# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/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/2025/11/07/peak-motifs.2025-11-07.144553_2025-11-07.144553_0jTHd8/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3) |  |  |  |
    ; oligos_7nt_mkv1_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; GhGAAGTGCAw
    ; Alignment reference
    a	0	1	0	3	3	0	0	0	0	3	2
    c	0	1	0	0	0	0	0	0	3	0	0
    g	3	0	3	0	0	3	0	3	0	0	0
    t	0	1	0	0	0	0	3	0	0	0	1
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3) |  |  |  |
    ; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; GhGAAGTGCAw
    ; cor=; Ncor=
    a	0	1	0	3	3	0	0	0	0	3	2
    c	0	1	0	0	0	0	0	0	3	0	0
    g	3	0	3	0	0	3	0	3	0	0	0
    t	0	1	0	0	0	0	3	0	0	0	1
oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2) |  |  |  |
    ; oligos_7nt_mkv1_m3 versus oligos_8nt_mkv1_m2; m=2/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.916667; GhGAAGTGCAw
    ; cor=; Ncor=
    a	0	1	0	3	3	0	0	0	0	3	2
    c	0	1	0	0	0	0	0	0	3	0	0
    g	3	0	3	0	0	3	0	3	0	0	0
    t	0	1	0	0	0	0	3	0	0	0	1
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m1; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.678706; --swAGTGmAr
    ; cor=; Ncor=
    a	0	0	1	3	6	0	0	0	2	6	3
    c	0	0	2	0	0	0	0	0	4	0	0
    g	0	0	3	1	0	6	0	6	0	0	2
    t	0	0	0	2	0	0	6	0	0	0	1

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --swAGTGmArw
    ; Alignment reference
    a	0	0	1	3	6	0	0	0	2	6	3	3
    c	0	0	2	0	0	0	0	0	4	0	0	1
    g	0	0	3	1	0	6	0	6	0	0	2	0
    t	0	0	0	2	0	0	6	0	0	0	1	2
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score=      1; --swAGTGmArw
    ; cor=; Ncor=
    a	0	0	1	3	6	0	0	0	2	6	3	3
    c	0	0	2	0	0	0	0	0	4	0	0	1
    g	0	0	3	1	0	6	0	6	0	0	2	0
    t	0	0	0	2	0	0	6	0	0	0	1	2
oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_8nt_mkv1_m2; m=2/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.754655; GhGAAGTGCAww
    ; cor=; Ncor=
    a	0	1	0	3	3	0	0	0	0	3	2	2
    c	0	1	0	0	0	0	0	0	3	0	0	0
    g	3	0	3	0	0	3	0	3	0	0	0	0
    t	0	1	0	0	0	0	3	0	0	0	1	1
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m3; m=3/3; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.678706; GhGAAGTGCAw-
    ; cor=; Ncor=
    a	0	1	0	3	3	0	0	0	0	3	2	0
    c	0	1	0	0	0	0	0	0	3	0	0	0
    g	3	0	3	0	0	3	0	3	0	0	0	0
    t	0	1	0	0	0	0	3	0	0	0	1	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 3 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; ctCTGTGGAwt
    ; Alignment reference
    a	0	1	0	0	1	0	0	0	5	3	1
    c	3	1	5	0	0	0	0	0	0	0	0
    g	1	1	0	0	4	0	4	5	0	0	1
    t	1	2	0	5	0	5	1	0	0	2	3
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; ctCTGTGGAwt
    ; cor=; Ncor=
    a	0	1	0	0	1	0	0	0	5	3	1
    c	3	1	5	0	0	0	0	0	0	0	0
    g	1	1	0	0	4	0	4	5	0	0	1
    t	1	2	0	5	0	5	1	0	0	2	3
oligos_8nt_mkv1_m1_shift0 (oligos_8nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_8nt_mkv1_m1; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.870312; ybCTGTGGAAk
    ; cor=; Ncor=
    a	0	0	0	0	0	0	0	0	3	3	0
    c	2	1	3	0	0	0	0	0	0	0	0
    g	0	1	0	0	3	0	3	3	0	0	1
    t	1	1	0	3	0	3	0	0	0	0	2

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv1_m4_shift0 (oligos_8nt_mkv1_m4) |  |  |  |
    ; oligos_8nt_mkv1_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; wAAAAGCTCCTry
    ; Alignment reference
    a	1	2	2	2	2	0	0	0	0	0	0	1	0
    c	0	0	0	0	0	0	2	0	2	2	0	0	1
    g	0	0	0	0	0	2	0	0	0	0	0	1	0
    t	1	0	0	0	0	0	0	2	0	0	2	0	1
oligos_8nt_mkv1_m4_shift0 (oligos_8nt_mkv1_m4) |  |  |  |
    ; oligos_8nt_mkv1_m4 versus oligos_8nt_mkv1_m4; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score=      1; wAAAAGCTCCTry
    ; cor=; Ncor=
    a	1	2	2	2	2	0	0	0	0	0	0	1	0
    c	0	0	0	0	0	0	2	0	2	2	0	0	1
    g	0	0	0	0	0	2	0	0	0	0	0	1	0
    t	1	0	0	0	0	0	0	2	0	0	2	0	1

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv1_m5_shift0 (oligos_8nt_mkv1_m5) |  |  |  |
    ; oligos_8nt_mkv1_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; vMCAATWTTARh
    ; Alignment reference
    a	2	1	0	4	4	0	3	0	0	4	3	1
    c	1	3	4	0	0	0	0	0	0	0	0	1
    g	1	0	0	0	0	0	0	0	0	0	1	0
    t	0	0	0	0	0	4	1	4	4	0	0	2
oligos_8nt_mkv1_m5_shift0 (oligos_8nt_mkv1_m5) |  |  |  |
    ; oligos_8nt_mkv1_m5 versus oligos_8nt_mkv1_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; vMCAATWTTARh
    ; cor=; Ncor=
    a	2	1	0	4	4	0	3	0	0	4	3	1
    c	1	3	4	0	0	0	0	0	0	0	0	1
    g	1	0	0	0	0	0	0	0	0	0	1	0
    t	0	0	0	0	0	4	1	4	4	0	0	2

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift4 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv1_m2_shift4 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=4; ncol=15; ----bhATGGCYCww
    ; Alignment reference
    a	0	0	0	0	1	2	8	0	0	0	1	0	0	3	2
    c	0	0	0	0	2	2	0	0	1	0	7	2	7	1	1
    g	0	0	0	0	3	1	0	0	7	7	0	0	1	1	0
    t	0	0	0	0	2	3	0	8	0	1	0	6	0	3	5
oligos_7nt_mkv1_m2_shift4 (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=4; score=      1; ----bhATGGCYCww
    ; cor=; Ncor=
    a	0	0	0	0	1	2	8	0	0	0	1	0	0	3	2
    c	0	0	0	0	2	2	0	0	1	0	7	2	7	1	1
    g	0	0	0	0	3	1	0	0	7	7	0	0	1	1	0
    t	0	0	0	0	2	3	0	8	0	1	0	6	0	3	5
oligos_8nt_mkv1_m3_shift0 (oligos_8nt_mkv1_m3) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_8nt_mkv1_m3; m=2/2; ncol2=12; w=-4; offset=-4; strand=D; shift=0; score=0.406473; rvCmCTATrGhT---
    ; cor=; Ncor=
    a	2	1	0	2	0	0	3	0	1	0	1	0	0	0	0
    c	0	1	3	1	3	0	0	0	0	0	1	0	0	0	0
    g	1	1	0	0	0	0	0	0	2	3	0	0	0	0	0
    t	0	0	0	0	0	3	0	3	0	0	1	3	0	0	0

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2) |  |  |  |
    ; oligos_8nt_mkv1_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; GhGAAGTGCAww
    ; Alignment reference
    a	0	1	0	3	3	0	0	0	0	3	2	2
    c	0	1	0	0	0	0	0	0	3	0	0	0
    g	3	0	3	0	0	3	0	3	0	0	0	0
    t	0	1	0	0	0	0	3	0	0	0	1	1
oligos_8nt_mkv1_m2_shift0 (oligos_8nt_mkv1_m2) |  |  |  |
    ; oligos_8nt_mkv1_m2 versus oligos_8nt_mkv1_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; GhGAAGTGCAww
    ; cor=; Ncor=
    a	0	1	0	3	3	0	0	0	0	3	2	2
    c	0	1	0	0	0	0	0	0	3	0	0	0
    g	3	0	3	0	0	3	0	3	0	0	0	0
    t	0	1	0	0	0	0	3	0	0	0	1	1
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3) |  |  |  |
    ; oligos_8nt_mkv1_m2 versus oligos_7nt_mkv1_m3; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.916667; GhGAAGTGCAw-
    ; cor=; Ncor=
    a	0	1	0	3	3	0	0	0	0	3	2	0
    c	0	1	0	0	0	0	0	0	3	0	0	0
    g	3	0	3	0	0	3	0	3	0	0	0	0
    t	0	1	0	0	0	0	3	0	0	0	1	0
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_8nt_mkv1_m2 versus oligos_6nt_mkv1_m1; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.754655; --swAGTGmArw
    ; cor=; Ncor=
    a	0	0	1	3	6	0	0	0	2	6	3	3
    c	0	0	2	0	0	0	0	0	4	0	0	1
    g	0	0	3	1	0	6	0	6	0	0	2	0
    t	0	0	0	2	0	0	6	0	0	0	1	2

## One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m1_shift0 (dyads_m1) |  |  |  |
    ; dyads_m1; m=0 (reference); ncol1=29; shift=0; ncol=29; rvAgGrwwytdaywhwdwwhdwwdAGAdk
    ; Alignment reference
    a	5	4	11	0	0	6	5	5	2	2	3	7	2	7	3	6	4	5	4	4	3	6	4	4	9	0	12	3	1
    c	2	3	0	2	0	1	1	0	3	1	0	1	5	0	4	0	2	2	0	4	1	1	1	0	1	0	0	1	1
    g	3	3	1	8	12	3	2	2	2	1	3	2	1	1	0	1	3	2	2	0	4	0	2	5	1	12	0	4	5
    t	2	2	0	2	0	2	4	5	5	8	6	2	4	4	5	5	3	3	6	4	4	5	5	3	1	0	0	4	5
dyads_m1_shift0 (dyads_m1) |  |  |  |
    ; dyads_m1 versus dyads_m1; m=1/1; ncol2=29; w=0; offset=0; strand=D; shift=0; score=      1; rvAgGrwwytdaywhwdwwhdwwdAGAdk
    ; cor=; Ncor=
    a	5	4	11	0	0	6	5	5	2	2	3	7	2	7	3	6	4	5	4	4	3	6	4	4	9	0	12	3	1
    c	2	3	0	2	0	1	1	0	3	1	0	1	5	0	4	0	2	2	0	4	1	1	1	0	1	0	0	1	1
    g	3	3	1	8	12	3	2	2	2	1	3	2	1	1	0	1	3	2	2	0	4	0	2	5	1	12	0	4	5
    t	2	2	0	2	0	2	4	5	5	8	6	2	4	4	5	5	3	3	6	4	4	5	5	3	1	0	0	4	5

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4) |  |  |  |
    ; oligos_7nt_mkv1_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; hdAAAAGAGsr
    ; Alignment reference
    a	1	1	4	4	4	4	0	4	0	0	2
    c	1	0	0	0	0	0	0	0	0	2	0
    g	0	2	0	0	0	0	4	0	4	2	2
    t	2	1	0	0	0	0	0	0	0	0	0
oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4) |  |  |  |
    ; oligos_7nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; hdAAAAGAGsr
    ; cor=; Ncor=
    a	1	1	4	4	4	4	0	4	0	0	2
    c	1	0	0	0	0	0	0	0	0	2	0
    g	0	2	0	0	0	0	4	0	4	2	2
    t	2	1	0	0	0	0	0	0	0	0	0

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv1_m3_shift0 (oligos_8nt_mkv1_m3) |  |  |  |
    ; oligos_8nt_mkv1_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; rvCmCTATrGhT
    ; Alignment reference
    a	2	1	0	2	0	0	3	0	1	0	1	0
    c	0	1	3	1	3	0	0	0	0	0	1	0
    g	1	1	0	0	0	0	0	0	2	3	0	0
    t	0	0	0	0	0	3	0	3	0	0	1	3
oligos_8nt_mkv1_m3_shift0 (oligos_8nt_mkv1_m3) |  |  |  |
    ; oligos_8nt_mkv1_m3 versus oligos_8nt_mkv1_m3; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; rvCmCTATrGhT
    ; cor=; Ncor=
    a	2	1	0	2	0	0	3	0	1	0	1	0
    c	0	1	3	1	3	0	0	0	0	0	1	0
    g	1	1	0	0	0	0	0	0	2	3	0	0
    t	0	0	0	0	0	3	0	3	0	0	1	3
oligos_7nt_mkv1_m2_shift4 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_8nt_mkv1_m3 versus oligos_7nt_mkv1_m2; m=2/2; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.406473; ----bhATGGCY
    ; cor=; Ncor=
    a	0	0	0	0	1	2	8	0	0	0	1	0
    c	0	0	0	0	2	2	0	0	1	0	7	2
    g	0	0	0	0	3	1	0	0	7	7	0	0
    t	0	0	0	0	2	3	0	8	0	1	0	6

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv1_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv1_m1_shift0 (oligos_8nt_mkv1_m1) |  |  |  |
    ; oligos_8nt_mkv1_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; ybCTGTGGAAkh
    ; Alignment reference
    a	0	0	0	0	0	0	0	0	3	3	0	1
    c	2	1	3	0	0	0	0	0	0	0	0	1
    g	0	1	0	0	3	0	3	3	0	0	1	0
    t	1	1	0	3	0	3	0	0	0	0	2	1
oligos_8nt_mkv1_m1_shift0 (oligos_8nt_mkv1_m1) |  |  |  |
    ; oligos_8nt_mkv1_m1 versus oligos_8nt_mkv1_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; ybCTGTGGAAkh
    ; cor=; Ncor=
    a	0	0	0	0	0	0	0	0	3	3	0	1
    c	2	1	3	0	0	0	0	0	0	0	0	1
    g	0	1	0	0	3	0	3	3	0	0	1	0
    t	1	1	0	3	0	3	0	0	0	0	2	1
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_8nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.870312; ctCTGTGGAwt-
    ; cor=; Ncor=
    a	0	1	0	0	1	0	0	0	5	3	1	0
    c	3	1	5	0	0	0	0	0	0	0	0	0
    g	1	1	0	0	4	0	4	5	0	0	1	0
    t	1	2	0	5	0	5	1	0	0	2	3	0