# 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.2025-06-19.092322_2025-06-19.092322_shBOom/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.2025-06-19.092322_2025-06-19.092322_shBOom/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_shift0 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5) |  |  |  |
    ; oligos_6-8nt_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; gyAGACCTTGcs
    ; Alignment reference
    a	15	11	53	1	51	3	5	1	1	1	13	13
    c	15	24	2	3	4	55	51	3	1	0	23	19
    g	21	10	3	56	5	3	3	2	2	59	11	18
    t	10	16	3	1	1	0	2	55	57	1	14	11