# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.092322_2025-06-19.092322_shBOom/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.2025-06-19.092322_2025-06-19.092322_shBOom/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## 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=11; shift=0; ncol=11; drTAcATAtay
    ; Alignment reference
    a	41	39	3	131	9	112	1	133	24	46	34
    c	27	31	0	5	87	7	0	5	29	26	36
    g	35	37	7	0	15	12	0	0	29	33	32
    t	36	32	129	3	28	8	138	1	57	34	37
oligos_6-8nt_m2_shift0 (oligos_6-8nt_m2) |  |  |  |
    ; oligos_6-8nt_m2 versus oligos_6-8nt_m2; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; drTAcATAtay
    ; cor=; Ncor=
    a	41	39	3	131	9	112	1	133	24	46	34
    c	27	31	0	5	87	7	0	5	29	26	36
    g	35	37	7	0	15	12	0	0	29	33	32
    t	36	32	129	3	28	8	138	1	57	34	37

## 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=12; shift=0; ncol=12; ccCCCCGCCCcy
    ; Alignment reference
    a	32	37	9	4	6	3	6	4	5	9	40	31
    c	81	87	179	190	183	179	50	192	185	182	89	91
    g	50	44	6	5	10	8	144	5	8	10	33	30
    t	40	35	9	4	4	13	3	2	5	2	41	51
oligos_6-8nt_m1_shift0 (oligos_6-8nt_m1) |  |  |  |
    ; oligos_6-8nt_m1 versus oligos_6-8nt_m1; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; ccCCCCGCCCcy
    ; cor=; Ncor=
    a	32	37	9	4	6	3	6	4	5	9	40	31
    c	81	87	179	190	183	179	50	192	185	182	89	91
    g	50	44	6	5	10	8	144	5	8	10	33	30
    t	40	35	9	4	4	13	3	2	5	2	41	51

## 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=10; shift=0; ncol=10; bsGCCGGCsv
    ; Alignment reference
    a	15	24	0	0	0	0	0	0	20	25
    c	31	25	0	98	98	0	0	98	29	27
    g	27	29	98	0	0	98	98	0	25	31
    t	25	20	0	0	0	0	0	0	24	15
oligos_6-8nt_m4_shift0 (oligos_6-8nt_m4) |  |  |  |
    ; oligos_6-8nt_m4 versus oligos_6-8nt_m4; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; bsGCCGGCsv
    ; cor=; Ncor=
    a	15	24	0	0	0	0	0	0	20	25
    c	31	25	0	98	98	0	0	98	29	27
    g	27	29	98	0	0	98	98	0	25	31
    t	25	20	0	0	0	0	0	0	24	15

## 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; cgCCAGCAGCms
    ; Alignment reference
    a	20	33	3	6	129	6	3	119	5	1	36	21
    c	60	32	113	127	5	6	137	7	4	131	38	46
    g	34	47	21	6	3	125	2	9	133	6	35	52
    t	28	30	5	3	5	5	0	7	0	4	33	23
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; cgCCAGCAGCms
    ; cor=; Ncor=
    a	20	33	3	6	129	6	3	119	5	1	36	21
    c	60	32	113	127	5	6	137	7	4	131	38	46
    g	34	47	21	6	3	125	2	9	133	6	35	52
    t	28	30	5	3	5	5	0	7	0	4	33	23

## 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; gyAGACCTTGcs
    ; Alignment reference
    a	15	11	53	1	51	3	5	1	1	1	13	13
    c	15	24	2	3	4	55	51	3	1	0	23	19
    g	21	10	3	56	5	3	3	2	2	59	11	18
    t	10	16	3	1	1	0	2	55	57	1	14	11
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; gyAGACCTTGcs
    ; cor=; Ncor=
    a	15	11	53	1	51	3	5	1	1	1	13	13
    c	15	24	2	3	4	55	51	3	1	0	23	19
    g	21	10	3	56	5	3	3	2	2	59	11	18
    t	10	16	3	1	1	0	2	55	57	1	14	11