# 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.2025-06-19.091929_2025-06-19.091929_ZGCM7J/results/discovered_motifs/oligos_6-8nt_m1/peak-motifs_oligos_6-8nt_m1.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.2025-06-19.091929_2025-06-19.091929_ZGCM7J/results/discovered_motifs/oligos_6-8nt_m1/peak-motifs_oligos_6-8nt_m1_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift0 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1) |  |  |  |
    ; oligos_6-8nt_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; ycgGCACGCCCsg
    ; Alignment reference
    a	26	26	13	2	0	116	3	1	3	2	10	22	31
    c	39	52	27	7	117	7	116	2	119	111	91	43	31
    g	31	25	71	113	7	3	3	122	4	10	21	34	36
    t	32	25	17	6	4	2	6	3	2	5	6	29	30