# 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_m5/peak-motifs_oligos_8nt_mkv2_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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/oligos_8nt_mkv2_m5/peak-motifs_oligos_8nt_mkv2_m5_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m5_shift5 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m5_shift5 (oligos_8nt_mkv2_m5) |  |  |  |
    ; oligos_8nt_mkv2_m5; m=0 (reference); ncol1=12; shift=5; ncol=17; -----wrGTGGAGGArr
    ; Alignment reference
    a	0	0	0	0	0	15	15	1	9	0	3	35	8	2	40	15	21
    c	0	0	0	0	0	2	8	0	1	3	0	1	0	0	1	3	4
    g	0	0	0	0	0	8	15	42	1	37	39	1	34	40	0	16	12
    t	0	0	0	0	0	18	5	0	32	3	1	6	1	1	2	9	6