# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.024047_2026-04-21.024047_gRzMOf/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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/2026/04/21/peak-motifs.2026-04-21.024047_2026-04-21.024047_gRzMOf/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## 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=10; shift=0; ncol=10; wrTTCAAAaw
    ; Alignment reference
    a	44	46	0	0	0	142	142	142	94	58
    c	30	24	0	0	142	0	0	0	15	13
    g	8	40	0	0	0	0	0	0	7	23
    t	60	32	142	142	0	0	0	0	26	48
positions_6nt_m2_shift0 (positions_6nt_m2) |  |  |  |
    ; positions_6nt_m2 versus positions_6nt_m2; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; wrTTCAAAaw
    ; cor=; Ncor=
    a	44	46	0	0	0	142	142	142	94	58
    c	30	24	0	0	142	0	0	0	15	13
    g	8	40	0	0	0	0	0	0	7	23
    t	60	32	142	142	0	0	0	0	26	48

## 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=11; shift=0; ncol=11; ywAAAAATwaw
    ; Alignment reference
    a	80	211	443	443	443	441	443	0	181	178	172
    c	122	89	0	0	0	0	0	0	58	81	25
    g	79	25	0	0	0	0	0	0	6	82	39
    t	162	118	0	0	0	2	0	443	198	102	207
positions_6nt_m1_shift0 (positions_6nt_m1) |  |  |  |
    ; positions_6nt_m1 versus positions_6nt_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; ywAAAAATwaw
    ; cor=; Ncor=
    a	80	211	443	443	443	441	443	0	181	178	172
    c	122	89	0	0	0	0	0	0	58	81	25
    g	79	25	0	0	0	0	0	0	6	82	39
    t	162	118	0	0	0	2	0	443	198	102	207