# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/02/26/peak-motifs.2026-02-26.234316_2026-02-26.234316_5Dj251/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/2026/02/26/peak-motifs.2026-02-26.234316_2026-02-26.234316_5Dj251/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## 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=15; shift=0; ncol=15; TCTCCATAACACAAG
    ; Alignment reference
    a	0	0	0	0	0	1	0	1	1	0	1	0	1	1	0
    c	0	1	0	1	1	0	0	0	0	1	0	1	0	0	0
    g	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
    t	1	0	1	0	0	0	1	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=15; w=0; offset=0; strand=D; shift=0; score=      1; TCTCCATAACACAAG
    ; cor=; Ncor=
    a	0	0	0	0	0	1	0	1	1	0	1	0	1	1	0
    c	0	1	0	1	1	0	0	0	0	1	0	1	0	0	0
    g	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
    t	1	0	1	0	0	0	1	0	0	0	0	0	0	0	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m3_shift0 ; 3 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; ttCCCTGCCyw
    ; Alignment reference
    a	1	1	0	0	0	0	0	0	0	0	3
    c	1	1	5	5	5	1	0	5	4	3	0
    g	1	1	0	0	0	0	5	0	0	0	0
    t	2	2	0	0	0	4	0	0	1	2	2
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3) |  |  |  |
    ; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; ttCCCTGCCyw
    ; cor=; Ncor=
    a	1	1	0	0	0	0	0	0	0	0	3
    c	1	1	5	5	5	1	0	5	4	3	0
    g	1	1	0	0	0	0	5	0	0	0	0
    t	2	2	0	0	0	4	0	0	1	2	2
oligos_7nt_mkv1_m2_rc_shift2 (oligos_7nt_mkv1_m2_rc) |  |  |  |
    ; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m2_rc; m=2/2; ncol2=13; w=0; offset=2; strand=R; shift=2; score=0.422322; --CCCCGCTTA
    ; cor=; Ncor=
    a	0	0	0	0	0	0	0	0	0	0	1
    c	0	0	1	1	1	1	0	1	0	0	0
    g	0	0	0	0	0	0	1	0	0	0	0
    t	0	0	0	0	0	0	0	0	1	1	0

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift5 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m1_shift5 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=5; ncol=15; -----CCCGCTTATC
    ; Alignment reference
    a	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
    c	0	0	0	0	0	1	1	1	0	1	0	0	0	0	1
    g	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
    t	0	0	0	0	0	0	0	0	0	0	1	1	0	1	0
oligos_6nt_mkv1_m1_shift5 (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=5; score=      1; -----CCCGCTTATC
    ; cor=; Ncor=
    a	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
    c	0	0	0	0	0	1	1	1	0	1	0	0	0	0	1
    g	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
    t	0	0	0	0	0	0	0	0	0	0	1	1	0	1	0
oligos_7nt_mkv1_m2_rc_shift4 (oligos_7nt_mkv1_m2_rc) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m2_rc; m=2/3; ncol2=13; w=-1; offset=-1; strand=R; shift=4; score=0.769231; ----CCCCGCTTATC
    ; cor=; Ncor=
    a	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0
    c	0	0	0	0	1	1	1	1	0	1	0	0	0	0	1
    g	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
    t	0	0	0	0	0	0	0	0	0	0	1	1	0	1	0
oligos_7nt_mkv1_m5_rc_shift0 (oligos_7nt_mkv1_m5_rc) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m5_rc; m=3/3; ncol2=11; w=-5; offset=-5; strand=R; shift=0; score=    0.4; CCTACCCCGCT----
    ; cor=; Ncor=
    a	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0
    c	1	1	0	0	1	1	1	1	0	1	0	0	0	0	0
    g	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0
    t	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 5 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=13; shift=0; ncol=13; GTGATAAGCGGGG
    ; Alignment reference
    a	0	0	0	1	0	1	1	0	0	0	0	0	0
    c	0	0	0	0	0	0	0	0	1	0	0	0	0
    g	1	0	1	0	0	0	0	1	0	1	1	1	1
    t	0	1	0	0	1	0	0	0	0	0	0	0	0
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/4; ncol2=13; w=0; offset=0; strand=D; shift=0; score=      1; GTGATAAGCGGGG
    ; cor=; Ncor=
    a	0	0	0	1	0	1	1	0	0	0	0	0	0
    c	0	0	0	0	0	0	0	0	1	0	0	0	0
    g	1	0	1	0	0	0	0	1	0	1	1	1	1
    t	0	1	0	0	1	0	0	0	0	0	0	0	0
oligos_6nt_mkv1_m1_rc_shift2 (oligos_6nt_mkv1_m1_rc) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m1_rc; m=2/4; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.769231; --GATAAGCGGG-
    ; cor=; Ncor=
    a	0	0	0	1	0	1	1	0	0	0	0	0	0
    c	0	0	0	0	0	0	0	0	1	0	0	0	0
    g	0	0	1	0	0	0	0	1	0	1	1	1	0
    t	0	0	0	0	1	0	0	0	0	0	0	0	0
oligos_7nt_mkv1_m3_rc_shift4 (oligos_7nt_mkv1_m3_rc) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m3_rc; m=3/4; ncol2=11; w=0; offset=4; strand=R; shift=4; score=0.422322; ----wrGGCAGGG
    ; cor=; Ncor=
    a	0	0	0	0	2	2	1	0	0	4	0	0	0
    c	0	0	0	0	0	0	0	0	5	0	0	0	0
    g	0	0	0	0	0	3	4	5	0	1	5	5	5
    t	0	0	0	0	3	0	0	0	0	0	0	0	0
oligos_7nt_mkv1_m5_shift6 (oligos_7nt_mkv1_m5) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m5; m=4/4; ncol2=11; w=0; offset=6; strand=D; shift=6; score=0.411765; ------AGCGGGG
    ; cor=; Ncor=
    a	0	0	0	0	0	0	1	0	0	0	0	0	0
    c	0	0	0	0	0	0	0	0	1	0	0	0	0
    g	0	0	0	0	0	0	0	1	0	1	1	1	1
    t	0	0	0	0	0	0	0	0	0	0	0	0	0

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m2_shift2 (oligos_6nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=10; shift=2; ncol=12; --AGAGTCAAmw
    ; Alignment reference
    a	0	0	2	0	2	0	0	0	2	2	1	1
    c	0	0	0	0	0	0	0	2	0	0	1	0
    g	0	0	0	2	0	2	0	0	0	0	0	0
    t	0	0	0	0	0	0	2	0	0	0	0	1
oligos_6nt_mkv1_m2_shift2 (oligos_6nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=2; score=      1; --AGAGTCAAmw
    ; cor=; Ncor=
    a	0	0	2	0	2	0	0	0	2	2	1	1
    c	0	0	0	0	0	0	0	2	0	0	1	0
    g	0	0	0	2	0	2	0	0	0	0	0	0
    t	0	0	0	0	0	0	2	0	0	0	0	1
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1; m=2/2; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.833333; srAGAGTCAAmw
    ; cor=; Ncor=
    a	0	1	2	0	2	0	0	0	2	2	1	1
    c	1	0	0	0	0	0	0	2	0	0	1	0
    g	1	1	0	2	0	2	0	0	0	0	0	0
    t	0	0	0	0	0	0	2	0	0	0	0	1

## 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=12; shift=0; ncol=12; srAGAGTCAAmw
    ; Alignment reference
    a	0	1	2	0	2	0	0	0	2	2	1	1
    c	1	0	0	0	0	0	0	2	0	0	1	0
    g	1	1	0	2	0	2	0	0	0	0	0	0
    t	0	0	0	0	0	0	2	0	0	0	0	1
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; srAGAGTCAAmw
    ; cor=; Ncor=
    a	0	1	2	0	2	0	0	0	2	2	1	1
    c	1	0	0	0	0	0	0	2	0	0	1	0
    g	1	1	0	2	0	2	0	0	0	0	0	0
    t	0	0	0	0	0	0	2	0	0	0	0	1
oligos_6nt_mkv1_m2_shift2 (oligos_6nt_mkv1_m2) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2; m=2/2; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.833333; --AGAGTCAAmw
    ; cor=; Ncor=
    a	0	0	2	0	2	0	0	0	2	2	1	1
    c	0	0	0	0	0	0	0	2	0	0	1	0
    g	0	0	0	2	0	2	0	0	0	0	0	0
    t	0	0	0	0	0	0	2	0	0	0	0	1

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m5_shift6 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv1_m5_shift6 (oligos_7nt_mkv1_m5) |  |  |  |
    ; oligos_7nt_mkv1_m5; m=0 (reference); ncol1=11; shift=6; ncol=17; ------AGCGGGGTAGG
    ; Alignment reference
    a	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0
    c	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
    g	0	0	0	0	0	0	0	1	0	1	1	1	1	0	0	1	1
    t	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
oligos_7nt_mkv1_m5_shift6 (oligos_7nt_mkv1_m5) |  |  |  |
    ; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=6; score=      1; ------AGCGGGGTAGG
    ; cor=; Ncor=
    a	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0
    c	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
    g	0	0	0	0	0	0	0	1	0	1	1	1	1	0	0	1	1
    t	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m2; m=2/3; ncol2=13; w=-6; offset=-6; strand=D; shift=0; score=0.411765; GTGATAAGCGGGG----
    ; cor=; Ncor=
    a	0	0	0	1	0	1	1	0	0	0	0	0	0	0	0	0	0
    c	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
    g	1	0	1	0	0	0	0	1	0	1	1	1	1	0	0	0	0
    t	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0
oligos_6nt_mkv1_m1_rc_shift2 (oligos_6nt_mkv1_m1_rc) |  |  |  |
    ; oligos_7nt_mkv1_m5 versus oligos_6nt_mkv1_m1_rc; m=3/3; ncol2=10; w=-4; offset=-4; strand=R; shift=2; score=    0.4; --GATAAGCGGG-----
    ; cor=; Ncor=
    a	0	0	0	1	0	1	1	0	0	0	0	0	0	0	0	0	0
    c	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0
    g	0	0	1	0	0	0	0	1	0	1	1	1	0	0	0	0	0
    t	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0