# 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_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.2026-02-26.135932_2026-02-26.135932_MeLHd6/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 ; 3 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=11; shift=0; ncol=11; hwTCACCAAcc
    ; Alignment reference
    a	10	7	2	0	24	0	0	24	23	5	5
    c	8	6	4	26	0	26	26	0	2	10	14
    g	1	3	1	0	0	0	0	0	0	5	1
    t	7	10	19	0	2	0	0	2	1	6	6
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=1/2; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.581606; --cYAMCwACC
    ; cor=; Ncor=
    a	0	0	13	0	97	26	0	37	99	14	1
    c	0	0	58	68	0	73	98	3	1	85	93
    g	0	0	13	2	1	1	0	1	0	0	0
    t	0	0	16	30	2	0	2	59	0	1	6
7242_MYB55_ArabidopsisPBM_20140210__shift3 (7242_MYB55_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus 7242_MYB55_ArabidopsisPBM_20140210_; m=2/2; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.467333; ---yACCTAMC
    ; cor=; Ncor=
    a	0	0	0	11	98	5	0	23	98	27	0
    c	0	0	0	36	0	95	99	5	0	73	96
    g	0	0	0	5	2	0	0	2	2	0	0
    t	0	0	0	48	0	0	1	70	0	0	4