# 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_m1/peak-motifs_oligos_6nt_mkv1_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/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/discovered_motifs/oligos_6nt_mkv1_m1/peak-motifs_oligos_6nt_mkv1_m1_vs_db_ArabidopsisPBM

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; ysCTCCTCkk
    ; Alignment reference
    a	2	3	0	0	0	0	0	0	1	4
    c	8	9	18	0	18	18	0	18	4	3
    g	3	5	0	0	0	0	0	0	6	5
    t	5	1	0	18	0	0	18	0	7	6
7274_TOE2_ArabidopsisPBM_20140210__shift3 (7274_TOE2_ArabidopsisPBM_20140210_) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus 7274_TOE2_ArabidopsisPBM_20140210_; m=1/1; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.405123; ---wCCTCGT
    ; cor=; Ncor=
    a	0	0	0	61	0	13	0	6	1	0
    c	0	0	0	2	92	85	0	92	0	0
    g	0	0	0	4	0	1	2	1	98	11
    t	0	0	0	33	8	1	98	1	1	89