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_6nt_mkv2_m1/peak-motifs_oligos_6nt_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_6nt_mkv2_m1/peak-motifs_oligos_6nt_mkv2_m1_vs_db_ArabidopsisPBM

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)
; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; ytcACCAACCCmm ; Alignment reference a 9 11 11 46 0 0 44 45 11 1 11 19 18 c 14 6 27 1 50 47 1 2 38 42 34 18 17 g 4 7 5 0 0 1 1 2 1 0 4 5 7 t 23 26 7 3 0 2 4 1 0 7 1 8 8

7237_MYB111_2_ArabidopsisPBM_20140210__rc_shift1 (7237_MYB111_2_ArabidopsisPBM_20140210__rc)
; oligos_6nt_mkv2_m1 versus 7237_MYB111_2_ArabidopsisPBM_20140210__rc; m=1/5; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.613959; -cYAMCwACCt-- ; cor=; Ncor= a 0 13 0 97 26 0 37 99 14 1 22 0 0 c 0 58 68 0 73 98 3 1 85 93 11 0 0 g 0 13 2 1 1 0 1 0 0 0 10 0 0 t 0 16 30 2 0 2 59 0 1 6 57 0 0

7242_MYB55_ArabidopsisPBM_20140210__shift2 (7242_MYB55_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv2_m1 versus 7242_MYB55_ArabidopsisPBM_20140210_; m=2/5; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.601847; --yACCTAMCGv- ; cor=; Ncor= a 0 0 11 98 5 0 23 98 27 0 12 25 0 c 0 0 36 0 95 99 5 0 73 96 5 28 0 g 0 0 5 2 0 0 2 2 0 0 76 30 0 t 0 0 48 0 0 1 70 0 0 4 7 17 0

7236_MYB111_ArabidopsisPBM_20140210__rc_shift1 (7236_MYB111_ArabidopsisPBM_20140210__rc)
; oligos_6nt_mkv2_m1 versus 7236_MYB111_ArabidopsisPBM_20140210__rc; m=3/5; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.578132; -syACCTAmCh-- ; cor=; Ncor= a 0 15 5 99 13 0 11 98 36 1 34 0 0 c 0 46 39 0 85 98 1 0 64 76 28 0 0 g 0 32 3 0 1 0 1 2 0 0 10 0 0 t 0 7 53 1 1 2 87 0 0 23 28 0 0

7238_MYB46_ArabidopsisPBM_20140210__rc_shift1 (7238_MYB46_ArabidopsisPBM_20140210__rc)
; oligos_6nt_mkv2_m1 versus 7238_MYB46_ArabidopsisPBM_20140210__rc; m=4/5; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.569328; -yyACCTAmCt-- ; cor=; Ncor= a 0 15 4 96 9 0 12 98 61 1 20 0 0 c 0 37 36 0 91 100 1 0 39 91 22 0 0 g 0 22 2 4 0 0 3 1 0 0 16 0 0 t 0 26 58 0 0 0 84 1 0 8 42 0 0

7243_MYB55_2_ArabidopsisPBM_20140210__rc_shift4 (7243_MYB55_2_ArabidopsisPBM_20140210__rc)
; oligos_6nt_mkv2_m1 versus 7243_MYB55_2_ArabidopsisPBM_20140210__rc; m=5/5; ncol2=10; w=0; offset=4; strand=R; shift=4; score=0.459937; ----cCAmCCAMC ; cor=; Ncor= a 0 0 0 0 13 2 96 54 1 17 91 28 2 c 0 0 0 0 62 83 2 44 98 69 0 70 89 g 0 0 0 0 11 5 0 1 0 3 8 1 1 t 0 0 0 0 14 10 2 1 1 11 1 1 8

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1)				; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; ytcACCAACCCmm ; Alignment reference a 9 11 11 46 0 0 44 45 11 1 11 19 18 c 14 6 27 1 50 47 1 2 38 42 34 18 17 g 4 7 5 0 0 1 1 2 1 0 4 5 7 t 23 26 7 3 0 2 4 1 0 7 1 8 8
7237_MYB111_2_ArabidopsisPBM_20140210__rc_shift1 (7237_MYB111_2_ArabidopsisPBM_20140210__rc)				; oligos_6nt_mkv2_m1 versus 7237_MYB111_2_ArabidopsisPBM_20140210__rc; m=1/5; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.613959; -cYAMCwACCt-- ; cor=; Ncor= a 0 13 0 97 26 0 37 99 14 1 22 0 0 c 0 58 68 0 73 98 3 1 85 93 11 0 0 g 0 13 2 1 1 0 1 0 0 0 10 0 0 t 0 16 30 2 0 2 59 0 1 6 57 0 0
7242_MYB55_ArabidopsisPBM_20140210__shift2 (7242_MYB55_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv2_m1 versus 7242_MYB55_ArabidopsisPBM_20140210_; m=2/5; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.601847; --yACCTAMCGv- ; cor=; Ncor= a 0 0 11 98 5 0 23 98 27 0 12 25 0 c 0 0 36 0 95 99 5 0 73 96 5 28 0 g 0 0 5 2 0 0 2 2 0 0 76 30 0 t 0 0 48 0 0 1 70 0 0 4 7 17 0
7236_MYB111_ArabidopsisPBM_20140210__rc_shift1 (7236_MYB111_ArabidopsisPBM_20140210__rc)				; oligos_6nt_mkv2_m1 versus 7236_MYB111_ArabidopsisPBM_20140210__rc; m=3/5; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.578132; -syACCTAmCh-- ; cor=; Ncor= a 0 15 5 99 13 0 11 98 36 1 34 0 0 c 0 46 39 0 85 98 1 0 64 76 28 0 0 g 0 32 3 0 1 0 1 2 0 0 10 0 0 t 0 7 53 1 1 2 87 0 0 23 28 0 0
7238_MYB46_ArabidopsisPBM_20140210__rc_shift1 (7238_MYB46_ArabidopsisPBM_20140210__rc)				; oligos_6nt_mkv2_m1 versus 7238_MYB46_ArabidopsisPBM_20140210__rc; m=4/5; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.569328; -yyACCTAmCt-- ; cor=; Ncor= a 0 15 4 96 9 0 12 98 61 1 20 0 0 c 0 37 36 0 91 100 1 0 39 91 22 0 0 g 0 22 2 4 0 0 3 1 0 0 16 0 0 t 0 26 58 0 0 0 84 1 0 8 42 0 0
7243_MYB55_2_ArabidopsisPBM_20140210__rc_shift4 (7243_MYB55_2_ArabidopsisPBM_20140210__rc)				; oligos_6nt_mkv2_m1 versus 7243_MYB55_2_ArabidopsisPBM_20140210__rc; m=5/5; ncol2=10; w=0; offset=4; strand=R; shift=4; score=0.459937; ----cCAmCCAMC ; cor=; Ncor= a 0 0 0 0 13 2 96 54 1 17 91 28 2 c 0 0 0 0 62 83 2 44 98 69 0 70 89 g 0 0 0 0 11 5 0 1 0 3 8 1 1 t 0 0 0 0 14 10 2 1 1 11 1 1 8