# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.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/2025/06/19/peak-motifs.2025-06-19.085523_2025-06-19.085523_UdMRwA/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift1 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m5_shift1 (oligos_6-8nt_m5) |  |  |  |
    ; oligos_6-8nt_m5; m=0 (reference); ncol1=11; shift=1; ncol=12; -gcCAAAATGgm
    ; Alignment reference
    a	0	161	157	46	553	573	579	583	8	32	160	162
    c	0	159	189	521	27	12	21	23	24	35	157	171
    g	0	188	151	51	39	33	23	24	20	556	182	153
    t	0	137	148	27	26	27	22	15	593	22	146	159