# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m1/peak-motifs_oligos_8nt_mkv1_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_plants_non-redundant_pfms_transfac.txt -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/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/oligos_8nt_mkv1_m1/peak-motifs_oligos_8nt_mkv1_m1_vs_db_JASPAR2024_CORE_plants_non-redundant

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv1_m1_shift0 (oligos_8nt_mkv1_m1) |  |  |  |
    ; oligos_8nt_mkv1_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; ybCTGTGGAAkh
    ; Alignment reference
    a	0	0	0	0	0	0	0	0	3	3	0	1
    c	2	1	3	0	0	0	0	0	0	0	0	1
    g	0	1	0	0	3	0	3	3	0	0	1	0
    t	1	1	0	3	0	3	0	0	0	0	2	1
MA2021.2_rc_shift1 (LBD13_rc) |  |  |  |
    ; oligos_8nt_mkv1_m1 versus MA2021.2_rc (LBD13_rc); m=1/1; ncol2=8; w=0; offset=1; strand=R; shift=1; score=0.476709; -aCGGTGGa---
    ; cor=; Ncor=
    a	0	628.0	18.0	8.0	9.0	72.0	17.0	39.0	635.0	0	0	0
    c	0	143.0	980.0	16.0	8.0	168.0	4.0	20.0	145.0	0	0	0
    g	0	227.0	11.0	1021.0	1031.0	6.0	1018.0	979.0	44.0	0	0	0
    t	0	57.0	46.0	10.0	7.0	809.0	16.0	17.0	231.0	0	0	0