# 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_7nt_mkv1_m1/peak-motifs_oligos_7nt_mkv1_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/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/discovered_motifs/oligos_7nt_mkv1_m1/peak-motifs_oligos_7nt_mkv1_m1_vs_db_ArabidopsisPBM

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; raAAAAAAAww
    ; Alignment reference
    a	32	29	69	70	73	71	70	71	74	33	33
    c	15	16	3	4	5	3	3	1	0	9	8
    g	22	19	7	5	2	5	4	4	4	18	19
    t	12	17	2	2	1	2	4	5	3	21	21
7217_DOF5.7_ArabidopsisPBM_20140210__shift2 (7217_DOF5.7_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus 7217_DOF5.7_ArabidopsisPBM_20140210_; m=1/1; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.54141; --raAAArrkg
    ; cor=; Ncor=
    a	0	0	39	45	68	97	90	36	48	10	18
    c	0	0	21	9	1	0	0	4	6	19	21
    g	0	0	27	22	7	1	8	59	44	46	41
    t	0	0	13	24	24	2	2	1	2	25	20