# 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.2026-01-25.181000_2026-01-25.181000_CpuIe4/results/discovered_motifs/positions_6-8nt_m2/peak-motifs_positions_6-8nt_m2.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.2026-01-25.181000_2026-01-25.181000_CpuIe4/results/discovered_motifs/positions_6-8nt_m2/peak-motifs_positions_6-8nt_m2_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: positions_6-8nt_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6-8nt_m2_shift0 (positions_6-8nt_m2) |  |  |  |
    ; positions_6-8nt_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; krGAGGGAda
    ; Alignment reference
    a	150	203	5	633	0	1	0	626	167	221
    c	135	152	2	0	3	0	0	0	110	131
    g	192	161	599	7	641	641	594	5	206	151
    t	167	128	38	4	0	2	50	13	161	141
z_shift1 (z) |  |  |  |
    ; positions_6-8nt_m2 versus z; m=1/1; ncol2=6; w=0; offset=1; strand=D; shift=1; score=0.429498; -TGAGtG---
    ; cor=; Ncor=
    a	0	2.04878	0	42	0	7.17073	1.02439	0	0	0
    c	0	7.17073	0	0	0	10.2439	5.12195	0	0	0
    g	0	3.07317	42	0	42	0	30.7317	0	0	0
    t	0	29.7073	0	0	0	24.5854	5.12195	0	0	0