# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.015247_2026-04-21.015247_DTyOML/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.2026-04-21.015247_2026-04-21.015247_DTyOML/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6nt_m1_shift2 (positions_6nt_m1) |  |  |  |
    ; positions_6nt_m1; m=0 (reference); ncol1=11; shift=2; ncol=13; --vwAAAATTCwr
    ; Alignment reference
    a	0	0	22	27	81	75	78	79	0	11	4	23	24
    c	0	0	24	14	1	0	1	2	0	0	78	2	12
    g	0	0	22	6	0	0	0	1	1	0	0	17	37
    t	0	0	14	35	0	7	3	0	81	71	0	40	9
positions_6nt_m1_shift2 (positions_6nt_m1) |  |  |  |
    ; positions_6nt_m1 versus positions_6nt_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=2; score=      1; --vwAAAATTCwr
    ; cor=; Ncor=
    a	0	0	22	27	81	75	78	79	0	11	4	23	24
    c	0	0	24	14	1	0	1	2	0	0	78	2	12
    g	0	0	22	6	0	0	0	1	1	0	0	17	37
    t	0	0	14	35	0	7	3	0	81	71	0	40	9
positions_6nt_m2_shift0 (positions_6nt_m2) |  |  |  |
    ; positions_6nt_m1 versus positions_6nt_m2; m=2/2; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.466699; twAAAAAAww---
    ; cor=; Ncor=
    a	115	130	507	507	507	507	507	507	130	182	0	0	0
    c	104	118	0	0	0	0	0	0	60	108	0	0	0
    g	119	105	0	0	0	0	0	0	56	46	0	0	0
    t	169	154	0	0	0	0	0	0	261	171	0	0	0

## One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 3 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; twAAAAAAww
    ; Alignment reference
    a	115	130	507	507	507	507	507	507	130	182
    c	104	118	0	0	0	0	0	0	60	108
    g	119	105	0	0	0	0	0	0	56	46
    t	169	154	0	0	0	0	0	0	261	171
positions_6nt_m2_shift0 (positions_6nt_m2) |  |  |  |
    ; positions_6nt_m2 versus positions_6nt_m2; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; twAAAAAAww
    ; cor=; Ncor=
    a	115	130	507	507	507	507	507	507	130	182
    c	104	118	0	0	0	0	0	0	60	108
    g	119	105	0	0	0	0	0	0	56	46
    t	169	154	0	0	0	0	0	0	261	171
positions_6nt_m1_shift2 (positions_6nt_m1) |  |  |  |
    ; positions_6nt_m2 versus positions_6nt_m1; m=2/2; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.466699; --vwAAAATT
    ; cor=; Ncor=
    a	0	0	22	27	81	75	78	79	0	11
    c	0	0	24	14	1	0	1	2	0	0
    g	0	0	22	6	0	0	0	1	1	0
    t	0	0	14	35	0	7	3	0	81	71