One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/07/22/compare-matrices_2026-07-22.144127_OuRJG2/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/ArabidopsisPBM/ArabidopsisPBM_2015-11-06.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/2026/07/22/compare-matrices_2026-07-22.144127_OuRJG2/compare-matrices.tab

One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift0 ; 7 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
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1oligos_6-8nt_m1)
; oligos_6-8nt_m1 (oligos_6-8nt_m1oligos_6-8nt_m1); m=0 (reference); ncol1=17; shift=0; ncol=17; wyhyTCACCAACCmCmh ; Alignment reference a 17 7 10 3 3 0 35 0 0 28 36 7 0 12 1 10 13 c 7 11 13 18 3 35 0 35 36 2 0 27 32 19 30 16 10 g 1 8 4 2 0 0 0 0 0 0 1 2 2 4 1 4 3 t 12 11 10 14 31 2 2 2 1 7 0 1 3 2 5 7 11

7237_MYB111_2_ArabidopsisPBM_20140210__rc_shift4 (7237_MYB111_2_ArabidopsisPBM_20140210__rc) 0.818 0.481 0.274 0.906 0.912 1 1 4 1 1 1.600 1
; oligos_6-8nt_m1 versus 7237_MYB111_2_ArabidopsisPBM_20140210__rc; m=1/6; ncol2=10; w=0; offset=4; strand=R; shift=4; score= 1.6; ----cYAMCwACCt--- ; cor=0.818; Ncor=0.481; logoDP=0.274; NsEucl=0.906; NSW=0.912; rcor=1; rNcor=1; rlogoDP=4; rNsEucl=1; rNSW=1; rank_mean=1.600; match_rank=1 a 0 0 0 0 13 0 97 26 0 37 99 14 1 22 0 0 0 c 0 0 0 0 58 68 0 73 98 3 1 85 93 11 0 0 0 g 0 0 0 0 13 2 1 1 0 1 0 0 0 10 0 0 0 t 0 0 0 0 16 30 2 0 2 59 0 1 6 57 0 0 0

7242_MYB55_ArabidopsisPBM_20140210__shift5 (7242_MYB55_ArabidopsisPBM_20140210_) 0.774 0.455 7.287 0.895 0.890 2 2 1 4 4 2.600 2
; oligos_6-8nt_m1 versus 7242_MYB55_ArabidopsisPBM_20140210_; m=2/6; ncol2=10; w=0; offset=5; strand=D; shift=5; score= 2.6; -----yACCTAMCGv-- ; cor=0.774; Ncor=0.455; logoDP=7.287; NsEucl=0.895; NSW=0.890; rcor=2; rNcor=2; rlogoDP=1; rNsEucl=4; rNSW=4; rank_mean=2.600; match_rank=2 a 0 0 0 0 0 11 98 5 0 23 98 27 0 12 25 0 0 c 0 0 0 0 0 36 0 95 99 5 0 73 96 5 28 0 0 g 0 0 0 0 0 5 2 0 0 2 2 0 0 76 30 0 0 t 0 0 0 0 0 48 0 0 1 70 0 0 4 7 17 0 0

7243_MYB55_2_ArabidopsisPBM_20140210__rc_shift7 (7243_MYB55_2_ArabidopsisPBM_20140210__rc) 0.742 0.436 0.433 0.898 0.897 3 3 3 3 3 3.000 3
; oligos_6-8nt_m1 versus 7243_MYB55_2_ArabidopsisPBM_20140210__rc; m=3/6; ncol2=10; w=0; offset=7; strand=R; shift=7; score= 3; -------cCAmCCAMCg ; cor=0.742; Ncor=0.436; logoDP=0.433; NsEucl=0.898; NSW=0.897; rcor=3; rNcor=3; rlogoDP=3; rNsEucl=3; rNSW=3; rank_mean=3.000; match_rank=3 a 0 0 0 0 0 0 0 13 2 96 54 1 17 91 28 2 24 c 0 0 0 0 0 0 0 62 83 2 44 98 69 0 70 89 14 g 0 0 0 0 0 0 0 11 5 0 1 0 3 8 1 1 54 t 0 0 0 0 0 0 0 14 10 2 1 1 11 1 1 8 8

7239_MYB46_2_ArabidopsisPBM_20140210__shift7 (7239_MYB46_2_ArabidopsisPBM_20140210_) 0.722 0.425 2.498 0.900 0.901 6 6 2 2 2 3.600 4
; oligos_6-8nt_m1 versus 7239_MYB46_2_ArabidopsisPBM_20140210_; m=4/6; ncol2=10; w=0; offset=7; strand=D; shift=7; score= 3.6; -------yyAACCAmCr ; cor=0.722; Ncor=0.425; logoDP=2.498; NsEucl=0.900; NSW=0.901; rcor=6; rNcor=6; rlogoDP=2; rNsEucl=2; rNSW=2; rank_mean=3.600; match_rank=4 a 0 0 0 0 0 0 0 16 5 92 82 1 21 82 25 6 31 c 0 0 0 0 0 0 0 29 53 3 13 96 68 1 64 72 19 g 0 0 0 0 0 0 0 24 13 3 2 1 7 16 2 3 39 t 0 0 0 0 0 0 0 31 29 2 3 2 4 1 9 19 11

7236_MYB111_ArabidopsisPBM_20140210__rc_shift4 (7236_MYB111_ArabidopsisPBM_20140210__rc) 0.737 0.433 0.267 0.889 0.876 5 5 5 5 5 5.000 5
; oligos_6-8nt_m1 versus 7236_MYB111_ArabidopsisPBM_20140210__rc; m=5/6; ncol2=10; w=0; offset=4; strand=R; shift=4; score= 5; ----syACCTAmCh--- ; cor=0.737; Ncor=0.433; logoDP=0.267; NsEucl=0.889; NSW=0.876; rcor=5; rNcor=5; rlogoDP=5; rNsEucl=5; rNSW=5; rank_mean=5.000; match_rank=5 a 0 0 0 0 15 5 99 13 0 11 98 36 1 34 0 0 0 c 0 0 0 0 46 39 0 85 98 1 0 64 76 28 0 0 0 g 0 0 0 0 32 3 0 1 0 1 2 0 0 10 0 0 0 t 0 0 0 0 7 53 1 1 2 87 0 0 23 28 0 0 0

7238_MYB46_ArabidopsisPBM_20140210__rc_shift4 (7238_MYB46_ArabidopsisPBM_20140210__rc) 0.740 0.435 0.264 0.889 0.876 4 4 6 6 6 5.200 6
; oligos_6-8nt_m1 versus 7238_MYB46_ArabidopsisPBM_20140210__rc; m=6/6; ncol2=10; w=0; offset=4; strand=R; shift=4; score= 5.2; ----yyACCTAmCt--- ; cor=0.740; Ncor=0.435; logoDP=0.264; NsEucl=0.889; NSW=0.876; rcor=4; rNcor=4; rlogoDP=6; rNsEucl=6; rNSW=6; rank_mean=5.200; match_rank=6 a 0 0 0 0 15 4 96 9 0 12 98 61 1 20 0 0 0 c 0 0 0 0 37 36 0 91 100 1 0 39 91 22 0 0 0 g 0 0 0 0 22 2 4 0 0 3 1 0 0 16 0 0 0 t 0 0 0 0 26 58 0 0 0 84 1 0 8 42 0 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1oligos_6-8nt_m1)													; oligos_6-8nt_m1 (oligos_6-8nt_m1oligos_6-8nt_m1); m=0 (reference); ncol1=17; shift=0; ncol=17; wyhyTCACCAACCmCmh ; Alignment reference a 17 7 10 3 3 0 35 0 0 28 36 7 0 12 1 10 13 c 7 11 13 18 3 35 0 35 36 2 0 27 32 19 30 16 10 g 1 8 4 2 0 0 0 0 0 0 1 2 2 4 1 4 3 t 12 11 10 14 31 2 2 2 1 7 0 1 3 2 5 7 11
7237_MYB111_2_ArabidopsisPBM_20140210__rc_shift4 (7237_MYB111_2_ArabidopsisPBM_20140210__rc)	0.818	0.481	0.274	0.906	0.912	1	1	4	1	1	1.600	1	; oligos_6-8nt_m1 versus 7237_MYB111_2_ArabidopsisPBM_20140210__rc; m=1/6; ncol2=10; w=0; offset=4; strand=R; shift=4; score= 1.6; ----cYAMCwACCt--- ; cor=0.818; Ncor=0.481; logoDP=0.274; NsEucl=0.906; NSW=0.912; rcor=1; rNcor=1; rlogoDP=4; rNsEucl=1; rNSW=1; rank_mean=1.600; match_rank=1 a 0 0 0 0 13 0 97 26 0 37 99 14 1 22 0 0 0 c 0 0 0 0 58 68 0 73 98 3 1 85 93 11 0 0 0 g 0 0 0 0 13 2 1 1 0 1 0 0 0 10 0 0 0 t 0 0 0 0 16 30 2 0 2 59 0 1 6 57 0 0 0
7242_MYB55_ArabidopsisPBM_20140210__shift5 (7242_MYB55_ArabidopsisPBM_20140210_)	0.774	0.455	7.287	0.895	0.890	2	2	1	4	4	2.600	2	; oligos_6-8nt_m1 versus 7242_MYB55_ArabidopsisPBM_20140210_; m=2/6; ncol2=10; w=0; offset=5; strand=D; shift=5; score= 2.6; -----yACCTAMCGv-- ; cor=0.774; Ncor=0.455; logoDP=7.287; NsEucl=0.895; NSW=0.890; rcor=2; rNcor=2; rlogoDP=1; rNsEucl=4; rNSW=4; rank_mean=2.600; match_rank=2 a 0 0 0 0 0 11 98 5 0 23 98 27 0 12 25 0 0 c 0 0 0 0 0 36 0 95 99 5 0 73 96 5 28 0 0 g 0 0 0 0 0 5 2 0 0 2 2 0 0 76 30 0 0 t 0 0 0 0 0 48 0 0 1 70 0 0 4 7 17 0 0
7243_MYB55_2_ArabidopsisPBM_20140210__rc_shift7 (7243_MYB55_2_ArabidopsisPBM_20140210__rc)	0.742	0.436	0.433	0.898	0.897	3	3	3	3	3	3.000	3	; oligos_6-8nt_m1 versus 7243_MYB55_2_ArabidopsisPBM_20140210__rc; m=3/6; ncol2=10; w=0; offset=7; strand=R; shift=7; score= 3; -------cCAmCCAMCg ; cor=0.742; Ncor=0.436; logoDP=0.433; NsEucl=0.898; NSW=0.897; rcor=3; rNcor=3; rlogoDP=3; rNsEucl=3; rNSW=3; rank_mean=3.000; match_rank=3 a 0 0 0 0 0 0 0 13 2 96 54 1 17 91 28 2 24 c 0 0 0 0 0 0 0 62 83 2 44 98 69 0 70 89 14 g 0 0 0 0 0 0 0 11 5 0 1 0 3 8 1 1 54 t 0 0 0 0 0 0 0 14 10 2 1 1 11 1 1 8 8
7239_MYB46_2_ArabidopsisPBM_20140210__shift7 (7239_MYB46_2_ArabidopsisPBM_20140210_)	0.722	0.425	2.498	0.900	0.901	6	6	2	2	2	3.600	4	; oligos_6-8nt_m1 versus 7239_MYB46_2_ArabidopsisPBM_20140210_; m=4/6; ncol2=10; w=0; offset=7; strand=D; shift=7; score= 3.6; -------yyAACCAmCr ; cor=0.722; Ncor=0.425; logoDP=2.498; NsEucl=0.900; NSW=0.901; rcor=6; rNcor=6; rlogoDP=2; rNsEucl=2; rNSW=2; rank_mean=3.600; match_rank=4 a 0 0 0 0 0 0 0 16 5 92 82 1 21 82 25 6 31 c 0 0 0 0 0 0 0 29 53 3 13 96 68 1 64 72 19 g 0 0 0 0 0 0 0 24 13 3 2 1 7 16 2 3 39 t 0 0 0 0 0 0 0 31 29 2 3 2 4 1 9 19 11
7236_MYB111_ArabidopsisPBM_20140210__rc_shift4 (7236_MYB111_ArabidopsisPBM_20140210__rc)	0.737	0.433	0.267	0.889	0.876	5	5	5	5	5	5.000	5	; oligos_6-8nt_m1 versus 7236_MYB111_ArabidopsisPBM_20140210__rc; m=5/6; ncol2=10; w=0; offset=4; strand=R; shift=4; score= 5; ----syACCTAmCh--- ; cor=0.737; Ncor=0.433; logoDP=0.267; NsEucl=0.889; NSW=0.876; rcor=5; rNcor=5; rlogoDP=5; rNsEucl=5; rNSW=5; rank_mean=5.000; match_rank=5 a 0 0 0 0 15 5 99 13 0 11 98 36 1 34 0 0 0 c 0 0 0 0 46 39 0 85 98 1 0 64 76 28 0 0 0 g 0 0 0 0 32 3 0 1 0 1 2 0 0 10 0 0 0 t 0 0 0 0 7 53 1 1 2 87 0 0 23 28 0 0 0
7238_MYB46_ArabidopsisPBM_20140210__rc_shift4 (7238_MYB46_ArabidopsisPBM_20140210__rc)	0.740	0.435	0.264	0.889	0.876	4	4	6	6	6	5.200	6	; oligos_6-8nt_m1 versus 7238_MYB46_ArabidopsisPBM_20140210__rc; m=6/6; ncol2=10; w=0; offset=4; strand=R; shift=4; score= 5.2; ----yyACCTAmCt--- ; cor=0.740; Ncor=0.435; logoDP=0.264; NsEucl=0.889; NSW=0.876; rcor=4; rNcor=4; rlogoDP=6; rNsEucl=6; rNSW=6; rank_mean=5.200; match_rank=6 a 0 0 0 0 15 4 96 9 0 12 98 61 1 20 0 0 0 c 0 0 0 0 37 36 0 91 100 1 0 39 91 22 0 0 0 g 0 0 0 0 22 2 4 0 0 3 1 0 0 16 0 0 0 t 0 0 0 0 26 58 0 0 0 84 1 0 8 42 0 0 0