# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.174057_2025-05-16.174057_O2IjFa/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.2025-05-16.174057_2025-05-16.174057_O2IjFa/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 2 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; sdGTAATCAkr
    ; Alignment reference
    a	2	3	1	2	10	9	0	0	10	1	4
    c	3	0	0	1	0	0	1	10	0	2	0
    g	4	3	9	0	0	0	0	0	0	3	4
    t	1	4	0	7	0	1	9	0	0	4	2
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; sdGTAATCAkr
    ; cor=; Ncor=
    a	2	3	1	2	10	9	0	0	10	1	4
    c	3	0	0	1	0	0	1	10	0	2	0
    g	4	3	9	0	0	0	0	0	0	3	4
    t	1	4	0	7	0	1	9	0	0	4	2

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv1_m3_shift1 (oligos_7nt_mkv1_m3) |  |  |  |
    ; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -msCACGCCGsC
    ; Alignment reference
    a	0	3	1	0	8	0	0	0	0	1	0	0
    c	0	5	5	10	0	10	0	9	9	1	6	7
    g	0	2	4	0	2	0	10	0	0	7	4	1
    t	0	0	0	0	0	0	0	1	1	1	0	2
oligos_7nt_mkv1_m3_shift1 (oligos_7nt_mkv1_m3) |  |  |  |
    ; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=1; score=      1; -msCACGCCGsC
    ; cor=; Ncor=
    a	0	3	1	0	8	0	0	0	0	1	0	0
    c	0	5	5	10	0	10	0	9	9	1	6	7
    g	0	2	4	0	2	0	10	0	0	7	4	1
    t	0	0	0	0	0	0	0	1	1	1	0	2
oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3) |  |  |  |
    ; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.894328; -ssCACGCCgs-
    ; cor=; Ncor=
    a	0	2	2	0	8	0	0	0	0	1	0	0
    c	0	4	4	8	0	9	0	8	9	2	5	0
    g	0	3	3	1	1	0	9	0	0	5	4	0
    t	0	0	0	0	0	0	0	1	0	1	0	0
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m1; m=3/4; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.714952; CmCCGCGCCgs-
    ; cor=; Ncor=
    a	1	4	0	0	3	0	0	0	0	3	0	0
    c	9	5	12	11	1	13	1	13	12	3	4	0
    g	3	3	0	1	9	0	12	0	0	5	8	0
    t	0	1	1	1	0	0	0	0	1	2	1	0
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m1; m=4/4; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.714952; CmCCGCGCCgs-
    ; cor=; Ncor=
    a	1	4	0	0	3	0	0	0	0	3	0	0
    c	9	5	12	11	1	13	1	13	12	3	4	0
    g	3	3	0	1	9	0	12	0	0	5	8	0
    t	0	1	1	1	0	0	0	0	1	2	1	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 5 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; CmCCGCGCCgs
    ; Alignment reference
    a	1	4	0	0	3	0	0	0	0	3	0
    c	9	5	12	11	1	13	1	13	12	3	4
    g	3	3	0	1	9	0	12	0	0	5	8
    t	0	1	1	1	0	0	0	0	1	2	1
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; CmCCGCGCCgs
    ; cor=; Ncor=
    a	1	4	0	0	3	0	0	0	0	3	0
    c	9	5	12	11	1	13	1	13	12	3	4
    g	3	3	0	1	9	0	12	0	0	5	8
    t	0	1	1	1	0	0	0	0	1	2	1
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; CmCCGCGCCgs
    ; cor=; Ncor=
    a	1	4	0	0	3	0	0	0	0	3	0
    c	9	5	12	11	1	13	1	13	12	3	4
    g	3	3	0	1	9	0	12	0	0	5	8
    t	0	1	1	1	0	0	0	0	1	2	1
oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m3; m=3/4; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.766447; -ssCACGCCgs
    ; cor=; Ncor=
    a	0	2	2	0	8	0	0	0	0	1	0
    c	0	4	4	8	0	9	0	8	9	2	5
    g	0	3	3	1	1	0	9	0	0	5	4
    t	0	0	0	0	0	0	0	1	0	1	0
oligos_7nt_mkv1_m3_shift1 (oligos_7nt_mkv1_m3) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m3; m=4/4; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.714952; -msCACGCCGs
    ; cor=; Ncor=
    a	0	3	1	0	8	0	0	0	0	1	0
    c	0	5	5	10	0	10	0	9	9	1	6
    g	0	2	4	0	2	0	10	0	0	7	4
    t	0	0	0	0	0	0	0	1	1	1	0

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift1 ; 5 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3) |  |  |  |
    ; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -ssCACGCCgs
    ; Alignment reference
    a	0	2	2	0	8	0	0	0	0	1	0
    c	0	4	4	8	0	9	0	8	9	2	5
    g	0	3	3	1	1	0	9	0	0	5	4
    t	0	0	0	0	0	0	0	1	0	1	0
oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3) |  |  |  |
    ; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/4; ncol2=10; w=0; offset=0; strand=D; shift=1; score=      1; -ssCACGCCgs
    ; cor=; Ncor=
    a	0	2	2	0	8	0	0	0	0	1	0
    c	0	4	4	8	0	9	0	8	9	2	5
    g	0	3	3	1	1	0	9	0	0	5	4
    t	0	0	0	0	0	0	0	1	0	1	0
oligos_7nt_mkv1_m3_shift1 (oligos_7nt_mkv1_m3) |  |  |  |
    ; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=1; score=0.894328; -msCACGCCGs
    ; cor=; Ncor=
    a	0	3	1	0	8	0	0	0	0	1	0
    c	0	5	5	10	0	10	0	9	9	1	6
    g	0	2	4	0	2	0	10	0	0	7	4
    t	0	0	0	0	0	0	0	1	1	1	0
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m1; m=3/4; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.766447; CmCCGCGCCgs
    ; cor=; Ncor=
    a	1	4	0	0	3	0	0	0	0	3	0
    c	9	5	12	11	1	13	1	13	12	3	4
    g	3	3	0	1	9	0	12	0	0	5	8
    t	0	1	1	1	0	0	0	0	1	2	1
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m1; m=4/4; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.766447; CmCCGCGCCgs
    ; cor=; Ncor=
    a	1	4	0	0	3	0	0	0	0	3	0
    c	9	5	12	11	1	13	1	13	12	3	4
    g	3	3	0	1	9	0	12	0	0	5	8
    t	0	1	1	1	0	0	0	0	1	2	1

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift0 ; 5 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=11; shift=0; ncol=11; CmCCGCGCCgs
    ; Alignment reference
    a	1	4	0	0	3	0	0	0	0	3	0
    c	9	5	12	11	1	13	1	13	12	3	4
    g	3	3	0	1	9	0	12	0	0	5	8
    t	0	1	1	1	0	0	0	0	1	2	1
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; CmCCGCGCCgs
    ; cor=; Ncor=
    a	1	4	0	0	3	0	0	0	0	3	0
    c	9	5	12	11	1	13	1	13	12	3	4
    g	3	3	0	1	9	0	12	0	0	5	8
    t	0	1	1	1	0	0	0	0	1	2	1
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; CmCCGCGCCgs
    ; cor=; Ncor=
    a	1	4	0	0	3	0	0	0	0	3	0
    c	9	5	12	11	1	13	1	13	12	3	4
    g	3	3	0	1	9	0	12	0	0	5	8
    t	0	1	1	1	0	0	0	0	1	2	1
oligos_6nt_mkv1_m3_shift1 (oligos_6nt_mkv1_m3) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m3; m=3/4; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.766447; -ssCACGCCgs
    ; cor=; Ncor=
    a	0	2	2	0	8	0	0	0	0	1	0
    c	0	4	4	8	0	9	0	8	9	2	5
    g	0	3	3	1	1	0	9	0	0	5	4
    t	0	0	0	0	0	0	0	1	0	1	0
oligos_7nt_mkv1_m3_shift1 (oligos_7nt_mkv1_m3) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m3; m=4/4; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.714952; -msCACGCCGs
    ; cor=; Ncor=
    a	0	3	1	0	8	0	0	0	0	1	0
    c	0	5	5	10	0	10	0	9	9	1	6
    g	0	2	4	0	2	0	10	0	0	7	4
    t	0	0	0	0	0	0	0	1	1	1	0

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; mrAAAAATkw
    ; Alignment reference
    a	4	4	11	11	11	11	11	0	2	6
    c	4	2	0	0	0	0	0	0	2	0
    g	2	4	0	0	0	0	0	0	4	2
    t	1	1	0	0	0	0	0	11	3	3
oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; mrAAAAATkw
    ; cor=; Ncor=
    a	4	4	11	11	11	11	11	0	2	6
    c	4	2	0	0	0	0	0	0	2	0
    g	2	4	0	0	0	0	0	0	4	2
    t	1	1	0	0	0	0	0	11	3	3