# 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_m3/peak-motifs_oligos_6-8nt_m3.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_m3/peak-motifs_oligos_6-8nt_m3_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3) |  |  |  |
    ; oligos_6-8nt_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; mmAACACAAmh
    ; Alignment reference
    a	949	1129	2938	3059	158	3134	181	2999	2977	1051	889
    c	973	884	251	176	2965	128	2938	207	224	880	938
    g	723	818	114	116	111	72	190	134	123	712	756
    t	807	621	149	101	218	118	143	112	128	809	869
eve_shift4 (eve) |  |  |  |
    ; oligos_6-8nt_m3 versus eve; m=1/1; ncol2=8; w=0; offset=4; strand=D; shift=4; score=0.425082; ----mACaaTw
    ; cor=; Ncor=
    a	0	0	0	0	8	18	1	13	13	0	9
    c	0	0	0	0	9	0	16	3	0	1	1
    g	0	0	0	0	3	2	0	4	3	0	1
    t	0	0	0	0	0	0	3	0	4	19	9