# 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_7nt_mkv2_m2/peak-motifs_oligos_7nt_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_7nt_mkv2_m2/peak-motifs_oligos_7nt_mkv2_m2_vs_db_footprintDB-plants

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift5 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2) |  |  |  |
    ; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=11; shift=5; ncol=16; -----wtCCTTTTCwt
    ; Alignment reference
    a	0	0	0	0	0	34	25	1	0	11	2	2	5	4	31	21
    c	0	0	0	0	0	7	15	94	93	2	15	10	5	97	13	19
    g	0	0	0	0	0	12	22	1	1	2	0	4	5	0	8	13
    t	0	0	0	0	0	48	39	5	7	86	84	85	86	0	49	48