# 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/dyads_m7/peak-motifs_dyads_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/dyads_m7/peak-motifs_dyads_m7_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m7_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m7_shift0 (dyads_m7) |  |  |  |
    ; dyads_m7; m=0 (reference); ncol1=21; shift=0; ncol=21; agrGAGAGaGAGAGAGAGAga
    ; Alignment reference
    a	437	175	436	80	707	66	713	59	476	62	715	49	717	49	692	47	686	59	637	141	448
    c	154	129	110	57	89	27	87	29	142	48	94	34	84	39	91	39	120	62	130	107	196
    g	206	540	293	761	75	807	57	819	227	797	73	824	72	820	100	821	70	783	108	616	207
    t	137	90	95	36	63	34	77	27	89	27	52	27	61	26	51	27	58	30	59	70	83
Trl_rc_shift8 (Trl_rc) |  |  |  |
    ; dyads_m7 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=8; strand=R; shift=8; score=0.521186; --------agaGaGAGmrmaA
    ; cor=; Ncor=
    a	0	0	0	0	0	0	0	0	42	17	46	7	50	11	62	0	40	26	30	41	57
    c	0	0	0	0	0	0	0	0	14	9	6	1	9	8	11	5	27	10	24	13	0
    g	0	0	0	0	0	0	0	0	3	47	16	56	12	56	0	72	3	41	19	8	10
    t	0	0	0	0	0	0	0	0	18	4	9	13	6	2	4	0	7	0	4	15	10