# 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_m1/peak-motifs_oligos_6-8nt_m1.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_m1/peak-motifs_oligos_6-8nt_m1_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1) |  |  |  |
    ; oligos_6-8nt_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; aartAAACAAAwa
    ; Alignment reference
    a	874	702	601	515	2215	2096	2225	61	2126	2128	2119	769	823
    c	472	561	318	319	47	92	71	2039	74	102	90	512	538
    g	479	560	1116	266	41	72	36	70	102	65	70	433	460
    t	563	565	353	1288	85	128	56	218	86	93	109	674	567
hb_shift1 (hb) |  |  |  |
    ; oligos_6-8nt_m1 versus hb; m=1/1; ncol2=9; w=0; offset=1; strand=D; shift=1; score=0.512827; -mayAAAAAa---
    ; cor=; Ncor=
    a	0	30.2913	47.4563	1.00971	96.932	101.981	104	97.9417	102.99	68.6602	0	0	0
    c	0	49.4757	16.1553	29.2816	1.00971	1.00971	0	1.00971	1.00971	8.07767	0	0	0
    g	0	21.2039	17.165	11.1068	4.03883	0	0	4.03883	0	12.1165	0	0	0
    t	0	3.02913	23.2233	62.6019	2.01942	1.00971	0	1.00971	0	15.1456	0	0	0