; compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/06/18/compare-matrices_2026-06-18.161301_2OKU9J/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -format2 tf -strand DR -lth cor 0.7 -lth Ncor 0.4 -uth match_rank 50 -return cor,Ncor,logoDP,NsEucl,NSW,match_rank,matrix_id,matrix_name,width,strand,offset,consensus,alignments_1ton -o $RSAT/public_html/tmp/www-data/2026/06/18/compare-matrices_2026-06-18.161301_2OKU9J/compare-matrices.tab
; Program version       	1.118
; Slow mode 
; Input files
;	file2 	/var/www/html/rsat/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf
;	file1 	/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/compare-matrices_2026-06-18.161301_2OKU9J/compare-matrices_query_matrices.transfac
; Output files
;	prefix       	/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/compare-matrices_2026-06-18.161301_2OKU9J/compare-matrices
;	match_table_html	/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/compare-matrices_2026-06-18.161301_2OKU9J/compare-matrices.html
;	alignments_1ton_html	/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/compare-matrices_2026-06-18.161301_2OKU9J/compare-matrices_alignments_1ton.html
;	html_index   	/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/compare-matrices_2026-06-18.161301_2OKU9J/compare-matrices_index.html
;	alignments_1ton	/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/compare-matrices_2026-06-18.161301_2OKU9J/compare-matrices_alignments_1ton.tab
;	match_table_txt	/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/compare-matrices_2026-06-18.161301_2OKU9J/compare-matrices.tab
; Matrices
;	file1	1 matrices	/var/www/html/rsat/public_html/tmp/www-data/2026/06/18/compare-matrices_2026-06-18.161301_2OKU9J/compare-matrices_query_matrices.transfac
;		file1	1	14	2524	hhwAAACCCTArww
;	file2	3463 matrices	/var/www/html/rsat/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf
;		file2		1		8		5		awmAGTTr
;		file2		2		8		3		rkTAGTTr
;		file2		3		8		5		wamaGTTr
;		file2		4		8		1		GTTAGTTA
;		file2		5		8		2		kwCwGTTr
;		file2		6		8		2		GTTAGTTr
;		file2		7		8		6		wwmaGTTr
;		file2		8		8		2		rsTkGTTr
;		file2		9		8		8		RkTwGKTr
;		file2		10		8		1		TACTGTTG
;		file2		11		8		4		WhhWGTTr
;		...	3453 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	NSW          	Normalized Sandelin-Wasserman similarity. NSW = SW/w
;	9	NsEucl       	relative Euclidian similarity. NsEucl = (max(dEucl) - dEucl)/max(dEucl)
;	10	w1           	Width of the first matrix
;	11	w2           	Width of the second matrix
;	12	w            	Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset)
;	13	W            	Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w
;	14	Wr           	Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W
;	15	wr1          	Alignment length relative to the width of the first matrix. wr1 = w/w1
;	16	wr2          	Alignment length relative to the width of the second matrix. wr2 = w/w2
;	17	strand       	"strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct;  R=reverse)
;	18	offset       	shift of the second matrix relative to the first matrix (negative:left; positive: right)
;	19	consensus1   	IUPAC consensus of matrix 1 (dots represent non-aligned columns)
;	20	consensus2   	IUPAC consensus of matrix 2 (dots represent non-aligned columns)
;	21	rcor         	Matching rank for cor
;	22	rNcor        	Matching rank for Ncor
;	23	rlogoDP      	Matching rank for logoDP
;	24	rNsEucl      	Matching rank for NsEucl
;	25	rNSW         	Matching rank for NSW
;	26	rank_mean    	Mean of the matching ranks on all selected metrics
;	27	match_rank   	Rank of the match (sorting by rank_mean)
#id1	id2	name1	name2	cor	Ncor	logoDP	NSW	NsEucl	w1	w2	w	W	Wr	wr1	wr2	strand	offset	consensus1	consensus2	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank
oligos_6nt_mkv4_m1	TRB1_MA2032.1_JASPAR	oligos_6nt_mkv4_m1	TRB1:MA2032.1:JASPAR	0.979	0.769	7.108	0.991	0.97100	14	11	11	14	0.7857	0.7857	1.0000	D	2	..wAAACCCTArw.	aaAACCCTArw                   	2	4	4	1	2	2.6000	1
oligos_6nt_mkv4_m1	TRB1_MA2032.2_JASPAR	oligos_6nt_mkv4_m1	TRB1:MA2032.2:JASPAR	0.985	0.633	7.105	0.992	0.96987	14	9	9	14	0.6429	0.6429	1.0000	D	3	...AAACCCTAr..	aAACCCTAr                     	1	13	5	2	1	4.4000	2
oligos_6nt_mkv4_m1	TBP3_MA1355.1_JASPAR	oligos_6nt_mkv4_m1	TBP3:MA1355.1:JASPAR	0.894	0.835	7.074	0.961	0.94751	14	15	14	15	0.9333	1.0000	0.9333	D	-1	hhwAAACCCTArww	.wwtwwrCCCTAAwt               	11	2	6	8	9	7.2000	3
oligos_6nt_mkv4_m1	TRB2_MA1355.2_JASPAR	oligos_6nt_mkv4_m1	TRB2:MA1355.2:JASPAR	0.897	0.705	7.068	0.954	0.93507	14	11	11	14	0.7857	0.7857	1.0000	D	3	...AAACCCTArww	wwrCCCTAAwt                   	10	6	7	10	11	8.8000	4
oligos_6nt_mkv4_m1	AT1G72740_MA1353.1_JASPAR	oligos_6nt_mkv4_m1	AT1G72740:MA1353.1:JASPAR	0.962	0.781	0.490	0.981	0.96153	14	15	13	16	0.8125	0.9286	0.8667	R	1	.hwAAACCCTArww	MWAAACCCTAAWY..               	5	3	35	4	4	10.2000	5
oligos_6nt_mkv4_m1	PNRC2_UN0276.1_JASPAR	oligos_6nt_mkv4_m1	PNRC2:UN0276.1:JASPAR	0.961	0.549	6.584	0.978	0.94785	14	8	8	14	0.5714	0.5714	1.0000	D	3	...AAACCCTA...	AAWMCCTA                      	6	24	9	7	6	10.4000	6
oligos_6nt_mkv4_m1	AT1G72740_MA1353.2_JASPAR	oligos_6nt_mkv4_m1	AT1G72740:MA1353.2:JASPAR	0.967	0.760	0.487	0.980	0.95788	14	11	11	14	0.7857	0.7857	1.0000	R	3	...AAACCCTArww	AAACCCTAAWY                   	3	5	36	5	5	10.8000	7
oligos_6nt_mkv4_m1	TBP3.ampDAP_M0621_AthalianaCistrome	oligos_6nt_mkv4_m1	TBP3.ampDAP:M0621:AthalianaCistrome	0.922	0.680	0.366	0.972	0.95530	14	19	14	19	0.7368	1.0000	0.7368	R	-4	hhwAAACCCTArww	....HHTAARCCCTAAWY.           	9	7	40	6	8	14.0000	8
oligos_6nt_mkv4_m1	AT1G72740.ampDAP_M0588_AthalianaCistrome	oligos_6nt_mkv4_m1	AT1G72740.ampDAP:M0588:AthalianaCistrome	0.965	0.570	0.278	0.984	0.96491	14	21	13	22	0.5909	0.9286	0.6190	R	1	.hwAAACCCTArww	MWAAACCCTAAWY........         	4	20	41	3	3	14.2000	9
oligos_6nt_mkv4_m1	1200010153_M1391_1.02_CISBP	oligos_6nt_mkv4_m1	1200010153:M1391_1.02:CISBP	0.882	0.630	5.269	0.952	0.93044	14	10	10	14	0.7143	0.7143	1.0000	D	4	....AACCCTArww	amCCCTAryy   	15	14	18	12	12	14.2000	10
oligos_6nt_mkv4_m1	MYBR101_SMH1_B73_1_m1_EEAD0453_EEADannot	oligos_6nt_mkv4_m1	MYBR101_SMH1_B73_1_m1:EEAD0453:EEADannot	0.854	0.671	6.560	0.937	0.92424	14	11	11	14	0.7857	0.7857	1.0000	D	1	.hwAAACCCTAr..	cywWrCCCTAr                   	21	8	10	16	16	14.2000	11
oligos_6nt_mkv4_m1	TRP5_MA1802.1_JASPAR	oligos_6nt_mkv4_m1	TRP5:MA1802.1:JASPAR	0.892	0.637	3.124	0.958	0.93483	14	10	10	14	0.7143	0.7143	1.0000	D	0	hhwAAACCCT....	swwAAACCyy                    	13	11	31	11	10	15.2000	12
oligos_6nt_mkv4_m1	LOC_Os01g51154_M1361_1.02_CISBP	oligos_6nt_mkv4_m1	LOC_Os01g51154:M1361_1.02:CISBP	0.872	0.623	4.354	0.948	0.92810	14	10	10	14	0.7143	0.7143	1.0000	D	4	....AACCCTArww	wrmCCTArhy   	18	15	24	13	13	16.6000	13
oligos_6nt_mkv4_m1	0100010593_M1389_1.02_CISBP	oligos_6nt_mkv4_m1	0100010593:M1389_1.02:CISBP	0.887	0.633	3.399	0.945	0.92614	14	10	10	14	0.7143	0.7143	1.0000	D	3	...AAACCCTArw.	wwAMCCTarw   	14	12	30	15	15	17.2000	14
oligos_6nt_mkv4_m1	TRP5_MA1802.2_JASPAR	oligos_6nt_mkv4_m1	TRP5:MA1802.2:JASPAR	0.945	0.472	3.093	0.972	0.93689	14	7	7	14	0.5000	0.5000	1.0000	D	2	..wAAACCC.....	wAAACCy                       	7	34	32	9	7	17.8000	15
oligos_6nt_mkv4_m1	MYB1-like_MA1030.1_JASPAR	oligos_6nt_mkv4_m1	MYB1-like:MA1030.1:JASPAR	0.872	0.623	4.293	0.948	0.92790	14	10	10	14	0.7143	0.7143	1.0000	D	4	....AACCCTArww	wrmCCTArhy      	19	16	26	14	14	17.8000	16
oligos_6nt_mkv4_m1	TRP2_MA1356.1_JASPAR	oligos_6nt_mkv4_m1	TRP2:MA1356.1:JASPAR	0.851	0.568	9.042	0.912	0.92051	14	21	14	21	0.6667	1.0000	0.6667	D	-3	hhwAAACCCTArww	...CcTAAACCCTAAAC....         	22	21	1	19	29	18.4000	17
oligos_6nt_mkv4_m1	MYBR101_SMH1_Mo17_1_EEAD0454_EEADannot	oligos_6nt_mkv4_m1	MYBR101_SMH1_Mo17_1:EEAD0454:EEADannot	0.821	0.657	6.160	0.929	0.92321	14	13	12	15	0.8000	0.8571	0.9231	D	-1	hhwAAACCCTAr..	.cCytwrCCCTAr                 	32	10	14	17	20	18.6000	18
oligos_6nt_mkv4_m1	TRP2.ampDAP_M0612_AthalianaCistrome	oligos_6nt_mkv4_m1	TRP2.ampDAP:M0612:AthalianaCistrome	0.851	0.567	9.009	0.912	0.92086	14	21	14	21	0.6667	1.0000	0.6667	D	-4	hhwAAACCCTArww	....CCTAAACCCTAAAC...         	24	22	2	18	27	18.6000	19
oligos_6nt_mkv4_m1	AL2G32420.t2_MYBRELATED_1_AT1G72740_EEAD0583_EEADannot	oligos_6nt_mkv4_m1	AL2G32420.t2_MYBRELATED_1_AT1G72740:EEAD0583:EEADannot	0.863	0.575	6.594	0.923	0.91229	14	11	10	15	0.6667	0.7143	0.9091	D	4	....AACCCTArww	AACCCTAAAC.                   	20	18	8	26	21	18.6000	20
oligos_6nt_mkv4_m1	LOC_Os01g51154.1_MYBRELATED_1_AT1G72740_EEAD0624_EEADannot	oligos_6nt_mkv4_m1	LOC_Os01g51154.1_MYBRELATED_1_AT1G72740:EEAD0624:EEADannot	0.840	0.593	6.315	0.918	0.91749	14	15	12	17	0.7059	0.8571	0.8000	D	-3	hhwAAACCCTAr..	...CCTAAACCCTAA               	27	17	13	21	24	20.4000	21
oligos_6nt_mkv4_m1	TRP1_MA1352.1_JASPAR	oligos_6nt_mkv4_m1	TRP1:MA1352.1:JASPAR	0.828	0.552	8.896	0.895	0.91360	14	21	14	21	0.6667	1.0000	0.6667	D	-2	hhwAAACCCTArww	..CCTAAACCCTAAAC.....         	28	23	3	24	33	22.2000	22
oligos_6nt_mkv4_m1	estExt_fgenesh1_pg.C_Chr_13.00010057_M1396_1.02_CISBP	oligos_6nt_mkv4_m1	estExt_fgenesh1_pg.C_Chr_13.00010057:M1396_1.02:CISBP	0.843	0.542	4.030	0.931	0.91234	14	9	9	14	0.6429	0.6429	1.0000	D	4	....AACCCTArw.	wrmCCTArh    	26	25	28	25	17	24.2000	23
oligos_6nt_mkv4_m1	Solyc07g040920.2.1_MYBRELATED_1_AT1G72740_EEAD0654_EEADannot	oligos_6nt_mkv4_m1	Solyc07g040920.2.1_MYBRELATED_1_AT1G72740:EEAD0654:EEADannot	0.851	0.479	5.238	0.921	0.90629	14	11	9	16	0.5625	0.6429	0.8182	D	5	.....ACCCTArww	ACCCTAAAC..                   	23	32	19	28	23	25.0000	24
oligos_6nt_mkv4_m1	XP_013589913.1_MYBRELATED_1_AT1G72740_EEAD0665_EEADannot	oligos_6nt_mkv4_m1	XP_013589913.1_MYBRELATED_1_AT1G72740:EEAD0665:EEADannot	0.851	0.478	5.176	0.921	0.90634	14	11	9	16	0.5625	0.6429	0.8182	D	5	.....ACCCTArww	ACCCTAAAC..                   	25	33	20	27	22	25.4000	25
oligos_6nt_mkv4_m1	P0510F09.23_MA1030.2_JASPAR	oligos_6nt_mkv4_m1	P0510F09.23:MA1030.2:JASPAR	0.873	0.436	4.281	0.929	0.89953	14	7	7	14	0.5000	0.5000	1.0000	D	4	....AACCCTA...	wrmCCTA                       	16	38	27	29	18	25.6000	26
oligos_6nt_mkv4_m1	AT4G12670.ampDAP_M0623_AthalianaCistrome	oligos_6nt_mkv4_m1	AT4G12670.ampDAP:M0623:AthalianaCistrome	0.774	0.516	6.418	0.898	0.91454	14	21	14	21	0.6667	1.0000	0.6667	D	-7	hhwAAACCCTArww	.......CmTAMACmYKAAAy         	36	27	12	22	31	25.6000	27
oligos_6nt_mkv4_m1	OsTRBF3_MA2404.1_JASPAR	oligos_6nt_mkv4_m1	OsTRBF3:MA2404.1:JASPAR	0.872	0.436	4.315	0.929	0.89948	14	7	7	14	0.5000	0.5000	1.0000	D	4	....AACCCTA...	wrmCCTA                       	17	39	25	30	19	26.0000	28
oligos_6nt_mkv4_m1	SRS7.DAP_M0745_AthalianaCistrome	oligos_6nt_mkv4_m1	SRS7.DAP:M0745:AthalianaCistrome	0.793	0.482	6.559	0.896	0.91366	14	23	14	23	0.6087	1.0000	0.6087	D	-4	hhwAAACCCTArww	....CCTAAACCCTAAAC.....       	35	31	11	23	32	26.4000	29
oligos_6nt_mkv4_m1	AT1G72740_MA1353.1_JASPAR	oligos_6nt_mkv4_m1	AT1G72740:MA1353.1:JASPAR	0.944	0.881	8.741	0.973	0.95638	14	15	14	15	0.9333	1.0000	0.9333	D	0	hhwAAACCCTArww	cctAAACCCTAAwy.               	8	1	39	42	42	26.4000	30
oligos_6nt_mkv4_m1	AT2G33550.DAP_M0787_AthalianaCistrome	oligos_6nt_mkv4_m1	AT2G33550.DAP:M0787:AthalianaCistrome	0.748	0.512	4.600	0.914	0.91867	14	18	13	19	0.6842	0.9286	0.7222	D	-5	hhwAAACCCTArw.	.....wawwwrCCCTwAa            	38	28	23	20	25	26.8000	31
oligos_6nt_mkv4_m1	TBP3_MA1355.1_JASPAR	oligos_6nt_mkv4_m1	TBP3:MA1355.1:JASPAR	0.893	0.658	7.064	0.961	0.94713	14	19	14	19	0.7368	1.0000	0.7368	D	-3	hhwAAACCCTArww	...whtwwrCCCTAAwt..           	12	9	34	41	40	27.2000	32
oligos_6nt_mkv4_m1	ATTRB2_M1346_1.02_CISBP	oligos_6nt_mkv4_m1	ATTRB2:M1346_1.02:CISBP	0.826	0.472	5.535	0.913	0.89563	14	8	8	14	0.5714	0.5714	1.0000	D	4	....AACCCTAr..	wrmCCTAr     	29	35	17	32	26	27.8000	33
oligos_6nt_mkv4_m1	TRB2_MA1073.1_JASPAR	oligos_6nt_mkv4_m1	TRB2:MA1073.1:JASPAR	0.825	0.471	5.555	0.912	0.89520	14	8	8	14	0.5714	0.5714	1.0000	D	4	....AACCCTAr..	wrmCCTAr        	30	36	16	33	28	28.6000	34
oligos_6nt_mkv4_m1	TRP2_MA1356.1_JASPAR	oligos_6nt_mkv4_m1	TRP2:MA1356.1:JASPAR	0.821	0.575	8.648	0.895	0.91330	14	20	14	20	0.7000	1.0000	0.7000	D	-4	hhwAAACCCTArww	....CCTAAACCCTAAAC..          	33	19	15	39	39	29.0000	35
oligos_6nt_mkv4_m1	estExt_fgenesh1_pg.C_Chr_03.00010061_M1394_1.02_CISBP	oligos_6nt_mkv4_m1	estExt_fgenesh1_pg.C_Chr_03.00010061:M1394_1.02:CISBP	0.811	0.521	2.886	0.906	0.89802	14	9	9	14	0.6429	0.6429	1.0000	D	3	...AAACCCTAr..	wwrmCCYar    	34	26	33	31	30	30.8000	36
oligos_6nt_mkv4_m1	TOE1_TOE1_3_ArabidopsisPBM	oligos_6nt_mkv4_m1	TOE1:TOE1_3:ArabidopsisPBM	0.715	0.511	4.640	0.870	0.88601	14	10	10	14	0.7143	0.7143	1.0000	D	3	...AAACCCTArw.	wAACCTTAAm                    	40	29	22	35	36	32.4000	37
oligos_6nt_mkv4_m1	TRP1_MA1352.1_JASPAR	oligos_6nt_mkv4_m1	TRP1:MA1352.1:JASPAR	0.822	0.500	8.551	0.897	0.91424	14	23	14	23	0.6087	1.0000	0.6087	D	-4	hhwAAACCCTArww	....CCTAAACCCTAAAC.....       	31	30	29	40	41	34.2000	38
oligos_6nt_mkv4_m1	STY1_STY1_ArabidopsisPBM	oligos_6nt_mkv4_m1	STY1:STY1:ArabidopsisPBM	0.731	0.439	4.797	0.868	0.87892	14	10	9	15	0.6000	0.6429	0.9000	R	5	.....ACCCTArww	RCCCTAGGG.                    	39	37	21	37	37	34.2000	39
oligos_6nt_mkv4_m1	NAC25_B73_1_m1_EEAD0471_EEADannot	oligos_6nt_mkv4_m1	NAC25_B73_1_m1:EEAD0471:EEADannot	0.764	0.402	0.486	0.890	0.89494	14	15	10	19	0.5263	0.7143	0.6667	R	-5	hhwAAACCCT....	.....CAAAAACTCT               	37	42	37	34	35	37.0000	40
oligos_6nt_mkv4_m1	Probable_6j4f_F_3D-footprint	oligos_6nt_mkv4_m1	Probable:6j4f_F:3D-footprint	0.713	0.408	0.461	0.893	0.88451	14	8	8	14	0.5714	0.5714	1.0000	R	0	hhwAAACC......	CTTNNACC                      	41	40	38	36	34	37.8000	41
oligos_6nt_mkv4_m1	TRFL5_M1316_1.02_CISBP	oligos_6nt_mkv4_m1	TRFL5:M1316_1.02:CISBP	0.705	0.403	0.266	0.833	0.85555	14	8	8	14	0.5714	0.5714	1.0000	R	4	....AACCCTAr..	TGCCCTAR     	42	41	42	38	38	40.2000	42
; Host name	rsat
; Job started	2026-06-18.161302
; Job done	2026-06-18.161322
; Seconds	12.45
;	user	12.45
;	system	1.12
;	cuser	5.89
;	csystem	1.55