# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.175855_2025-05-16.175855_ID8f2H/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/2025/05/16/peak-motifs.2025-05-16.175855_2025-05-16.175855_ID8f2H/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; skCGsCGAmm
    ; Alignment reference
    a	0	1	0	0	1	0	0	8	4	3
    c	5	1	10	0	3	10	0	0	3	3
    g	3	4	0	10	6	0	10	1	2	2
    t	2	4	0	0	0	0	0	1	1	2
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; skCGsCGAmm
    ; cor=; Ncor=
    a	0	1	0	0	1	0	0	8	4	3
    c	5	1	10	0	3	10	0	0	3	3
    g	3	4	0	10	6	0	10	1	2	2
    t	2	4	0	0	0	0	0	1	1	2
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m2; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.857456; ckCGGCGAAc
    ; cor=; Ncor=
    a	0	1	0	0	0	0	0	4	4	1
    c	3	0	5	0	0	5	0	0	1	2
    g	1	2	0	5	5	0	5	0	0	1
    t	1	2	0	0	0	0	0	1	0	1

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; ckCGGCGAAct
    ; Alignment reference
    a	0	1	0	0	0	0	0	4	4	1	1
    c	3	0	5	0	0	5	0	0	1	2	1
    g	1	2	0	5	5	0	5	0	0	1	1
    t	1	2	0	0	0	0	0	1	0	1	2
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; ckCGGCGAAct
    ; cor=; Ncor=
    a	0	1	0	0	0	0	0	4	4	1	1
    c	3	0	5	0	0	5	0	0	1	2	1
    g	1	2	0	5	5	0	5	0	0	1	1
    t	1	2	0	0	0	0	0	1	0	1	2
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m1; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.857456; skCGsCGAmm-
    ; cor=; Ncor=
    a	0	1	0	0	1	0	0	8	4	3	0
    c	5	1	10	0	3	10	0	0	3	3	0
    g	3	4	0	10	6	0	10	1	2	2	0
    t	2	4	0	0	0	0	0	1	1	2	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; kmACAGGTGag
    ; Alignment reference
    a	0	2	5	0	5	0	0	0	0	2	1
    c	0	3	0	5	0	0	0	0	0	1	1
    g	2	0	0	0	0	5	5	0	5	1	2
    t	3	0	0	0	0	0	0	5	0	1	1
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; kmACAGGTGag
    ; cor=; Ncor=
    a	0	2	5	0	5	0	0	0	0	2	1
    c	0	3	0	5	0	0	0	0	0	1	1
    g	2	0	0	0	0	5	5	0	5	1	2
    t	3	0	0	0	0	0	0	5	0	1	1