# 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/oligos_6-8nt_m4/peak-motifs_oligos_6-8nt_m4.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/oligos_6-8nt_m4/peak-motifs_oligos_6-8nt_m4_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4) |  |  |  |
    ; oligos_6-8nt_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; wrTAyATAya
    ; Alignment reference
    a	607	949	20	2377	126	1841	4	2324	446	933
    c	502	392	33	21	1426	149	26	27	617	437
    g	435	630	16	0	211	229	55	21	360	449
    t	855	428	2330	1	636	180	2314	27	976	580
Antp_shift4 (Antp) |  |  |  |
    ; oligos_6-8nt_m4 versus Antp; m=1/1; ncol2=6; w=0; offset=4; strand=D; shift=4; score=0.424092; ----mATAAw
    ; cor=; Ncor=
    a	0	0	0	0	10.5	18	0	16.5	18	7.5
    c	0	0	0	0	4.5	0	0	0	0	0
    g	0	0	0	0	3	0	0	1.5	0	0
    t	0	0	0	0	0	0	18	0	0	10.5