# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.012409_2025-05-16.012409_IdvjkC/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.2025-05-16.012409_2025-05-16.012409_IdvjkC/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; kwGAATCGAwa
    ; Alignment reference
    a	14	19	2	54	53	4	7	3	51	18	19
    c	9	8	1	0	1	0	44	2	3	8	14
    g	16	11	51	2	1	3	2	48	2	10	13
    t	19	20	4	2	3	51	5	5	2	22	12
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; kwGAATCGAwa
    ; cor=; Ncor=
    a	14	19	2	54	53	4	7	3	51	18	19
    c	9	8	1	0	1	0	44	2	3	8	14
    g	16	11	51	2	1	3	2	48	2	10	13
    t	19	20	4	2	3	51	5	5	2	22	12

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=14; shift=0; ncol=14; waAAATAATAAwww
    ; Alignment reference
    a	39	37	66	77	76	7	78	77	7	73	78	32	42	34
    c	10	19	2	1	3	0	1	1	1	4	3	10	7	14
    g	9	12	4	3	1	2	3	3	3	3	1	15	11	8
    t	25	15	11	2	3	74	1	2	72	3	1	26	23	27
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score=      1; waAAATAATAAwww
    ; cor=; Ncor=
    a	39	37	66	77	76	7	78	77	7	73	78	32	42	34
    c	10	19	2	1	3	0	1	1	1	4	3	10	7	14
    g	9	12	4	3	1	2	3	3	3	3	1	15	11	8
    t	25	15	11	2	3	74	1	2	72	3	1	26	23	27
oligos_6nt_test_vs_ctrl_m1_shift2 (oligos_6nt_test_vs_ctrl_m1) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m1; m=2/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.776658; --waATAATAATaw
    ; cor=; Ncor=
    a	0	0	61	65	131	10	139	132	8	139	130	15	81	57
    c	0	0	15	21	10	0	0	3	3	3	9	8	14	25
    g	0	0	19	27	1	8	8	6	7	1	2	3	29	16
    t	0	0	54	36	7	131	2	8	131	6	8	123	25	51
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m4; m=3/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.72635; amAAATAATrw---
    ; cor=; Ncor=
    a	15	10	33	33	33	0	33	33	0	12	17	0	0	0
    c	6	10	0	0	0	0	0	0	0	4	5	0	0	0
    g	4	6	0	0	0	0	0	0	0	10	2	0	0	0
    t	8	7	0	0	0	33	0	0	33	7	9	0	0	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=11; shift=1; ncol=12; -amAAATAATrw
    ; Alignment reference
    a	0	15	10	33	33	33	0	33	33	0	12	17
    c	0	6	10	0	0	0	0	0	0	0	4	5
    g	0	4	6	0	0	0	0	0	0	0	10	2
    t	0	8	7	0	0	0	33	0	0	33	7	9
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=1; score=      1; -amAAATAATrw
    ; cor=; Ncor=
    a	0	15	10	33	33	33	0	33	33	0	12	17
    c	0	6	10	0	0	0	0	0	0	0	4	5
    g	0	4	6	0	0	0	0	0	0	0	10	2
    t	0	8	7	0	0	0	33	0	0	33	7	9
oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m2; m=2/3; ncol2=14; w=0; offset=0; strand=D; shift=1; score=0.72635; -waAAATAATAA
    ; cor=; Ncor=
    a	0	39	37	66	77	76	7	78	77	7	73	78
    c	0	10	19	2	1	3	0	1	1	1	4	3
    g	0	9	12	4	3	1	2	3	3	3	3	1
    t	0	25	15	11	2	3	74	1	2	72	3	1
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m1; m=3/3; ncol2=12; w=-1; offset=-1; strand=D; shift=0; score=0.710646; waATAATAATaw
    ; cor=; Ncor=
    a	61	65	131	10	139	132	8	139	130	15	81	57
    c	15	21	10	0	0	3	3	3	9	8	14	25
    g	19	27	1	8	8	6	7	1	2	3	29	16
    t	54	36	7	131	2	8	131	6	8	123	25	51

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_test_vs_ctrl_m1_shift2 (oligos_6nt_test_vs_ctrl_m1) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --waATAATAATaw
    ; Alignment reference
    a	0	0	61	65	131	10	139	132	8	139	130	15	81	57
    c	0	0	15	21	10	0	0	3	3	3	9	8	14	25
    g	0	0	19	27	1	8	8	6	7	1	2	3	29	16
    t	0	0	54	36	7	131	2	8	131	6	8	123	25	51
oligos_6nt_test_vs_ctrl_m1_shift2 (oligos_6nt_test_vs_ctrl_m1) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score=      1; --waATAATAATaw
    ; cor=; Ncor=
    a	0	0	61	65	131	10	139	132	8	139	130	15	81	57
    c	0	0	15	21	10	0	0	3	3	3	9	8	14	25
    g	0	0	19	27	1	8	8	6	7	1	2	3	29	16
    t	0	0	54	36	7	131	2	8	131	6	8	123	25	51
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m2; m=2/3; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.776658; waAAATAATAAwww
    ; cor=; Ncor=
    a	39	37	66	77	76	7	78	77	7	73	78	32	42	34
    c	10	19	2	1	3	0	1	1	1	4	3	10	7	14
    g	9	12	4	3	1	2	3	3	3	3	1	15	11	8
    t	25	15	11	2	3	74	1	2	72	3	1	26	23	27
oligos_7nt_test_vs_ctrl_m4_shift3 (oligos_7nt_test_vs_ctrl_m4) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=3/3; ncol2=11; w=0; offset=1; strand=D; shift=3; score=0.710646; ---amAAATAATrw
    ; cor=; Ncor=
    a	0	0	0	15	10	33	33	33	0	33	33	0	12	17
    c	0	0	0	6	10	0	0	0	0	0	0	0	4	5
    g	0	0	0	4	6	0	0	0	0	0	0	0	10	2
    t	0	0	0	8	7	0	0	0	33	0	0	33	7	9

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=11; shift=0; ncol=11; wrCACCTGAww
    ; Alignment reference
    a	22	20	2	55	2	2	2	3	42	15	20
    c	11	8	45	0	52	49	2	1	6	5	10
    g	7	16	3	0	0	4	0	54	4	11	9
    t	18	14	8	3	4	3	54	0	6	27	19
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; wrCACCTGAww
    ; cor=; Ncor=
    a	22	20	2	55	2	2	2	3	42	15	20
    c	11	8	45	0	52	49	2	1	6	5	10
    g	7	16	3	0	0	4	0	54	4	11	9
    t	18	14	8	3	4	3	54	0	6	27	19

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wwAGCAACArh
    ; Alignment reference
    a	33	23	83	6	4	77	64	0	80	27	29
    c	12	14	1	1	79	1	10	78	5	19	26
    g	20	19	1	71	1	2	8	4	2	22	10
    t	23	32	3	10	4	8	6	6	1	20	23
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; wwAGCAACArh
    ; cor=; Ncor=
    a	33	23	83	6	4	77	64	0	80	27	29
    c	12	14	1	1	79	1	10	78	5	19	26
    g	20	19	1	71	1	2	8	4	2	22	10
    t	23	32	3	10	4	8	6	6	1	20	23

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; rtCATCGATGay
    ; Alignment reference
    a	7	4	2	20	0	0	1	19	2	1	9	4
    c	4	4	18	0	2	20	1	1	0	1	5	7
    g	7	5	1	0	1	1	20	2	0	18	4	4
    t	4	9	1	2	19	1	0	0	20	2	4	7
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; rtCATCGATGay
    ; cor=; Ncor=
    a	7	4	2	20	0	0	1	19	2	1	9	4
    c	4	4	18	0	2	20	1	1	0	1	5	7
    g	7	5	1	0	1	1	20	2	0	18	4	4
    t	4	9	1	2	19	1	0	0	20	2	4	7