# 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_m3/peak-motifs_dyads_m3.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_m3/peak-motifs_dyads_m3_vs_db_footprintDB

## One-to-n matrix alignment; reference matrix: dyads_m3_shift2 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m3_shift2 (dyads_m3) |  |  |  |
    ; dyads_m3; m=0 (reference); ncol1=30; shift=2; ncol=32; --thACCttsctyysmbwyrycrtrkyCAGtr
    ; Alignment reference
    a	0	0	5	12	30	0	0	9	9	5	5	8	9	8	6	15	1	13	5	17	2	6	16	6	15	7	7	0	29	1	6	12
    c	0	0	7	13	6	37	35	6	7	12	18	6	11	12	13	11	11	4	15	2	14	13	6	8	5	7	12	34	0	1	5	3
    g	0	0	9	1	0	0	1	7	9	13	5	4	4	4	10	6	12	9	1	12	7	9	12	9	15	13	8	0	7	35	8	14
    t	0	0	16	11	1	0	1	15	12	7	9	19	13	13	8	5	13	11	16	6	14	9	3	14	2	10	10	3	1	0	18	8