# 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.2026-01-25.202113_2026-01-25.202113_GYd2gc/results/discovered_motifs/dyads_m8/peak-motifs_dyads_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.2026-01-25.202113_2026-01-25.202113_GYd2gc/results/discovered_motifs/dyads_m8/peak-motifs_dyads_m8_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m8_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m8_shift0 (dyads_m8) |  |  |  |
    ; dyads_m8; m=0 (reference); ncol1=22; shift=0; ncol=22; agrGAGAGAGAGmGAGAGaGag
    ; Alignment reference
    a	142	38	142	29	198	25	211	17	211	12	221	12	146	15	216	16	222	14	184	32	140	40
    c	44	47	32	23	28	12	33	10	30	13	25	12	85	11	29	13	39	18	52	21	63	35
    g	67	170	85	219	36	235	25	248	25	255	21	255	28	254	25	250	12	241	33	216	53	183
    t	32	30	26	14	23	13	16	10	19	5	18	6	26	5	15	6	12	12	16	16	29	27
Trl_rc_shift4 (Trl_rc) |  |  |  |
    ; dyads_m8 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=4; strand=R; shift=4; score=0.492951; ----agaGaGAGmrmaA-----
    ; cor=; Ncor=
    a	0	0	0	0	42	17	46	7	50	11	62	0	40	26	30	41	57	0	0	0	0	0
    c	0	0	0	0	14	9	6	1	9	8	11	5	27	10	24	13	0	0	0	0	0	0
    g	0	0	0	0	3	47	16	56	12	56	0	72	3	41	19	8	10	0	0	0	0	0
    t	0	0	0	0	18	4	9	13	6	2	4	0	7	0	4	15	10	0	0	0	0	0