# 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.2025-06-19.091816_2025-06-19.091816_x3rpdD/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3.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.2025-06-19.091816_2025-06-19.091816_x3rpdD/results/discovered_motifs/oligos_6-8nt_m3/peak-motifs_oligos_6-8nt_m3_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift1 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m3_shift1 (oligos_6-8nt_m3) |  |  |  |
    ; oligos_6-8nt_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -skGCACGCvs
    ; Alignment reference
    a	0	27	25	0	0	125	0	0	0	35	22
    c	0	41	25	0	125	0	125	0	125	35	36
    g	0	32	36	125	0	0	0	125	0	34	38
    t	0	25	39	0	0	0	0	0	0	21	29