# 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_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.2026-01-25.202113_2026-01-25.202113_GYd2gc/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=18; shift=0; ncol=18; ctCTCTCTCTCTCTCtct
    ; Alignment reference
    a	43	38	14	16	17	17	10	23	7	22	10	22	15	21	14	44	29	56
    c	240	58	322	30	330	28	346	23	340	32	337	19	331	35	321	68	254	76
    g	44	89	23	65	17	47	13	48	18	42	14	52	18	39	19	84	45	58
    t	57	199	25	273	20	292	15	290	19	288	23	291	20	289	30	188	56	194
Trl_shift3 (Trl) |  |  |  |
    ; dyads_m2 versus Trl; m=1/1; ncol2=13; w=0; offset=3; strand=D; shift=3; score=0.592713; ---TtkykCTCtCtct--
    ; cor=; Ncor=
    a	0	0	0	10	15	4	0	7	0	4	2	6	13	9	4	18	0	0
    c	0	0	0	10	8	19	41	3	72	0	56	12	56	16	47	3	0	0
    g	0	0	0	0	13	24	10	27	5	11	8	9	1	6	9	14	0	0
    t	0	0	0	57	41	30	26	40	0	62	11	50	7	46	17	42	0	0