One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/07/compare-matrices_2019-07-07.122532_zWKXQk/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_2019-07-07.122532_zWKXQk/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift9 ; 14 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_shift9 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=13; shift=9; ncol=22; ---------wkGGCGGGAAAwt ; Alignment reference a 0 0 0 0 0 0 0 0 0 19 13 10 1 9 4 1 4 64 57 51 24 17 c 0 0 0 0 0 0 0 0 0 6 2 7 0 56 0 4 1 3 1 3 8 15 g 0 0 0 0 0 0 0 0 0 15 18 52 71 0 66 64 65 2 10 11 17 16 t 0 0 0 0 0 0 0 0 0 32 39 3 0 7 2 3 2 3 4 7 23 24

E2Fb_E2Fb_Athamap_rc_shift12 (E2Fb:E2Fb:Athamap_rc) 0.988 0.608 0.447 0.956 0.984 1 4 11 2 1 3.800 1
; dyads_test_vs_ctrl_m1 versus E2Fb_E2Fb_Athamap_rc (E2Fb:E2Fb:Athamap_rc); m=1/13; ncol2=8; w=8; offset=3; strand=R; shift=12; score= 3.8; ------------GCGGGAAW-- ; cor=0.988; Ncor=0.608; logoDP=0.447; NsEucl=0.956; NSW=0.984; rcor=1; rNcor=4; rlogoDP=11; rNsEucl=2; rNSW=1; rank_mean=3.800; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 3 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 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 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0

E2Fc_E2Fc_Athamap_rc_shift8 (E2Fc:E2Fc:Athamap_rc) 0.961 0.687 0.891 0.956 0.981 3 3 9 1 3 3.800 2
; dyads_test_vs_ctrl_m1 versus E2Fc_E2Fc_Athamap_rc (E2Fc:E2Fc:Athamap_rc); m=2/13; ncol2=11; w=10; offset=-1; strand=R; shift=8; score= 3.8; --------wwkgGCGGGAA--- ; cor=0.961; Ncor=0.687; logoDP=0.891; NsEucl=0.956; NSW=0.981; rcor=3; rNcor=3; rlogoDP=9; rNsEucl=1; rNSW=3; rank_mean=3.800; match_rank=2 a 0 0 0 0 0 0 0 0 2 2 0 1 0 0 0 0 0 4 4 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1 0 5 0 1 0 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 0 t 0 0 0 0 0 0 0 0 3 3 3 0 0 0 0 0 0 1 1 0 0 0

DEL1.ampDAP_M0365_AthalianaCistrome_shift6 (DEL1.ampDAP:M0365:AthalianaCistrome) 0.942 0.706 8.909 0.935 0.949 6 1 2 6 6 4.200 3
; dyads_test_vs_ctrl_m1 versus DEL1.ampDAP_M0365_AthalianaCistrome (DEL1.ampDAP:M0365:AthalianaCistrome); m=3/13; ncol2=15; w=12; offset=-3; strand=D; shift=6; score= 4.2; ------tTTTTGGCGGGAAAA- ; cor=0.942; Ncor=0.706; logoDP=8.909; NsEucl=0.935; NSW=0.949; rcor=6; rNcor=1; rlogoDP=2; rNsEucl=6; rNSW=6; rank_mean=4.200; match_rank=3 a 0 0 0 0 0 0 136 64 16 9 10 5 2 1 0 0 10 581 584 541 419 0 c 0 0 0 0 0 0 6 2 0 0 1 4 0 583 0 11 3 0 0 5 33 0 g 0 0 0 0 0 0 125 12 0 1 3 571 582 0 583 572 569 3 0 9 16 0 t 0 0 0 0 0 0 317 506 568 574 570 4 0 0 1 1 2 0 0 29 116 0

DEL2.ampDAP_M0366_AthalianaCistrome_shift6 (DEL2.ampDAP:M0366:AthalianaCistrome) 0.940 0.705 9.076 0.933 0.946 7 2 1 7 7 4.800 5
; dyads_test_vs_ctrl_m1 versus DEL2.ampDAP_M0366_AthalianaCistrome (DEL2.ampDAP:M0366:AthalianaCistrome); m=5/13; ncol2=15; w=12; offset=-3; strand=D; shift=6; score= 4.8; ------tTTTTGGCGGGAAAA- ; cor=0.940; Ncor=0.705; logoDP=9.076; NsEucl=0.933; NSW=0.946; rcor=7; rNcor=2; rlogoDP=1; rNsEucl=7; rNSW=7; rank_mean=4.800; match_rank=5 a 0 0 0 0 0 0 114 57 26 20 8 3 0 1 1 1 0 545 549 526 425 0 c 0 0 0 0 0 0 5 1 2 0 1 2 0 548 0 8 6 0 0 7 28 0 g 0 0 0 0 0 0 135 7 1 4 3 543 549 0 547 540 542 4 0 6 12 0 t 0 0 0 0 0 0 295 484 520 525 537 1 0 0 1 0 1 0 0 10 84 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m1_shift9 (dyads_test_vs_ctrl_m1)													; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=13; shift=9; ncol=22; ---------wkGGCGGGAAAwt ; Alignment reference a 0 0 0 0 0 0 0 0 0 19 13 10 1 9 4 1 4 64 57 51 24 17 c 0 0 0 0 0 0 0 0 0 6 2 7 0 56 0 4 1 3 1 3 8 15 g 0 0 0 0 0 0 0 0 0 15 18 52 71 0 66 64 65 2 10 11 17 16 t 0 0 0 0 0 0 0 0 0 32 39 3 0 7 2 3 2 3 4 7 23 24
E2Fb_E2Fb_Athamap_rc_shift12 (E2Fb:E2Fb:Athamap_rc)	0.988	0.608	0.447	0.956	0.984	1	4	11	2	1	3.800	1	; dyads_test_vs_ctrl_m1 versus E2Fb_E2Fb_Athamap_rc (E2Fb:E2Fb:Athamap_rc); m=1/13; ncol2=8; w=8; offset=3; strand=R; shift=12; score= 3.8; ------------GCGGGAAW-- ; cor=0.988; Ncor=0.608; logoDP=0.447; NsEucl=0.956; NSW=0.984; rcor=1; rNcor=4; rlogoDP=11; rNsEucl=2; rNSW=1; rank_mean=3.800; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 3 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 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 0 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
E2Fc_E2Fc_Athamap_rc_shift8 (E2Fc:E2Fc:Athamap_rc)	0.961	0.687	0.891	0.956	0.981	3	3	9	1	3	3.800	2	; dyads_test_vs_ctrl_m1 versus E2Fc_E2Fc_Athamap_rc (E2Fc:E2Fc:Athamap_rc); m=2/13; ncol2=11; w=10; offset=-1; strand=R; shift=8; score= 3.8; --------wwkgGCGGGAA--- ; cor=0.961; Ncor=0.687; logoDP=0.891; NsEucl=0.956; NSW=0.981; rcor=3; rNcor=3; rlogoDP=9; rNsEucl=1; rNSW=3; rank_mean=3.800; match_rank=2 a 0 0 0 0 0 0 0 0 2 2 0 1 0 0 0 0 0 4 4 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 1 0 5 0 1 0 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 0 t 0 0 0 0 0 0 0 0 3 3 3 0 0 0 0 0 0 1 1 0 0 0
DEL1.ampDAP_M0365_AthalianaCistrome_shift6 (DEL1.ampDAP:M0365:AthalianaCistrome)	0.942	0.706	8.909	0.935	0.949	6	1	2	6	6	4.200	3	; dyads_test_vs_ctrl_m1 versus DEL1.ampDAP_M0365_AthalianaCistrome (DEL1.ampDAP:M0365:AthalianaCistrome); m=3/13; ncol2=15; w=12; offset=-3; strand=D; shift=6; score= 4.2; ------tTTTTGGCGGGAAAA- ; cor=0.942; Ncor=0.706; logoDP=8.909; NsEucl=0.935; NSW=0.949; rcor=6; rNcor=1; rlogoDP=2; rNsEucl=6; rNSW=6; rank_mean=4.200; match_rank=3 a 0 0 0 0 0 0 136 64 16 9 10 5 2 1 0 0 10 581 584 541 419 0 c 0 0 0 0 0 0 6 2 0 0 1 4 0 583 0 11 3 0 0 5 33 0 g 0 0 0 0 0 0 125 12 0 1 3 571 582 0 583 572 569 3 0 9 16 0 t 0 0 0 0 0 0 317 506 568 574 570 4 0 0 1 1 2 0 0 29 116 0
DEL2.ampDAP_M0366_AthalianaCistrome_shift6 (DEL2.ampDAP:M0366:AthalianaCistrome)	0.940	0.705	9.076	0.933	0.946	7	2	1	7	7	4.800	5	; dyads_test_vs_ctrl_m1 versus DEL2.ampDAP_M0366_AthalianaCistrome (DEL2.ampDAP:M0366:AthalianaCistrome); m=5/13; ncol2=15; w=12; offset=-3; strand=D; shift=6; score= 4.8; ------tTTTTGGCGGGAAAA- ; cor=0.940; Ncor=0.705; logoDP=9.076; NsEucl=0.933; NSW=0.946; rcor=7; rNcor=2; rlogoDP=1; rNsEucl=7; rNSW=7; rank_mean=4.800; match_rank=5 a 0 0 0 0 0 0 114 57 26 20 8 3 0 1 1 1 0 545 549 526 425 0 c 0 0 0 0 0 0 5 1 2 0 1 2 0 548 0 8 6 0 0 7 28 0 g 0 0 0 0 0 0 135 7 1 4 3 543 549 0 547 540 542 4 0 6 12 0 t 0 0 0 0 0 0 295 484 520 525 537 1 0 0 1 0 1 0 0 10 84 0