# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/03/24/peak-motifs.2026-03-24.175732_2026-03-24.175732_d4HBn3/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/2026/03/24/peak-motifs.2026-03-24.175732_2026-03-24.175732_d4HBn3/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; atATACATAta
    ; Alignment reference
    a	168	66	308	6	332	10	314	11	331	60	167
    c	52	73	12	19	9	259	7	18	5	75	56
    g	52	49	11	8	8	15	13	7	7	43	48
    t	83	167	24	322	6	71	21	319	12	177	84
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; atATACATAta
    ; cor=; Ncor=
    a	168	66	308	6	332	10	314	11	331	60	167
    c	52	73	12	19	9	259	7	18	5	75	56
    g	52	49	11	8	8	15	13	7	7	43	48
    t	83	167	24	322	6	71	21	319	12	177	84
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m1; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.891277; awATAcATATw
    ; cor=; Ncor=
    a	148	72	251	15	249	25	256	19	248	2	119
    c	29	60	2	4	7	184	2	7	1	23	34
    g	38	31	7	3	8	10	4	1	9	3	39
    t	56	108	11	249	7	52	9	244	13	243	79

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3) |  |  |  |
    ; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; dmCAGCTGwh
    ; Alignment reference
    a	39	38	0	130	0	2	1	5	35	40
    c	19	34	128	1	0	134	1	1	32	37
    g	38	32	1	1	134	0	0	130	32	19
    t	40	32	7	4	2	0	134	0	37	40
oligos_6nt_mkv2_m3_shift0 (oligos_6nt_mkv2_m3) |  |  |  |
    ; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; dmCAGCTGwh
    ; cor=; Ncor=
    a	39	38	0	130	0	2	1	5	35	40
    c	19	34	128	1	0	134	1	1	32	37
    g	38	32	1	1	134	0	0	130	32	19
    t	40	32	7	4	2	0	134	0	37	40

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5) |  |  |  |
    ; oligos_6nt_mkv2_m5; m=0 (reference); ncol1=10; shift=0; ncol=10; hwTCATCAth
    ; Alignment reference
    a	17	19	0	0	61	0	0	61	15	17
    c	17	9	0	61	0	0	61	0	9	17
    g	11	10	0	0	0	0	0	0	14	7
    t	16	23	61	0	0	61	0	0	23	20
oligos_6nt_mkv2_m5_shift0 (oligos_6nt_mkv2_m5) |  |  |  |
    ; oligos_6nt_mkv2_m5 versus oligos_6nt_mkv2_m5; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; hwTCATCAth
    ; cor=; Ncor=
    a	17	19	0	0	61	0	0	61	15	17
    c	17	9	0	61	0	0	61	0	9	17
    g	11	10	0	0	0	0	0	0	14	7
    t	16	23	61	0	0	61	0	0	23	20

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; ymkCCGCCGay
    ; Alignment reference
    a	48	57	43	8	9	17	14	7	6	82	38
    c	70	61	28	195	204	9	182	198	4	41	71
    g	39	48	90	2	0	170	8	5	199	43	50
    t	62	53	58	14	6	23	15	9	10	53	60
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; ymkCCGCCGay
    ; cor=; Ncor=
    a	48	57	43	8	9	17	14	7	6	82	38
    c	70	61	28	195	204	9	182	198	4	41	71
    g	39	48	90	2	0	170	8	5	199	43	50
    t	62	53	58	14	6	23	15	9	10	53	60

## One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_7nt_m1_shift0 (positions_7nt_m1) |  |  |  |
    ; positions_7nt_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; awAAGCAAAyr
    ; Alignment reference
    a	53	33	109	111	0	0	96	97	109	21	42
    c	17	13	0	1	0	101	4	3	3	39	12
    g	20	24	1	1	116	1	8	8	2	24	34
    t	27	47	7	4	1	15	9	9	3	33	29
positions_7nt_m1_shift0 (positions_7nt_m1) |  |  |  |
    ; positions_7nt_m1 versus positions_7nt_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; awAAGCAAAyr
    ; cor=; Ncor=
    a	53	33	109	111	0	0	96	97	109	21	42
    c	17	13	0	1	0	101	4	3	3	39	12
    g	20	24	1	1	116	1	8	8	2	24	34
    t	27	47	7	4	1	15	9	9	3	33	29
positions_6nt_m1_shift2 (positions_6nt_m1) |  |  |  |
    ; positions_7nt_m1 versus positions_6nt_m1; m=2/2; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.585892; --srGCAAACd
    ; cor=; Ncor=
    a	0	0	16	25	0	0	72	71	72	0	27
    c	0	0	19	12	0	72	0	0	0	72	9
    g	0	0	22	19	72	0	0	0	0	0	18
    t	0	0	15	16	0	0	0	1	0	0	18

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 3 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=14; shift=0; ncol=14; rrCTATCGATAGyy
    ; Alignment reference
    a	27	23	7	4	64	1	0	5	70	8	63	12	16	15
    c	13	16	51	6	2	0	67	2	3	0	1	4	19	19
    g	19	19	4	1	0	3	2	67	0	2	6	51	16	13
    t	15	16	12	63	8	70	5	0	1	64	4	7	23	27
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4) |  |  |  |
    ; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=0; score=      1; rrCTATCGATAGyy
    ; cor=; Ncor=
    a	27	23	7	4	64	1	0	5	70	8	63	12	16	15
    c	13	16	51	6	2	0	67	2	3	0	1	4	19	19
    g	19	19	4	1	0	3	2	67	0	2	6	51	16	13
    t	15	16	12	63	8	70	5	0	1	64	4	7	23	27
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4) |  |  |  |
    ; oligos_7nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=2/2; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.78708; -awTATCGATAwt-
    ; cor=; Ncor=
    a	0	54	75	16	161	2	5	11	174	13	137	51	44	0
    c	0	43	34	15	4	0	158	4	2	0	10	18	37	0
    g	0	37	18	10	0	2	4	158	0	4	15	34	43	0
    t	0	44	51	137	13	174	11	5	2	161	16	75	54	0

## 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; yaCACACACac
    ; Alignment reference
    a	67	158	11	316	16	322	18	326	12	186	77
    c	153	58	329	17	322	17	323	13	308	63	135
    g	46	81	8	17	9	16	9	14	22	46	66
    t	98	67	16	14	17	9	14	11	22	69	86
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; yaCACACACac
    ; cor=; Ncor=
    a	67	158	11	316	16	322	18	326	12	186	77
    c	153	58	329	17	322	17	323	13	308	63	135
    g	46	81	8	17	9	16	9	14	22	46	66
    t	98	67	16	14	17	9	14	11	22	69	86

## One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
positions_6nt_m1_shift2 (positions_6nt_m1) |  |  |  |
    ; positions_6nt_m1; m=0 (reference); ncol1=10; shift=2; ncol=12; --srGCAAACdw
    ; Alignment reference
    a	0	0	16	25	0	0	72	71	72	0	27	24
    c	0	0	19	12	0	72	0	0	0	72	9	12
    g	0	0	22	19	72	0	0	0	0	0	18	17
    t	0	0	15	16	0	0	0	1	0	0	18	19
positions_6nt_m1_shift2 (positions_6nt_m1) |  |  |  |
    ; positions_6nt_m1 versus positions_6nt_m1; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=2; score=      1; --srGCAAACdw
    ; cor=; Ncor=
    a	0	0	16	25	0	0	72	71	72	0	27	24
    c	0	0	19	12	0	72	0	0	0	72	9	12
    g	0	0	22	19	72	0	0	0	0	0	18	17
    t	0	0	15	16	0	0	0	1	0	0	18	19
positions_7nt_m1_shift0 (positions_7nt_m1) |  |  |  |
    ; positions_6nt_m1 versus positions_7nt_m1; m=2/2; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.585892; awAAGCAAAyr-
    ; cor=; Ncor=
    a	53	33	109	111	0	0	96	97	109	21	42	0
    c	17	13	0	1	0	101	4	3	3	39	12	0
    g	20	24	1	1	116	1	8	8	2	24	34	0
    t	27	47	7	4	1	15	9	9	3	33	29	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 3 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=12; shift=0; ncol=12; awATAcATATwt
    ; Alignment reference
    a	148	72	251	15	249	25	256	19	248	2	119	60
    c	29	60	2	4	7	184	2	7	1	23	34	48
    g	38	31	7	3	8	10	4	1	9	3	39	32
    t	56	108	11	249	7	52	9	244	13	243	79	131
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; awATAcATATwt
    ; cor=; Ncor=
    a	148	72	251	15	249	25	256	19	248	2	119	60
    c	29	60	2	4	7	184	2	7	1	23	34	48
    g	38	31	7	3	8	10	4	1	9	3	39	32
    t	56	108	11	249	7	52	9	244	13	243	79	131
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m2; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.891277; atATACATAta-
    ; cor=; Ncor=
    a	168	66	308	6	332	10	314	11	331	60	167	0
    c	52	73	12	19	9	259	7	18	5	75	56	0
    g	52	49	11	8	8	15	13	7	7	43	48	0
    t	83	167	24	322	6	71	21	319	12	177	84	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; arGAGGAGGArs
    ; Alignment reference
    a	37	29	8	86	5	4	86	6	2	88	30	20
    c	20	10	3	5	2	9	4	4	10	1	18	37
    g	20	45	83	0	89	83	0	84	84	4	38	27
    t	19	12	2	5	0	0	6	2	0	3	10	12
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; arGAGGAGGArs
    ; cor=; Ncor=
    a	37	29	8	86	5	4	86	6	2	88	30	20
    c	20	10	3	5	2	9	4	4	10	1	18	37
    g	20	45	83	0	89	83	0	84	84	4	38	27
    t	19	12	2	5	0	0	6	2	0	3	10	12

## 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=12; shift=0; ncol=12; tyTCTCTCTCtc
    ; Alignment reference
    a	20	16	1	4	1	5	3	2	0	7	9	22
    c	23	47	5	96	5	93	1	98	1	82	19	43
    g	20	9	10	0	3	1	1	0	5	6	21	18
    t	42	33	89	5	96	6	100	5	99	10	56	22
oligos_7nt_mkv2_m3_shift0 (oligos_7nt_mkv2_m3) |  |  |  |
    ; oligos_7nt_mkv2_m3 versus oligos_7nt_mkv2_m3; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; tyTCTCTCTCtc
    ; cor=; Ncor=
    a	20	16	1	4	1	5	3	2	0	7	9	22
    c	23	47	5	96	5	93	1	98	1	82	19	43
    g	20	9	10	0	3	1	1	0	5	6	21	18
    t	42	33	89	5	96	6	100	5	99	10	56	22

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4) |  |  |  |
    ; oligos_6nt_mkv2_m4; m=0 (reference); ncol1=12; shift=1; ncol=13; -awTATCGATAwt
    ; Alignment reference
    a	0	54	75	16	161	2	5	11	174	13	137	51	44
    c	0	43	34	15	4	0	158	4	2	0	10	18	37
    g	0	37	18	10	0	2	4	158	0	4	15	34	43
    t	0	44	51	137	13	174	11	5	2	161	16	75	54
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4) |  |  |  |
    ; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/2; ncol2=12; w=0; offset=0; strand=D; shift=1; score=      1; -awTATCGATAwt
    ; cor=; Ncor=
    a	0	54	75	16	161	2	5	11	174	13	137	51	44
    c	0	43	34	15	4	0	158	4	2	0	10	18	37
    g	0	37	18	10	0	2	4	158	0	4	15	34	43
    t	0	44	51	137	13	174	11	5	2	161	16	75	54
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4) |  |  |  |
    ; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=2/2; ncol2=14; w=-1; offset=-1; strand=D; shift=0; score=0.78708; rrCTATCGATAGy
    ; cor=; Ncor=
    a	27	23	7	4	64	1	0	5	70	8	63	12	16
    c	13	16	51	6	2	0	67	2	3	0	1	4	19
    g	19	19	4	1	0	3	2	67	0	2	6	51	16
    t	15	16	12	63	8	70	5	0	1	64	4	7	23