# 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_m1/peak-motifs_oligos_8nt_mkv2_m1.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_m1/peak-motifs_oligos_8nt_mkv2_m1_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m1_shift2 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m1_shift2 (oligos_8nt_mkv2_m1) |  |  |  |
    ; oligos_8nt_mkv2_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --wyCTTACTACww
    ; Alignment reference
    a	0	0	17	9	1	3	1	40	2	2	43	2	17	20
    c	0	0	6	12	43	1	3	1	38	1	1	40	8	4
    g	0	0	4	5	1	0	0	1	2	1	1	2	2	2
    t	0	0	19	20	1	42	42	4	4	42	1	2	19	20