# 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_m2/peak-motifs_positions_6nt_m2.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_m2/peak-motifs_positions_6nt_m2_vs_db_DMMPMM_drosophila

## One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6nt_m2_shift0 (positions_6nt_m2) |  |  |  |
    ; positions_6nt_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; waCTATCGATAstw
    ; Alignment reference
    a	37	37	3	12	83	2	3	1	85	2	73	8	21	32
    c	14	14	67	10	3	2	90	0	2	5	2	47	16	16
    g	14	22	17	3	5	2	0	91	4	0	12	31	17	13
    t	28	20	6	68	2	87	0	1	2	86	6	7	39	32
Dref_rc_shift2 (Dref_rc) |  |  |  |
    ; positions_6nt_m2 versus Dref_rc; m=1/1; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.634776; --yTATCGwTAt--
    ; cor=; Ncor=
    a	0	0	0	0	10	0	0	0	6.66667	1.11111	7.77778	2.22222	0	0
    c	0	0	6.66667	1.11111	0	0	8.88889	0	0	0	1.11111	0	0	0
    g	0	0	0	1.11111	0	0	0	10	0	1.11111	0	1.11111	0	0
    t	0	0	3.33333	7.77778	0	10	1.11111	0	3.33333	7.77778	1.11111	6.66667	0	0