# 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.2026-01-25.201729_2026-01-25.201729_P12xBT/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6.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.2026-01-25.201729_2026-01-25.201729_P12xBT/results/discovered_motifs/dyads_m6/peak-motifs_dyads_m6_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m6_shift0 (dyads_m6) |  |  |  |
    ; dyads_m6; m=0 (reference); ncol1=22; shift=0; ncol=22; agrGAGAGrGAGAGAGAGAGag
    ; Alignment reference
    a	125	36	113	18	195	22	190	19	129	8	189	9	192	9	186	16	189	14	173	27	127	40
    c	39	40	32	12	17	8	22	10	34	17	25	14	24	10	24	14	31	13	42	17	46	32
    g	59	149	83	209	25	212	20	213	68	217	19	220	20	223	25	213	14	217	18	191	59	154
    t	27	25	22	11	13	8	18	8	19	8	17	7	14	8	15	7	16	6	17	15	18	24
Trl_rc_shift8 (Trl_rc) |  |  |  |
    ; dyads_m6 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=8; strand=R; shift=8; score=0.484677; --------agaGaGAGmrmaA-
    ; cor=; Ncor=
    a	0	0	0	0	0	0	0	0	42	17	46	7	50	11	62	0	40	26	30	41	57	0
    c	0	0	0	0	0	0	0	0	14	9	6	1	9	8	11	5	27	10	24	13	0	0
    g	0	0	0	0	0	0	0	0	3	47	16	56	12	56	0	72	3	41	19	8	10	0
    t	0	0	0	0	0	0	0	0	18	4	9	13	6	2	4	0	7	0	4	15	10	0