# 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_m8/peak-motifs_oligos_6-8nt_m8.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_m8/peak-motifs_oligos_6-8nt_m8_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m8_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m8_shift0 (oligos_6-8nt_m8) |  |  |  |
    ; oligos_6-8nt_m8; m=0 (reference); ncol1=14; shift=0; ncol=14; agAGAGAGmGAGag
    ; Alignment reference
    a	994	451	1769	160	1792	102	1845	112	705	108	1804	142	986	408
    c	454	356	160	92	213	70	140	46	1215	80	176	86	498	337
    g	461	1198	165	1923	83	1997	89	1996	156	1989	146	1907	385	1205
    t	308	212	123	42	129	48	143	63	141	40	91	82	348	267
Trl_rc_shift0 (Trl_rc) |  |  |  |
    ; oligos_6-8nt_m8 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.732476; agaGaGAGmrmaA-
    ; cor=; Ncor=
    a	42	17	46	7	50	11	62	0	40	26	30	41	57	0
    c	14	9	6	1	9	8	11	5	27	10	24	13	0	0
    g	3	47	16	56	12	56	0	72	3	41	19	8	10	0
    t	18	4	9	13	6	2	4	0	7	0	4	15	10	0