/vh/rsat/rsat/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_footprintDB.tab 
 compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5.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/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_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/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5.tf
 Output files
	alignments_1ton	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_footprintDB_alignments_1ton.tab
	match_table_txt	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_footprintDB.tab
	html_index   	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_footprintDB_index.html
	alignments_1ton_html	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_footprintDB_alignments_1ton.html
	match_table_html	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_footprintDB.html
	prefix       	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_footprintDB
 Matrices
	file1	1 matrices	$RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5.tf
		file1	1	12	43	dtAACCCGGAtg
	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
positions_8nt_m5 5241_ELF1_full_HumanTF_1.0_ positions_8nt_m5 5241_ELF1_full_HumanTF_1.0_ 0.875 0.625 6.444 0.593 0.932 1.3557 0.91767 12 12 10 14 0.7143 0.8333 0.8333 D 2 ..AACCCGGAtg AACCCGGAAG.. 8 4 6 4 6 14 10 7.4286 1
positions_8nt_m5 5801_SPDEF_DBD_1_HumanTF_1.0_ positions_8nt_m5 5801_SPDEF_DBD_1_HumanTF_1.0_ 0.896 0.576 6.197 0.552 0.947 0.9566 0.92316 12 11 9 14 0.6429 0.7500 0.8182 D 3 ...ACCCGGAtg AmCCGGATg.. 6 11 10 9 3 10 4 7.5714 2
positions_8nt_m5 2542_MA0280.1_JASPAR_CORE_2009_ positions_8nt_m5 2542_MA0280.1_JASPAR_CORE_2009_ 0.962 0.481 5.286 0.476 0.979 0.2526 0.94077 12 6 6 12 0.5000 0.5000 1.0000 D 5 .....CCGGAt. CCGGar 1 21 14 16 1 1 1 7.8571 3
positions_8nt_m5 5804_SPDEF_full_1_HumanTF_1.0_ positions_8nt_m5 5804_SPDEF_full_1_HumanTF_1.0_ 0.890 0.572 6.290 0.545 0.943 1.0305 0.92024 12 11 9 14 0.6429 0.7500 0.8182 D 3 ...ACCCGGAtg AmCCGGATg.. 7 13 8 11 4 11 7 8.7143 4
positions_8nt_m5 6044_1dux_F_3D-footprint_20130124_ positions_8nt_m5 6044_1dux_F_3D-footprint_20130124_ 0.932 0.544 3.997 0.523 0.972 0.3989 0.93620 12 7 7 12 0.5833 0.5833 1.0000 D 5 .....CCGGAtg cCGGAng 2 18 25 13 2 2 2 9.1429 5
positions_8nt_m5 5240_ELF1_DBD_HumanTF_1.0_ positions_8nt_m5 5240_ELF1_DBD_HumanTF_1.0_ 0.861 0.615 6.286 0.579 0.928 1.4413 0.91511 12 12 10 14 0.7143 0.8333 0.8333 D 2 ..AACCCGGAtg aACCCGGAAG.. 9 5 9 5 10 15 11 9.1429 6
positions_8nt_m5 5242_ELF3_DBD_HumanTF_1.0_ positions_8nt_m5 5242_ELF3_DBD_HumanTF_1.0_ 0.855 0.611 6.522 0.577 0.923 1.5308 0.91251 12 12 10 14 0.7143 0.8333 0.8333 D 2 ..AACCCGGAtg wACCCGGAAG.. 10 6 5 6 14 18 14 10.4286 7
positions_8nt_m5 2539_MA0275.1_JASPAR_CORE_2009_ positions_8nt_m5 2539_MA0275.1_JASPAR_CORE_2009_ 0.921 0.461 4.424 0.458 0.960 0.4845 0.91797 12 6 6 12 0.5000 0.5000 1.0000 D 5 .....CCGGAt. CCGGAw 3 24 22 19 5 3 3 11.2857 8
positions_8nt_m5 5244_ELF4_full_HumanTF_1.0_ positions_8nt_m5 5244_ELF4_full_HumanTF_1.0_ 0.846 0.604 6.024 0.563 0.920 1.5933 0.91074 12 12 10 14 0.7143 0.8333 0.8333 D 2 ..AACCCGGAtg aACCCGGAAG.. 13 7 11 7 16 20 16 12.8571 9
positions_8nt_m5 7494_MECP2_f1_HOCOMOCO_v9_ positions_8nt_m5 7494_MECP2_f1_HOCOMOCO_v9_ 0.897 0.449 5.318 0.456 0.943 0.6836 0.90256 12 6 6 12 0.5000 0.5000 1.0000 D 5 .....CCGGAt. CCGGrr 4 27 13 20 20 4 6 13.4286 10
positions_8nt_m5 5243_ELF3_full_HumanTF_1.0_ positions_8nt_m5 5243_ELF3_full_HumanTF_1.0_ 0.849 0.566 6.362 0.530 0.920 1.5986 0.91060 12 13 10 15 0.6667 0.8333 0.7692 D 2 ..AACCCGGAtg wACCCGGAAG... 12 16 7 12 17 21 17 14.5714 11
positions_8nt_m5 5239_EHF_full_HumanTF_1.0_ positions_8nt_m5 5239_EHF_full_HumanTF_1.0_ 0.832 0.594 5.347 0.553 0.920 1.6077 0.91034 12 12 10 14 0.7143 0.8333 0.8333 D 2 ..AACCCGGAtg wACCCGGAAG.. 18 8 12 8 18 22 18 14.8571 12
positions_8nt_m5 7366_ERG_f1_HOCOMOCO_v9_ positions_8nt_m5 7366_ERG_f1_HOCOMOCO_v9_ 0.896 0.418 4.791 0.417 0.945 0.7743 0.91111 12 10 7 15 0.4667 0.5833 0.7000 D 5 .....CCGGAtg CCGGAAr... 5 33 18 23 15 6 5 15.0000 13
positions_8nt_m5 1889_PB0024.1_JASPAR_CORE_2009_ positions_8nt_m5 1889_PB0024.1_JASPAR_CORE_2009_ 0.763 0.572 6.615 0.607 0.910 2.1710 0.91318 12 16 12 16 0.7500 1.0000 0.7500 D -1 dtAACCCGGAtg .mvwACCCGCATv... 31 14 3 2 12 34 22 16.8571 14
positions_8nt_m5 1869_MA0421.1_JASPAR_CORE_2009_ positions_8nt_m5 1869_MA0421.1_JASPAR_CORE_2009_ 0.787 0.656 8.133 0.634 0.882 2.3620 0.89133 12 10 10 12 0.8333 0.8333 1.0000 D 0 dtAACCCGGA.. TTTACCCGGm 23 1 1 1 25 37 33 17.2857 15
positions_8nt_m5 7360_ELK1_f1_HOCOMOCO_v9_ positions_8nt_m5 7360_ELK1_f1_HOCOMOCO_v9_ 0.850 0.458 3.086 0.437 0.936 0.9024 0.90404 12 8 7 13 0.5385 0.5833 0.8750 D 5 .....CCGGAtg CCGGAAr. 11 25 29 22 19 7 9 17.4286 16
positions_8nt_m5 3767_UP00070_UniPROBE_20120919_ positions_8nt_m5 3767_UP00070_UniPROBE_20120919_ 0.762 0.572 6.606 0.606 0.909 2.1762 0.91307 12 16 12 16 0.7500 1.0000 0.7500 D -1 dtAACCCGGAtg .mvwACCCGCATv... 33 15 4 3 13 35 23 18.0000 17
positions_8nt_m5 3735_UP00038_UniPROBE_20120919_ positions_8nt_m5 3735_UP00038_UniPROBE_20120919_ 0.776 0.582 4.519 0.466 0.918 1.9601 0.91750 12 16 12 16 0.7500 1.0000 0.7500 R -1 dtAACCCGGAtg .ARDATCCGGATG... 27 9 20 17 7 29 19 18.2857 18
positions_8nt_m5 1935_PB0077.1_JASPAR_CORE_2009_ positions_8nt_m5 1935_PB0077.1_JASPAR_CORE_2009_ 0.775 0.582 4.519 0.465 0.918 1.9669 0.91736 12 16 12 16 0.7500 1.0000 0.7500 R -1 dtAACCCGGAtg .ARWATCCGGATG... 28 10 21 18 8 30 20 19.2857 19
positions_8nt_m5 7355_EHF_si_HOCOMOCO_v9_ positions_8nt_m5 7355_EHF_si_HOCOMOCO_v9_ 0.786 0.561 4.957 0.519 0.904 1.9118 0.90223 12 12 10 14 0.7143 0.8333 0.8333 D 2 ..AACCCGGAtg wAcMmGGAAr.. 24 17 17 14 21 26 26 20.7143 20
positions_8nt_m5 2601_MA0363.1_JASPAR_CORE_2009_ positions_8nt_m5 2601_MA0363.1_JASPAR_CORE_2009_ 0.768 0.576 6.819 0.548 0.881 2.1346 0.88521 12 9 9 12 0.7500 0.7500 1.0000 D 0 dtAACCCGG... rTTACCCkg 30 12 2 10 29 31 34 21.1429 21
positions_8nt_m5 2487_MA0098.1_JASPAR_CORE_2009_ positions_8nt_m5 2487_MA0098.1_JASPAR_CORE_2009_ 0.841 0.421 0.238 -0.094 0.937 0.7502 0.89792 12 6 6 12 0.5000 0.5000 1.0000 R 6 ......CGGAtg MGGAWR 14 31 37 35 22 5 8 21.7143 22
positions_8nt_m5 4939_Eip74EF_DrosophilaTF_1.1_ positions_8nt_m5 4939_Eip74EF_DrosophilaTF_1.1_ 0.762 0.538 4.566 0.501 0.910 2.1607 0.91338 12 17 12 17 0.7059 1.0000 0.7059 D 0 dtAACCCGGAtg mgAAyCMGGAAr..... 34 19 19 15 11 33 21 21.7143 23
positions_8nt_m5 2420_MA0026.1_JASPAR_CORE_2009_ positions_8nt_m5 2420_MA0026.1_JASPAR_CORE_2009_ 0.814 0.475 3.947 0.447 0.908 1.2908 0.88524 12 7 7 12 0.5833 0.5833 1.0000 D 5 .....CCGGAtg CMGGAAr 20 22 26 21 28 12 24 21.8571 24
positions_8nt_m5 3995_UP00305_UniPROBE_20120919_ positions_8nt_m5 3995_UP00305_UniPROBE_20120919_ 0.797 0.461 1.660 0.050 0.925 1.6566 0.91726 12 18 11 19 0.5789 0.9167 0.6111 R -7 dtAACCCGGAt. .......KMSRCCCGRRW 21 23 33 33 9 24 12 22.1429 25
positions_8nt_m5 6163_1k79_A_3D-footprint_20130124_ positions_8nt_m5 6163_1k79_A_3D-footprint_20130124_ 0.839 0.419 0.288 -0.128 0.924 0.9060 0.88782 12 6 6 12 0.5000 0.5000 1.0000 R 6 ......CGGAtg CGGAAA 15 32 36 36 26 8 13 23.7143 26
positions_8nt_m5 6164_1k7a_A_3D-footprint_20130124_ positions_8nt_m5 6164_1k7a_A_3D-footprint_20130124_ 0.835 0.418 0.293 -0.129 0.922 0.9322 0.88622 12 6 6 12 0.5000 0.5000 1.0000 R 6 ......CGGAtg CGGAAA 16 34 35 37 27 9 15 24.7143 27
positions_8nt_m5 7373_ETS1_si_HOCOMOCO_v9_ positions_8nt_m5 7373_ETS1_si_HOCOMOCO_v9_ 0.784 0.422 3.525 0.396 0.908 1.2926 0.88515 12 8 7 13 0.5385 0.5833 0.8750 D 5 .....CCGGAtg cmGGAWg. 25 30 27 27 30 13 25 25.2857 28
positions_8nt_m5 2690_PF0003.1_JASPAR_CORE_2009_ positions_8nt_m5 2690_PF0003.1_JASPAR_CORE_2009_ 0.818 0.440 4.987 0.413 0.884 1.6263 0.87118 12 8 7 13 0.5385 0.5833 0.8750 D 5 .....CCGGAtg SCGGAAG. 19 28 16 25 36 23 32 25.5714 29
positions_8nt_m5 5368_GCM2_DBD_HumanTF_1.0_ positions_8nt_m5 5368_GCM2_DBD_HumanTF_1.0_ 0.753 0.627 2.654 0.276 0.893 2.1413 0.89653 12 10 10 12 0.8333 0.8333 1.0000 R 2 ..AACCCGGAtg YRCCCGCATV 36 2 31 29 23 32 29 26.0000 30
positions_8nt_m5 5365_GCM1_DBD_HumanTF_1.0_ positions_8nt_m5 5365_GCM1_DBD_HumanTF_1.0_ 0.752 0.627 2.703 0.265 0.886 2.2852 0.89311 12 10 10 12 0.8333 0.8333 1.0000 R 2 ..AACCCGGAtg TACCCGCATR 37 3 30 30 24 36 31 27.2857 31
positions_8nt_m5 2614_MA0380.1_JASPAR_CORE_2009_ positions_8nt_m5 2614_MA0380.1_JASPAR_CORE_2009_ 0.776 0.453 2.226 0.151 0.895 1.4698 0.87753 12 7 7 12 0.5833 0.5833 1.0000 R 4 ....CCCGGAt. YCCGGRR 26 26 32 32 33 16 27 27.4286 32
positions_8nt_m5 4969_gcm_DrosophilaTF_1.1_ positions_8nt_m5 4969_gcm_DrosophilaTF_1.1_ 0.788 0.525 3.378 0.245 0.880 1.9180 0.87759 12 8 8 12 0.6667 0.6667 1.0000 R 3 ...ACCCGGAt. RCCCGCAT 22 20 28 31 32 27 35 27.8571 33
positions_8nt_m5 5356_GABPA_full_HumanTF_1.0_ positions_8nt_m5 5356_GABPA_full_HumanTF_1.0_ 0.762 0.436 5.246 0.416 0.879 1.9432 0.87679 12 10 8 14 0.5714 0.6667 0.8000 D 4 ....CCCGGAtg aCCGGAAG.. 32 29 15 24 34 28 36 28.2857 34
positions_8nt_m5 2649_MA0430.1_JASPAR_CORE_2009_ positions_8nt_m5 2649_MA0430.1_JASPAR_CORE_2009_ 0.771 0.415 4.167 0.400 0.890 1.5406 0.87462 12 8 7 13 0.5385 0.5833 0.8750 D 5 .....CCGGAtg yCGGAGT. 29 36 24 26 35 19 30 28.4286 35
positions_8nt_m5 7361_ELK3_f1_HOCOMOCO_v9_ positions_8nt_m5 7361_ELK3_f1_HOCOMOCO_v9_ 0.756 0.403 4.254 0.373 0.894 1.6976 0.88484 12 11 8 15 0.5333 0.6667 0.7273 D 4 ....CCCGGAtg mChGGAAr... 35 37 23 28 31 25 28 29.5714 36
positions_8nt_m5 6730_4b06_A_3D-footprint_20130124_ positions_8nt_m5 6730_4b06_A_3D-footprint_20130124_ 0.835 0.417 1.421 0.018 0.876 1.4830 0.85648 12 6 6 12 0.5000 0.5000 1.0000 R 6 ......CGGAtg CGGAAG 17 35 34 34 37 17 37 30.1429 37 
 Host name	biow
 Job started	2014-09-05.203818
 Job done	2014-09-05.203900
 Seconds	31.8
	user	31.8
	system	0.79
	cuser	7.85
;	csystem	1.49