; compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.motif.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB
; Program version       	1.118
; Quick mode 
; Input files
;	file2 	/var/www/html/rsat/public_html/motif_databases/footprintDB/footprintDB.motif.tf
;	file1 	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf
; Output files
;	alignments_1ton	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB_alignments_1ton.tab
;	html_index   	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB_index.html
;	match_table_txt	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB.tab
;	prefix       	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB
;	match_table_html	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB.html
;	alignments_1ton_html	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB_alignments_1ton.html
; Matrices
;	file1	1 matrices	/var/www/html/rsat/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2.tf
;		file1	1	20	31
;	file2	13863 matrices	/var/www/html/rsat/public_html/motif_databases/footprintDB/footprintDB.motif.tf
;		file2		1		17		1.01
;		file2		2		7		96
;		file2		3		8		5
;		file2		4		8		3
;		file2		5		8		5
;		file2		6		8		1
;		file2		7		8		2
;		file2		8		8		2
;		file2		9		8		6
;		file2		10		8		2
;		file2		11		8		8
;		...	13853 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	w1           	Width of the first matrix
;	8	w2           	Width of the second matrix
;	9	w            	Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset)
;	10	W            	Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w
;	11	Wr           	Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W
;	12	wr1          	Alignment length relative to the width of the first matrix. wr1 = w/w1
;	13	wr2          	Alignment length relative to the width of the second matrix. wr2 = w/w2
;	14	strand       	"strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct;  R=reverse)
;	15	offset       	shift of the second matrix relative to the first matrix (negative:left; positive: right)
#id1	id2	name1	name2	cor	Ncor	w1	w2	w	W	Wr	wr1	wr2	strand	offset
dyads_m2	CG1856/ttk-PF_SOLEXA_FBgn0003870/FlyZincFinger	dyads_m2	CG1856:ttk-PF_SOLEXA_FBgn0003870:FlyZincFinger	0.823	0.453	20	11	11	20	0.5500	0.5500	1.0000	D	0
dyads_m2	Signal/4y5w_AC/3D-footprint	dyads_m2	Signal:4y5w_AC:3D-footprint	0.798	0.435	20	14	12	22	0.5455	0.6000	0.8571	D	-2
dyads_m2	RS1/5mhk_CDJ/3D-footprint	dyads_m2	RS1:5mhk_CDJ:3D-footprint	0.711	0.427	20	12	12	20	0.6000	0.6000	1.0000	D	7
dyads_m2	Erf-a/MA1853.1/JASPAR	dyads_m2	Erf-a:MA1853.1:JASPAR	0.705	0.423	20	20	15	25	0.6000	0.7500	0.7500	D	-5
dyads_m2	EFNCRG00000000350/M1766_1.02/CISBP	dyads_m2	EFNCRG00000000350:M1766_1.02:CISBP	0.832	0.416	20	10	10	20	0.5000	0.5000	1.0000	D	9
dyads_m2	FLI1_HUMAN.H10MO.A|M01137/FLI1_HUMAN.H10MO.A|M01137/HOCOMOCO	dyads_m2	FLI1_HUMAN.H10MO.A|M01137:FLI1_HUMAN.H10MO.A|M01137:HOCOMOCO	0.715	0.408	20	13	12	21	0.5714	0.6000	0.9231	D	-1
dyads_m2	aod-5/M1735_1.02/CISBP	dyads_m2	aod-5:M1735_1.02:CISBP	0.803	0.401	20	10	10	20	0.5000	0.5000	1.0000	D	9
; Host name	rsat
; Job started	2025-03-02.091227
; Job done	2025-03-02.091233
; Seconds	5.6
;	user	5.6
;	system	0.13
;	cuser	0.52
;	csystem	0.06
