# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/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/2025/02/25/peak-motifs.2025-02-25.153813_2025-02-25.153813_MpHLQf/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3) |  |  |  |
    ; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; rtATATATat
    ; Alignment reference
    a	14	7	30	0	32	0	33	0	18	5
    c	8	8	3	1	1	2	1	2	3	8
    g	9	3	2	0	2	1	1	3	8	8
    t	4	17	0	34	0	32	0	30	6	14
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3) |  |  |  |
    ; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; rtATATATat
    ; cor=; Ncor=
    a	14	7	30	0	32	0	33	0	18	5
    c	8	8	3	1	1	2	1	2	3	8
    g	9	3	2	0	2	1	1	3	8	8
    t	4	17	0	34	0	32	0	30	6	14

## 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; syCGTCGTCsb
    ; Alignment reference
    a	6	8	0	0	2	0	0	1	1	6	6
    c	15	15	44	7	5	44	4	2	44	12	14
    g	21	11	2	38	4	1	41	4	1	23	13
    t	4	12	0	1	35	1	1	39	0	5	13
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; syCGTCGTCsb
    ; cor=; Ncor=
    a	6	8	0	0	2	0	0	1	1	6	6
    c	15	15	44	7	5	44	4	2	44	12	14
    g	21	11	2	38	4	1	41	4	1	23	13
    t	4	12	0	1	35	1	1	39	0	5	13

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m1_shift1 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=10; shift=1; ncol=11; -ysCTCCTCkk
    ; Alignment reference
    a	0	2	3	0	0	0	0	0	0	1	4
    c	0	8	9	18	0	18	18	0	18	4	3
    g	0	3	5	0	0	0	0	0	0	6	5
    t	0	5	1	0	18	0	0	18	0	7	6
oligos_6nt_mkv1_m1_shift1 (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=1; score=      1; -ysCTCCTCkk
    ; cor=; Ncor=
    a	0	2	3	0	0	0	0	0	0	1	4
    c	0	8	9	18	0	18	18	0	18	4	3
    g	0	3	5	0	0	0	0	0	0	6	5
    t	0	5	1	0	18	0	0	18	0	7	6
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m3; m=2/2; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.808137; yyCCTCCTCkk
    ; cor=; Ncor=
    a	1	5	2	0	0	0	0	0	0	4	5
    c	12	7	19	25	0	24	20	1	23	2	4
    g	4	5	3	0	0	0	5	1	1	7	8
    t	8	8	1	0	25	1	0	23	1	12	8

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4) |  |  |  |
    ; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; sgAGGTAGwm
    ; Alignment reference
    a	3	3	16	0	0	0	18	0	6	5
    c	7	4	0	0	2	0	0	1	3	5
    g	5	7	0	17	16	0	0	16	4	4
    t	3	4	2	1	0	18	0	1	5	4
oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4) |  |  |  |
    ; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; sgAGGTAGwm
    ; cor=; Ncor=
    a	3	3	16	0	0	0	18	0	6	5
    c	7	4	0	0	2	0	0	1	3	5
    g	5	7	0	17	16	0	0	16	4	4
    t	3	4	2	1	0	18	0	1	5	4

## 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; raAAAAAAAww
    ; Alignment reference
    a	32	29	69	70	73	71	70	71	74	33	33
    c	15	16	3	4	5	3	3	1	0	9	8
    g	22	19	7	5	2	5	4	4	4	18	19
    t	12	17	2	2	1	2	4	5	3	21	21
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; raAAAAAAAww
    ; cor=; Ncor=
    a	32	29	69	70	73	71	70	71	74	33	33
    c	15	16	3	4	5	3	3	1	0	9	8
    g	22	19	7	5	2	5	4	4	4	18	19
    t	12	17	2	2	1	2	4	5	3	21	21

## 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=12; shift=0; ncol=12; yyCCTCCTCkkc
    ; Alignment reference
    a	1	5	2	0	0	0	0	0	0	4	5	3
    c	12	7	19	25	0	24	20	1	23	2	4	13
    g	4	5	3	0	0	0	5	1	1	7	8	3
    t	8	8	1	0	25	1	0	23	1	12	8	6
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3) |  |  |  |
    ; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; yyCCTCCTCkkc
    ; cor=; Ncor=
    a	1	5	2	0	0	0	0	0	0	4	5	3
    c	12	7	19	25	0	24	20	1	23	2	4	13
    g	4	5	3	0	0	0	5	1	1	7	8	3
    t	8	8	1	0	25	1	0	23	1	12	8	6
oligos_6nt_mkv1_m1_shift1 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m1; m=2/2; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.808137; -ysCTCCTCkk-
    ; cor=; Ncor=
    a	0	2	3	0	0	0	0	0	0	1	4	0
    c	0	8	9	18	0	18	18	0	18	4	3	0
    g	0	3	5	0	0	0	0	0	0	6	5	0
    t	0	5	1	0	18	0	0	18	0	7	6	0

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m5_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5) |  |  |  |
    ; oligos_6nt_mkv1_m5; m=0 (reference); ncol1=10; shift=2; ncol=12; --scCGCCGCsg
    ; Alignment reference
    a	0	0	2	2	0	0	0	0	0	0	5	3
    c	0	0	8	10	21	0	21	21	0	21	6	5
    g	0	0	9	5	0	21	0	0	21	0	6	11
    t	0	0	2	4	0	0	0	0	0	0	4	2
oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5) |  |  |  |
    ; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m5; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score=      1; --scCGCCGCsg
    ; cor=; Ncor=
    a	0	0	2	2	0	0	0	0	0	0	5	3
    c	0	0	8	10	21	0	21	21	0	21	6	5
    g	0	0	9	5	0	21	0	0	21	0	6	11
    t	0	0	2	4	0	0	0	0	0	0	4	2
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m5 versus oligos_7nt_mkv1_m2; m=2/3; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.648406; shCCCGCCGhs-
    ; cor=; Ncor=
    a	4	6	0	2	0	0	2	0	0	6	1	0
    c	8	6	21	18	21	0	20	23	0	8	10	0
    g	10	5	2	2	2	23	0	0	23	3	7	0
    t	1	6	0	1	0	0	1	0	0	6	5	0
oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m2; m=3/3; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.543838; vcCCCGCCsc--
    ; cor=; Ncor=
    a	6	3	0	0	0	0	0	0	4	3	0	0
    c	8	9	22	22	22	0	22	22	6	10	0	0
    g	7	5	0	0	0	22	0	0	11	4	0	0
    t	1	5	0	0	0	0	0	0	1	5	0	0

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift0 ; 4 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; vcCCCGCCsc
    ; Alignment reference
    a	6	3	0	0	0	0	0	0	4	3
    c	8	9	22	22	22	0	22	22	6	10
    g	7	5	0	0	0	22	0	0	11	4
    t	1	5	0	0	0	0	0	0	1	5
oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; vcCCCGCCsc
    ; cor=; Ncor=
    a	6	3	0	0	0	0	0	0	4	3
    c	8	9	22	22	22	0	22	22	6	10
    g	7	5	0	0	0	22	0	0	11	4
    t	1	5	0	0	0	0	0	0	1	5
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=2/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.853035; shCCCGCCGh
    ; cor=; Ncor=
    a	4	6	0	2	0	0	2	0	0	6
    c	8	6	21	18	21	0	20	23	0	8
    g	10	5	2	2	2	23	0	0	23	3
    t	1	6	0	1	0	0	1	0	0	6
oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5) |  |  |  |
    ; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m5; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.543838; --scCGCCGC
    ; cor=; Ncor=
    a	0	0	2	2	0	0	0	0	0	0
    c	0	0	8	10	21	0	21	21	0	21
    g	0	0	9	5	0	21	0	0	21	0
    t	0	0	2	4	0	0	0	0	0	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 4 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; shCCCGCCGhs
    ; Alignment reference
    a	4	6	0	2	0	0	2	0	0	6	1
    c	8	6	21	18	21	0	20	23	0	8	10
    g	10	5	2	2	2	23	0	0	23	3	7
    t	1	6	0	1	0	0	1	0	0	6	5
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; shCCCGCCGhs
    ; cor=; Ncor=
    a	4	6	0	2	0	0	2	0	0	6	1
    c	8	6	21	18	21	0	20	23	0	8	10
    g	10	5	2	2	2	23	0	0	23	3	7
    t	1	6	0	1	0	0	1	0	0	6	5
oligos_6nt_mkv1_m2_shift0 (oligos_6nt_mkv1_m2) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=2/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.853035; vcCCCGCCsc-
    ; cor=; Ncor=
    a	6	3	0	0	0	0	0	0	4	3	0
    c	8	9	22	22	22	0	22	22	6	10	0
    g	7	5	0	0	0	22	0	0	11	4	0
    t	1	5	0	0	0	0	0	0	1	5	0
oligos_6nt_mkv1_m5_shift2 (oligos_6nt_mkv1_m5) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m5; m=3/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.648406; --scCGCCGCs
    ; cor=; Ncor=
    a	0	0	2	2	0	0	0	0	0	0	5
    c	0	0	8	10	21	0	21	21	0	21	6
    g	0	0	9	5	0	21	0	0	21	0	6
    t	0	0	2	4	0	0	0	0	0	0	4

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv1_m5_shift0 (oligos_7nt_mkv1_m5) |  |  |  |
    ; oligos_7nt_mkv1_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; wvtAGTACTAct
    ; Alignment reference
    a	10	5	2	17	0	0	18	0	0	13	3	4
    c	0	5	2	0	4	0	0	14	0	2	7	3
    g	3	5	2	0	14	0	0	3	0	1	4	1
    t	5	3	12	1	0	18	0	1	18	2	4	10
oligos_7nt_mkv1_m5_shift0 (oligos_7nt_mkv1_m5) |  |  |  |
    ; oligos_7nt_mkv1_m5 versus oligos_7nt_mkv1_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; wvtAGTACTAct
    ; cor=; Ncor=
    a	10	5	2	17	0	0	18	0	0	13	3	4
    c	0	5	2	0	4	0	0	14	0	2	7	3
    g	3	5	2	0	14	0	0	3	0	1	4	1
    t	5	3	12	1	0	18	0	1	18	2	4	10