# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.150933_2026-01-05.150933_rtRXPK/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/2026/01/05/peak-motifs.2026-01-05.150933_2026-01-05.150933_rtRXPK/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; rsAGACCAGvm
    ; Alignment reference
    a	16	10	51	1	54	1	0	43	2	17	17
    c	13	16	2	3	1	48	52	4	4	18	17
    g	15	20	1	51	0	4	2	2	49	15	12
    t	12	10	2	1	1	3	2	7	1	6	10
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; rsAGACCAGvm
    ; cor=; Ncor=
    a	16	10	51	1	54	1	0	43	2	17	17
    c	13	16	2	3	1	48	52	4	4	18	17
    g	15	20	1	51	0	4	2	2	49	15	12
    t	12	10	2	1	1	3	2	7	1	6	10

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; syyCCTGAAATaa
    ; Alignment reference
    a	5	5	6	4	0	1	1	26	28	23	3	10	10
    c	9	9	11	21	29	1	0	0	1	2	1	6	6
    g	12	7	4	2	0	2	28	2	0	2	4	7	7
    t	3	8	8	2	0	25	0	1	0	2	21	6	6
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score=      1; syyCCTGAAATaa
    ; cor=; Ncor=
    a	5	5	6	4	0	1	1	26	28	23	3	10	10
    c	9	9	11	21	29	1	0	0	1	2	1	6	6
    g	12	7	4	2	0	2	28	2	0	2	4	7	7
    t	3	8	8	2	0	25	0	1	0	2	21	6	6

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; hyCTTTCAAAwa
    ; Alignment reference
    a	13	10	1	4	2	4	1	42	41	42	16	15
    c	13	11	32	1	0	1	36	1	0	1	8	10
    g	6	7	6	0	3	4	4	0	1	0	9	10
    t	12	16	5	39	39	35	3	1	2	1	11	9
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; hyCTTTCAAAwa
    ; cor=; Ncor=
    a	13	10	1	4	2	4	1	42	41	42	16	15
    c	13	11	32	1	0	1	36	1	0	1	8	10
    g	6	7	6	0	3	4	4	0	1	0	9	10
    t	12	16	5	39	39	35	3	1	2	1	11	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; vbGACTGGCgs
    ; Alignment reference
    a	15	4	1	50	1	1	1	4	2	12	10
    c	19	18	6	2	53	5	2	0	47	13	23
    g	16	19	49	3	2	2	52	47	5	20	16
    t	6	15	0	1	0	48	1	5	2	11	7
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; vbGACTGGCgs
    ; cor=; Ncor=
    a	15	4	1	50	1	1	1	4	2	12	10
    c	19	18	6	2	53	5	2	0	47	13	23
    g	16	19	49	3	2	2	52	47	5	20	16
    t	6	15	0	1	0	48	1	5	2	11	7

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=14; shift=0; ncol=14; dhcAAAACTTagyy
    ; Alignment reference
    a	10	8	5	25	26	25	29	3	0	3	20	2	7	5
    c	2	11	16	3	0	4	1	28	1	2	2	2	8	8
    g	9	4	4	2	2	1	1	0	0	3	6	21	6	7
    t	10	8	6	1	3	1	0	0	30	23	3	6	10	11
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/3; ncol2=14; w=0; offset=0; strand=D; shift=0; score=      1; dhcAAAACTTagyy
    ; cor=; Ncor=
    a	10	8	5	25	26	25	29	3	0	3	20	2	7	5
    c	2	11	16	3	0	4	1	28	1	2	2	2	8	8
    g	9	4	4	2	2	1	1	0	0	3	6	21	6	7
    t	10	8	6	1	3	1	0	0	30	23	3	6	10	11
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/3; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.769646; ywyAAAACTTTtd-
    ; cor=; Ncor=
    a	9	14	7	37	36	34	37	2	0	3	3	10	11	0
    c	14	9	13	1	1	0	4	33	0	2	2	10	5	0
    g	7	7	9	2	0	2	0	3	3	3	3	10	11	0
    t	11	11	12	1	4	5	0	3	38	33	33	11	14	0
oligos_7nt_test_vs_ctrl_m3_shift2 (oligos_7nt_test_vs_ctrl_m3) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m3; m=3/3; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.574228; --gsAAACTCAvy-
    ; cor=; Ncor=
    a	0	0	21	17	77	77	76	5	5	2	75	23	20	0
    c	0	0	17	25	2	6	3	72	5	72	1	28	27	0
    g	0	0	27	26	3	2	3	6	3	4	6	24	15	0
    t	0	0	20	17	3	0	3	2	72	7	3	10	23	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m3_shift2 (oligos_7nt_test_vs_ctrl_m3) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=2; ncol=13; --gsAAACTCAvy
    ; Alignment reference
    a	0	0	21	17	77	77	76	5	5	2	75	23	20
    c	0	0	17	25	2	6	3	72	5	72	1	28	27
    g	0	0	27	26	3	2	3	6	3	4	6	24	15
    t	0	0	20	17	3	0	3	2	72	7	3	10	23
oligos_7nt_test_vs_ctrl_m3_shift2 (oligos_7nt_test_vs_ctrl_m3) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=2; score=      1; --gsAAACTCAvy
    ; cor=; Ncor=
    a	0	0	21	17	77	77	76	5	5	2	75	23	20
    c	0	0	17	25	2	6	3	72	5	72	1	28	27
    g	0	0	27	26	3	2	3	6	3	4	6	24	15
    t	0	0	20	17	3	0	3	2	72	7	3	10	23
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5; m=2/2; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.574228; dhcAAAACTTagy
    ; cor=; Ncor=
    a	10	8	5	25	26	25	29	3	0	3	20	2	7
    c	2	11	16	3	0	4	1	28	1	2	2	2	8
    g	9	4	4	2	2	1	1	0	0	3	6	21	6
    t	10	8	6	1	3	1	0	0	30	23	3	6	10

## 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=13; shift=0; ncol=13; wwtTAAAAAAAhm
    ; Alignment reference
    a	26	27	12	6	73	70	71	73	72	76	72	22	27
    c	17	18	9	3	2	10	5	5	3	2	4	24	28
    g	16	14	9	8	3	4	3	3	6	6	4	16	13
    t	27	27	56	69	8	2	7	5	5	2	6	24	18
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=13; w=0; offset=0; strand=D; shift=0; score=      1; wwtTAAAAAAAhm
    ; cor=; Ncor=
    a	26	27	12	6	73	70	71	73	72	76	72	22	27
    c	17	18	9	3	2	10	5	5	3	2	4	24	28
    g	16	14	9	8	3	4	3	3	6	6	4	16	13
    t	27	27	56	69	8	2	7	5	5	2	6	24	18

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; mvATGACAAmr
    ; Alignment reference
    a	13	16	41	1	2	44	3	46	46	16	17
    c	17	15	5	1	0	5	46	3	0	15	10
    g	12	15	2	4	48	1	2	2	4	11	16
    t	10	6	4	46	2	2	1	1	2	10	9
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; mvATGACAAmr
    ; cor=; Ncor=
    a	13	16	41	1	2	44	3	46	46	16	17
    c	17	15	5	1	0	5	46	3	0	15	10
    g	12	15	2	4	48	1	2	2	4	11	16
    t	10	6	4	46	2	2	1	1	2	10	9

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; masTTTACAAad
    ; Alignment reference
    a	14	17	6	6	1	3	45	3	43	33	16	15
    c	14	9	14	1	1	0	0	34	1	6	10	3
    g	8	9	19	3	1	4	0	3	1	2	8	15
    t	9	10	6	35	42	38	0	5	0	4	11	12
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; masTTTACAAad
    ; cor=; Ncor=
    a	14	17	6	6	1	3	45	3	43	33	16	15
    c	14	9	14	1	1	0	0	34	1	6	10	3
    g	8	9	19	3	1	4	0	3	1	2	8	15
    t	9	10	6	35	42	38	0	5	0	4	11	12

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=13; shift=1; ncol=14; -haAAAGTTTTrwr
    ; Alignment reference
    a	0	14	11	33	33	38	3	0	5	4	1	12	11	11
    c	0	11	10	3	3	3	3	0	2	0	2	9	7	7
    g	0	5	10	2	2	0	33	4	0	1	1	13	9	14
    t	0	11	10	3	3	0	2	37	34	36	37	7	14	9
oligos_6nt_test_vs_ctrl_m2_shift1 (oligos_6nt_test_vs_ctrl_m2) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=1; score=      1; -haAAAGTTTTrwr
    ; cor=; Ncor=
    a	0	14	11	33	33	38	3	0	5	4	1	12	11	11
    c	0	11	10	3	3	3	3	0	2	0	2	9	7	7
    g	0	5	10	2	2	0	33	4	0	1	1	13	9	14
    t	0	11	10	3	3	0	2	37	34	36	37	7	14	9
oligos_6nt_test_vs_ctrl_m5_rc_shift0 (oligos_6nt_test_vs_ctrl_m5_rc) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5_rc; m=2/2; ncol2=14; w=-1; offset=-1; strand=R; shift=0; score=0.769646; rrctAAGTTTTgdh
    ; cor=; Ncor=
    a	11	10	6	3	23	30	0	0	1	3	1	6	8	10
    c	7	6	21	6	3	0	0	1	1	2	2	4	4	9
    g	8	8	2	2	2	1	28	1	4	0	3	16	11	2
    t	5	7	2	20	3	0	3	29	25	26	25	5	8	10