# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.022353_2026-04-21.022353_CcghX5/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/2026/04/21/peak-motifs.2026-04-21.022353_2026-04-21.022353_CcghX5/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; bmGCAAGACdr
    ; Alignment reference
    a	2	43	0	19	115	116	0	132	3	51	64
    c	38	48	0	113	0	0	16	0	113	2	20
    g	56	17	116	0	1	16	111	0	16	41	48
    t	36	24	16	0	16	0	5	0	0	38	0
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; bmGCAAGACdr
    ; cor=; Ncor=
    a	2	43	0	19	115	116	0	132	3	51	64
    c	38	48	0	113	0	0	16	0	113	2	20
    g	56	17	116	0	1	16	111	0	16	41	48
    t	36	24	16	0	16	0	5	0	0	38	0

## 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; mhGCACTCCGy
    ; Alignment reference
    a	32	19	16	0	72	16	0	0	0	4	18
    c	33	32	0	75	3	54	0	75	75	3	19
    g	3	1	59	0	0	3	0	0	0	52	3
    t	7	23	0	0	0	2	75	0	0	16	35
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; mhGCACTCCGy
    ; cor=; Ncor=
    a	32	19	16	0	72	16	0	0	0	4	18
    c	33	32	0	75	3	54	0	75	75	3	19
    g	3	1	59	0	0	3	0	0	0	52	3
    t	7	23	0	0	0	2	75	0	0	16	35

## 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; TCTGGCTTCAym
    ; Alignment reference
    a	11	1	0	0	0	0	0	0	0	48	0	28
    c	0	44	0	0	0	57	11	0	59	9	31	19
    g	0	13	0	59	59	0	0	0	0	0	1	0
    t	48	1	59	0	0	2	48	59	0	2	27	12
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; TCTGGCTTCAym
    ; cor=; Ncor=
    a	11	1	0	0	0	0	0	0	0	48	0	28
    c	0	44	0	0	0	57	11	0	59	9	31	19
    g	0	13	0	59	59	0	0	0	0	0	1	0
    t	48	1	59	0	0	2	48	59	0	2	27	12

## 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=11; shift=0; ncol=11; aaACGACACvm
    ; Alignment reference
    a	67	49	111	16	1	95	0	94	0	33	46
    c	16	26	0	94	0	0	98	16	98	32	36
    g	16	19	0	0	108	0	0	0	0	40	12
    t	12	17	0	1	2	16	13	1	13	6	17
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5) |  |  |  |
    ; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; aaACGACACvm
    ; cor=; Ncor=
    a	67	49	111	16	1	95	0	94	0	33	46
    c	16	26	0	94	0	0	98	16	98	32	36
    g	16	19	0	0	108	0	0	0	0	40	12
    t	12	17	0	1	2	16	13	1	13	6	17

## 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; TtTGGTGAAck
    ; Alignment reference
    a	19	29	3	16	3	0	0	136	151	32	21
    c	4	22	3	0	3	0	0	0	0	101	8
    g	18	4	0	131	147	5	150	16	2	10	83
    t	112	98	147	6	0	148	3	1	0	10	41
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; TtTGGTGAAck
    ; cor=; Ncor=
    a	19	29	3	16	3	0	0	136	151	32	21
    c	4	22	3	0	3	0	0	0	0	101	8
    g	18	4	0	131	147	5	150	16	2	10	83
    t	112	98	147	6	0	148	3	1	0	10	41