One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/discovered_motifs/oligos_6nt_mkv1_m4/peak-motifs_oligos_6nt_mkv1_m4.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/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/discovered_motifs/oligos_6nt_mkv1_m4/peak-motifs_oligos_6nt_mkv1_m4_vs_db_ArabidopsisPBM

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4)
; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=3; ncol=13; ---sgAGGTAGwm ; Alignment reference a 0 0 0 3 3 16 0 0 0 18 0 6 5 c 0 0 0 7 4 0 0 2 0 0 1 3 5 g 0 0 0 5 7 0 17 16 0 0 16 4 4 t 0 0 0 3 4 2 1 0 18 0 1 5 4

7265_STY1_2_ArabidopsisPBM_20140210__rc_shift2 (7265_STY1_2_ArabidopsisPBM_20140210__rc)
; oligos_6nt_mkv1_m4 versus 7265_STY1_2_ArabidopsisPBM_20140210__rc; m=1/5; ncol2=10; w=-1; offset=-1; strand=R; shift=2; score=0.578813; --rCTAGCTAGt- ; cor=; Ncor= a 0 0 31 3 5 91 2 2 5 91 3 16 0 c 0 0 8 89 1 0 1 95 4 3 5 20 0 g 0 0 50 5 3 4 95 1 0 1 89 23 0 t 0 0 11 3 91 5 2 2 91 5 3 41 0

7237_MYB111_2_ArabidopsisPBM_20140210__shift5 (7237_MYB111_2_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m4 versus 7237_MYB111_2_ArabidopsisPBM_20140210_; m=2/5; ncol2=10; w=0; offset=2; strand=D; shift=5; score=0.526712; -----aGGTwGKT ; cor=; Ncor= a 0 0 0 0 0 57 6 1 0 59 2 0 2 c 0 0 0 0 0 10 0 0 0 1 0 1 1 g 0 0 0 0 0 11 93 85 1 3 98 73 0 t 0 0 0 0 0 22 1 14 99 37 0 26 97

7236_MYB111_ArabidopsisPBM_20140210__shift1 (7236_MYB111_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m4 versus 7236_MYB111_ArabidopsisPBM_20140210_; m=3/5; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.506784; -dGkTAGGTrs-- ; cor=; Ncor= a 0 28 23 0 0 87 2 1 1 53 7 0 0 c 0 10 0 0 2 1 0 1 0 3 32 0 0 g 0 28 76 64 0 1 98 85 0 39 46 0 0 t 0 34 1 36 98 11 0 13 99 5 15 0 0

7238_MYB46_ArabidopsisPBM_20140210__shift1 (7238_MYB46_ArabidopsisPBM_20140210_)
; oligos_6nt_mkv1_m4 versus 7238_MYB46_ArabidopsisPBM_20140210_; m=4/5; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.499562; -aGkTAGGTrr-- ; cor=; Ncor= a 0 42 8 0 1 84 0 0 0 58 26 0 0 c 0 16 0 0 1 3 0 0 4 2 22 0 0 g 0 22 91 39 0 1 100 91 0 36 37 0 0 t 0 20 1 61 98 12 0 9 96 4 15 0 0

7242_MYB55_ArabidopsisPBM_20140210__rc_shift0 (7242_MYB55_ArabidopsisPBM_20140210__rc)
; oligos_6nt_mkv1_m4 versus 7242_MYB55_ArabidopsisPBM_20140210__rc; m=5/5; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.407551; bCGKTAGGTr--- ; cor=; Ncor= a 17 7 4 0 0 70 1 0 0 48 0 0 0 c 30 76 0 0 2 2 0 0 2 5 0 0 0 g 28 5 96 73 0 5 99 95 0 36 0 0 0 t 25 12 0 27 98 23 0 5 98 11 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4)				; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=3; ncol=13; ---sgAGGTAGwm ; Alignment reference a 0 0 0 3 3 16 0 0 0 18 0 6 5 c 0 0 0 7 4 0 0 2 0 0 1 3 5 g 0 0 0 5 7 0 17 16 0 0 16 4 4 t 0 0 0 3 4 2 1 0 18 0 1 5 4
7265_STY1_2_ArabidopsisPBM_20140210__rc_shift2 (7265_STY1_2_ArabidopsisPBM_20140210__rc)				; oligos_6nt_mkv1_m4 versus 7265_STY1_2_ArabidopsisPBM_20140210__rc; m=1/5; ncol2=10; w=-1; offset=-1; strand=R; shift=2; score=0.578813; --rCTAGCTAGt- ; cor=; Ncor= a 0 0 31 3 5 91 2 2 5 91 3 16 0 c 0 0 8 89 1 0 1 95 4 3 5 20 0 g 0 0 50 5 3 4 95 1 0 1 89 23 0 t 0 0 11 3 91 5 2 2 91 5 3 41 0
7237_MYB111_2_ArabidopsisPBM_20140210__shift5 (7237_MYB111_2_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m4 versus 7237_MYB111_2_ArabidopsisPBM_20140210_; m=2/5; ncol2=10; w=0; offset=2; strand=D; shift=5; score=0.526712; -----aGGTwGKT ; cor=; Ncor= a 0 0 0 0 0 57 6 1 0 59 2 0 2 c 0 0 0 0 0 10 0 0 0 1 0 1 1 g 0 0 0 0 0 11 93 85 1 3 98 73 0 t 0 0 0 0 0 22 1 14 99 37 0 26 97
7236_MYB111_ArabidopsisPBM_20140210__shift1 (7236_MYB111_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m4 versus 7236_MYB111_ArabidopsisPBM_20140210_; m=3/5; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.506784; -dGkTAGGTrs-- ; cor=; Ncor= a 0 28 23 0 0 87 2 1 1 53 7 0 0 c 0 10 0 0 2 1 0 1 0 3 32 0 0 g 0 28 76 64 0 1 98 85 0 39 46 0 0 t 0 34 1 36 98 11 0 13 99 5 15 0 0
7238_MYB46_ArabidopsisPBM_20140210__shift1 (7238_MYB46_ArabidopsisPBM_20140210_)				; oligos_6nt_mkv1_m4 versus 7238_MYB46_ArabidopsisPBM_20140210_; m=4/5; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.499562; -aGkTAGGTrr-- ; cor=; Ncor= a 0 42 8 0 1 84 0 0 0 58 26 0 0 c 0 16 0 0 1 3 0 0 4 2 22 0 0 g 0 22 91 39 0 1 100 91 0 36 37 0 0 t 0 20 1 61 98 12 0 9 96 4 15 0 0
7242_MYB55_ArabidopsisPBM_20140210__rc_shift0 (7242_MYB55_ArabidopsisPBM_20140210__rc)				; oligos_6nt_mkv1_m4 versus 7242_MYB55_ArabidopsisPBM_20140210__rc; m=5/5; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.407551; bCGKTAGGTr--- ; cor=; Ncor= a 17 7 4 0 0 70 1 0 0 48 0 0 0 c 30 76 0 0 2 2 0 0 2 5 0 0 0 g 28 5 96 73 0 5 99 95 0 36 0 0 0 t 25 12 0 27 98 23 0 5 98 11 0 0 0