# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.142119_2026-03-30.142119_XX18DY/results/discovered_motifs/dyads_test_vs_ctrl_m1/peak-motifs_dyads_test_vs_ctrl_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/2026/03/30/peak-motifs.2026-03-30.142119_2026-03-30.142119_XX18DY/results/discovered_motifs/dyads_test_vs_ctrl_m1/peak-motifs_dyads_test_vs_ctrl_m1_vs_db_footprintDB

## One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift7 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_test_vs_ctrl_m1_shift7 (dyads_test_vs_ctrl_m1) |  |  |  |
    ; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=7; ncol=19; -------twCTTtwAAAwt
    ; Alignment reference
    a	0	0	0	0	0	0	0	11	12	0	0	0	11	21	47	47	47	20	10
    c	0	0	0	0	0	0	0	4	9	47	0	0	7	2	0	0	0	10	7
    g	0	0	0	0	0	0	0	10	9	0	0	0	8	10	0	0	0	5	9
    t	0	0	0	0	0	0	0	22	17	0	47	47	21	14	0	0	0	12	21