# 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_m4/peak-motifs_dyads_m4.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_m4/peak-motifs_dyads_m4_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: dyads_m4_shift7 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m4_shift7 (dyads_m4) |  |  |  |
    ; dyads_m4; m=0 (reference); ncol1=10; shift=7; ncol=17; -------whACCAAAww
    ; Alignment reference
    a	0	0	0	0	0	0	0	18	19	63	0	0	61	63	63	25	25
    c	0	0	0	0	0	0	0	12	16	0	63	62	0	0	0	9	12
    g	0	0	0	0	0	0	0	13	10	0	0	1	2	0	0	11	4
    t	0	0	0	0	0	0	0	20	18	0	0	0	0	0	0	18	22