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_7nt_mkv2_m1/peak-motifs_oligos_7nt_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_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_vs_db_ArabidopsisPBM

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)
; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; mtTcACCAACCCmm ; Alignment reference a 15 7 3 4 34 1 0 33 35 4 1 4 11 11 c 10 6 2 22 1 34 35 0 1 31 29 29 14 13 g 3 2 3 4 0 0 0 1 0 2 1 4 4 5 t 9 22 29 7 2 2 2 3 1 0 6 0 8 8

7242_MYB55_ArabidopsisPBM_20140210__shift3 (7242_MYB55_ArabidopsisPBM_20140210_)
; oligos_7nt_mkv2_m1 versus 7242_MYB55_ArabidopsisPBM_20140210_; m=1/3; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.550159; ---yACCTAMCGv- ; cor=; Ncor= a 0 0 0 11 98 5 0 23 98 27 0 12 25 0 c 0 0 0 36 0 95 99 5 0 73 96 5 28 0 g 0 0 0 5 2 0 0 2 2 0 0 76 30 0 t 0 0 0 48 0 0 1 70 0 0 4 7 17 0

7237_MYB111_2_ArabidopsisPBM_20140210__rc_shift2 (7237_MYB111_2_ArabidopsisPBM_20140210__rc)
; oligos_7nt_mkv2_m1 versus 7237_MYB111_2_ArabidopsisPBM_20140210__rc; m=2/3; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.547096; --cYAMCwACCt-- ; cor=; Ncor= a 0 0 13 0 97 26 0 37 99 14 1 22 0 0 c 0 0 58 68 0 73 98 3 1 85 93 11 0 0 g 0 0 13 2 1 1 0 1 0 0 0 10 0 0 t 0 0 16 30 2 0 2 59 0 1 6 57 0 0

7236_MYB111_ArabidopsisPBM_20140210__rc_shift2 (7236_MYB111_ArabidopsisPBM_20140210__rc)
; oligos_7nt_mkv2_m1 versus 7236_MYB111_ArabidopsisPBM_20140210__rc; m=3/3; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.503565; --syACCTAmCh-- ; cor=; Ncor= a 0 0 15 5 99 13 0 11 98 36 1 34 0 0 c 0 0 46 39 0 85 98 1 0 64 76 28 0 0 g 0 0 32 3 0 1 0 1 2 0 0 10 0 0 t 0 0 7 53 1 1 2 87 0 0 23 28 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1)				; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; mtTcACCAACCCmm ; Alignment reference a 15 7 3 4 34 1 0 33 35 4 1 4 11 11 c 10 6 2 22 1 34 35 0 1 31 29 29 14 13 g 3 2 3 4 0 0 0 1 0 2 1 4 4 5 t 9 22 29 7 2 2 2 3 1 0 6 0 8 8
7242_MYB55_ArabidopsisPBM_20140210__shift3 (7242_MYB55_ArabidopsisPBM_20140210_)				; oligos_7nt_mkv2_m1 versus 7242_MYB55_ArabidopsisPBM_20140210_; m=1/3; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.550159; ---yACCTAMCGv- ; cor=; Ncor= a 0 0 0 11 98 5 0 23 98 27 0 12 25 0 c 0 0 0 36 0 95 99 5 0 73 96 5 28 0 g 0 0 0 5 2 0 0 2 2 0 0 76 30 0 t 0 0 0 48 0 0 1 70 0 0 4 7 17 0
7237_MYB111_2_ArabidopsisPBM_20140210__rc_shift2 (7237_MYB111_2_ArabidopsisPBM_20140210__rc)				; oligos_7nt_mkv2_m1 versus 7237_MYB111_2_ArabidopsisPBM_20140210__rc; m=2/3; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.547096; --cYAMCwACCt-- ; cor=; Ncor= a 0 0 13 0 97 26 0 37 99 14 1 22 0 0 c 0 0 58 68 0 73 98 3 1 85 93 11 0 0 g 0 0 13 2 1 1 0 1 0 0 0 10 0 0 t 0 0 16 30 2 0 2 59 0 1 6 57 0 0
7236_MYB111_ArabidopsisPBM_20140210__rc_shift2 (7236_MYB111_ArabidopsisPBM_20140210__rc)				; oligos_7nt_mkv2_m1 versus 7236_MYB111_ArabidopsisPBM_20140210__rc; m=3/3; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.503565; --syACCTAmCh-- ; cor=; Ncor= a 0 0 15 5 99 13 0 11 98 36 1 34 0 0 c 0 0 46 39 0 85 98 1 0 64 76 28 0 0 g 0 0 32 3 0 1 0 1 2 0 0 10 0 0 t 0 0 7 53 1 1 2 87 0 0 23 28 0 0