# 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_m3/peak-motifs_oligos_7nt_mkv2_m3.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_m3/peak-motifs_oligos_7nt_mkv2_m3_vs_db_ArabidopsisPBM

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3) |  |  |  |
    ; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; whACCAAACmh
    ; Alignment reference
    a	8	8	25	0	0	22	26	21	0	7	8
    c	3	7	0	26	27	1	1	5	26	9	11
    g	3	3	2	1	0	2	0	1	0	5	1
    t	13	9	0	0	0	2	0	0	1	6	7
7238_MYB46_ArabidopsisPBM_20140210__rc_shift0 (7238_MYB46_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_7nt_mkv2_m3 versus 7238_MYB46_ArabidopsisPBM_20140210__rc; m=1/5; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.750475; 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
7242_MYB55_ArabidopsisPBM_20140210__shift1 (7242_MYB55_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_7nt_mkv2_m3 versus 7242_MYB55_ArabidopsisPBM_20140210_; m=2/5; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.713903; -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
7244_MYB59_ArabidopsisPBM_20140210__rc_shift0 (7244_MYB59_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_7nt_mkv2_m3 versus 7244_MYB59_ArabidopsisPBM_20140210__rc; m=3/5; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.706551; 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
7236_MYB111_ArabidopsisPBM_20140210__rc_shift0 (7236_MYB111_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_7nt_mkv2_m3 versus 7236_MYB111_ArabidopsisPBM_20140210__rc; m=4/5; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.680343; 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
7237_MYB111_2_ArabidopsisPBM_20140210__rc_shift0 (7237_MYB111_2_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_7nt_mkv2_m3 versus 7237_MYB111_2_ArabidopsisPBM_20140210__rc; m=5/5; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.675321; cYAMCwACCt-
    ; cor=; Ncor=
    a	13	0	97	26	0	37	99	14	1	22	0
    c	58	68	0	73	98	3	1	85	93	11	0
    g	13	2	1	1	0	1	0	0	0	10	0
    t	16	30	2	0	2	59	0	1	6	57	0