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

## One-to-n matrix alignment; reference matrix: dyads_m3_shift7 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m3_shift7 (dyads_m3) |  |  |  |
    ; dyads_m3; m=0 (reference); ncol1=18; shift=7; ncol=25; -------mmCTThtwthhwwTTCwt
    ; Alignment reference
    a	0	0	0	0	0	0	0	24	23	1	0	1	21	13	22	16	18	21	25	20	1	3	0	25	14
    c	0	0	0	0	0	0	0	17	18	64	1	1	19	16	11	15	17	20	14	14	0	0	66	15	13
    g	0	0	0	0	0	0	0	10	9	0	2	0	7	10	6	9	7	8	9	8	0	1	0	5	11
    t	0	0	0	0	0	0	0	15	16	1	63	64	19	27	27	26	24	17	18	24	65	62	0	21	28