# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184256_2025-05-16.184256_DOHBqC/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/2025/05/16/peak-motifs.2025-05-16.184256_2025-05-16.184256_DOHBqC/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m1; m=0 (reference); ncol1=13; shift=2; ncol=15; --mAGCCAGCCAGCC
    ; Alignment reference
    a	0	0	32	59	1	1	1	63	1	0	0	62	1	2	3
    c	0	0	33	0	8	62	63	1	8	65	63	0	0	58	58
    g	0	0	0	5	56	1	0	0	56	0	1	3	64	4	3
    t	0	0	0	1	0	1	1	1	0	0	1	0	0	1	1
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=2; score=      1; --mAGCCAGCCAGCC
    ; cor=; Ncor=
    a	0	0	32	59	1	1	1	63	1	0	0	62	1	2	3
    c	0	0	33	0	8	62	63	1	8	65	63	0	0	58	58
    g	0	0	0	5	56	1	0	0	56	0	1	3	64	4	3
    t	0	0	0	1	0	1	1	1	0	0	1	0	0	1	1
oligos_6nt_mkv1_m2_rc_shift0 (oligos_6nt_mkv1_m2_rc) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_6nt_mkv1_m2_rc; m=2/3; ncol2=16; w=-2; offset=-2; strand=R; shift=0; score=0.743816; sCmAGCCAGCCArsC
    ; cor=; Ncor=
    a	3	3	55	108	0	0	1	104	2	2	2	106	63	2	7
    c	56	97	54	1	2	105	106	2	6	100	102	0	4	42	89
    g	47	4	0	0	104	4	1	2	100	4	3	3	41	63	8
    t	3	5	0	0	3	0	1	1	1	3	2	0	1	2	5
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_6nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=3/3; ncol2=17; w=-2; offset=-2; strand=D; shift=0; score=0.600748; sCmAGCCAGCCAAGC
    ; cor=; Ncor=
    a	2	2	33	54	0	0	0	53	2	0	1	55	53	0	3
    c	34	49	22	1	0	51	53	1	3	52	52	0	0	2	47
    g	18	2	0	0	52	4	1	1	50	2	2	0	2	52	3
    t	1	2	0	0	3	0	1	0	0	1	0	0	0	1	2

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m2_shift1 (oligos_6nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=16; shift=1; ncol=17; -kGsyTGGCTGGCTkGs
    ; Alignment reference
    a	0	5	5	2	1	0	2	3	1	1	1	0	3	0	0	5	3
    c	0	4	8	63	41	3	3	4	100	2	1	4	104	0	0	4	47
    g	0	57	89	42	4	0	102	100	6	2	106	105	2	1	54	97	56
    t	0	43	7	2	63	106	2	2	2	104	1	0	0	108	55	3	3
oligos_6nt_mkv1_m2_shift1 (oligos_6nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m2; m=1/3; ncol2=16; w=0; offset=0; strand=D; shift=1; score=      1; -kGsyTGGCTGGCTkGs
    ; cor=; Ncor=
    a	0	5	5	2	1	0	2	3	1	1	1	0	3	0	0	5	3
    c	0	4	8	63	41	3	3	4	100	2	1	4	104	0	0	4	47
    g	0	57	89	42	4	0	102	100	6	2	106	105	2	1	54	97	56
    t	0	43	7	2	63	106	2	2	2	104	1	0	0	108	55	3	3
oligos_7nt_mkv1_m1_rc_shift0 (oligos_7nt_mkv1_m1_rc) |  |  |  |
    ; oligos_6nt_mkv1_m2 versus oligos_7nt_mkv1_m1_rc; m=2/3; ncol2=17; w=-1; offset=-1; strand=R; shift=0; score= 0.9005; TGGCTTGGCTGGCTkGs
    ; cor=; Ncor=
    a	1	2	2	1	0	0	0	1	0	0	1	0	3	0	0	2	1
    c	3	1	3	52	2	0	2	2	50	1	1	4	52	0	0	2	18
    g	1	48	47	2	0	0	52	52	3	1	53	51	0	1	22	49	34
    t	50	4	3	0	53	55	1	0	2	53	0	0	0	54	33	2	2
oligos_6nt_mkv1_m1_rc_shift2 (oligos_6nt_mkv1_m1_rc) |  |  |  |
    ; oligos_6nt_mkv1_m2 versus oligos_6nt_mkv1_m1_rc; m=3/3; ncol2=13; w=0; offset=1; strand=R; shift=2; score=0.743816; --GGCTGGCTGGCTk--
    ; cor=; Ncor=
    a	0	0	1	1	0	0	1	0	0	1	1	1	0	1	0	0	0
    c	0	0	3	4	64	3	1	0	56	0	0	1	56	5	0	0	0
    g	0	0	58	58	0	0	63	65	8	1	63	62	8	0	33	0	0
    t	0	0	3	2	1	62	0	0	1	63	1	1	1	59	32	0	0

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m4_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4) |  |  |  |
    ; oligos_6nt_mkv1_m4; m=0 (reference); ncol1=10; shift=0; ncol=10; dgCAGAGAgw
    ; Alignment reference
    a	4	2	0	10	0	10	0	10	1	4
    c	0	2	10	0	0	0	0	0	2	1
    g	3	5	0	0	10	0	10	0	6	2
    t	3	1	0	0	0	0	0	0	1	3
oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4) |  |  |  |
    ; oligos_6nt_mkv1_m4 versus oligos_6nt_mkv1_m4; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; dgCAGAGAgw
    ; cor=; Ncor=
    a	4	2	0	10	0	10	0	10	1	4
    c	0	2	10	0	0	0	0	0	2	1
    g	3	5	0	0	10	0	10	0	6	2
    t	3	1	0	0	0	0	0	0	1	3
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_6nt_mkv1_m4 versus oligos_7nt_mkv1_m2; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.891545; drCAGAGAGr
    ; cor=; Ncor=
    a	2	2	0	7	0	7	0	7	0	3
    c	0	1	7	0	0	0	0	0	0	1
    g	3	3	0	0	7	0	7	0	6	2
    t	2	1	0	0	0	0	0	0	1	1

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m1_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; sCmAGCCAGCCAAGCCA
    ; Alignment reference
    a	2	2	33	54	0	0	0	53	2	0	1	55	53	0	3	4	50
    c	34	49	22	1	0	51	53	1	3	52	52	0	0	2	47	48	1
    g	18	2	0	0	52	4	1	1	50	2	2	0	2	52	3	1	3
    t	1	2	0	0	3	0	1	0	0	1	0	0	0	1	2	2	1
oligos_7nt_mkv1_m1_shift0 (oligos_7nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_7nt_mkv1_m1; m=1/3; ncol2=17; w=0; offset=0; strand=D; shift=0; score=      1; sCmAGCCAGCCAAGCCA
    ; cor=; Ncor=
    a	2	2	33	54	0	0	0	53	2	0	1	55	53	0	3	4	50
    c	34	49	22	1	0	51	53	1	3	52	52	0	0	2	47	48	1
    g	18	2	0	0	52	4	1	1	50	2	2	0	2	52	3	1	3
    t	1	2	0	0	3	0	1	0	0	1	0	0	0	1	2	2	1
oligos_6nt_mkv1_m2_rc_shift0 (oligos_6nt_mkv1_m2_rc) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m2_rc; m=2/3; ncol2=16; w=0; offset=0; strand=R; shift=0; score= 0.9005; sCmAGCCAGCCArsCm-
    ; cor=; Ncor=
    a	3	3	55	108	0	0	1	104	2	2	2	106	63	2	7	43	0
    c	56	97	54	1	2	105	106	2	6	100	102	0	4	42	89	57	0
    g	47	4	0	0	104	4	1	2	100	4	3	3	41	63	8	4	0
    t	3	5	0	0	3	0	1	1	1	3	2	0	1	2	5	5	0
oligos_6nt_mkv1_m1_shift2 (oligos_6nt_mkv1_m1) |  |  |  |
    ; oligos_7nt_mkv1_m1 versus oligos_6nt_mkv1_m1; m=3/3; ncol2=13; w=0; offset=2; strand=D; shift=2; score=0.600748; --mAGCCAGCCAGCC--
    ; cor=; Ncor=
    a	0	0	32	59	1	1	1	63	1	0	0	62	1	2	3	0	0
    c	0	0	33	0	8	62	63	1	8	65	63	0	0	58	58	0	0
    g	0	0	0	5	56	1	0	0	56	0	1	3	64	4	3	0	0
    t	0	0	0	1	0	1	1	1	0	0	1	0	0	1	1	0	0

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3) |  |  |  |
    ; oligos_6nt_mkv1_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; ycATTGTGhg
    ; Alignment reference
    a	2	2	9	0	0	0	0	0	3	2
    c	3	3	0	0	0	0	0	0	3	1
    g	1	2	0	0	0	9	0	9	0	5
    t	3	2	0	9	9	0	9	0	3	1
oligos_6nt_mkv1_m3_shift0 (oligos_6nt_mkv1_m3) |  |  |  |
    ; oligos_6nt_mkv1_m3 versus oligos_6nt_mkv1_m3; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; ycATTGTGhg
    ; cor=; Ncor=
    a	2	2	9	0	0	0	0	0	3	2
    c	3	3	0	0	0	0	0	0	3	1
    g	1	2	0	0	0	9	0	9	0	5
    t	3	2	0	9	9	0	9	0	3	1

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv1_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_7nt_mkv1_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; drCAGAGAGrv
    ; Alignment reference
    a	2	2	0	7	0	7	0	7	0	3	2
    c	0	1	7	0	0	0	0	0	0	1	2
    g	3	3	0	0	7	0	7	0	6	2	2
    t	2	1	0	0	0	0	0	0	1	1	1
oligos_7nt_mkv1_m2_shift0 (oligos_7nt_mkv1_m2) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_7nt_mkv1_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; drCAGAGAGrv
    ; cor=; Ncor=
    a	2	2	0	7	0	7	0	7	0	3	2
    c	0	1	7	0	0	0	0	0	0	1	2
    g	3	3	0	0	7	0	7	0	6	2	2
    t	2	1	0	0	0	0	0	0	1	1	1
oligos_6nt_mkv1_m4_shift0 (oligos_6nt_mkv1_m4) |  |  |  |
    ; oligos_7nt_mkv1_m2 versus oligos_6nt_mkv1_m4; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.891545; dgCAGAGAgw-
    ; cor=; Ncor=
    a	4	2	0	10	0	10	0	10	1	4	0
    c	0	2	10	0	0	0	0	0	2	1	0
    g	3	5	0	0	10	0	10	0	6	2	0
    t	3	1	0	0	0	0	0	0	1	3	0