# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/12/19/peak-motifs.2025-12-19.115413_2025-12-19.115413_FZ7H1y/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/2025/12/19/peak-motifs.2025-12-19.115413_2025-12-19.115413_FZ7H1y/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift3 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4) |  |  |  |
    ; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=14; shift=3; ncol=17; ---yywkAGGCCTmwrr
    ; Alignment reference
    a	0	0	0	1	0	2	1	8	0	0	0	0	0	3	4	4	4
    c	0	0	0	3	4	1	0	0	0	0	8	8	0	4	1	0	0
    g	0	0	0	0	0	1	4	0	8	8	0	0	0	0	1	4	3
    t	0	0	0	4	4	4	3	0	0	0	0	0	8	1	2	0	1
oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4) |  |  |  |
    ; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=3; score=      1; ---yywkAGGCCTmwrr
    ; cor=; Ncor=
    a	0	0	0	1	0	2	1	8	0	0	0	0	0	3	4	4	4
    c	0	0	0	3	4	1	0	0	0	0	8	8	0	4	1	0	0
    g	0	0	0	0	0	1	4	0	8	8	0	0	0	0	1	4	3
    t	0	0	0	4	4	4	3	0	0	0	0	0	8	1	2	0	1
oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4) |  |  |  |
    ; oligos_6nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=2/2; ncol2=20; w=-3; offset=-3; strand=D; shift=0; score= 0.6833; ysryywkAGGCCTmwrr
    ; cor=; Ncor=
    a	0	0	1	0	0	1	0	2	0	0	0	0	0	1	1	1	1
    c	1	1	0	1	1	0	0	0	0	0	2	2	0	1	0	0	0
    g	0	1	1	0	0	0	1	0	2	2	0	0	0	0	0	1	1
    t	1	0	0	1	1	1	1	0	0	0	0	0	2	0	1	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; TAAAATATCAA
    ; Alignment reference
    a	3	35	41	37	41	0	41	0	2	32	36
    c	1	2	0	0	0	0	0	1	39	2	1
    g	3	4	0	0	0	0	0	0	0	3	1
    t	34	0	0	4	0	41	0	40	0	4	3
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3) |  |  |  |
    ; oligos_7nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; TAAAATATCAA
    ; cor=; Ncor=
    a	3	35	41	37	41	0	41	0	2	32	36
    c	1	2	0	0	0	0	0	1	39	2	1
    g	3	4	0	0	0	0	0	0	0	3	1
    t	34	0	0	4	0	41	0	40	0	4	3
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3) |  |  |  |
    ; oligos_7nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; TAAAATATCAA
    ; cor=; Ncor=
    a	3	35	41	37	41	0	41	0	2	32	36
    c	1	2	0	0	0	0	0	1	39	2	1
    g	3	4	0	0	0	0	0	0	0	3	1
    t	34	0	0	4	0	41	0	40	0	4	3

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 3 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=14; shift=0; ncol=14; aswGAGTTGAAyvy
    ; Alignment reference
    a	7	1	4	0	11	0	1	1	0	11	10	1	3	1
    c	2	4	0	0	0	0	0	0	0	0	1	5	4	5
    g	0	4	1	11	0	11	0	0	10	0	0	1	3	1
    t	2	2	6	0	0	0	10	10	1	0	0	4	1	4
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=0; score=      1; aswGAGTTGAAyvy
    ; cor=; Ncor=
    a	7	1	4	0	11	0	1	1	0	11	10	1	3	1
    c	2	4	0	0	0	0	0	0	0	0	1	5	4	5
    g	0	4	1	11	0	11	0	0	10	0	0	1	3	1
    t	2	2	6	0	0	0	10	10	1	0	0	4	1	4
oligos_6nt_mkv1_m2_rc_shift1 (oligos_6nt_mkv1_m2_rc) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m2_rc; m=2/2; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.834905; -bdGAGTTGAAys-
    ; cor=; Ncor=
    a	0	2	5	0	16	3	1	1	0	16	15	1	3	0
    c	0	6	0	0	0	0	0	0	0	0	1	5	4	0
    g	0	4	4	16	0	13	0	2	15	0	0	1	8	0
    t	0	4	7	0	0	0	15	13	1	0	0	9	1	0

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift0 ; 4 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=14; shift=0; ncol=14; TCCATTCCATTCCA
    ; Alignment reference
    a	0	3	3	44	2	0	2	3	46	2	0	3	7	40
    c	0	35	36	0	0	0	43	42	0	3	0	42	35	1
    g	2	2	5	2	0	0	1	0	1	0	1	1	2	5
    t	46	8	4	2	46	48	2	3	1	43	47	2	4	2
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score=      1; TCCATTCCATTCCA
    ; cor=; Ncor=
    a	0	3	3	44	2	0	2	3	46	2	0	3	7	40
    c	0	35	36	0	0	0	43	42	0	3	0	42	35	1
    g	2	2	5	2	0	0	1	0	1	0	1	1	2	5
    t	46	8	4	2	46	48	2	3	1	43	47	2	4	2
oligos_7nt_mkv1_m1_rc_shift0 (oligos_7nt_mkv1_m1_rc) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m1_rc; m=2/3; ncol2=15; w=0; offset=0; strand=R; shift=0; score=0.932269; TCCATTCCATTCCA
    ; cor=; Ncor=
    a	1	4	3	43	2	0	2	3	44	2	0	2	6	41
    c	0	33	37	0	0	0	43	41	1	2	0	41	37	1
    g	1	2	5	2	0	1	1	0	1	0	1	1	0	3
    t	45	8	2	2	45	46	1	3	1	43	46	3	4	2
oligos_6nt_mkv1_m2_shift2 (oligos_6nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m2; m=3/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.621589; --srTTCAACTChv
    ; cor=; Ncor=
    a	0	0	1	9	0	0	1	13	15	0	0	0	7	4
    c	0	0	8	1	0	0	15	2	0	13	0	16	4	4
    g	0	0	4	5	1	0	0	0	0	0	0	0	0	6
    t	0	0	3	1	15	16	0	1	1	3	16	0	5	2

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift2 ; 5 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=12; shift=2; ncol=14; --srTTCAACTChv
    ; Alignment reference
    a	0	0	1	9	0	0	1	13	15	0	0	0	7	4
    c	0	0	8	1	0	0	15	2	0	13	0	16	4	4
    g	0	0	4	5	1	0	0	0	0	0	0	0	0	6
    t	0	0	3	1	15	16	0	1	1	3	16	0	5	2
oligos_6nt_mkv1_m2_shift2 (oligos_6nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=2; score=      1; --srTTCAACTChv
    ; cor=; Ncor=
    a	0	0	1	9	0	0	1	13	15	0	0	0	7	4
    c	0	0	8	1	0	0	15	2	0	13	0	16	4	4
    g	0	0	4	5	1	0	0	0	0	0	0	0	0	6
    t	0	0	3	1	15	16	0	1	1	3	16	0	5	2
oligos_7nt_mkv1_m2_rc_shift1 (oligos_7nt_mkv1_m2_rc) |  |  |  |
    ; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m2_rc; m=2/4; ncol2=14; w=-1; offset=-1; strand=R; shift=1; score=0.834905; -rbrTTCAACTCws
    ; cor=; Ncor=
    a	0	4	1	4	0	0	1	10	10	0	0	0	6	2
    c	0	1	3	1	0	0	10	0	0	11	0	11	1	4
    g	0	5	4	5	1	0	0	0	0	0	0	0	0	4
    t	0	1	3	1	10	11	0	1	1	0	11	0	4	1
oligos_6nt_mkv1_m1_shift0 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m1; m=3/4; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.621589; TCCATTCCATTCCA
    ; cor=; Ncor=
    a	0	3	3	44	2	0	2	3	46	2	0	3	7	40
    c	0	35	36	0	0	0	43	42	0	3	0	42	35	1
    g	2	2	5	2	0	0	1	0	1	0	1	1	2	5
    t	46	8	4	2	46	48	2	3	1	43	47	2	4	2
oligos_7nt_mkv1_m1_rc_shift0 (oligos_7nt_mkv1_m1_rc) |  |  |  |
    ; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1_rc; m=4/4; ncol2=15; w=-2; offset=-2; strand=R; shift=0; score=0.569648; TCCATTCCATTCCA
    ; cor=; Ncor=
    a	1	4	3	43	2	0	2	3	44	2	0	2	6	41
    c	0	33	37	0	0	0	43	41	1	2	0	41	37	1
    g	1	2	5	2	0	1	1	0	1	0	1	1	0	3
    t	45	8	2	2	45	46	1	3	1	43	46	3	4	2

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 4 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=15; shift=0; ncol=15; ATGGAATGGAATGGA
    ; Alignment reference
    a	40	2	4	3	46	43	1	3	1	46	45	2	2	8	45
    c	1	3	0	1	1	0	1	0	1	1	0	2	5	2	1
    g	4	1	37	41	0	2	1	41	43	0	0	0	37	33	0
    t	2	41	6	2	0	2	44	3	2	0	2	43	3	4	1
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/3; ncol2=15; w=0; offset=0; strand=D; shift=0; score=      1; ATGGAATGGAATGGA
    ; cor=; Ncor=
    a	40	2	4	3	46	43	1	3	1	46	45	2	2	8	45
    c	1	3	0	1	1	0	1	0	1	1	0	2	5	2	1
    g	4	1	37	41	0	2	1	41	43	0	0	0	37	33	0
    t	2	41	6	2	0	2	44	3	2	0	2	43	3	4	1
oligos_6nt_mkv1_m1_rc_shift1 (oligos_6nt_mkv1_m1_rc) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m1_rc; m=2/3; ncol2=14; w=0; offset=1; strand=R; shift=1; score=0.932269; -TGGAATGGAATGGA
    ; cor=; Ncor=
    a	0	2	4	2	47	43	1	3	2	48	46	2	4	8	46
    c	0	5	2	1	1	0	1	0	1	0	0	2	5	2	2
    g	0	1	35	42	0	3	0	42	43	0	0	0	36	35	0
    t	0	40	7	3	0	2	46	3	2	0	2	44	3	3	0
oligos_6nt_mkv1_m2_rc_shift1 (oligos_6nt_mkv1_m2_rc) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2_rc; m=3/3; ncol2=12; w=0; offset=1; strand=R; shift=1; score=0.569648; -bdGAGTTGAAys--
    ; cor=; Ncor=
    a	0	2	5	0	16	3	1	1	0	16	15	1	3	0	0
    c	0	6	0	0	0	0	0	0	0	0	1	5	4	0	0
    g	0	4	4	16	0	13	0	2	15	0	0	1	8	0	0
    t	0	4	7	0	0	0	15	13	1	0	0	9	1	0	0

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift0 ; 3 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=11; shift=0; ncol=11; TAAAATATCAA
    ; Alignment reference
    a	3	35	41	37	41	0	41	0	2	32	36
    c	1	2	0	0	0	0	0	1	39	2	1
    g	3	4	0	0	0	0	0	0	0	3	1
    t	34	0	0	4	0	41	0	40	0	4	3
oligos_7nt_mkv1_m3_shift0 (oligos_7nt_mkv1_m3) |  |  |  |
    ; oligos_6nt_mkv1_m3 versus oligos_7nt_mkv1_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; TAAAATATCAA
    ; cor=; Ncor=
    a	3	35	41	37	41	0	41	0	2	32	36
    c	1	2	0	0	0	0	0	1	39	2	1
    g	3	4	0	0	0	0	0	0	0	3	1
    t	34	0	0	4	0	41	0	40	0	4	3
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3) |  |  |  |
    ; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; TAAAATATCAA
    ; cor=; Ncor=
    a	3	35	41	37	41	0	41	0	2	32	36
    c	1	2	0	0	0	0	0	1	39	2	1
    g	3	4	0	0	0	0	0	0	0	3	1
    t	34	0	0	4	0	41	0	40	0	4	3

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m4_shift0 ; 3 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=20; shift=0; ncol=20; ysryywkAGGCCTmwrrysr
    ; Alignment reference
    a	0	0	1	0	0	1	0	2	0	0	0	0	0	1	1	1	1	0	0	1
    c	1	1	0	1	1	0	0	0	0	0	2	2	0	1	0	0	0	1	1	0
    g	0	1	1	0	0	0	1	0	2	2	0	0	0	0	0	1	1	0	1	1
    t	1	0	0	1	1	1	1	0	0	0	0	0	2	0	1	0	0	1	0	0
oligos_7nt_mkv1_m4_shift0 (oligos_7nt_mkv1_m4) |  |  |  |
    ; oligos_7nt_mkv1_m4 versus oligos_7nt_mkv1_m4; m=1/2; ncol2=20; w=0; offset=0; strand=D; shift=0; score=      1; ysryywkAGGCCTmwrrysr
    ; cor=; Ncor=
    a	0	0	1	0	0	1	0	2	0	0	0	0	0	1	1	1	1	0	0	1
    c	1	1	0	1	1	0	0	0	0	0	2	2	0	1	0	0	0	1	1	0
    g	0	1	1	0	0	0	1	0	2	2	0	0	0	0	0	1	1	0	1	1
    t	1	0	0	1	1	1	1	0	0	0	0	0	2	0	1	0	0	1	0	0
oligos_6nt_mkv1_m4_shift3 (oligos_6nt_mkv1_m4) |  |  |  |
    ; oligos_7nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=2/2; ncol2=14; w=0; offset=3; strand=D; shift=3; score= 0.6833; ---yywkAGGCCTmwrr---
    ; cor=; Ncor=
    a	0	0	0	1	0	2	1	8	0	0	0	0	0	3	4	4	4	0	0	0
    c	0	0	0	3	4	1	0	0	0	0	8	8	0	4	1	0	0	0	0	0
    g	0	0	0	0	0	1	4	0	8	8	0	0	0	0	1	4	3	0	0	0
    t	0	0	0	4	4	4	3	0	0	0	0	0	8	1	2	0	1	0	0	0

## 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; myCAAAGTAysy
    ; Alignment reference
    a	41	2	2	61	63	61	0	1	62	0	1	2
    c	21	19	57	0	0	1	0	0	0	42	35	36
    g	0	2	2	2	0	0	61	0	1	1	21	1
    t	1	40	2	0	0	1	2	62	0	20	6	24
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; myCAAAGTAysy
    ; cor=; Ncor=
    a	41	2	2	61	63	61	0	1	62	0	1	2
    c	21	19	57	0	0	1	0	0	0	42	35	36
    g	0	2	2	2	0	0	61	0	1	1	21	1
    t	1	40	2	0	0	1	2	62	0	20	6	24

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m5_shift0 (oligos_6nt_mkv1_m5) |  |  |  |
    ; oligos_6nt_mkv1_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; GTACATAAAAT
    ; Alignment reference
    a	2	1	40	0	39	0	40	40	34	36	4
    c	0	3	0	40	1	0	0	0	0	1	1
    g	33	3	0	0	0	0	0	0	0	1	0
    t	5	33	0	0	0	40	0	0	6	2	35
oligos_6nt_mkv1_m5_shift0 (oligos_6nt_mkv1_m5) |  |  |  |
    ; oligos_6nt_mkv1_m5 versus oligos_6nt_mkv1_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; GTACATAAAAT
    ; cor=; Ncor=
    a	2	1	40	0	39	0	40	40	34	36	4
    c	0	3	0	40	1	0	0	0	0	1	1
    g	33	3	0	0	0	0	0	0	0	1	0
    t	5	33	0	0	0	40	0	0	6	2	35