benchmark_result_slow.tab
 compare-matrices  -v 1 -file1 DemoCompMat.txt -file2 $RSAT/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -format transfac -lth Ncor2 0.7 -lth w 3 -mode profiles -return matrix_id,cor,Ncor,Ncor1,Ncor2,w,offset,strand -o benchmark_result_slow.tab
 Program version       	1.117
 Input files
	file2 	$RSAT/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf
	file1 	DemoCompMat.txt
 Output files
	match_table_txt	benchmark_result_slow.tab
	html_index   	benchmark_result_slow_index.html
	output_prefix	benchmark_result_slow
	match_table_html	benchmark_result_slow.html
 Matrices
	file1	6 matrices	DemoCompMat.txt
	file2	130 matrices	$RSAT/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf
	file1	1	12	392	tgCATrACAAwr
	file1	2	12	565	wtATGCAAATgw
	file1	3	11	246	wtATGyTAAtk
	file1	4	20	233	byCwTTGwyATGCAaATGdr
	file1	5	21	56	srTATGyGCATATGCAwATrw
	file1	6	11	663	AAAAAAAAAAA
	file2	1	9	185	GCCcbrrGs
	file2	2	6	20	CACGTG
	file2	3	6	24	yGCGTG
	file2	4	22	24	hwwrGmACryyvtGTwCchrms
	file2	5	11	40	CTAGGTGTGAA
	file2	6	20	12	drvkcasygrwGcRkrrCsr
	file2	7	14	13	TGAmCTTTGmmCyt
	file2	8	12	39	rrrTGCAATmcc
	file2	9	8	10	TTTsGCGC
	file2	10	11	23	TTAyGTAAyrt
	file2	11	11	10	waRTdRWkbyc
	file2	12	10	28	varcCGGAAr
	file2	13	14	27	aAGAyAAGATAAba
	file2	14	14	28	bmaasRTAAACAaw
	file2	15	8	20	GTAAACAw
	file2	16	8	16	vshvwGTA
	file2	17	8	23	wwdayATA
	file2	18	5	53	gGATr
	file2	19	6	63	wGATwg
	file2	20	10	53	ymAATCacwg
	file2	21	11	18	tAwTGTTTATw
	file2	22	12	47	gwwTRTTTdTTY
	file2	23	12	31	ksdTrTTTrTwT
	file2	24	12	18	krTTACryAAth
	file2	25	14	21	gGTTAATwwTTamc
	file2	26	12	54	gCGCAGCTGCKy
	file2	27	12	20	rAAAryGAAAsy
	file2	28	18	12	sGAAAGyGAAAsyrwwwm
	file2	29	10	58	CTATTTwTAG
	file2	30	12	16	mrrCArCwGswG
	file2	31	6	20	yGGGGA
	file2	32	10	16	bkAKGGGkrr
	file2	33	10	17	rrmCACGTGr
	file2	34	11	21	rAsCACGTGGt
	file2	35	16	116	myyrrCCAATsrgmrs
	file2	36	10	38	GGGrmTTyCC
	file2	37	7	17	wTAAktg
	file2	38	20	28	sTrGGTCAcsgTGACCyAcW
	file2	39	8	31	wgTCAykb
	file2	40	30	21	rAAwawwwkcmmmwacymcmcymmcmcymc
	file2	41	14	43	TTyACGCwTsAvTk
	file2	42	12	18	hcATCAATCAww
	file2	43	10	25	wwcwAGGTCA
	file2	44	14	36	wwwAwbTAGGTCAr
	file2	45	20	11	MCMCmAMmCAmCMmCmmmsm
	file2	46	15	10	RGGTCAwcGrGTTCA
	file2	47	5	59	AATTA
	file2	48	9	20	ACCGGAAGy
	file2	49	9	76	rAACAATrG
	file2	50	9	31	yhyATTGTs
	file2	51	7	49	wsmGGAA
	file2	52	12	46	GCCCWTATAwGG
	file2	53	9	28	kwwaACAAw
	file2	54	7	23	wAACAAT
	file2	55	20	10	bayyTCCCAkmaTkCmwyGm
	file2	56	6	34	sATGAC
	file2	57	12	12	yRCATTCCwsbg
	file2	58	12	44	mgAmCAKMTGkT
	file2	59	10	29	srTCTGGmwt
	file2	60	7	30	CACGTGr
	file2	61	6	17	rCCATc
	file2	62	6	40	ywTCCk
	file2	63	8	51	grCvGTTG
	file2	64	10	17	sGGrmwTTCC
	file2	65	6	41	CACCTk
	file2	66	11	18	GGGGrwyYCCC
	file2	67	20	17	msGRACATGyCCGGGCATGT
	file2	68	10	18	gGGraTTTCC
	file2	69	15	389	sTATAWAwrssssss
	file2	70	10	59	wwmCwTwkvt
	file2	71	11	12	RGGGTwwCAGc
	file2	72	18	9	rrrAacAtwmyGTyCtrw
	file2	73	13	67	rGgbCAAAGkyCa
	file2	74	17	25	AAAGGTCAAAGGTCAAc
	file2	75	15	33	gsmmCCyWrGGkkkm
	file2	76	8	15	GCTGAcks
	file2	77	14	16	TGGCAssrwGCCAA
	file2	78	9	24	ytrAGTRsm
	file2	79	7	20	aTACTTA
	file2	80	8	38	TAATTrsy
	file2	81	6	16	mTCCAC
	file2	82	10	20	bwACGTCCGc
	file2	83	6	31	cTAATk
	file2	84	7	43	mCAAcms
	file2	85	13	20	wAATTAATTAwyy
	file2	86	9	44	waywTCCkk
	file2	87	19	913	ygrCCAsyAGrkGGCrsyr
	file2	88	18	2949	ctgskgsggrswGATAAg
	file2	89	12	3656	rgsyCAAGGTCA
	file2	90	15	1369	ywTTswyATGCAaAt
	file2	91	15	669	cywTTGTyaTgcaaA
	file2	92	10	613	TTCCaGGAAr
	file2	93	14	4090	CCrGyyyrarCCrG
	file2	94	14	481	sssgsCbvGGCCTs
	file2	95	10	227	mgCACGTGGc
	file2	96	11	897	TGTTTrCwywg
	file2	97	18	105	GGAAGGAAGGAAGGAAGG
	file2	98	11	993	CCGGAAGygvc
	file2	99	11	4000	rsWGATAAgrr
	file2	100	10	4349	wGGGyGkGGc
	file2	101	21	1606	tTCAGcACCatGGACAGckcC
	file2	102	11	2000	ktyTGTGGttw
	file2	103	15	2085	cayTTCChrGAAryc
	file2	104	10	438	msCACGTGGc
	file2	105	12	811	TRTTTACwywgg
	file2	106	20	475	vkscmaGGtCAcccTGaCCy
	file2	107	15	864	strGGgcArAGGkcA
	file2	108	11	20	rTGACwmAGCA
	file2	109	6	27	ATyAAA
	file2	110	7	26	TTTTCCA
	file2	111	12	9	yyAATrwTTAAC
	file2	112	10	25	mCyCmaGGGA
	file2	113	12	24	TGymwGGGGkcr
	file2	114	8	13	CAGGAArT
	file2	115	8	13	kGTAAACA
	file2	116	8	16	CdbwAATk
	file2	117	17	23	rGkTCAysgrsAGKTCA
	file2	118	8	14	aAGGTCAc
	file2	119	6	6912	yTGGCa
	file2	120	11	15	yGCGTGGGcGk
	file2	121	14	18	GGGGCCcwmGGGGG
	file2	122	7	23	cAAGCTT
	file2	123	7	42	AGGAAGT
	file2	124	8	11	TGACGYcA
	file2	125	7	18	TGAmTCA
	file2	126	10	35	CCCCkCCCCC
	file2	127	9	18	TtkygCAAy
	file2	128	18	357	cwrGGTCAsgkTGmCCys
	file2	129	8	104	vbACGTGc
	file2	130	6	22	CwTTGT
 Threshold values
	Parameter      	Lower	Upper
	w              	3	none
	ncor2          	0.7	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	Ncor1        	Normalized correlation. Ncor1 = cor * w / w1
	8	Ncor2        	Normalized correlation. Ncor2 = cor * w / w2
	9	w1           	Width of the first matrix
	10	w2           	Width of the second matrix
	11	w            	Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset)
	12	W            	Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w
	13	Wr           	Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W
	14	wr1          	Alignment length relative to the width of the first matrix. wr1 = w/w1
	15	wr2          	Alignment length relative to the width of the second matrix. wr2 = w/w2
	16	strand       	"strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct;  R=reverse)
	17	offset       	shift of the second matrix relative to the first matrix (negative:left; positive: right)
	18	consensus1   	IUPAC consensus of matrix 1 (dots represent non-aligned columns)
	19	consensus2   	IUPAC consensus of matrix 2 (dots represent non-aligned columns)
id1 id2 name1 name2 cor Ncor Ncor1 Ncor2 w1 w2 w W Wr wr1 wr2 strand offset consensus1 consensus2
oligos_7nt_mkv5_m1 MA0067.1 oligos_7nt_mkv5_m1 Pax2 0.702 0.468 0.468 0.702 12 8 8 12 0.6667 0.6667 1.0000 R 1 .gCATrACA... VMRTGACW
oligos_7nt_mkv5_m1 MA0077.1 oligos_7nt_mkv5_m1 SOX9 0.790 0.486 0.527 0.702 12 9 8 13 0.6154 0.6667 0.8889 D 4 ....TrACAAwr rAACAATr.
oligos_7nt_mkv5_m1 MA0078.1 oligos_7nt_mkv5_m1 Sox17 0.914 0.457 0.533 0.711 12 9 7 14 0.5000 0.5833 0.7778 R 5 .....rACAAwr SACAATR..
oligos_7nt_mkv5_m1 MA0084.1 oligos_7nt_mkv5_m1 SRY 0.745 0.559 0.559 0.745 12 9 9 12 0.7500 0.7500 1.0000 D 2 ..CATrACAAw. kwwaACAAw
oligos_7nt_mkv5_m1 MA0087.1 oligos_7nt_mkv5_m1 Sox5 0.828 0.483 0.483 0.828 12 7 7 12 0.5833 0.5833 1.0000 D 4 ....TrACAAw. wAACAAT
oligos_7nt_mkv5_m1 MA0089.1 oligos_7nt_mkv5_m1 NFE2L1::MafG 0.842 0.421 0.421 0.842 12 6 6 12 0.5000 0.5000 1.0000 D 2 ..CATrAC.... sATGAC
oligos_7nt_mkv5_m1 MA0142.1 oligos_7nt_mkv5_m1 Pou5f1 0.944 0.755 0.944 0.755 12 15 12 15 0.8000 1.0000 0.8000 R -3 tgCATrACAAwr ...TGCATRWSAAWR
oligos_7nt_mkv5_m1 MA0143.1 oligos_7nt_mkv5_m1 Sox2 0.962 0.769 0.962 0.769 12 15 12 15 0.8000 1.0000 0.8000 R -2 tgCATrACAAwr ..TGCATRACAAWR.
oligos_7nt_mkv5_m1 MA0442.1 oligos_7nt_mkv5_m1 SOX10 0.945 0.472 0.472 0.945 12 6 6 12 0.5000 0.5000 1.0000 R 6 ......ACAAwr ACAAWG
oligos_7nt_mkv5_m2 MA0075.1 oligos_7nt_mkv5_m2 Prrx2 0.751 0.313 0.313 0.751 12 5 5 12 0.4167 0.4167 1.0000 D 7 .......AATgw AATTA
oligos_7nt_mkv5_m2 MA0132.1 oligos_7nt_mkv5_m2 Pdx1 0.752 0.376 0.376 0.752 12 6 6 12 0.5000 0.5000 1.0000 D 5 .....CAAATg. cTAATk
oligos_7nt_mkv5_m3 MA0075.1 oligos_7nt_mkv5_m3 Prrx2 0.886 0.403 0.403 0.886 11 5 5 11 0.4545 0.4545 1.0000 R 6 ......TAAtk TAATT
oligos_7nt_mkv5_m3 MA0132.1 oligos_7nt_mkv5_m3 Pdx1 0.928 0.506 0.506 0.928 11 6 6 11 0.5455 0.5455 1.0000 D 5 .....yTAAtk cTAATk
positions_7nt_m1 MA0077.1 positions_7nt_m1 SOX9 0.766 0.345 0.345 0.766 20 9 9 20 0.4500 0.4500 1.0000 R 1 .yCwTTGwyA.......... CYATTGTTY
positions_7nt_m1 MA0078.1 positions_7nt_m1 Sox17 0.845 0.380 0.380 0.845 20 9 9 20 0.4500 0.4500 1.0000 D 0 byCwTTGwy........... yhyATTGTs
positions_7nt_m1 MA0087.1 positions_7nt_m1 Sox5 0.807 0.282 0.282 0.807 20 7 7 20 0.3500 0.3500 1.0000 R 3 ...wTTGwyA.......... ATTGTTW
positions_7nt_m1 MA0089.1 positions_7nt_m1 NFE2L1::MafG 0.736 0.221 0.221 0.736 20 6 6 20 0.3000 0.3000 1.0000 R 6 ......GwyATG........ GTCATS
positions_7nt_m1 MA0095.1 positions_7nt_m1 YY1 0.756 0.227 0.227 0.756 20 6 6 20 0.3000 0.3000 1.0000 R 14 ..............aATGdr GATGGY
positions_7nt_m1 MA0142.1 positions_7nt_m1 Pou5f1 0.989 0.742 0.742 0.989 20 15 15 20 0.7500 0.7500 1.0000 D 2 ..CwTTGwyATGCAaAT... ywTTswyATGCAaAt
positions_7nt_m1 MA0143.1 positions_7nt_m1 Sox2 0.948 0.711 0.711 0.948 20 15 15 20 0.7500 0.7500 1.0000 D 1 .yCwTTGwyATGCAaA.... cywTTGTyaTgcaaA
positions_7nt_m1 MA0442.1 positions_7nt_m1 SOX10 0.947 0.284 0.284 0.947 20 6 6 20 0.3000 0.3000 1.0000 D 2 ..CwTTGw............ CwTTGT
positions_7nt_m2 MA0033.1 positions_7nt_m2 FOXL1 0.757 0.288 0.288 0.757 21 8 8 21 0.3810 0.3810 1.0000 R 10 ..........TATGCAwA... TATRTHWW
 Host name	caminante-6.local
 Job started	2013-03-05.165441
 Job done	2013-03-05.165444
 Seconds	3.41
	user	3.41
	system	0.02
	cuser	0
;	csystem	0