# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7.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/2025/11/26/peak-motifs.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/dyads_m7/peak-motifs_dyads_m7_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: dyads_m7_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m7_shift0 (dyads_m7) |  |  |  |
    ; dyads_m7; m=0 (reference); ncol1=14; shift=0; ncol=14; acAyACACACAyac
    ; Alignment reference
    a	1763	381	2620	124	2741	84	2776	70	2703	73	2647	156	1615	405
    c	455	1780	115	863	58	2638	31	2656	75	2647	89	786	455	1694
    g	374	287	105	76	65	58	59	35	66	71	78	168	440	391
    t	319	463	71	1848	47	131	45	150	67	120	97	1801	401	421
twi_shift5 (twi) |  |  |  |
    ; dyads_m7 versus twi; m=1/1; ncol2=8; w=0; offset=5; strand=D; shift=5; score=0.414302; -----mACAyaTG-
    ; cor=; Ncor=
    a	0	0	0	0	0	10.6667	12.8	0	16	1.06667	10.6667	0	1.06667	0
    c	0	0	0	0	0	5.33333	3.2	16	0	7.46667	3.2	3.2	0	0
    g	0	0	0	0	0	0	0	0	0	1.06667	2.13333	1.06667	13.8667	0
    t	0	0	0	0	0	0	0	0	0	6.4	0	11.7333	1.06667	0