# 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_m2/peak-motifs_dyads_m2.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_m2/peak-motifs_dyads_m2_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m2_shift0 (dyads_m2) |  |  |  |
    ; dyads_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; tccCTCTCyCTCTCyct
    ; Alignment reference
    a	133	107	47	51	65	16	31	24	54	61	57	14	41	26	73	152	156
    c	248	507	595	798	81	909	52	848	568	780	87	891	39	824	589	474	245
    g	189	177	111	65	83	27	48	51	105	59	78	34	73	83	74	170	199
    t	431	210	248	87	772	49	870	78	274	101	779	62	848	68	265	205	401
Trl_shift0 (Trl) |  |  |  |
    ; dyads_m2 versus Trl; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.622227; TtkykCTCtCtct----
    ; cor=; Ncor=
    a	10	15	4	0	7	0	4	2	6	13	9	4	18	0	0	0	0
    c	10	8	19	41	3	72	0	56	12	56	16	47	3	0	0	0	0
    g	0	13	24	10	27	5	11	8	9	1	6	9	14	0	0	0	0
    t	57	41	30	26	40	0	62	11	50	7	46	17	42	0	0	0	0