# 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.2026-02-26.135932_2026-02-26.135932_MeLHd6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_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/2026/02/26/peak-motifs.2026-02-26.135932_2026-02-26.135932_MeLHd6/results/discovered_motifs/oligos_7nt_mkv2_m4/peak-motifs_oligos_7nt_mkv2_m4_vs_db_ArabidopsisPBM

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m4_shift2 (oligos_7nt_mkv2_m4) |  |  |  |
    ; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=2; ncol=14; --yhAACGGCGwwd
    ; Alignment reference
    a	0	0	3	5	15	16	1	0	1	0	2	4	7	7
    c	0	0	5	5	0	0	14	1	2	14	0	1	2	0
    g	0	0	2	0	1	0	0	15	13	0	13	3	2	4
    t	0	0	6	6	0	0	1	0	0	2	1	8	5	5
7240_MYB52_ArabidopsisPBM_20140210__shift0 (7240_MYB52_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_7nt_mkv2_m4 versus 7240_MYB52_ArabidopsisPBM_20140210_; m=1/2; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.475064; 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
7218_DOF5.7_2_ArabidopsisPBM_20140210__rc_shift0 (7218_DOF5.7_2_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_7nt_mkv2_m4 versus 7218_DOF5.7_2_ArabidopsisPBM_20140210__rc; m=2/2; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.415556; mGTTAACGwt----
    ; cor=; Ncor=
    a	25	5	5	6	96	96	4	2	25	24	0	0	0	0
    c	52	1	3	3	2	2	94	2	13	24	0	0	0	0
    g	11	90	5	3	1	0	0	94	15	8	0	0	0	0
    t	12	4	87	88	1	2	2	2	47	44	0	0	0	0