One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/07/compare-matrices_2019-07-07.144429_PSav84/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/2019/07/07/compare-matrices_2019-07-07.144429_PSav84/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift10 ; 15 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NsEucl NSW rcor rNcor rlogoDP rNsEucl rNSW rank_mean match_rank Aligned matrices

dyads_test_vs_ctrl_m1_shift10 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=11; shift=10; ncol=21; ----------kgGCGGGAArw ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 12 16 3 9 1 3 2 60 63 26 19 c 0 0 0 0 0 0 0 0 0 0 13 14 2 53 1 1 2 5 1 16 14 g 0 0 0 0 0 0 0 0 0 0 18 22 60 0 63 61 62 1 3 18 16 t 0 0 0 0 0 0 0 0 0 0 24 15 2 5 2 2 1 1 0 7 18

E2Fa_E2Fa_Athamap_rc_shift12 (E2Fa:E2Fa:Athamap_rc) 0.972 0.707 0.409 0.945 0.976 1 1 13 1 1 3.400 1
; dyads_test_vs_ctrl_m1 versus E2Fa_E2Fa_Athamap_rc (E2Fa:E2Fa:Athamap_rc); m=1/14; ncol2=8; w=8; offset=2; strand=R; shift=12; score= 3.4; ------------GCGGGAAw- ; cor=0.972; Ncor=0.707; logoDP=0.409; NsEucl=0.945; NSW=0.976; rcor=1; rNcor=1; rlogoDP=13; rNsEucl=1; rNSW=1; rank_mean=3.400; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 3 0 3 3 3 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0

E2Fb_E2Fb_Athamap_rc_shift12 (E2Fb:E2Fb:Athamap_rc) 0.971 0.706 0.411 0.943 0.974 2 2 12 2 2 4.000 2
; dyads_test_vs_ctrl_m1 versus E2Fb_E2Fb_Athamap_rc (E2Fb:E2Fb:Athamap_rc); m=2/14; ncol2=8; w=8; offset=2; strand=R; shift=12; score= 4; ------------GCGGGAAW- ; cor=0.971; Ncor=0.706; logoDP=0.411; NsEucl=0.943; NSW=0.974; rcor=2; rNcor=2; rlogoDP=12; rNsEucl=2; rNSW=2; rank_mean=4.000; match_rank=2 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 3 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 4 0 4 4 4 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0

E2Fc_E2Fc_Athamap_rc_shift8 (E2Fc:E2Fc:Athamap_rc) 0.943 0.653 1.012 0.943 0.971 3 3 10 3 3 4.400 3
; dyads_test_vs_ctrl_m1 versus E2Fc_E2Fc_Athamap_rc (E2Fc:E2Fc:Athamap_rc); m=3/14; ncol2=11; w=9; offset=-2; strand=R; shift=8; score= 4.4; --------wwkgGCGGGAA-- ; cor=0.943; Ncor=0.653; logoDP=1.012; NsEucl=0.943; NSW=0.971; rcor=3; rNcor=3; rlogoDP=10; rNsEucl=3; rNSW=3; rank_mean=4.400; match_rank=3 a 0 0 0 0 0 0 0 0 2 2 0 1 0 0 0 0 0 4 4 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1 0 5 0 1 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2 3 5 0 5 4 5 0 0 0 0 t 0 0 0 0 0 0 0 0 3 3 3 0 0 0 0 0 0 1 1 0 0

DEL1.ampDAP_M0365_AthalianaCistrome_shift6 (DEL1.ampDAP:M0365:AthalianaCistrome) 0.878 0.644 8.361 0.912 0.915 6 4 2 6 6 4.800 4
; dyads_test_vs_ctrl_m1 versus DEL1.ampDAP_M0365_AthalianaCistrome (DEL1.ampDAP:M0365:AthalianaCistrome); m=4/14; ncol2=15; w=11; offset=-4; strand=D; shift=6; score= 4.8; ------tTTTTGGCGGGAAAA ; cor=0.878; Ncor=0.644; logoDP=8.361; NsEucl=0.912; NSW=0.915; rcor=6; rNcor=4; rlogoDP=2; rNsEucl=6; rNSW=6; rank_mean=4.800; match_rank=4 a 0 0 0 0 0 0 136 64 16 9 10 5 2 1 0 0 10 581 584 541 419 c 0 0 0 0 0 0 6 2 0 0 1 4 0 583 0 11 3 0 0 5 33 g 0 0 0 0 0 0 125 12 0 1 3 571 582 0 583 572 569 3 0 9 16 t 0 0 0 0 0 0 317 506 568 574 570 4 0 0 1 1 2 0 0 29 116

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m1_shift10 (dyads_test_vs_ctrl_m1)													; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=11; shift=10; ncol=21; ----------kgGCGGGAArw ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 12 16 3 9 1 3 2 60 63 26 19 c 0 0 0 0 0 0 0 0 0 0 13 14 2 53 1 1 2 5 1 16 14 g 0 0 0 0 0 0 0 0 0 0 18 22 60 0 63 61 62 1 3 18 16 t 0 0 0 0 0 0 0 0 0 0 24 15 2 5 2 2 1 1 0 7 18
E2Fa_E2Fa_Athamap_rc_shift12 (E2Fa:E2Fa:Athamap_rc)	0.972	0.707	0.409	0.945	0.976	1	1	13	1	1	3.400	1	; dyads_test_vs_ctrl_m1 versus E2Fa_E2Fa_Athamap_rc (E2Fa:E2Fa:Athamap_rc); m=1/14; ncol2=8; w=8; offset=2; strand=R; shift=12; score= 3.4; ------------GCGGGAAw- ; cor=0.972; Ncor=0.707; logoDP=0.409; NsEucl=0.945; NSW=0.976; rcor=1; rNcor=1; rlogoDP=13; rNsEucl=1; rNSW=1; rank_mean=3.400; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 3 0 3 3 3 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
E2Fb_E2Fb_Athamap_rc_shift12 (E2Fb:E2Fb:Athamap_rc)	0.971	0.706	0.411	0.943	0.974	2	2	12	2	2	4.000	2	; dyads_test_vs_ctrl_m1 versus E2Fb_E2Fb_Athamap_rc (E2Fb:E2Fb:Athamap_rc); m=2/14; ncol2=8; w=8; offset=2; strand=R; shift=12; score= 4; ------------GCGGGAAW- ; cor=0.971; Ncor=0.706; logoDP=0.411; NsEucl=0.943; NSW=0.974; rcor=2; rNcor=2; rlogoDP=12; rNsEucl=2; rNSW=2; rank_mean=4.000; match_rank=2 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 3 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 4 0 4 4 4 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
E2Fc_E2Fc_Athamap_rc_shift8 (E2Fc:E2Fc:Athamap_rc)	0.943	0.653	1.012	0.943	0.971	3	3	10	3	3	4.400	3	; dyads_test_vs_ctrl_m1 versus E2Fc_E2Fc_Athamap_rc (E2Fc:E2Fc:Athamap_rc); m=3/14; ncol2=11; w=9; offset=-2; strand=R; shift=8; score= 4.4; --------wwkgGCGGGAA-- ; cor=0.943; Ncor=0.653; logoDP=1.012; NsEucl=0.943; NSW=0.971; rcor=3; rNcor=3; rlogoDP=10; rNsEucl=3; rNSW=3; rank_mean=4.400; match_rank=3 a 0 0 0 0 0 0 0 0 2 2 0 1 0 0 0 0 0 4 4 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1 0 5 0 1 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 2 3 5 0 5 4 5 0 0 0 0 t 0 0 0 0 0 0 0 0 3 3 3 0 0 0 0 0 0 1 1 0 0
DEL1.ampDAP_M0365_AthalianaCistrome_shift6 (DEL1.ampDAP:M0365:AthalianaCistrome)	0.878	0.644	8.361	0.912	0.915	6	4	2	6	6	4.800	4	; dyads_test_vs_ctrl_m1 versus DEL1.ampDAP_M0365_AthalianaCistrome (DEL1.ampDAP:M0365:AthalianaCistrome); m=4/14; ncol2=15; w=11; offset=-4; strand=D; shift=6; score= 4.8; ------tTTTTGGCGGGAAAA ; cor=0.878; Ncor=0.644; logoDP=8.361; NsEucl=0.912; NSW=0.915; rcor=6; rNcor=4; rlogoDP=2; rNsEucl=6; rNSW=6; rank_mean=4.800; match_rank=4 a 0 0 0 0 0 0 136 64 16 9 10 5 2 1 0 0 10 581 584 541 419 c 0 0 0 0 0 0 6 2 0 0 1 4 0 583 0 11 3 0 0 5 33 g 0 0 0 0 0 0 125 12 0 1 3 571 582 0 583 572 569 3 0 9 16 t 0 0 0 0 0 0 317 506 568 574 570 4 0 0 1 1 2 0 0 29 116