# 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/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.2026-01-25.180905_2026-01-25.180905_kvVFaU/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m7_shift1 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m7_shift1 (dyads_m7) |  |  |  |
    ; dyads_m7; m=0 (reference); ncol1=19; shift=1; ncol=20; -yyCTCyyyctcyyyCTCyy
    ; Alignment reference
    a	0	423	426	86	69	71	289	396	357	312	460	340	339	370	446	82	87	73	327	428
    c	0	885	617	2072	75	2103	638	923	700	1137	411	1132	664	925	592	2073	77	2116	646	869
    g	0	320	424	71	36	48	457	372	343	423	351	372	477	325	372	68	38	31	478	363
    t	0	628	789	27	2076	34	872	565	856	384	1034	412	776	636	846	33	2054	36	805	596
Trl_shift0 (Trl) |  |  |  |
    ; dyads_m7 versus Trl; m=1/1; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.427559; TtkykCTCtCtct-------
    ; cor=; Ncor=
    a	10	15	4	0	7	0	4	2	6	13	9	4	18	0	0	0	0	0	0	0
    c	10	8	19	41	3	72	0	56	12	56	16	47	3	0	0	0	0	0	0	0
    g	0	13	24	10	27	5	11	8	9	1	6	9	14	0	0	0	0	0	0	0
    t	57	41	30	26	40	0	62	11	50	7	46	17	42	0	0	0	0	0	0	0