# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.091929_2025-06-19.091929_ZGCM7J/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/2025/06/19/peak-motifs.2025-06-19.091929_2025-06-19.091929_ZGCM7J/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5) |  |  |  |
    ; oligos_6-8nt_m5; m=0 (reference); ncol1=13; shift=0; ncol=13; bscCCCATGCAbs
    ; Alignment reference
    a	12	19	9	2	2	2	95	3	3	3	86	23	17
    c	32	26	67	90	89	91	3	3	6	92	7	26	35
    g	30	41	12	1	3	3	1	1	87	3	7	25	32
    t	26	14	12	7	6	4	1	93	4	2	0	26	16
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5) |  |  |  |
    ; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score=      1; bscCCCATGCAbs
    ; cor=; Ncor=
    a	12	19	9	2	2	2	95	3	3	3	86	23	17
    c	32	26	67	90	89	91	3	3	6	92	7	26	35
    g	30	41	12	1	3	3	1	1	87	3	7	25	32
    t	26	14	12	7	6	4	1	93	4	2	0	26	16

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1) |  |  |  |
    ; oligos_6-8nt_m1; m=0 (reference); ncol1=13; shift=0; ncol=13; ycgGCACGCCCsg
    ; Alignment reference
    a	26	26	13	2	0	116	3	1	3	2	10	22	31
    c	39	52	27	7	117	7	116	2	119	111	91	43	31
    g	31	25	71	113	7	3	3	122	4	10	21	34	36
    t	32	25	17	6	4	2	6	3	2	5	6	29	30
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1) |  |  |  |
    ; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score=      1; ycgGCACGCCCsg
    ; cor=; Ncor=
    a	26	26	13	2	0	116	3	1	3	2	10	22	31
    c	39	52	27	7	117	7	116	2	119	111	91	43	31
    g	31	25	71	113	7	3	3	122	4	10	21	34	36
    t	32	25	17	6	4	2	6	3	2	5	6	29	30

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3) |  |  |  |
    ; oligos_6-8nt_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCCCCGCCCcs
    ; Alignment reference
    a	58	58	11	14	14	13	15	6	7	7	61	48
    c	110	114	282	280	281	275	42	292	286	291	121	118
    g	91	94	14	15	11	9	244	11	10	14	58	95
    t	56	49	8	6	9	18	14	6	12	3	75	54
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3) |  |  |  |
    ; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; ssCCCCGCCCcs
    ; cor=; Ncor=
    a	58	58	11	14	14	13	15	6	7	7	61	48
    c	110	114	282	280	281	275	42	292	286	291	121	118
    g	91	94	14	15	11	9	244	11	10	14	58	95
    t	56	49	8	6	9	18	14	6	12	3	75	54

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4) |  |  |  |
    ; oligos_6-8nt_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; yvTACCGTAss
    ; Alignment reference
    a	28	43	5	137	0	9	3	7	133	29	35
    c	52	40	8	3	147	124	7	8	7	51	43
    g	36	42	5	11	5	15	142	7	12	41	45
    t	41	32	139	6	5	9	5	135	5	36	34
oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4) |  |  |  |
    ; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; yvTACCGTAss
    ; cor=; Ncor=
    a	28	43	5	137	0	9	3	7	133	29	35
    c	52	40	8	3	147	124	7	8	7	51	43
    g	36	42	5	11	5	15	142	7	12	41	45
    t	41	32	139	6	5	9	5	135	5	36	34

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2) |  |  |  |
    ; oligos_6-8nt_m2; m=0 (reference); ncol1=12; shift=0; ncol=12; ssCCCATCGCvs
    ; Alignment reference
    a	22	20	3	9	7	123	3	1	6	5	37	29
    c	46	45	130	132	137	4	6	137	5	140	43	54
    g	50	55	9	4	3	12	19	6	135	2	44	40
    t	30	28	6	3	1	9	120	4	2	1	24	25
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2) |  |  |  |
    ; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; ssCCCATCGCvs
    ; cor=; Ncor=
    a	22	20	3	9	7	123	3	1	6	5	37	29
    c	46	45	130	132	137	4	6	137	5	140	43	54
    g	50	55	9	4	3	12	19	6	135	2	44	40
    t	30	28	6	3	1	9	120	4	2	1	24	25