# 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_m2/peak-motifs_dyads_m2.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_m2/peak-motifs_dyads_m2_vs_db_footprintDB

## One-to-n matrix alignment; reference matrix: dyads_m2_shift5 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m2_shift5 (dyads_m2) |  |  |  |
    ; dyads_m2; m=0 (reference); ncol1=20; shift=5; ncol=25; -----mmGGAmdywabrwymCGAmr
    ; Alignment reference
    a	0	0	0	0	0	13	15	0	1	26	9	9	4	10	15	4	13	9	5	13	0	0	29	11	10
    c	0	0	0	0	0	11	9	3	0	5	11	4	16	6	4	9	4	7	10	8	31	0	1	8	6
    g	0	0	0	0	0	6	5	24	30	0	4	8	2	6	5	10	10	3	7	7	0	31	1	5	11
    t	0	0	0	0	0	1	2	4	0	0	7	10	9	9	7	8	4	12	9	3	0	0	0	7	4