# 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_m4/peak-motifs_oligos_6-8nt_m4.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_m4/peak-motifs_oligos_6-8nt_m4_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift3 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m4_shift3 (oligos_6-8nt_m4) |  |  |  |
    ; oligos_6-8nt_m4; m=0 (reference); ncol1=11; shift=3; ncol=14; ---yvTACCGTAss
    ; Alignment reference
    a	0	0	0	28	43	5	137	0	9	3	7	133	29	35
    c	0	0	0	52	40	8	3	147	124	7	8	7	51	43
    g	0	0	0	36	42	5	11	5	15	142	7	12	41	45
    t	0	0	0	41	32	139	6	5	9	5	135	5	36	34