# 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_m6/peak-motifs_oligos_6-8nt_m6.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_m6/peak-motifs_oligos_6-8nt_m6_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m6_shift0 (oligos_6-8nt_m6) |  |  |  |
    ; oligos_6-8nt_m6; m=0 (reference); ncol1=12; shift=0; ncol=12; vmaATCGATtkb
    ; Alignment reference
    a	458	571	1111	1593	40	41	81	1641	90	308	349	402
    c	446	480	201	48	36	1597	41	44	32	139	360	455
    g	454	362	141	30	44	41	1598	36	48	201	481	447
    t	403	348	308	90	1641	82	41	40	1591	1113	571	457
Dref_rc_shift1 (Dref_rc) |  |  |  |
    ; oligos_6-8nt_m6 versus Dref_rc; m=1/1; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.631936; -yTATCGwTAt-
    ; cor=; Ncor=
    a	0	0	0	10	0	0	0	6.66667	1.11111	7.77778	2.22222	0
    c	0	6.66667	1.11111	0	0	8.88889	0	0	0	1.11111	0	0
    g	0	0	1.11111	0	0	0	10	0	1.11111	0	1.11111	0
    t	0	3.33333	7.77778	0	10	1.11111	0	3.33333	7.77778	1.11111	6.66667	0