# 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.2026-02-26.135827_2026-02-26.135827_NiTe41/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1.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.2026-02-26.135827_2026-02-26.135827_NiTe41/results/discovered_motifs/oligos_7nt_mkv2_m1/peak-motifs_oligos_7nt_mkv2_m1_vs_db_ArabidopsisPBM

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; mtTcACCAACCCmm
    ; Alignment reference
    a	15	7	3	4	34	1	0	33	35	4	1	4	11	11
    c	10	6	2	22	1	34	35	0	1	31	29	29	14	13
    g	3	2	3	4	0	0	0	1	0	2	1	4	4	5
    t	9	22	29	7	2	2	2	3	1	0	6	0	8	8
7242_MYB55_ArabidopsisPBM_20140210__shift3 (7242_MYB55_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus 7242_MYB55_ArabidopsisPBM_20140210_; m=1/3; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.550159; ---yACCTAMCGv-
    ; cor=; Ncor=
    a	0	0	0	11	98	5	0	23	98	27	0	12	25	0
    c	0	0	0	36	0	95	99	5	0	73	96	5	28	0
    g	0	0	0	5	2	0	0	2	2	0	0	76	30	0
    t	0	0	0	48	0	0	1	70	0	0	4	7	17	0
7237_MYB111_2_ArabidopsisPBM_20140210__rc_shift2 (7237_MYB111_2_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus 7237_MYB111_2_ArabidopsisPBM_20140210__rc; m=2/3; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.547096; --cYAMCwACCt--
    ; cor=; Ncor=
    a	0	0	13	0	97	26	0	37	99	14	1	22	0	0
    c	0	0	58	68	0	73	98	3	1	85	93	11	0	0
    g	0	0	13	2	1	1	0	1	0	0	0	10	0	0
    t	0	0	16	30	2	0	2	59	0	1	6	57	0	0
7236_MYB111_ArabidopsisPBM_20140210__rc_shift2 (7236_MYB111_ArabidopsisPBM_20140210__rc) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus 7236_MYB111_ArabidopsisPBM_20140210__rc; m=3/3; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.503565; --syACCTAmCh--
    ; cor=; Ncor=
    a	0	0	15	5	99	13	0	11	98	36	1	34	0	0
    c	0	0	46	39	0	85	98	1	0	64	76	28	0	0
    g	0	0	32	3	0	1	0	1	2	0	0	10	0	0
    t	0	0	7	53	1	1	2	87	0	0	23	28	0	0