# 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.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3.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.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/dyads_m3/peak-motifs_dyads_m3_vs_db_DrosophilaTFs

## One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m3_shift0 (dyads_m3) |  |  |  |
    ; dyads_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; agCAGCAGCAGCag
    ; Alignment reference
    a	3023	732	205	4256	205	120	4427	196	120	4310	275	188	3102	833
    c	572	721	4047	152	229	4354	108	164	4365	138	232	4152	534	744
    g	704	2845	257	245	4149	96	157	4245	93	192	4045	171	729	2643
    t	468	469	258	114	184	197	75	162	189	127	215	256	402	547
4933_Adf1_DrosophilaTF_1.1__rc_shift0 (4933_Adf1_DrosophilaTF_1.1__rc) |  |  |  |
    ; dyads_m3 versus 4933_Adf1_DrosophilaTF_1.1__rc; m=1/1; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.705504; drCrGmrGsAGC--
    ; cor=; Ncor=
    a	33	50	0	50	0	50	50	0	0	1	0	0	0	0
    c	0	0	1	0	0	50	0	0	50	0	0	1	0	0
    g	33	50	0	50	1	0	50	1	50	0	1	0	0	0
    t	34	0	0	0	0	0	0	0	0	0	0	0	0	0