# 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_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.2025-06-19.091929_2025-06-19.091929_ZGCM7J/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_shift1 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m2_shift1 (oligos_6-8nt_m2) |  |  |  |
    ; oligos_6-8nt_m2; m=0 (reference); ncol1=12; shift=1; ncol=13; -ssCCCATCGCvs
    ; Alignment reference
    a	0	22	20	3	9	7	123	3	1	6	5	37	29
    c	0	46	45	130	132	137	4	6	137	5	140	43	54
    g	0	50	55	9	4	3	12	19	6	135	2	44	40
    t	0	30	28	6	3	1	9	120	4	2	1	24	25