# 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_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.2026-01-25.180941_2026-01-25.180941_K9UVGH/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=20; shift=0; ncol=20; tctCTCTCTCTCTCTCTCtc
    ; Alignment reference
    a	147	126	110	69	83	58	83	52	77	38	89	43	95	40	102	40	111	49	172	114
    c	288	819	185	1046	137	1080	140	1116	114	1144	91	1135	101	1130	88	1123	108	1068	219	817
    g	259	146	212	84	186	81	180	60	137	47	135	40	163	44	149	48	137	76	208	164
    t	614	217	801	109	902	89	905	80	980	79	993	90	949	94	969	97	952	115	709	213
Trl_shift0 (Trl) |  |  |  |
    ; dyads_m2 versus Trl; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.553802; 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