# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m4/peak-motifs_oligos_8nt_mkv2_m4_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m4_shift4 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m4_shift4 (oligos_8nt_mkv2_m4) |  |  |  |
    ; oligos_8nt_mkv2_m4; m=0 (reference); ncol1=12; shift=4; ncol=16; ----wwGTGACAGAkw
    ; Alignment reference
    a	0	0	0	0	18	13	3	1	1	34	4	35	3	36	9	13
    c	0	0	0	0	4	3	0	2	0	0	30	1	2	1	1	5
    g	0	0	0	0	5	6	35	2	37	2	3	2	34	0	15	9
    t	0	0	0	0	12	17	1	34	1	3	2	1	0	2	14	12