# 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_m3/peak-motifs_oligos_6-8nt_m3.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_m3/peak-motifs_oligos_6-8nt_m3_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift5 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m3_shift5 (oligos_6-8nt_m3) |  |  |  |
    ; oligos_6-8nt_m3; m=0 (reference); ncol1=12; shift=5; ncol=17; -----ssCCCCGCCCcs
    ; Alignment reference
    a	0	0	0	0	0	58	58	11	14	14	13	15	6	7	7	61	48
    c	0	0	0	0	0	110	114	282	280	281	275	42	292	286	291	121	118
    g	0	0	0	0	0	91	94	14	15	11	9	244	11	10	14	58	95
    t	0	0	0	0	0	56	49	8	6	9	18	14	6	12	3	75	54