/vh/rsat/rsat/public_html/tmp/apache/2014/09/06/peak-motifs.2014-09-06.011249_2014-09-06.011249_H1RYPN/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_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/dyads_m3/peak-motifs_dyads_m3.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/dyads_m3/peak-motifs_dyads_m3_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/dyads_m3/peak-motifs_dyads_m3.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/dyads_m3/peak-motifs_dyads_m3_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/dyads_m3/peak-motifs_dyads_m3_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/dyads_m3/peak-motifs_dyads_m3_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/dyads_m3/peak-motifs_dyads_m3_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/dyads_m3/peak-motifs_dyads_m3_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/dyads_m3/peak-motifs_dyads_m3_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/dyads_m3/peak-motifs_dyads_m3.tf
		file1	1	11	11	ymGATCAAAtw
	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
dyads_m3 2526_MA0151.1_JASPAR_CORE_2009_ dyads_m3 2526_MA0151.1_JASPAR_CORE_2009_ 0.887 0.484 8.694 0.469 0.920 0.9602 0.88452 11 6 6 11 0.5455 0.5455 1.0000 D 3 ...ATCAAA.. ATyAAA 5 17 5 9 22 5 7 10.0000 1
dyads_m3 1939_PB0082.1_JASPAR_CORE_2009_ dyads_m3 1939_PB0082.1_JASPAR_CORE_2009_ 0.799 0.517 8.434 0.552 0.903 2.1345 0.90608 11 17 11 17 0.6471 1.0000 0.6471 D -2 ymGATCAAAtw ..wasATCAAAGg.... 16 11 7 6 3 17 10 10.0000 2
dyads_m3 6733_4euw_A_3D-footprint_20130124_ dyads_m3 6733_4euw_A_3D-footprint_20130124_ 0.883 0.481 7.280 0.491 0.927 0.8773 0.88961 11 6 6 11 0.5455 0.5455 1.0000 D 4 ....TCAAAt. TcAAAg 6 18 12 8 20 4 5 10.4286 3
dyads_m3 5048_ZmHOX2a_2__Athamap_20091028_ dyads_m3 5048_ZmHOX2a_2__Athamap_20091028_ 0.940 0.598 0.123 -0.161 0.967 0.4560 0.93179 11 7 7 11 0.6364 0.6364 1.0000 R 0 ymGATCA.... CMGATCA 2 4 31 31 1 2 2 10.4286 4
dyads_m3 2653_MA0434.1_JASPAR_CORE_2009_ dyads_m3 2653_MA0434.1_JASPAR_CORE_2009_ 0.862 0.464 6.479 0.443 0.928 1.0135 0.89830 11 9 7 13 0.5385 0.6364 0.7778 D -2 ymGATCA.... ..ymrATCm 9 21 15 10 15 6 4 11.4286 5
dyads_m3 1940_PB0083.1_JASPAR_CORE_2009_ dyads_m3 1940_PB0083.1_JASPAR_CORE_2009_ 0.795 0.515 7.733 0.554 0.902 2.1605 0.90551 11 17 11 17 0.6471 1.0000 0.6471 D -2 ymGATCAAAtw ..wasWTCAAAGg.... 18 13 10 4 5 19 12 11.5714 6
dyads_m3 3755_UP00058_UniPROBE_20120919_ dyads_m3 3755_UP00058_UniPROBE_20120919_ 0.796 0.515 8.422 0.550 0.902 2.1652 0.90541 11 17 11 17 0.6471 1.0000 0.6471 D -2 ymGATCAAAtw ..wwsATCAAAGg.... 17 12 8 7 6 20 13 11.8571 7
dyads_m3 7482_LEF1_f1_HOCOMOCO_v9_ dyads_m3 7482_LEF1_f1_HOCOMOCO_v9_ 0.917 0.500 2.545 0.028 0.939 0.7262 0.89957 11 6 6 11 0.5455 0.5455 1.0000 R 3 ...ATCAAA.. WWCAAA 3 15 26 26 13 3 3 12.7143 8
dyads_m3 3751_UP00054_UniPROBE_20120919_ dyads_m3 3751_UP00054_UniPROBE_20120919_ 0.795 0.514 7.843 0.554 0.901 2.1670 0.90537 11 17 11 17 0.6471 1.0000 0.6471 D -2 ymGATCAAAtw ..wasWTCAAAGg.... 19 14 9 5 7 21 14 12.7143 9
dyads_m3 1795_MA0237.1_JASPAR_CORE_2009_ dyads_m3 1795_MA0237.1_JASPAR_CORE_2009_ 0.888 0.646 2.118 0.068 0.915 1.3602 0.89691 11 8 8 11 0.7273 0.7273 1.0000 R 2 ..GATCAAAt. KWTCAAAR 4 3 27 24 16 9 9 13.1429 10
dyads_m3 2329_CN0166.1_JASPAR_CORE_2009_ dyads_m3 2329_CN0166.1_JASPAR_CORE_2009_ 0.864 0.407 8.500 0.387 0.917 1.3229 0.89834 11 14 8 17 0.4706 0.7273 0.5714 D -6 ymGATCAA... ......GAGATCAA 7 32 6 18 14 8 8 13.2857 11
dyads_m3 6387_2a07_K_3D-footprint_20130124_ dyads_m3 6387_2a07_K_3D-footprint_20130124_ 0.958 0.436 0.093 -0.128 0.972 0.2820 0.92490 11 5 5 11 0.4545 0.4545 1.0000 R 5 .....CAAAt. CAAAT 1 25 33 30 2 1 1 13.2857 12
dyads_m3 3061_FNR_RegulonDB_7.5_ dyads_m3 3061_FNR_RegulonDB_7.5_ 0.863 0.406 6.313 0.409 0.924 1.2158 0.90254 11 14 8 17 0.4706 0.7273 0.5714 D -6 ymGATCAA... ......wayATCAA 8 33 16 17 11 7 6 14.0000 13
dyads_m3 5494_LEF1_DBD_HumanTF_1.0_ dyads_m3 5494_LEF1_DBD_HumanTF_1.0_ 0.777 0.570 11.529 0.608 0.876 2.7363 0.89367 11 15 11 15 0.7333 1.0000 0.7333 D -1 ymGATCAAAtw .AAGATCAAAGg... 21 5 1 3 17 29 23 14.1429 14
dyads_m3 3780_UP00083_UniPROBE_20120919_ dyads_m3 3780_UP00083_UniPROBE_20120919_ 0.803 0.520 3.634 0.097 0.902 2.1520 0.90570 11 17 11 17 0.6471 1.0000 0.6471 R -2 ymGATCAAAtw ..WASATCAAAGG.... 14 9 23 21 4 18 11 14.2857 15
dyads_m3 5900_Tcf7_DBD_HumanTF_1.0_ dyads_m3 5900_Tcf7_DBD_HumanTF_1.0_ 0.766 0.702 11.009 0.742 0.870 2.8493 0.89149 11 12 11 12 0.9167 1.0000 0.9167 D -1 ymGATCAAAtw .AASATCAAAGg 24 1 2 1 19 31 27 15.0000 16
dyads_m3 3764_UP00067_UniPROBE_20120919_ dyads_m3 3764_UP00067_UniPROBE_20120919_ 0.805 0.521 3.757 0.094 0.901 2.1757 0.90518 11 17 11 17 0.6471 1.0000 0.6471 R -2 ymGATCAAAtw ..WASATCAAAGG.... 12 7 22 22 9 23 16 15.8571 17
dyads_m3 2684_PB0084.1_JASPAR_CORE_2009_ dyads_m3 2684_PB0084.1_JASPAR_CORE_2009_ 0.801 0.518 3.622 0.097 0.901 2.1747 0.90520 11 17 11 17 0.6471 1.0000 0.6471 R -2 ymGATCAAAtw ..WASATCAAAGG.... 15 10 24 20 8 22 15 16.2857 18
dyads_m3 1904_PB0040.1_JASPAR_CORE_2009_ dyads_m3 1904_PB0040.1_JASPAR_CORE_2009_ 0.805 0.521 3.773 0.092 0.901 2.1768 0.90516 11 17 11 17 0.6471 1.0000 0.6471 R -2 ymGATCAAAtw ..WASATCAAAGG.... 13 8 21 23 10 24 17 16.5714 19
dyads_m3 5863_TCF7L1_full_HumanTF_1.0_ dyads_m3 5863_TCF7L1_full_HumanTF_1.0_ 0.750 0.688 10.294 0.720 0.863 3.0152 0.88838 11 12 11 12 0.9167 1.0000 0.9167 D -1 ymGATCAAAtw .AAGATCAAAGG 33 2 3 2 21 33 28 17.4286 20
dyads_m3 6753_6gat_A_3D-footprint_20130124_ dyads_m3 6753_6gat_A_3D-footprint_20130124_ 0.805 0.439 4.748 0.415 0.885 1.3769 0.86171 11 6 6 11 0.5455 0.5455 1.0000 D 1 .mGATCA.... CnATCA 11 24 18 16 29 10 20 18.2857 21
dyads_m3 7299_ARI3A_do_HOCOMOCO_v9_ dyads_m3 7299_ARI3A_do_HOCOMOCO_v9_ 0.781 0.409 4.796 0.423 0.895 2.3089 0.90232 11 21 11 21 0.5238 1.0000 0.5238 D -7 ymGATCAAAtw .......rrwATcWAAwt... 20 31 17 14 12 25 18 19.5714 22
dyads_m3 7300_ARI3A_f1_HOCOMOCO_v9_ dyads_m3 7300_ARI3A_f1_HOCOMOCO_v9_ 0.764 0.417 8.757 0.415 0.829 2.0579 0.83094 11 6 6 11 0.5455 0.5455 1.0000 D 3 ...ATCAAA.. ATTAAA 26 28 4 15 33 15 33 22.0000 23
dyads_m3 3893_UP00198_UniPROBE_20120919_ dyads_m3 3893_UP00198_UniPROBE_20120919_ 0.758 0.426 6.826 0.431 0.871 2.3132 0.88050 11 14 9 16 0.5625 0.8182 0.6429 D -5 ymGATCAAA.. .....ssmATCAaw 30 26 13 12 23 26 25 22.1429 24
dyads_m3 2872_PH0014.1_JASPAR_CORE_2009_ dyads_m3 2872_PH0014.1_JASPAR_CORE_2009_ 0.758 0.426 6.826 0.431 0.871 2.3132 0.88050 11 14 9 16 0.5625 0.8182 0.6429 D -5 ymGATCAAA.. .....ssmATCAaw 30 26 13 12 23 26 25 22.1429 25
dyads_m3 7604_RARG_f1_HOCOMOCO_v9_ dyads_m3 7604_RARG_f1_HOCOMOCO_v9_ 0.759 0.414 7.379 0.439 0.848 1.8216 0.84094 11 6 6 11 0.5455 0.5455 1.0000 D 1 .mGATCA.... AGKTCA 29 30 11 11 32 14 31 22.5714 26
dyads_m3 2255_CN0092.1_JASPAR_CORE_2009_ dyads_m3 2255_CN0092.1_JASPAR_CORE_2009_ 0.761 0.465 4.160 0.101 0.875 2.7440 0.89352 11 18 11 18 0.6111 1.0000 0.6111 R -5 ymGATCAAAtw .....CAAATCAAATT.. 28 20 20 19 18 30 24 22.7143 27
dyads_m3 2760_PF0073.1_JASPAR_CORE_2009_ dyads_m3 2760_PF0073.1_JASPAR_CORE_2009_ 0.828 0.452 0.121 -0.177 0.877 1.4711 0.85706 11 6 6 11 0.5455 0.5455 1.0000 R 4 ....TCAAAt. TCAAAG 10 23 32 32 30 11 22 22.8571 28
dyads_m3 2619_MA0389.1_JASPAR_CORE_2009_ dyads_m3 2619_MA0389.1_JASPAR_CORE_2009_ 0.776 0.452 1.017 0.016 0.884 1.6212 0.87138 11 8 7 12 0.5833 0.6364 0.8750 R -1 ymGATCA.... .KAGATCT 22 22 28 27 27 13 21 22.8571 29
dyads_m3 2559_MA0301.1_JASPAR_CORE_2009_ dyads_m3 2559_MA0301.1_JASPAR_CORE_2009_ 0.773 0.416 0.195 -0.115 0.885 1.6057 0.87200 11 9 7 13 0.5385 0.6364 0.7778 R -2 ymGATCA.... ..TRGATCT 23 29 30 29 26 12 19 24.0000 30
dyads_m3 1838_MA0326.1_JASPAR_CORE_2009_ dyads_m3 1838_MA0326.1_JASPAR_CORE_2009_ 0.764 0.555 2.550 -0.043 0.847 2.4465 0.86175 11 8 8 11 0.7273 0.7273 1.0000 R 1 .mGATCAAA.. YGAGCAAA 27 6 25 28 28 28 32 24.8571 31
dyads_m3 1793_MA0235.1_JASPAR_CORE_2009_ dyads_m3 1793_MA0235.1_JASPAR_CORE_2009_ 0.764 0.486 0.204 -0.181 0.850 2.1064 0.85339 11 7 7 11 0.6364 0.6364 1.0000 R 1 .mGATCAA... HAATCAA 25 16 29 33 31 16 30 25.7143 32
dyads_m3 2350_CN0187.1_JASPAR_CORE_2009_ dyads_m3 2350_CN0187.1_JASPAR_CORE_2009_ 0.755 0.472 4.329 0.067 0.854 2.9292 0.87898 11 15 10 16 0.6250 0.9091 0.6667 R -5 ymGATCAAAt. .....AAGAWCAAAG 32 19 19 25 25 32 29 25.8571 33 
 Host name	biow
 Job started	2014-09-06.011734
 Job done	2014-09-06.011811
 Seconds	29.82
	user	29.82
	system	0.59
	cuser	5.97
;	csystem	1.24