# 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_m2/peak-motifs_oligos_7nt_mkv2_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/oligos_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_vs_db_ArabidopsisPBM

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2) |  |  |  |
    ; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; wyACCAACCrm
    ; Alignment reference
    a	14	7	33	2	0	29	34	5	1	12	9
    c	5	13	1	32	35	2	0	30	31	8	20
    g	2	6	0	0	0	1	2	1	2	10	2
    t	15	10	2	2	1	4	0	0	2	6	5
7242_MYB55_ArabidopsisPBM_20140210__shift1 (7242_MYB55_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_7nt_mkv2_m2 versus 7242_MYB55_ArabidopsisPBM_20140210_; m=1/6; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.779089; -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
7237_MYB111_2_ArabidopsisPBM_20140210__rc_shift0 (7237_MYB111_2_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_7nt_mkv2_m2 versus 7237_MYB111_2_ArabidopsisPBM_20140210__rc; m=2/6; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.777914; 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
7236_MYB111_ArabidopsisPBM_20140210__rc_shift0 (7236_MYB111_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_7nt_mkv2_m2 versus 7236_MYB111_ArabidopsisPBM_20140210__rc; m=3/6; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.71753; 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
7238_MYB46_ArabidopsisPBM_20140210__rc_shift0 (7238_MYB46_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_7nt_mkv2_m2 versus 7238_MYB46_ArabidopsisPBM_20140210__rc; m=4/6; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.708774; 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
7243_MYB55_2_ArabidopsisPBM_20140210__rc_shift0 (7243_MYB55_2_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_7nt_mkv2_m2 versus 7243_MYB55_2_ArabidopsisPBM_20140210__rc; m=5/6; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.678076; cCAmCCAMCg-
    ; cor=; Ncor=
    a	13	2	96	54	1	17	91	28	2	24	0
    c	62	83	2	44	98	69	0	70	89	14	0
    g	11	5	0	1	0	3	8	1	1	54	0
    t	14	10	2	1	1	11	1	1	8	8	0
7239_MYB46_2_ArabidopsisPBM_20140210__shift3 (7239_MYB46_2_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_7nt_mkv2_m2 versus 7239_MYB46_2_ArabidopsisPBM_20140210_; m=6/6; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.492998; ---yyAACCAm
    ; cor=; Ncor=
    a	0	0	0	16	5	92	82	1	21	82	25
    c	0	0	0	29	53	3	13	96	68	1	64
    g	0	0	0	24	13	3	2	1	7	16	2
    t	0	0	0	31	29	2	3	2	4	1	9