# 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_m2/peak-motifs_oligos_6-8nt_m2.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_m2/peak-motifs_oligos_6-8nt_m2_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift2 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m2_shift2 (oligos_6-8nt_m2) |  |  |  |
    ; oligos_6-8nt_m2; m=0 (reference); ncol1=11; shift=2; ncol=13; --drTAcATAtay
    ; Alignment reference
    a	0	0	41	39	3	131	9	112	1	133	24	46	34
    c	0	0	27	31	0	5	87	7	0	5	29	26	36
    g	0	0	35	37	7	0	15	12	0	0	29	33	32
    t	0	0	36	32	129	3	28	8	138	1	57	34	37