# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.091816_2025-06-19.091816_x3rpdD/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5.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/2025/06/19/peak-motifs.2025-06-19.091816_2025-06-19.091816_x3rpdD/results/discovered_motifs/oligos_6-8nt_m5/peak-motifs_oligos_6-8nt_m5_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift9 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m5_shift9 (oligos_6-8nt_m5) |  |  |  |
    ; oligos_6-8nt_m5; m=0 (reference); ncol1=12; shift=9; ncol=21; ---------csCCACGCCCcc
    ; Alignment reference
    a	0	0	0	0	0	0	0	0	0	26	17	1	1	123	9	9	3	6	4	36	30
    c	0	0	0	0	0	0	0	0	0	62	67	141	152	14	124	4	138	142	146	65	56
    g	0	0	0	0	0	0	0	0	0	38	40	11	2	9	13	136	13	4	2	31	31
    t	0	0	0	0	0	0	0	0	0	29	31	2	0	9	9	6	1	3	3	23	38