 8 2 21 33 27 17.0000 14
oligos_6nt_mkv2 1000_UP00185_UniPROBE_20120919_ oligos_6nt_mkv2 1000_UP00185_UniPROBE_20120919_ 0.780 0.505 6.380 0.516 0.899 2.2270 0.90407 11 17 11 17 0.6471 1.0000 0.6471 D -3 taGATCAATrw ...ymCATCAAwmw... 21 10 23 8 13 29 18 17.4286 15
oligos_6nt_mkv2 2984_PH0134.1_JASPAR_CORE_2009_ oligos_6nt_mkv2 2984_PH0134.1_JASPAR_CORE_2009_ 0.780 0.505 6.380 0.516 0.899 2.2270 0.90407 11 17 11 17 0.6471 1.0000 0.6471 D -3 taGATCAATrw ...ymCATCAAwmw... 21 10 23 8 13 29 18 17.4286 16
oligos_6nt_mkv2 5195_CUX1_DBD_1_HumanTF_1.0_ oligos_6nt_mkv2 5195_CUX1_DBD_1_HumanTF_1.0_ 0.854 0.405 7.521 0.397 0.920 1.4468 0.90550 11 17 9 19 0.4737 0.8182 0.5294 D -8 taGATCAAT.. ........strATCrAT 11 34 16 25 12 15 11 17.7143 17
oligos_6nt_mkv2 2329_CN0166.1_JASPAR_CORE_2009_ oligos_6nt_mkv2 2329_CN0166.1_JASPAR_CORE_2009_ 0.850 0.400 8.262 0.376 0.910 1.4456 0.89373 11 14 8 17 0.4706 0.7273 0.5714 D -6 taGATCAA... ......GAGATCAA 12 35 9 27 20 14 14 18.7143 18
oligos_6nt_mkv2 6138_1j5n_A_3D-footprint_20130124_ oligos_6nt_mkv2 6138_1j5n_A_3D-footprint_20130124_ 0.773 0.492 9.628 0.518 0.854 2.0478 0.85545 11 7 7 11 0.6364 0.6364 1.0000 D 3 ...ATCAATr. AACAATc 24 12 5 7 31 25 31 19.2857 19
oligos_6nt_mkv2 3788_UP00091_UniPROBE_20120919_ oligos_6nt_mkv2 3788_UP00091_UniPROBE_20120919_ 0.753 0.517 7.714 0.528 0.884 2.5561 0.89723 11 16 11 16 0.6875 1.0000 0.6875 D -2 taGATCAATrw ..drgAACAATwa... 32 8 12 5 17 35 26 19.2857 20
oligos_6nt_mkv2 2682_PB0072.1_JASPAR_CORE_2009_ oligos_6nt_mkv2 2682_PB0072.1_JASPAR_CORE_2009_ 0.753 0.517 7.665 0.527 0.884 2.5547 0.89725 11 16 11 16 0.6875 1.0000 0.6875 D -2 taGATCAATrw ..drgAACAATwa... 33 9 15 6 16 34 25 19.7143 21
oligos_6nt_mkv2 7440_HNF6_f1_HOCOMOCO_v9_ oligos_6nt_mkv2 7440_HNF6_f1_HOCOMOCO_v9_ 0.805 0.681 0.872 -0.173 0.905 2.0928 0.90701 11 13 11 13 0.8462 1.0000 0.8462 R -2 taGATCAATrw ..WAARTCAATAW 17 3 30 35 11 26 16 19.7143 22
oligos_6nt_mkv2 7627_SOX10_si_HOCOMOCO_v9_ oligos_6nt_mkv2 7627_SOX10_si_HOCOMOCO_v9_ 0.801 0.437 5.845 0.418 0.894 1.2695 0.86722 11 6 6 11 0.5455 0.5455 1.0000 D 5 .....CAATrw CAAwGr 19 19 27 19 28 11 20 20.4286 23
oligos_6nt_mkv2 6753_6gat_A_3D-footprint_20130124_ oligos_6nt_mkv2 6753_6gat_A_3D-footprint_20130124_ 0.803 0.438 4.707 0.416 0.888 1.3459 0.86328 11 6 6 11 0.5455 0.5455 1.0000 D 1 .aGATCA.... CnATCA 18 18 28 20 29 12 23 21.1429 24
oligos_6nt_mkv2 3061_FNR_RegulonDB_7.5_ oligos_6nt_mkv2 3061_FNR_RegulonDB_7.5_ 0.863 0.406 6.281 0.405 0.902 1.5678 0.88933 11 14 8 17 0.4706 0.7273 0.5714 R -6 taGATCAA... ......TWRATCAA 10 33 26 24 22 17 17 21.2857 25
oligos_6nt_mkv2 1741_MA0182.1_JASPAR_CORE_2009_ oligos_6nt_mkv2 1741_MA0182.1_JASPAR_CORE_2009_ 0.826 0.413 0.779 -0.103 0.909 1.0956 0.87665 11 7 6 12 0.5000 0.5455 0.8571 R 5 .....CAATrw YAATWA. 14 27 32 31 25 7 15 21.5714 26
oligos_6nt_mkv2 7634_SOX5_f1_HOCOMOCO_v9_ oligos_6nt_mkv2 7634_SOX5_f1_HOCOMOCO_v9_ 0.767 0.488 6.350 0.491 0.857 2.0035 0.85702 11 7 7 11 0.6364 0.6364 1.0000 D 3 ...ATCAATr. AACAATr 27 14 25 11 30 24 30 23.0000 27
oligos_6nt_mkv2 3893_UP00198_UniPROBE_20120919_ oligos_6nt_mkv2 3893_UP00198_UniPROBE_20120919_ 0.761 0.428 6.819 0.429 0.876 2.2370 0.88249 11 14 9 16 0.5625 0.8182 0.6429 D -5 taGATCAAT.. .....ssmATCAaw 28 21 20 15 23 31 28 23.7143 28
oligos_6nt_mkv2 2872_PH0014.1_JASPAR_CORE_2009_ oligos_6nt_mkv2 2872_PH0014.1_JASPAR_CORE_2009_ 0.761 0.428 6.819 0.429 0.876 2.2370 0.88249 11 14 9 16 0.5625 0.8182 0.6429 D -5 taGATCAAT.. .....ssmATCAaw 28 21 20 15 23 31 28 23.7143 29
oligos_6nt_mkv2 2619_MA0389.1_JASPAR_CORE_2009_ oligos_6nt_mkv2 2619_MA0389.1_JASPAR_CORE_2009_ 0.771 0.450 0.785 -0.004 0.885 1.6162 0.87158 11 8 7 12 0.5833 0.6364 0.8750 R -1 taGATCA.... .KAGATCT 25 17 31 30 27 18 24 24.5714 30
oligos_6nt_mkv2 2559_MA0301.1_JASPAR_CORE_2009_ oligos_6nt_mkv2 2559_MA0301.1_JASPAR_CORE_2009_ 0.776 0.418 0.126 -0.106 0.890 1.5448 0.87445 11 9 7 13 0.5385 0.6364 0.7778 R -2 taGATCA.... ..TRGATCT 23 25 35 32 26 16 22 25.5714 31
oligos_6nt_mkv2 7604_RARG_f1_HOCOMOCO_v9_ oligos_6nt_mkv2 7604_RARG_f1_HOCOMOCO_v9_ 0.752 0.410 7.248 0.429 0.846 1.8446 0.83994 11 6 6 11 0.5455 0.5455 1.0000 D 1 .aGATCA.... AGKTCA 34 30 17 14 33 19 33 25.7143 32
oligos_6nt_mkv2 2526_MA0151.1_JASPAR_CORE_2009_ oligos_6nt_mkv2 2526_MA0151.1_JASPAR_CORE_2009_ 0.758 0.414 8.186 0.386 0.834 1.9973 0.83345 11 6 6 11 0.5455 0.5455 1.0000 D 3 ...ATCAAT.. ATyAAA 31 26 10 26 35 23 35 26.5714 33
oligos_6nt_mkv2 1793_MA0235.1_JASPAR_CORE_2009_ oligos_6nt_mkv2 1793_MA0235.1_JASPAR_CORE_2009_ 0.759 0.483 0.148 -0.170 0.848 2.1244 0.85277 11 7 7 11 0.6364 0.6364 1.0000 R 1 .aGATCAA... HAATCAA 30 15 33 34 32 27 32 29.0000 34
oligos_6nt_mkv2 2670_MF0011.1_JASPAR_CORE_2009_ oligos_6nt_mkv2 2670_MF0011.1_JASPAR_CORE_2009_ 0.751 0.410 1.677 0.106 0.835 1.9840 0.83400 11 6 6 11 0.5455 0.5455 1.0000 R 3 ...ATCAAT.. AACAAW 35 31 29 29 34 22 34 30.5714 35 
 Host name	biow
 Job started	2014-09-06.011407
 Job done	2014-09-06.011454
 Seconds	31.81
	user	31.82
	system	0.95
	cuser	12.37
;	csystem	1.49