# 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_m2/peak-motifs_oligos_8nt_mkv2_m2.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_m2/peak-motifs_oligos_8nt_mkv2_m2_vs_db_ArabidopsisPBM

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m2_shift2 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m2_shift2 (oligos_8nt_mkv2_m2) |  |  |  |
    ; oligos_8nt_mkv2_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --ywAACGGCGTtw
    ; Alignment reference
    a	0	0	4	9	15	16	1	0	2	0	0	1	3	5
    c	0	0	6	1	1	0	16	1	2	17	0	0	4	1
    g	0	0	2	0	2	1	0	16	14	0	18	1	4	3
    t	0	0	6	8	0	1	1	1	0	1	0	16	7	9
7240_MYB52_ArabidopsisPBM_20140210__shift0 (7240_MYB52_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_8nt_mkv2_m2 versus 7240_MYB52_ArabidopsisPBM_20140210_; m=1/1; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.460582; amcTAACGGw----
    ; cor=; Ncor=
    a	64	49	24	10	92	87	2	9	13	46	0	0	0	0
    c	8	30	52	11	1	10	92	5	2	18	0	0	0	0
    g	17	15	10	4	4	1	3	79	79	9	0	0	0	0
    t	11	6	14	75	3	2	3	7	6	27	0	0	0	0