One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.135827_2026-02-26.135827_NiTe41/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/ArabidopsisPBM/ArabidopsisPBM_2015-11-06.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/2026/02/26/peak-motifs.2026-02-26.135827_2026-02-26.135827_NiTe41/results/discovered_motifs/oligos_8nt_mkv2_m1/peak-motifs_oligos_8nt_mkv2_m1_vs_db_ArabidopsisPBM

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m1_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)
; oligos_8nt_mkv2_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; mtTCACCAACCmCmm ; Alignment reference a 12 5 3 0 27 1 0 26 26 4 0 8 4 11 9 c 9 6 3 22 0 28 29 0 1 24 27 17 20 10 9 g 2 2 0 3 0 0 0 0 2 1 0 3 2 6 4 t 6 16 23 4 2 0 0 3 0 0 2 1 3 2 7

7237_MYB111_2_ArabidopsisPBM_20140210__rc_shift2 (7237_MYB111_2_ArabidopsisPBM_20140210__rc)
; oligos_8nt_mkv2_m1 versus 7237_MYB111_2_ArabidopsisPBM_20140210__rc; m=1/6; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.540576; --cYAMCwACCt--- ; cor=; Ncor= a 0 0 13 0 97 26 0 37 99 14 1 22 0 0 0 c 0 0 58 68 0 73 98 3 1 85 93 11 0 0 0 g 0 0 13 2 1 1 0 1 0 0 0 10 0 0 0 t 0 0 16 30 2 0 2 59 0 1 6 57 0 0 0

7242_MYB55_ArabidopsisPBM_20140210__shift3 (7242_MYB55_ArabidopsisPBM_20140210_)
; oligos_8nt_mkv2_m1 versus 7242_MYB55_ArabidopsisPBM_20140210_; m=2/6; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.520683; ---yACCTAMCGv-- ; cor=; Ncor= a 0 0 0 11 98 5 0 23 98 27 0 12 25 0 0 c 0 0 0 36 0 95 99 5 0 73 96 5 28 0 0 g 0 0 0 5 2 0 0 2 2 0 0 76 30 0 0 t 0 0 0 48 0 0 1 70 0 0 4 7 17 0 0

7243_MYB55_2_ArabidopsisPBM_20140210__rc_shift5 (7243_MYB55_2_ArabidopsisPBM_20140210__rc)
; oligos_8nt_mkv2_m1 versus 7243_MYB55_2_ArabidopsisPBM_20140210__rc; m=3/6; ncol2=10; w=0; offset=5; strand=R; shift=5; score=0.496655; -----cCAmCCAMCg ; cor=; Ncor= a 0 0 0 0 0 13 2 96 54 1 17 91 28 2 24 c 0 0 0 0 0 62 83 2 44 98 69 0 70 89 14 g 0 0 0 0 0 11 5 0 1 0 3 8 1 1 54 t 0 0 0 0 0 14 10 2 1 1 11 1 1 8 8

7236_MYB111_ArabidopsisPBM_20140210__rc_shift2 (7236_MYB111_ArabidopsisPBM_20140210__rc)
; oligos_8nt_mkv2_m1 versus 7236_MYB111_ArabidopsisPBM_20140210__rc; m=4/6; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.484147; --syACCTAmCh--- ; cor=; Ncor= a 0 0 15 5 99 13 0 11 98 36 1 34 0 0 0 c 0 0 46 39 0 85 98 1 0 64 76 28 0 0 0 g 0 0 32 3 0 1 0 1 2 0 0 10 0 0 0 t 0 0 7 53 1 1 2 87 0 0 23 28 0 0 0

7238_MYB46_ArabidopsisPBM_20140210__rc_shift2 (7238_MYB46_ArabidopsisPBM_20140210__rc)
; oligos_8nt_mkv2_m1 versus 7238_MYB46_ArabidopsisPBM_20140210__rc; m=5/6; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.483323; --yyACCTAmCt--- ; cor=; Ncor= a 0 0 15 4 96 9 0 12 98 61 1 20 0 0 0 c 0 0 37 36 0 91 100 1 0 39 91 22 0 0 0 g 0 0 22 2 4 0 0 3 1 0 0 16 0 0 0 t 0 0 26 58 0 0 0 84 1 0 8 42 0 0 0

7239_MYB46_2_ArabidopsisPBM_20140210__shift5 (7239_MYB46_2_ArabidopsisPBM_20140210_)
; oligos_8nt_mkv2_m1 versus 7239_MYB46_2_ArabidopsisPBM_20140210_; m=6/6; ncol2=10; w=0; offset=5; strand=D; shift=5; score= 0.4743; -----yyAACCAmCr ; cor=; Ncor= a 0 0 0 0 0 16 5 92 82 1 21 82 25 6 31 c 0 0 0 0 0 29 53 3 13 96 68 1 64 72 19 g 0 0 0 0 0 24 13 3 2 1 7 16 2 3 39 t 0 0 0 0 0 31 29 2 3 2 4 1 9 19 11

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m1_shift0 (oligos_8nt_mkv2_m1)				; oligos_8nt_mkv2_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; mtTCACCAACCmCmm ; Alignment reference a 12 5 3 0 27 1 0 26 26 4 0 8 4 11 9 c 9 6 3 22 0 28 29 0 1 24 27 17 20 10 9 g 2 2 0 3 0 0 0 0 2 1 0 3 2 6 4 t 6 16 23 4 2 0 0 3 0 0 2 1 3 2 7
7237_MYB111_2_ArabidopsisPBM_20140210__rc_shift2 (7237_MYB111_2_ArabidopsisPBM_20140210__rc)				; oligos_8nt_mkv2_m1 versus 7237_MYB111_2_ArabidopsisPBM_20140210__rc; m=1/6; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.540576; --cYAMCwACCt--- ; cor=; Ncor= a 0 0 13 0 97 26 0 37 99 14 1 22 0 0 0 c 0 0 58 68 0 73 98 3 1 85 93 11 0 0 0 g 0 0 13 2 1 1 0 1 0 0 0 10 0 0 0 t 0 0 16 30 2 0 2 59 0 1 6 57 0 0 0
7242_MYB55_ArabidopsisPBM_20140210__shift3 (7242_MYB55_ArabidopsisPBM_20140210_)				; oligos_8nt_mkv2_m1 versus 7242_MYB55_ArabidopsisPBM_20140210_; m=2/6; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.520683; ---yACCTAMCGv-- ; cor=; Ncor= a 0 0 0 11 98 5 0 23 98 27 0 12 25 0 0 c 0 0 0 36 0 95 99 5 0 73 96 5 28 0 0 g 0 0 0 5 2 0 0 2 2 0 0 76 30 0 0 t 0 0 0 48 0 0 1 70 0 0 4 7 17 0 0
7243_MYB55_2_ArabidopsisPBM_20140210__rc_shift5 (7243_MYB55_2_ArabidopsisPBM_20140210__rc)				; oligos_8nt_mkv2_m1 versus 7243_MYB55_2_ArabidopsisPBM_20140210__rc; m=3/6; ncol2=10; w=0; offset=5; strand=R; shift=5; score=0.496655; -----cCAmCCAMCg ; cor=; Ncor= a 0 0 0 0 0 13 2 96 54 1 17 91 28 2 24 c 0 0 0 0 0 62 83 2 44 98 69 0 70 89 14 g 0 0 0 0 0 11 5 0 1 0 3 8 1 1 54 t 0 0 0 0 0 14 10 2 1 1 11 1 1 8 8
7236_MYB111_ArabidopsisPBM_20140210__rc_shift2 (7236_MYB111_ArabidopsisPBM_20140210__rc)				; oligos_8nt_mkv2_m1 versus 7236_MYB111_ArabidopsisPBM_20140210__rc; m=4/6; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.484147; --syACCTAmCh--- ; cor=; Ncor= a 0 0 15 5 99 13 0 11 98 36 1 34 0 0 0 c 0 0 46 39 0 85 98 1 0 64 76 28 0 0 0 g 0 0 32 3 0 1 0 1 2 0 0 10 0 0 0 t 0 0 7 53 1 1 2 87 0 0 23 28 0 0 0
7238_MYB46_ArabidopsisPBM_20140210__rc_shift2 (7238_MYB46_ArabidopsisPBM_20140210__rc)				; oligos_8nt_mkv2_m1 versus 7238_MYB46_ArabidopsisPBM_20140210__rc; m=5/6; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.483323; --yyACCTAmCt--- ; cor=; Ncor= a 0 0 15 4 96 9 0 12 98 61 1 20 0 0 0 c 0 0 37 36 0 91 100 1 0 39 91 22 0 0 0 g 0 0 22 2 4 0 0 3 1 0 0 16 0 0 0 t 0 0 26 58 0 0 0 84 1 0 8 42 0 0 0
7239_MYB46_2_ArabidopsisPBM_20140210__shift5 (7239_MYB46_2_ArabidopsisPBM_20140210_)				; oligos_8nt_mkv2_m1 versus 7239_MYB46_2_ArabidopsisPBM_20140210_; m=6/6; ncol2=10; w=0; offset=5; strand=D; shift=5; score= 0.4743; -----yyAACCAmCr ; cor=; Ncor= a 0 0 0 0 0 16 5 92 82 1 21 82 25 6 31 c 0 0 0 0 0 29 53 3 13 96 68 1 64 72 19 g 0 0 0 0 0 24 13 3 2 1 7 16 2 3 39 t 0 0 0 0 0 31 29 2 3 2 4 1 9 19 11