# 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/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2.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/oligos_6nt_mkv2_m2/peak-motifs_oligos_6nt_mkv2_m2_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift6 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m2_shift6 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=10; shift=6; ncol=16; ------wdTAGTAAdw
    ; Alignment reference
    a	0	0	0	0	0	0	22	16	0	55	0	0	55	55	17	20
    c	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	4
    g	0	0	0	0	0	0	9	14	0	0	55	0	0	0	16	12
    t	0	0	0	0	0	0	16	17	55	0	0	55	0	0	14	19