# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.091816_2025-06-19.091816_x3rpdD/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.2025-06-19.091816_2025-06-19.091816_x3rpdD/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## 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=13; shift=0; ncol=13; cssCCGCCGCCss
    ; Alignment reference
    a	32	21	31	5	5	5	2	2	7	7	10	35	32
    c	59	60	55	141	142	9	142	141	14	137	136	55	51
    g	35	43	45	5	4	141	9	7	136	6	4	48	43
    t	31	33	26	6	6	2	4	7	0	7	7	19	31
oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4) |  |  |  |
    ; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score=      1; cssCCGCCGCCss
    ; cor=; Ncor=
    a	32	21	31	5	5	5	2	2	7	7	10	35	32
    c	59	60	55	141	142	9	142	141	14	137	136	55	51
    g	35	43	45	5	4	141	9	7	136	6	4	48	43
    t	31	33	26	6	6	2	4	7	0	7	7	19	31

## 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=11; shift=0; ncol=11; ssCCAACCcss
    ; Alignment reference
    a	24	29	3	1	113	122	0	0	13	15	25
    c	38	42	116	113	1	1	120	119	76	45	33
    g	32	34	3	8	9	0	1	4	20	45	42
    t	31	20	3	3	2	2	4	2	16	20	25
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1) |  |  |  |
    ; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; ssCCAACCcss
    ; cor=; Ncor=
    a	24	29	3	1	113	122	0	0	13	15	25
    c	38	42	116	113	1	1	120	119	76	45	33
    g	32	34	3	8	9	0	1	4	20	45	42
    t	31	20	3	3	2	2	4	2	16	20	25

## 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=14; shift=0; ncol=14; cscCCCATTCCGcs
    ; Alignment reference
    a	19	17	8	5	2	2	63	1	1	0	1	2	9	16
    c	27	27	47	56	71	68	9	3	8	78	65	5	40	23
    g	14	24	14	13	4	6	3	2	5	1	7	69	13	25
    t	19	11	10	5	2	3	4	73	65	0	6	3	17	15
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2) |  |  |  |
    ; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score=      1; cscCCCATTCCGcs
    ; cor=; Ncor=
    a	19	17	8	5	2	2	63	1	1	0	1	2	9	16
    c	27	27	47	56	71	68	9	3	8	78	65	5	40	23
    g	14	24	14	13	4	6	3	2	5	1	7	69	13	25
    t	19	11	10	5	2	3	4	73	65	0	6	3	17	15

## 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=12; shift=0; ncol=12; csCCACGCCCcc
    ; Alignment reference
    a	26	17	1	1	123	9	9	3	6	4	36	30
    c	62	67	141	152	14	124	4	138	142	146	65	56
    g	38	40	11	2	9	13	136	13	4	2	31	31
    t	29	31	2	0	9	9	6	1	3	3	23	38
oligos_6-8nt_m5_shift0 (oligos_6-8nt_m5) |  |  |  |
    ; oligos_6-8nt_m5 versus oligos_6-8nt_m5; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; csCCACGCCCcc
    ; cor=; Ncor=
    a	26	17	1	1	123	9	9	3	6	4	36	30
    c	62	67	141	152	14	124	4	138	142	146	65	56
    g	38	40	11	2	9	13	136	13	4	2	31	31
    t	29	31	2	0	9	9	6	1	3	3	23	38

## 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=10; shift=0; ncol=10; skGCACGCvs
    ; Alignment reference
    a	27	25	0	0	125	0	0	0	35	22
    c	41	25	0	125	0	125	0	125	35	36
    g	32	36	125	0	0	0	125	0	34	38
    t	25	39	0	0	0	0	0	0	21	29
oligos_6-8nt_m3_shift0 (oligos_6-8nt_m3) |  |  |  |
    ; oligos_6-8nt_m3 versus oligos_6-8nt_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; skGCACGCvs
    ; cor=; Ncor=
    a	27	25	0	0	125	0	0	0	35	22
    c	41	25	0	125	0	125	0	125	35	36
    g	32	36	125	0	0	0	125	0	34	38
    t	25	39	0	0	0	0	0	0	21	29