# 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/dyads_m4/peak-motifs_dyads_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/dyads_m4/peak-motifs_dyads_m4_vs_db_ArabidopsisPBM

## One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m4_shift0 (dyads_m4) |  |  |  |
    ; dyads_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; waACCAAACmm
    ; Alignment reference
    a	5	7	16	0	0	11	16	16	0	5	7
    c	2	3	0	16	16	1	0	0	16	5	6
    g	3	3	0	0	0	2	0	0	0	3	1
    t	6	3	0	0	0	2	0	0	0	3	2
7238_MYB46_ArabidopsisPBM_20140210__rc_shift0 (7238_MYB46_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; dyads_m4 versus 7238_MYB46_ArabidopsisPBM_20140210__rc; m=1/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.739175; yyACCTAmCt-
    ; cor=; Ncor=
    a	15	4	96	9	0	12	98	61	1	20	0
    c	37	36	0	91	100	1	0	39	91	22	0
    g	22	2	4	0	0	3	1	0	0	16	0
    t	26	58	0	0	0	84	1	0	8	42	0
7244_MYB59_ArabidopsisPBM_20140210__rc_shift0 (7244_MYB59_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; dyads_m4 versus 7244_MYB59_ArabidopsisPBM_20140210__rc; m=2/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.727915; kkACCTAAyt-
    ; cor=; Ncor=
    a	24	16	92	2	2	7	95	86	8	20	0
    c	16	2	0	95	96	2	1	11	55	16	0
    g	28	27	4	1	0	4	1	1	1	5	0
    t	32	55	4	2	2	87	3	2	36	59	0
7242_MYB55_ArabidopsisPBM_20140210__shift1 (7242_MYB55_ArabidopsisPBM_20140210_) |  |  |  |
    ; dyads_m4 versus 7242_MYB55_ArabidopsisPBM_20140210_; m=3/4; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.678908; -yACCTAMCGv
    ; cor=; Ncor=
    a	0	11	98	5	0	23	98	27	0	12	25
    c	0	36	0	95	99	5	0	73	96	5	28
    g	0	5	2	0	0	2	2	0	0	76	30
    t	0	48	0	0	1	70	0	0	4	7	17
7236_MYB111_ArabidopsisPBM_20140210__rc_shift0 (7236_MYB111_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; dyads_m4 versus 7236_MYB111_ArabidopsisPBM_20140210__rc; m=4/4; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.661078; syACCTAmCh-
    ; cor=; Ncor=
    a	15	5	99	13	0	11	98	36	1	34	0
    c	46	39	0	85	98	1	0	64	76	28	0
    g	32	3	0	1	0	1	2	0	0	10	0
    t	7	53	1	1	2	87	0	0	23	28	0