# 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.2026-01-25.180905_2026-01-25.180905_kvVFaU/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.2026-01-25.180905_2026-01-25.180905_kvVFaU/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=14; shift=0; ncol=14; acgCACTCACctay
    ; Alignment reference
    a	336	229	199	113	1001	22	76	27	984	29	222	165	328	216
    c	276	407	193	832	26	1046	54	1004	36	1030	616	238	274	376
    g	243	206	572	77	45	26	33	31	43	36	106	132	242	243
    t	264	277	155	97	47	25	956	57	56	24	175	584	275	284
z_rc_shift3 (z_rc) |  |  |  |
    ; oligos_6-8nt_m4 versus z_rc; m=1/1; ncol2=6; w=0; offset=3; strand=R; shift=3; score=0.410393; ---CaCTCA-----
    ; cor=; Ncor=
    a	0	0	0	5.12195	24.5854	0	0	0	29.7073	0	0	0	0	0
    c	0	0	0	30.7317	0	42	0	42	3.07317	0	0	0	0	0
    g	0	0	0	5.12195	10.2439	0	0	0	7.17073	0	0	0	0	0
    t	0	0	0	1.02439	7.17073	0	42	0	2.04878	0	0	0	0	0