# 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_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_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/oligos_8nt_mkv2_m3/peak-motifs_oligos_8nt_mkv2_m3_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m3_shift4 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m3_shift4 (oligos_8nt_mkv2_m3) |  |  |  |
    ; oligos_8nt_mkv2_m3; m=0 (reference); ncol1=12; shift=4; ncol=16; ----rwGGAGGAGAwr
    ; Alignment reference
    a	0	0	0	0	12	16	3	3	36	0	5	35	3	35	16	18
    c	0	0	0	0	1	4	0	0	4	0	2	2	1	0	4	2
    g	0	0	0	0	21	6	36	38	0	41	35	3	36	6	10	13
    t	0	0	0	0	8	16	3	1	2	1	0	2	2	1	12	9