# 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/DrosophilaTFs/DrosophilaTFs_2015-11-06.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_DrosophilaTFs

## 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
4983_sd_DrosophilaTF_1.1__rc_shift6 (4983_sd_DrosophilaTF_1.1__rc) |  |  |  |
    ; dyads_m7 versus 4983_sd_DrosophilaTF_1.1__rc; m=1/1; ncol2=9; w=0; offset=6; strand=R; shift=6; score=0.417491; ------AnAmATny
    ; cor=; Ncor=
    a	0	0	0	0	0	0	1	25	1	50	1	0	25	0
    c	0	0	0	0	0	0	0	25	0	50	0	0	25	50
    g	0	0	0	0	0	0	0	25	0	0	0	0	25	0
    t	0	0	0	0	0	0	0	25	0	0	0	1	25	50