# 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.2026-01-25.180941_2026-01-25.180941_K9UVGH/results/discovered_motifs/oligos_6-8nt_m7/peak-motifs_oligos_6-8nt_m7.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.2026-01-25.180941_2026-01-25.180941_K9UVGH/results/discovered_motifs/oligos_6-8nt_m7/peak-motifs_oligos_6-8nt_m7_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m7_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m7_shift0 (oligos_6-8nt_m7) |  |  |  |
    ; oligos_6-8nt_m7; m=0 (reference); ncol1=16; shift=0; ncol=16; gaGAGAGAGmGAGaga
    ; Alignment reference
    a	221	629	103	976	66	983	52	998	58	517	58	956	71	823	166	594
    c	166	228	76	97	43	124	27	83	26	508	58	103	53	199	164	248
    g	738	225	1005	83	1096	54	1123	65	1119	117	1086	119	1072	115	776	261
    t	112	155	53	81	32	76	35	91	34	95	35	59	41	100	131	134
Trl_rc_shift1 (Trl_rc) |  |  |  |
    ; oligos_6-8nt_m7 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=1; strand=R; shift=1; score=0.67147; -agaGaGAGmrmaA--
    ; cor=; Ncor=
    a	0	42	17	46	7	50	11	62	0	40	26	30	41	57	0	0
    c	0	14	9	6	1	9	8	11	5	27	10	24	13	0	0	0
    g	0	3	47	16	56	12	56	0	72	3	41	19	8	10	0	0
    t	0	18	4	9	13	6	2	4	0	7	0	4	15	10	0	0