# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184046_2025-05-16.184046_ZEi16E/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.2025-05-16.184046_2025-05-16.184046_ZEi16E/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---gsCCCGCChy
    ; Alignment reference
    a	0	0	0	6	4	0	0	0	0	0	0	8	3
    c	0	0	0	5	12	32	32	32	0	32	31	14	14
    g	0	0	0	14	10	0	0	0	32	0	1	2	3
    t	0	0	0	7	6	0	0	0	0	0	0	8	12
oligos_6nt_mkv2_m2_shift3 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=3; score=      1; ---gsCCCGCChy
    ; cor=; Ncor=
    a	0	0	0	6	4	0	0	0	0	0	0	8	3
    c	0	0	0	5	12	32	32	32	0	32	31	14	14
    g	0	0	0	14	10	0	0	0	32	0	1	2	3
    t	0	0	0	7	6	0	0	0	0	0	0	8	12
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc) |  |  |  |
    ; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1_rc; m=2/3; ncol2=12; w=-3; offset=-3; strand=R; shift=0; score=0.610268; cyGGCCCCGCcc-
    ; cor=; Ncor=
    a	4	9	2	3	2	0	1	0	0	2	7	3	0
    c	19	14	3	1	35	38	35	35	0	32	22	23	0
    g	7	6	34	35	2	1	1	4	38	4	7	8	0
    t	9	10	0	0	0	0	2	0	1	1	3	5	0
oligos_6nt_mkv2_m1_rc_shift1 (oligos_6nt_mkv2_m1_rc) |  |  |  |
    ; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m1_rc; m=3/3; ncol2=10; w=-2; offset=-2; strand=R; shift=1; score=0.548811; -yrGCCCCGmc--
    ; cor=; Ncor=
    a	0	4	8	1	0	0	1	0	0	8	7	0	0
    c	0	15	5	0	32	30	31	32	0	16	16	0	0
    g	0	5	17	31	0	2	0	0	32	7	6	0	0
    t	0	8	2	0	0	0	0	0	0	1	3	0	0

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --gkCGGGGCyr
    ; Alignment reference
    a	0	0	3	1	0	0	0	0	0	0	2	8
    c	0	0	6	7	32	0	0	2	0	31	17	5
    g	0	0	16	16	0	32	31	30	32	0	5	15
    t	0	0	7	8	0	0	1	0	0	1	8	4
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=2; score=      1; --gkCGGGGCyr
    ; cor=; Ncor=
    a	0	0	3	1	0	0	0	0	0	0	2	8
    c	0	0	6	7	32	0	0	2	0	31	17	5
    g	0	0	16	16	0	32	31	30	32	0	5	15
    t	0	0	7	8	0	0	1	0	0	1	8	4
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/3; ncol2=12; w=-1; offset=-1; strand=D; shift=1; score=0.797323; -ggGCGGGGCCr
    ; cor=; Ncor=
    a	0	5	3	1	1	0	2	0	0	0	0	10
    c	0	8	7	4	38	4	1	1	2	35	34	6
    g	0	23	22	32	0	35	35	38	35	1	3	14
    t	0	3	7	2	0	0	1	0	2	3	2	9
oligos_6nt_mkv2_m2_rc_shift0 (oligos_6nt_mkv2_m2_rc) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=3/3; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.548811; rdGGCGGGsc--
    ; cor=; Ncor=
    a	12	8	0	0	0	0	0	0	6	7	0	0
    c	3	2	1	0	32	0	0	0	10	14	0	0
    g	14	14	31	32	0	32	32	32	12	5	0	0
    t	3	8	0	0	0	0	0	0	4	6	0	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5) |  |  |  |
    ; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=12; shift=0; ncol=12; ykCTACTMArwr
    ; Alignment reference
    a	2	1	0	0	9	0	0	8	11	7	6	5
    c	5	2	11	1	0	10	0	3	0	0	1	1
    g	1	3	0	0	1	1	0	0	0	3	1	4
    t	3	5	0	10	1	0	11	0	0	1	3	1
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5) |  |  |  |
    ; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; ykCTACTMArwr
    ; cor=; Ncor=
    a	2	1	0	0	9	0	0	8	11	7	6	5
    c	5	2	11	1	0	10	0	3	0	0	1	1
    g	1	3	0	0	1	1	0	0	0	3	1	4
    t	3	5	0	10	1	0	11	0	0	1	3	1

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3) |  |  |  |
    ; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; vwCTTGAACty
    ; Alignment reference
    a	6	8	0	1	0	0	21	20	1	5	3
    c	7	3	22	1	2	0	0	0	19	4	11
    g	9	3	0	0	3	21	0	2	0	3	1
    t	0	8	0	20	17	1	1	0	2	10	7
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3) |  |  |  |
    ; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; vwCTTGAACty
    ; cor=; Ncor=
    a	6	8	0	1	0	0	21	20	1	5	3
    c	7	3	22	1	2	0	0	0	19	4	11
    g	9	3	0	0	3	21	0	2	0	3	1
    t	0	8	0	20	17	1	1	0	2	10	7

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4) |  |  |  |
    ; oligos_7nt_mkv2_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; gsGATTACAGgy
    ; Alignment reference
    a	2	0	0	11	0	0	11	0	11	1	1	1
    c	0	3	0	0	1	1	0	10	0	0	2	6
    g	8	8	12	1	0	0	1	0	0	11	8	2
    t	2	1	0	0	11	11	0	2	1	0	1	3
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4) |  |  |  |
    ; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; gsGATTACAGgy
    ; cor=; Ncor=
    a	2	0	0	11	0	0	11	0	11	1	1	1
    c	0	3	0	0	1	1	0	10	0	0	2	6
    g	8	8	12	1	0	0	1	0	0	11	8	2
    t	2	1	0	0	11	11	0	2	1	0	1	3

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2) |  |  |  |
    ; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; ykCCTCCCGrs
    ; Alignment reference
    a	3	1	1	0	1	0	1	0	0	8	4
    c	7	4	19	19	0	21	19	21	0	3	8
    g	5	9	1	2	0	0	0	0	21	8	7
    t	6	7	0	0	20	0	1	0	0	2	2
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2) |  |  |  |
    ; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; ykCCTCCCGrs
    ; cor=; Ncor=
    a	3	1	1	0	1	0	1	0	0	8	4
    c	7	4	19	19	0	21	19	21	0	3	8
    g	5	9	1	2	0	0	0	0	21	8	7
    t	6	7	0	0	20	0	1	0	0	2	2

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -ggGCGGGGCCrg
    ; Alignment reference
    a	0	5	3	1	1	0	2	0	0	0	0	10	9
    c	0	8	7	4	38	4	1	1	2	35	34	6	7
    g	0	23	22	32	0	35	35	38	35	1	3	14	19
    t	0	3	7	2	0	0	1	0	2	3	2	9	4
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=1; score=      1; -ggGCGGGGCCrg
    ; cor=; Ncor=
    a	0	5	3	1	1	0	2	0	0	0	0	10	9
    c	0	8	7	4	38	4	1	1	2	35	34	6	7
    g	0	23	22	32	0	35	35	38	35	1	3	14	19
    t	0	3	7	2	0	0	1	0	2	3	2	9	4
oligos_6nt_mkv2_m1_shift2 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=2; score=0.797323; --gkCGGGGCyr-
    ; cor=; Ncor=
    a	0	0	3	1	0	0	0	0	0	0	2	8	0
    c	0	0	6	7	32	0	0	2	0	31	17	5	0
    g	0	0	16	16	0	32	31	30	32	0	5	15	0
    t	0	0	7	8	0	0	1	0	0	1	8	4	0
oligos_6nt_mkv2_m2_rc_shift0 (oligos_6nt_mkv2_m2_rc) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2_rc; m=3/3; ncol2=10; w=-1; offset=-1; strand=R; shift=0; score=0.610268; rdGGCGGGsc---
    ; cor=; Ncor=
    a	12	8	0	0	0	0	0	0	6	7	0	0	0
    c	3	2	1	0	32	0	0	0	10	14	0	0	0
    g	14	14	31	32	0	32	32	32	12	5	0	0	0
    t	3	8	0	0	0	0	0	0	4	6	0	0	0