# 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_m5/peak-motifs_dyads_m5.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_m5/peak-motifs_dyads_m5_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: dyads_m5_shift2 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m5_shift2 (dyads_m5) |  |  |  |
    ; dyads_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --wwCGAwyACAha
    ; Alignment reference
    a	0	0	21	18	1	0	52	24	12	48	4	54	19	22
    c	0	0	10	13	58	0	3	13	15	3	49	2	15	14
    g	0	0	13	11	1	57	2	8	12	1	2	2	8	10
    t	0	0	16	18	0	3	3	15	21	8	5	2	18	14