# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.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/2025/03/02/peak-motifs.2025-03-02.091145_2025-03-02.091145_IYXNXa/results/discovered_motifs/dyads_m1/peak-motifs_dyads_m1_vs_db_footprintDB

## One-to-n matrix alignment; reference matrix: dyads_m1_shift5 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m1_shift5 (dyads_m1) |  |  |  |
    ; dyads_m1; m=0 (reference); ncol1=13; shift=5; ncol=18; -----mrGCArvwGGAyw
    ; Alignment reference
    a	0	0	0	0	0	8	16	1	0	25	17	10	10	0	3	28	5	11
    c	0	0	0	0	0	12	2	1	27	0	2	8	2	1	0	0	13	6
    g	0	0	0	0	0	3	7	26	1	0	8	8	4	27	24	0	3	3
    t	0	0	0	0	0	5	3	0	0	3	1	2	12	0	1	0	7	8