# 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/dyads_m2/peak-motifs_dyads_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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/dyads_m2/peak-motifs_dyads_m2_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: dyads_m2_shift1 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m2_shift1 (dyads_m2) |  |  |  |
    ; dyads_m2; m=0 (reference); ncol1=14; shift=1; ncol=15; -adGGAGAGAAGGrd
    ; Alignment reference
    a	0	24	19	10	10	46	4	48	3	49	51	2	9	25	17
    c	0	5	5	2	5	1	3	1	3	1	0	1	3	7	6
    g	0	14	15	41	39	5	44	4	49	6	5	48	43	15	15
    t	0	14	18	4	3	5	6	4	2	1	1	6	2	10	19