# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/25/peak-motifs.2026-01-25.201729_2026-01-25.201729_P12xBT/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/DMMPMM_drosophila/dmmpmm_PCM.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/2026/01/25/peak-motifs.2026-01-25.201729_2026-01-25.201729_P12xBT/results/discovered_motifs/oligos_6nt_mkv3_m5/peak-motifs_oligos_6nt_mkv3_m5_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv3_m5_shift0 (oligos_6nt_mkv3_m5) |  |  |  |
    ; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; hyACTCAChmy
    ; Alignment reference
    a	29	22	103	1	3	1	99	1	31	29	28
    c	34	43	3	111	3	109	3	110	37	45	29
    g	22	16	0	2	0	1	0	3	12	16	21
    t	30	34	9	1	109	4	13	1	35	25	37
z_rc_shift1 (z_rc) |  |  |  |
    ; oligos_6nt_mkv3_m5 versus z_rc; m=1/1; ncol2=6; w=0; offset=1; strand=R; shift=1; score=0.50615; -CaCTCA----
    ; cor=; Ncor=
    a	0	5.12195	24.5854	0	0	0	29.7073	0	0	0	0
    c	0	30.7317	0	42	0	42	3.07317	0	0	0	0
    g	0	5.12195	10.2439	0	0	0	7.17073	0	0	0	0
    t	0	1.02439	7.17073	0	42	0	2.04878	0	0	0	0