# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.142119_2026-03-30.142119_XX18DY/results/discovered_motifs/oligos_6-8nt_m1/peak-motifs_oligos_6-8nt_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.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/2026/03/30/peak-motifs.2026-03-30.142119_2026-03-30.142119_XX18DY/results/discovered_motifs/oligos_6-8nt_m1/peak-motifs_oligos_6-8nt_m1_vs_db_footprintDB

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift5 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m1_shift5 (oligos_6-8nt_m1) |  |  |  |
    ; oligos_6-8nt_m1; m=0 (reference); ncol1=10; shift=5; ncol=15; -----awAGTAGGww
    ; Alignment reference
    a	0	0	0	0	0	13	12	20	0	3	24	0	0	8	10
    c	0	0	0	0	0	3	1	3	0	1	2	0	1	3	6
    g	0	0	0	0	0	5	6	1	26	1	0	26	25	4	2
    t	0	0	0	0	0	5	7	2	0	21	0	0	0	11	8