# 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_6nt_m1/peak-motifs_positions_6nt_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_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6nt_m1_shift0 (positions_6nt_m1) |  |  |  |
    ; positions_6nt_m1; m=0 (reference); ncol1=14; shift=0; ncol=14; wacTATCGATAgyw
    ; Alignment reference
    a	34	40	7	11	88	2	0	0	92	2	69	8	19	34
    c	13	14	65	15	3	1	97	0	2	4	2	17	25	16
    g	17	24	17	2	4	2	0	97	1	3	15	65	14	13
    t	33	19	8	69	2	92	0	0	2	88	11	7	39	34
Dref_shift2 (Dref) |  |  |  |
    ; positions_6nt_m1 versus Dref; m=1/1; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.632364; --aTAwCGATAr--
    ; cor=; Ncor=
    a	0	0	6.66667	1.11111	7.77778	3.33333	0	1.11111	10	0	7.77778	3.33333	0	0
    c	0	0	1.11111	0	1.11111	0	10	0	0	0	1.11111	0	0	0
    g	0	0	0	1.11111	0	0	0	8.88889	0	0	1.11111	6.66667	0	0
    t	0	0	2.22222	7.77778	1.11111	6.66667	0	0	0	10	0	0	0	0