# 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.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9.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.2026-01-25.181029_2026-01-25.181029_PUJ88V/results/discovered_motifs/dyads_m9/peak-motifs_dyads_m9_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m9_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m9_shift0 (dyads_m9) |  |  |  |
    ; dyads_m9; m=0 (reference); ncol1=17; shift=0; ncol=17; agrGAGAGAGAGAGrga
    ; Alignment reference
    a	1657	610	1459	259	2892	258	2908	225	2732	196	2915	150	2821	221	1338	635	1635
    c	567	464	338	225	234	97	234	90	266	91	205	86	241	119	426	447	622
    g	702	1976	1356	2812	153	2993	149	3025	284	3045	182	3108	200	2952	1465	1993	798
    t	494	370	267	124	141	72	129	80	138	88	118	76	158	128	191	345	365
Trl_rc_shift4 (Trl_rc) |  |  |  |
    ; dyads_m9 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=4; strand=R; shift=4; score=0.661031; ----agaGaGAGmrmaA
    ; cor=; Ncor=
    a	0	0	0	0	42	17	46	7	50	11	62	0	40	26	30	41	57
    c	0	0	0	0	14	9	6	1	9	8	11	5	27	10	24	13	0
    g	0	0	0	0	3	47	16	56	12	56	0	72	3	41	19	8	10
    t	0	0	0	0	18	4	9	13	6	2	4	0	7	0	4	15	10