# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/03/19/peak-motifs.2026-03-19.135349_2026-03-19.135349_WDqUmM/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/2026/03/19/peak-motifs.2026-03-19.135349_2026-03-19.135349_WDqUmM/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift0 ; 4 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; wdyACTGTAcw
    ; Alignment reference
    a	32	31	6	111	2	0	3	2	120	17	35
    c	18	26	60	4	112	2	0	0	2	45	24
    g	25	32	24	2	0	3	117	0	0	30	22
    t	47	33	32	5	8	117	2	120	0	30	41
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; wdyACTGTAcw
    ; cor=; Ncor=
    a	32	31	6	111	2	0	3	2	120	17	35
    c	18	26	60	4	112	2	0	0	2	45	24
    g	25	32	24	2	0	3	117	0	0	30	22
    t	47	33	32	5	8	117	2	120	0	30	41
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1_rc; m=2/3; ncol2=13; w=0; offset=0; strand=R; shift=0; score=0.755393; wsTACTGTACw
    ; cor=; Ncor=
    a	47	21	1	102	5	14	3	0	105	4	32
    c	12	32	8	4	99	2	0	3	3	91	19
    g	24	42	7	4	2	2	106	4	2	10	20
    t	30	18	97	3	7	95	4	106	3	8	42
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m3; m=3/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.700938; -wyATTGTAmw
    ; cor=; Ncor=
    a	0	22	13	65	0	2	4	0	65	17	18
    c	0	13	22	0	0	0	1	0	0	25	11
    g	0	9	13	0	0	0	51	1	0	9	6
    t	0	21	17	0	65	63	9	64	0	14	30

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m4_shift1 ; 4 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=10; shift=1; ncol=11; -ycCTTCTCck
    ; Alignment reference
    a	0	8	9	1	0	0	3	0	1	5	7
    c	0	16	24	49	1	2	46	3	48	24	10
    g	0	12	8	0	1	0	0	3	0	11	20
    t	0	15	10	1	49	49	2	45	2	11	14
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4) |  |  |  |
    ; oligos_6nt_mkv2_m4 versus oligos_6nt_mkv2_m4; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=1; score=      1; -ycCTTCTCck
    ; cor=; Ncor=
    a	0	8	9	1	0	0	3	0	1	5	7
    c	0	16	24	49	1	2	46	3	48	24	10
    g	0	12	8	0	1	0	0	3	0	11	20
    t	0	15	10	1	49	49	2	45	2	11	14
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5) |  |  |  |
    ; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m5; m=2/3; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.872581; gbCCTTCTCyy
    ; cor=; Ncor=
    a	22	20	6	9	5	5	3	2	3	17	24
    c	25	27	88	89	3	2	96	3	94	35	28
    g	40	31	5	5	4	8	3	5	6	24	23
    t	19	28	7	3	94	91	4	96	3	30	31
oligos_7nt_mkv2_m7_rc_shift2 (oligos_7nt_mkv2_m7_rc) |  |  |  |
    ; oligos_6nt_mkv2_m4 versus oligos_7nt_mkv2_m7_rc; m=3/3; ncol2=12; w=0; offset=1; strand=R; shift=2; score=0.510393; --cvTTCTCGT
    ; cor=; Ncor=
    a	0	0	6	12	0	1	0	1	2	0	0
    c	0	0	14	10	3	0	35	2	34	1	0
    g	0	0	9	10	2	4	2	1	0	34	1
    t	0	0	8	5	32	32	0	33	1	2	36

## 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; ybTACGACTCsc
    ; Alignment reference
    a	8	6	4	38	0	0	43	1	1	2	7	6
    c	12	12	1	3	43	1	1	40	2	37	17	20
    g	9	11	4	2	1	39	0	1	0	1	12	8
    t	15	15	35	1	0	4	0	2	41	4	8	10
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; ybTACGACTCsc
    ; cor=; Ncor=
    a	8	6	4	38	0	0	43	1	1	2	7	6
    c	12	12	1	3	43	1	1	40	2	37	17	20
    g	9	11	4	2	1	39	0	1	0	1	12	8
    t	15	15	35	1	0	4	0	2	41	4	8	10

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m6_shift4 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m6_shift4 (oligos_6nt_mkv2_m6) |  |  |  |
    ; oligos_6nt_mkv2_m6; m=0 (reference); ncol1=10; shift=4; ncol=14; ----yaGTACTAcw
    ; Alignment reference
    a	0	0	0	0	16	30	2	1	73	4	0	73	16	24
    c	0	0	0	0	19	10	0	0	0	68	0	1	25	9
    g	0	0	0	0	8	17	69	0	0	0	0	0	15	10
    t	0	0	0	0	31	17	3	73	1	2	74	0	18	31
oligos_6nt_mkv2_m6_shift4 (oligos_6nt_mkv2_m6) |  |  |  |
    ; oligos_6nt_mkv2_m6 versus oligos_6nt_mkv2_m6; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=4; score=      1; ----yaGTACTAcw
    ; cor=; Ncor=
    a	0	0	0	0	16	30	2	1	73	4	0	73	16	24
    c	0	0	0	0	19	10	0	0	0	68	0	1	25	9
    g	0	0	0	0	8	17	69	0	0	0	0	0	15	10
    t	0	0	0	0	31	17	3	73	1	2	74	0	18	31
oligos_7nt_mkv2_m1_rc_shift0 (oligos_7nt_mkv2_m1_rc) |  |  |  |
    ; oligos_6nt_mkv2_m6 versus oligos_7nt_mkv2_m1_rc; m=2/2; ncol2=13; w=-4; offset=-4; strand=R; shift=0; score=0.45911; wsTACTGTACwrk-
    ; cor=; Ncor=
    a	47	21	1	102	5	14	3	0	105	4	32	43	14	0
    c	12	32	8	4	99	2	0	3	3	91	19	15	17	0
    g	24	42	7	4	2	2	106	4	2	10	20	35	38	0
    t	30	18	97	3	7	95	4	106	3	8	42	20	44	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift0 ; 4 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=11; shift=0; ncol=11; gbCCTTCTCyy
    ; Alignment reference
    a	22	20	6	9	5	5	3	2	3	17	24
    c	25	27	88	89	3	2	96	3	94	35	28
    g	40	31	5	5	4	8	3	5	6	24	23
    t	19	28	7	3	94	91	4	96	3	30	31
oligos_7nt_mkv2_m5_shift0 (oligos_7nt_mkv2_m5) |  |  |  |
    ; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m5; m=1/3; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; gbCCTTCTCyy
    ; cor=; Ncor=
    a	22	20	6	9	5	5	3	2	3	17	24
    c	25	27	88	89	3	2	96	3	94	35	28
    g	40	31	5	5	4	8	3	5	6	24	23
    t	19	28	7	3	94	91	4	96	3	30	31
oligos_6nt_mkv2_m4_shift1 (oligos_6nt_mkv2_m4) |  |  |  |
    ; oligos_7nt_mkv2_m5 versus oligos_6nt_mkv2_m4; m=2/3; ncol2=10; w=0; offset=1; strand=D; shift=1; score=0.872581; -ycCTTCTCck
    ; cor=; Ncor=
    a	0	8	9	1	0	0	3	0	1	5	7
    c	0	16	24	49	1	2	46	3	48	24	10
    g	0	12	8	0	1	0	0	3	0	11	20
    t	0	15	10	1	49	49	2	45	2	11	14
oligos_7nt_mkv2_m7_rc_shift2 (oligos_7nt_mkv2_m7_rc) |  |  |  |
    ; oligos_7nt_mkv2_m5 versus oligos_7nt_mkv2_m7_rc; m=3/3; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.478654; --cvTTCTCGT
    ; cor=; Ncor=
    a	0	0	6	12	0	1	0	1	2	0	0
    c	0	0	14	10	3	0	35	2	34	1	0
    g	0	0	9	10	2	4	2	1	0	34	1
    t	0	0	8	5	32	32	0	33	1	2	36

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m7_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m7_shift0 (oligos_7nt_mkv2_m7) |  |  |  |
    ; oligos_7nt_mkv2_m7; m=0 (reference); ncol1=12; shift=0; ncol=12; rrAACGAGAAbg
    ; Alignment reference
    a	15	10	30	36	2	1	33	0	32	32	5	8
    c	9	6	3	1	34	0	1	2	4	2	10	9
    g	10	12	0	0	1	34	2	35	0	3	10	14
    t	3	9	4	0	0	2	1	0	1	0	12	6
oligos_7nt_mkv2_m7_shift0 (oligos_7nt_mkv2_m7) |  |  |  |
    ; oligos_7nt_mkv2_m7 versus oligos_7nt_mkv2_m7; m=1/4; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; rrAACGAGAAbg
    ; cor=; Ncor=
    a	15	10	30	36	2	1	33	0	32	32	5	8
    c	9	6	3	1	34	0	1	2	4	2	10	9
    g	10	12	0	0	1	34	2	35	0	3	10	14
    t	3	9	4	0	0	2	1	0	1	0	12	6
oligos_6nt_mkv2_m8_shift0 (oligos_6nt_mkv2_m8) |  |  |  |
    ; oligos_7nt_mkv2_m7 versus oligos_6nt_mkv2_m8; m=2/4; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.875982; rrAACGAGAac-
    ; cor=; Ncor=
    a	25	24	64	76	3	3	77	2	71	31	18	0
    c	12	14	5	4	74	1	2	5	5	18	26	0
    g	31	26	5	0	4	76	3	72	1	17	19	0
    t	15	19	9	3	2	3	1	4	6	17	20	0
oligos_6nt_mkv2_m4_rc_shift3 (oligos_6nt_mkv2_m4_rc) |  |  |  |
    ; oligos_7nt_mkv2_m7 versus oligos_6nt_mkv2_m4_rc; m=3/4; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.510393; ---mgGAGAAGg
    ; cor=; Ncor=
    a	0	0	0	14	11	2	45	2	49	49	1	10
    c	0	0	0	20	11	0	3	0	0	1	0	8
    g	0	0	0	10	24	48	3	46	2	1	49	24
    t	0	0	0	7	5	1	0	3	0	0	1	9
oligos_7nt_mkv2_m5_rc_shift3 (oligos_7nt_mkv2_m5_rc) |  |  |  |
    ; oligos_7nt_mkv2_m7 versus oligos_7nt_mkv2_m5_rc; m=4/4; ncol2=11; w=0; offset=3; strand=R; shift=3; score=0.478654; ---rrGAGAAGG
    ; cor=; Ncor=
    a	0	0	0	31	30	3	96	4	91	94	3	7
    c	0	0	0	23	24	6	5	3	8	4	5	5
    g	0	0	0	28	35	94	3	96	2	3	89	88
    t	0	0	0	24	17	3	2	3	5	5	9	6

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=12; shift=2; ncol=14; --crTGCATGCAyg
    ; Alignment reference
    a	0	0	36	58	8	6	10	149	2	7	7	134	27	27
    c	0	0	58	26	9	2	135	0	3	2	139	3	43	33
    g	0	0	33	43	3	139	2	3	0	135	2	9	26	58
    t	0	0	27	27	134	7	7	2	149	10	6	8	58	36
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m2; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score=      1; --crTGCATGCAyg
    ; cor=; Ncor=
    a	0	0	36	58	8	6	10	149	2	7	7	134	27	27
    c	0	0	58	26	9	2	135	0	3	2	139	3	43	33
    g	0	0	33	43	3	139	2	3	0	135	2	9	26	58
    t	0	0	27	27	134	7	7	2	149	10	6	8	58	36
oligos_7nt_mkv2_m6_rc_shift0 (oligos_7nt_mkv2_m6_rc) |  |  |  |
    ; oligos_6nt_mkv2_m2 versus oligos_7nt_mkv2_m6_rc; m=2/3; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.604313; skCGTGCATGca--
    ; cor=; Ncor=
    a	20	25	10	11	1	7	3	97	1	2	22	36	0	0
    c	34	20	82	6	3	0	98	4	6	2	39	24	0	0
    g	29	28	4	85	2	93	1	1	4	93	18	20	0	0
    t	21	31	8	2	98	4	2	2	93	7	25	24	0	0
oligos_6nt_mkv2_m9_shift0 (oligos_6nt_mkv2_m9) |  |  |  |
    ; oligos_6nt_mkv2_m2 versus oligos_6nt_mkv2_m9; m=3/3; ncol2=10; w=-2; offset=-2; strand=D; shift=0; score=0.423632; vrCGTGCAyk----
    ; cor=; Ncor=
    a	16	18	0	0	0	0	0	62	6	8	0	0	0	0
    c	23	12	62	0	0	0	62	0	20	12	0	0	0	0
    g	16	20	0	62	0	62	0	0	13	23	0	0	0	0
    t	7	12	0	0	62	0	0	0	23	19	0	0	0	0

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m10_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m10_shift0 (oligos_6nt_mkv2_m10) |  |  |  |
    ; oligos_6nt_mkv2_m10; m=0 (reference); ncol1=10; shift=0; ncol=10; ryAGTCTAyk
    ; Alignment reference
    a	14	5	40	1	0	1	0	43	9	10
    c	9	15	1	0	1	42	0	0	16	4
    g	16	10	2	41	2	0	0	0	6	17
    t	4	13	0	1	40	0	43	0	12	12
oligos_6nt_mkv2_m10_shift0 (oligos_6nt_mkv2_m10) |  |  |  |
    ; oligos_6nt_mkv2_m10 versus oligos_6nt_mkv2_m10; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; ryAGTCTAyk
    ; cor=; Ncor=
    a	14	5	40	1	0	1	0	43	9	10
    c	9	15	1	0	1	42	0	0	16	4
    g	16	10	2	41	2	0	0	0	6	17
    t	4	13	0	1	40	0	43	0	12	12

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m7_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m7_shift0 (oligos_6nt_mkv2_m7) |  |  |  |
    ; oligos_6nt_mkv2_m7; m=0 (reference); ncol1=10; shift=0; ncol=10; ddAAAATAms
    ; Alignment reference
    a	26	33	81	83	87	87	14	73	24	22
    c	18	5	0	0	0	1	0	9	27	23
    g	23	24	7	2	2	0	5	1	20	24
    t	24	29	3	6	2	3	72	8	20	22
oligos_6nt_mkv2_m7_shift0 (oligos_6nt_mkv2_m7) |  |  |  |
    ; oligos_6nt_mkv2_m7 versus oligos_6nt_mkv2_m7; m=1/1; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; ddAAAATAms
    ; cor=; Ncor=
    a	26	33	81	83	87	87	14	73	24	22
    c	18	5	0	0	0	1	0	9	27	23
    g	23	24	7	2	2	0	5	1	20	24
    t	24	29	3	6	2	3	72	8	20	22

## 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=12; shift=0; ncol=12; sbACTCCCTGby
    ; Alignment reference
    a	11	9	46	1	2	1	6	2	2	4	9	9
    c	16	14	0	46	0	45	42	48	2	2	13	13
    g	15	14	2	2	1	2	1	0	1	43	13	12
    t	9	14	3	2	48	3	2	1	46	2	16	17
oligos_7nt_mkv2_m2_shift0 (oligos_7nt_mkv2_m2) |  |  |  |
    ; oligos_7nt_mkv2_m2 versus oligos_7nt_mkv2_m2; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; sbACTCCCTGby
    ; cor=; Ncor=
    a	11	9	46	1	2	1	6	2	2	4	9	9
    c	16	14	0	46	0	45	42	48	2	2	13	13
    g	15	14	2	2	1	2	1	0	1	43	13	12
    t	9	14	3	2	48	3	2	1	46	2	16	17

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m8_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m8_shift0 (oligos_6nt_mkv2_m8) |  |  |  |
    ; oligos_6nt_mkv2_m8; m=0 (reference); ncol1=11; shift=0; ncol=11; rrAACGAGAac
    ; Alignment reference
    a	25	24	64	76	3	3	77	2	71	31	18
    c	12	14	5	4	74	1	2	5	5	18	26
    g	31	26	5	0	4	76	3	72	1	17	19
    t	15	19	9	3	2	3	1	4	6	17	20
oligos_6nt_mkv2_m8_shift0 (oligos_6nt_mkv2_m8) |  |  |  |
    ; oligos_6nt_mkv2_m8 versus oligos_6nt_mkv2_m8; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; rrAACGAGAac
    ; cor=; Ncor=
    a	25	24	64	76	3	3	77	2	71	31	18
    c	12	14	5	4	74	1	2	5	5	18	26
    g	31	26	5	0	4	76	3	72	1	17	19
    t	15	19	9	3	2	3	1	4	6	17	20
oligos_7nt_mkv2_m7_shift0 (oligos_7nt_mkv2_m7) |  |  |  |
    ; oligos_6nt_mkv2_m8 versus oligos_7nt_mkv2_m7; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.875982; rrAACGAGAAb
    ; cor=; Ncor=
    a	15	10	30	36	2	1	33	0	32	32	5
    c	9	6	3	1	34	0	1	2	4	2	10
    g	10	12	0	0	1	34	2	35	0	3	10
    t	3	9	4	0	0	2	1	0	1	0	12

## 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; ssGCTAGCss
    ; Alignment reference
    a	7	10	0	0	0	49	1	0	8	10
    c	17	15	0	48	0	0	0	49	17	15
    g	15	16	49	0	0	0	47	0	14	16
    t	10	8	0	1	49	0	1	0	10	8
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; ssGCTAGCss
    ; cor=; Ncor=
    a	7	10	0	0	0	49	1	0	8	10
    c	17	15	0	48	0	0	0	49	17	15
    g	15	16	49	0	0	0	47	0	14	16
    t	10	8	0	1	49	0	1	0	10	8

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m6_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m6_shift2 (oligos_7nt_mkv2_m6) |  |  |  |
    ; oligos_7nt_mkv2_m6; m=0 (reference); ncol1=12; shift=2; ncol=14; --tgCATGCACGms
    ; Alignment reference
    a	0	0	24	25	7	93	2	2	4	98	2	8	31	21
    c	0	0	20	18	93	4	1	1	93	2	85	4	28	29
    g	0	0	24	39	2	6	4	98	0	3	6	82	20	34
    t	0	0	36	22	2	1	97	3	7	1	11	10	25	20
oligos_7nt_mkv2_m6_shift2 (oligos_7nt_mkv2_m6) |  |  |  |
    ; oligos_7nt_mkv2_m6 versus oligos_7nt_mkv2_m6; m=1/3; ncol2=12; w=0; offset=0; strand=D; shift=2; score=      1; --tgCATGCACGms
    ; cor=; Ncor=
    a	0	0	24	25	7	93	2	2	4	98	2	8	31	21
    c	0	0	20	18	93	4	1	1	93	2	85	4	28	29
    g	0	0	24	39	2	6	4	98	0	3	6	82	20	34
    t	0	0	36	22	2	1	97	3	7	1	11	10	25	20
oligos_6nt_mkv2_m9_rc_shift4 (oligos_6nt_mkv2_m9_rc) |  |  |  |
    ; oligos_7nt_mkv2_m6 versus oligos_6nt_mkv2_m9_rc; m=2/3; ncol2=10; w=0; offset=2; strand=R; shift=4; score=0.747965; ----mrTGCACGyb
    ; cor=; Ncor=
    a	0	0	0	0	19	23	0	0	0	62	0	0	12	7
    c	0	0	0	0	23	13	0	0	62	0	62	0	20	16
    g	0	0	0	0	12	20	0	62	0	0	0	62	12	23
    t	0	0	0	0	8	6	62	0	0	0	0	0	18	16
oligos_6nt_mkv2_m2_shift0 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_7nt_mkv2_m6 versus oligos_6nt_mkv2_m2; m=3/3; ncol2=12; w=-2; offset=-2; strand=D; shift=0; score=0.604313; crTGCATGCAyg--
    ; cor=; Ncor=
    a	36	58	8	6	10	149	2	7	7	134	27	27	0	0
    c	58	26	9	2	135	0	3	2	139	3	43	33	0	0
    g	33	43	3	139	2	3	0	135	2	9	26	58	0	0
    t	27	27	134	7	7	2	149	10	6	8	58	36	0	0

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3) |  |  |  |
    ; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=10; shift=1; ncol=11; -wyATTGTAmw
    ; Alignment reference
    a	0	22	13	65	0	2	4	0	65	17	18
    c	0	13	22	0	0	0	1	0	0	25	11
    g	0	9	13	0	0	0	51	1	0	9	6
    t	0	21	17	0	65	63	9	64	0	14	30
oligos_6nt_mkv2_m3_shift1 (oligos_6nt_mkv2_m3) |  |  |  |
    ; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m3; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=1; score=      1; -wyATTGTAmw
    ; cor=; Ncor=
    a	0	22	13	65	0	2	4	0	65	17	18
    c	0	13	22	0	0	0	1	0	0	25	11
    g	0	9	13	0	0	0	51	1	0	9	6
    t	0	21	17	0	65	63	9	64	0	14	30
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m3 versus oligos_6nt_mkv2_m1; m=2/2; ncol2=11; w=-1; offset=-1; strand=D; shift=0; score=0.700938; wdyACTGTAcw
    ; cor=; Ncor=
    a	32	31	6	111	2	0	3	2	120	17	35
    c	18	26	60	4	112	2	0	0	2	45	24
    g	25	32	24	2	0	3	117	0	0	30	22
    t	47	33	32	5	8	117	2	120	0	30	41

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=13; shift=1; ncol=14; -mywGTACAGTAsw
    ; Alignment reference
    a	0	44	20	42	8	3	106	4	95	7	3	97	18	30
    c	0	38	35	20	10	2	4	106	2	2	4	7	42	24
    g	0	17	15	19	91	3	3	0	2	99	4	8	32	12
    t	0	14	43	32	4	105	0	3	14	5	102	1	21	47
oligos_7nt_mkv2_m1_shift1 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/3; ncol2=13; w=0; offset=0; strand=D; shift=1; score=      1; -mywGTACAGTAsw
    ; cor=; Ncor=
    a	0	44	20	42	8	3	106	4	95	7	3	97	18	30
    c	0	38	35	20	10	2	4	106	2	2	4	7	42	24
    g	0	17	15	19	91	3	3	0	2	99	4	8	32	12
    t	0	14	43	32	4	105	0	3	14	5	102	1	21	47
oligos_6nt_mkv2_m1_rc_shift3 (oligos_6nt_mkv2_m1_rc) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1_rc; m=2/3; ncol2=11; w=0; offset=2; strand=R; shift=3; score=0.755393; ---wgTACAGTrhw
    ; cor=; Ncor=
    a	0	0	0	41	30	0	120	2	117	8	5	32	33	47
    c	0	0	0	22	30	0	0	117	3	0	2	24	32	25
    g	0	0	0	24	45	2	0	0	2	112	4	60	26	18
    t	0	0	0	35	17	120	2	3	0	2	111	6	31	32
oligos_6nt_mkv2_m6_rc_shift0 (oligos_6nt_mkv2_m6_rc) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m6_rc; m=3/3; ncol2=10; w=-1; offset=-1; strand=R; shift=0; score=0.45911; wgTAGTACtr----
    ; cor=; Ncor=
    a	31	18	0	74	2	1	73	3	17	31	0	0	0	0
    c	10	15	0	0	0	0	0	69	17	8	0	0	0	0
    g	9	25	1	0	68	0	0	0	10	19	0	0	0	0
    t	24	16	73	0	4	73	1	2	30	16	0	0	0	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m4_shift0 ; 2 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=11; shift=0; ncol=11; rwCACTGAChw
    ; Alignment reference
    a	27	27	7	78	4	1	2	81	3	27	29
    c	19	19	81	6	83	3	1	3	83	23	17
    g	23	20	0	3	1	2	86	5	0	16	19
    t	22	25	3	4	3	85	2	2	5	25	26
oligos_7nt_mkv2_m4_shift0 (oligos_7nt_mkv2_m4) |  |  |  |
    ; oligos_7nt_mkv2_m4 versus oligos_7nt_mkv2_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; rwCACTGAChw
    ; cor=; Ncor=
    a	27	27	7	78	4	1	2	81	3	27	29
    c	19	19	81	6	83	3	1	3	83	23	17
    g	23	20	0	3	1	2	86	5	0	16	19
    t	22	25	3	4	3	85	2	2	5	25	26

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m9_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m9_shift0 (oligos_6nt_mkv2_m9) |  |  |  |
    ; oligos_6nt_mkv2_m9; m=0 (reference); ncol1=10; shift=0; ncol=10; vrCGTGCAyk
    ; Alignment reference
    a	16	18	0	0	0	0	0	62	6	8
    c	23	12	62	0	0	0	62	0	20	12
    g	16	20	0	62	0	62	0	0	13	23
    t	7	12	0	0	62	0	0	0	23	19
oligos_6nt_mkv2_m9_shift0 (oligos_6nt_mkv2_m9) |  |  |  |
    ; oligos_6nt_mkv2_m9 versus oligos_6nt_mkv2_m9; m=1/3; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; vrCGTGCAyk
    ; cor=; Ncor=
    a	16	18	0	0	0	0	0	62	6	8
    c	23	12	62	0	0	0	62	0	20	12
    g	16	20	0	62	0	62	0	0	13	23
    t	7	12	0	0	62	0	0	0	23	19
oligos_7nt_mkv2_m6_rc_shift0 (oligos_7nt_mkv2_m6_rc) |  |  |  |
    ; oligos_6nt_mkv2_m9 versus oligos_7nt_mkv2_m6_rc; m=2/3; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.747965; skCGTGCATG
    ; cor=; Ncor=
    a	20	25	10	11	1	7	3	97	1	2
    c	34	20	82	6	3	0	98	4	6	2
    g	29	28	4	85	2	93	1	1	4	93
    t	21	31	8	2	98	4	2	2	93	7
oligos_6nt_mkv2_m2_shift2 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_6nt_mkv2_m9 versus oligos_6nt_mkv2_m2; m=3/3; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.423632; --crTGCATG
    ; cor=; Ncor=
    a	0	0	36	58	8	6	10	149	2	7
    c	0	0	58	26	9	2	135	0	3	2
    g	0	0	33	43	3	139	2	3	0	135
    t	0	0	27	27	134	7	7	2	149	10