# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/04/28/peak-motifs.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1.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/2025/04/28/peak-motifs.2025-04-28.044641_2025-04-28.044641_ntYsd5/results/discovered_motifs/positions_7nt_m1/peak-motifs_positions_7nt_m1_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_7nt_m1_shift0 (positions_7nt_m1) |  |  |  |
    ; positions_7nt_m1; m=0 (reference); ncol1=16; shift=0; ncol=16; awacTATCGATAgtwt
    ; Alignment reference
    a	35	29	51	7	8	77	1	1	0	84	2	65	7	16	33	15
    c	17	13	9	56	12	4	2	87	0	1	5	3	18	12	13	21
    g	21	13	12	18	3	5	1	0	87	2	4	12	56	9	13	17
    t	15	33	16	7	65	2	84	0	1	1	77	8	7	51	29	35
Dref_rc_shift3 (Dref_rc) |  |  |  |
    ; positions_7nt_m1 versus Dref_rc; m=1/1; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.554241; ---yTATCGwTAt---
    ; cor=; Ncor=
    a	0	0	0	0	0	10	0	0	0	6.66667	1.11111	7.77778	2.22222	0	0	0
    c	0	0	0	6.66667	1.11111	0	0	8.88889	0	0	0	1.11111	0	0	0	0
    g	0	0	0	0	1.11111	0	0	0	10	0	1.11111	0	1.11111	0	0	0
    t	0	0	0	3.33333	7.77778	0	10	1.11111	0	3.33333	7.77778	1.11111	6.66667	0	0	0