# 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_m2/peak-motifs_dyads_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.2026-02-26.135932_2026-02-26.135932_MeLHd6/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_ArabidopsisPBM

## One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m2_shift0 (dyads_m2) |  |  |  |
    ; dyads_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; tyACCwayyCCCwy
    ; Alignment reference
    a	4	3	18	0	1	7	13	2	3	3	1	0	9	3
    c	5	7	1	22	20	5	5	9	9	16	20	22	3	8
    g	5	3	0	0	1	1	1	4	2	3	0	0	4	2
    t	8	9	3	0	0	9	3	7	8	0	1	0	6	9
7236_MYB111_ArabidopsisPBM_20140210__rc_shift0 (7236_MYB111_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; dyads_m2 versus 7236_MYB111_ArabidopsisPBM_20140210__rc; m=1/2; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.564103; syACCTAmCh----
    ; cor=; Ncor=
    a	15	5	99	13	0	11	98	36	1	34	0	0	0	0
    c	46	39	0	85	98	1	0	64	76	28	0	0	0	0
    g	32	3	0	1	0	1	2	0	0	10	0	0	0	0
    t	7	53	1	1	2	87	0	0	23	28	0	0	0	0
7238_MYB46_ArabidopsisPBM_20140210__rc_shift0 (7238_MYB46_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; dyads_m2 versus 7238_MYB46_ArabidopsisPBM_20140210__rc; m=2/2; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.541028; yyACCTAmCt----
    ; cor=; Ncor=
    a	15	4	96	9	0	12	98	61	1	20	0	0	0	0
    c	37	36	0	91	100	1	0	39	91	22	0	0	0	0
    g	22	2	4	0	0	3	1	0	0	16	0	0	0	0
    t	26	58	0	0	0	84	1	0	8	42	0	0	0	0