# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/discovered_motifs/oligos_6nt_mkv1_m3/peak-motifs_oligos_6nt_mkv1_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/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/discovered_motifs/oligos_6nt_mkv1_m3/peak-motifs_oligos_6nt_mkv1_m3_vs_db_ArabidopsisPBM

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3) |  |  |  |
    ; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; rtATATATat
    ; Alignment reference
    a	14	7	30	0	32	0	33	0	18	5
    c	8	8	3	1	1	2	1	2	3	8
    g	9	3	2	0	2	1	1	3	8	8
    t	4	17	0	34	0	32	0	30	6	14
7186_AHL20_ArabidopsisPBM_20140210__shift0 (7186_AHL20_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_6nt_mkv1_m3 versus 7186_AHL20_ArabidopsisPBM_20140210_; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.76704; wAATATATTw
    ; cor=; Ncor=
    a	44	95	88	8	87	13	90	11	3	44
    c	16	1	0	1	0	0	1	1	1	10
    g	11	1	1	0	0	0	1	0	1	21
    t	29	3	11	91	13	87	8	88	95	25
7185_AHL12_3_ArabidopsisPBM_20140210__shift1 (7185_AHL12_3_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_6nt_mkv1_m3 versus 7185_AHL12_3_ArabidopsisPBM_20140210_; m=2/2; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.578425; -wAwwwwwwT
    ; cor=; Ncor=
    a	0	42	83	44	55	36	64	43	54	11
    c	0	11	2	1	1	0	0	1	1	4
    g	0	11	5	1	1	0	0	1	0	2
    t	0	36	10	54	43	64	36	55	45	83