# 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_m10/peak-motifs_dyads_m10.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_m10/peak-motifs_dyads_m10_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m10_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m10_shift0 (dyads_m10) |  |  |  |
    ; dyads_m10; m=0 (reference); ncol1=23; shift=0; ncol=23; agrGAGaGrGAGAGAGAGAGaga
    ; Alignment reference
    a	91	30	91	14	153	12	112	14	106	7	155	4	155	8	158	9	156	8	150	17	135	33	99
    c	34	31	30	11	11	5	26	8	24	13	22	11	20	8	17	8	23	8	23	10	31	22	35
    g	49	123	58	166	22	177	24	172	54	173	16	179	14	179	15	180	9	180	17	166	26	133	45
    t	27	17	22	10	15	7	39	7	17	8	8	7	12	6	11	4	13	5	11	8	9	13	22
Trl_rc_shift10 (Trl_rc) |  |  |  |
    ; dyads_m10 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=10; strand=R; shift=10; score=0.484208; ----------agaGaGAGmrmaA
    ; cor=; Ncor=
    a	0	0	0	0	0	0	0	0	0	0	42	17	46	7	50	11	62	0	40	26	30	41	57
    c	0	0	0	0	0	0	0	0	0	0	14	9	6	1	9	8	11	5	27	10	24	13	0
    g	0	0	0	0	0	0	0	0	0	0	3	47	16	56	12	56	0	72	3	41	19	8	10
    t	0	0	0	0	0	0	0	0	0	0	18	4	9	13	6	2	4	0	7	0	4	15	10