# 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_m9/peak-motifs_dyads_m9.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_m9/peak-motifs_dyads_m9_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m9_shift3 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m9_shift3 (dyads_m9) |  |  |  |
    ; dyads_m9; m=0 (reference); ncol1=10; shift=3; ncol=13; ---ykCTTTTCyy
    ; Alignment reference
    a	0	0	0	92	123	0	0	0	9	1	0	102	117
    c	0	0	0	168	84	511	0	0	0	0	511	145	140
    g	0	0	0	83	166	0	0	0	0	0	0	123	116
    t	0	0	0	168	138	0	511	511	502	510	0	141	138
Kr_rc_shift0 (Kr_rc) |  |  |  |
    ; dyads_m9 versus Kr_rc; m=1/1; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.40095; taACCCtTTt---
    ; cor=; Ncor=
    a	5	30	40	1	1	2	5	2	1	5	0	0	0
    c	7	4	2	34	39	41	7	2	3	9	0	0	0
    g	6	5	0	4	0	0	10	8	3	7	0	0	0
    t	27	6	3	6	5	2	23	33	38	24	0	0	0