# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2025/05/22/peak-motifs.2025-05-22.140140_2025-05-22.140140_quAEhD/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/2025/05/22/peak-motifs.2025-05-22.140140_2025-05-22.140140_quAEhD/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=12; shift=0; ncol=12; rbGGAAAAATww
    ; Alignment reference
    a	23	15	4	3	63	68	69	66	56	8	22	23
    c	12	18	3	3	3	1	0	3	8	5	12	12
    g	21	20	59	64	4	0	1	0	4	2	10	17
    t	15	18	5	1	1	2	1	2	3	56	27	19
oligos_6nt_test_vs_ctrl_m4_shift0 (oligos_6nt_test_vs_ctrl_m4) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m4; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; rbGGAAAAATww
    ; cor=; Ncor=
    a	23	15	4	3	63	68	69	66	56	8	22	23
    c	12	18	3	3	3	1	0	3	8	5	12	12
    g	21	20	59	64	4	0	1	0	4	2	10	17
    t	15	18	5	1	1	2	1	2	3	56	27	19

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=14; shift=0; ncol=14; mrCATGGGAACAyw
    ; Alignment reference
    a	9	6	4	17	0	1	2	2	20	20	3	21	5	6
    c	6	4	15	1	3	3	0	1	1	0	18	0	8	5
    g	2	7	1	1	1	16	18	18	1	0	0	0	2	3
    t	5	5	2	3	18	2	2	1	0	2	1	1	7	8
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m5; m=1/2; ncol2=14; w=0; offset=0; strand=D; shift=0; score=      1; mrCATGGGAACAyw
    ; cor=; Ncor=
    a	9	6	4	17	0	1	2	2	20	20	3	21	5	6
    c	6	4	15	1	3	3	0	1	1	0	18	0	8	5
    g	2	7	1	1	1	16	18	18	1	0	0	0	2	3
    t	5	5	2	3	18	2	2	1	0	2	1	1	7	8
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m3; m=2/2; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.654446; --rwTGGGAACrm-
    ; cor=; Ncor=
    a	0	0	33	24	2	1	4	8	80	79	9	27	22	0
    c	0	0	9	20	3	3	4	9	3	2	67	16	30	0
    g	0	0	23	15	3	74	73	66	2	0	3	22	17	0
    t	0	0	20	26	77	7	4	2	0	4	6	20	16	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; aaACGGTTAcm
    ; Alignment reference
    a	18	23	53	2	6	3	0	2	47	14	18
    c	14	11	1	54	6	1	2	2	2	17	19
    g	14	12	3	1	42	51	1	0	5	14	11
    t	12	12	1	1	4	3	55	54	4	13	10
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m1; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; aaACGGTTAcm
    ; cor=; Ncor=
    a	18	23	53	2	6	3	0	2	47	14	18
    c	14	11	1	54	6	1	2	2	2	17	19
    g	14	12	3	1	42	51	1	0	5	14	11
    t	12	12	1	1	4	3	55	54	4	13	10

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; dbtAAAGCGah
    ; Alignment reference
    a	17	10	13	55	54	55	1	1	0	26	17
    c	10	16	6	0	1	4	4	55	1	11	16
    g	17	18	4	2	2	0	50	1	55	11	11
    t	15	15	36	2	2	0	4	2	3	11	15
oligos_6nt_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m2; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; dbtAAAGCGah
    ; cor=; Ncor=
    a	17	10	13	55	54	55	1	1	0	26	17
    c	10	16	6	0	1	4	4	55	1	11	16
    g	17	18	4	2	2	0	50	1	55	11	11
    t	15	15	36	2	2	0	4	2	3	11	15
oligos_7nt_test_vs_ctrl_m3_rc_shift0 (oligos_7nt_test_vs_ctrl_m3_rc) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m3_rc; m=2/2; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.773038; arTAAAGCTma
    ; cor=; Ncor=
    a	16	18	6	56	56	57	4	2	2	18	26
    c	15	12	6	1	1	2	1	54	2	25	11
    g	15	17	1	2	2	0	49	2	2	11	10
    t	15	14	48	2	2	2	7	3	55	7	14

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; tbtTGGCCAama
    ; Alignment reference
    a	21	16	11	0	0	2	3	2	85	50	22	29
    c	18	23	16	1	1	2	81	84	1	11	28	21
    g	19	27	10	0	85	82	2	2	2	16	21	18
    t	30	22	51	87	2	2	2	0	0	11	17	20
oligos_6nt_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m1 versus oligos_6nt_test_vs_ctrl_m1; m=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; tbtTGGCCAama
    ; cor=; Ncor=
    a	21	16	11	0	0	2	3	2	85	50	22	29
    c	18	23	16	1	1	2	81	84	1	11	28	21
    g	19	27	10	0	85	82	2	2	2	16	21	18
    t	30	22	51	87	2	2	2	0	0	11	17	20

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=11; shift=1; ncol=12; -wtgAGAATCgr
    ; Alignment reference
    a	0	17	9	3	48	0	48	44	2	1	11	17
    c	0	10	11	8	0	1	0	4	3	40	12	8
    g	0	8	11	33	1	46	1	1	2	5	14	15
    t	0	14	18	5	0	2	0	0	42	3	12	9
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score=      1; -wtgAGAATCgr
    ; cor=; Ncor=
    a	0	17	9	3	48	0	48	44	2	1	11	17
    c	0	10	11	8	0	1	0	4	3	40	12	8
    g	0	8	11	33	1	46	1	1	2	5	14	15
    t	0	14	18	5	0	2	0	0	42	3	12	9
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m2; m=2/2; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.815051; rwyGAGAATCcr
    ; cor=; Ncor=
    a	12	10	2	0	30	1	30	27	0	3	5	13
    c	5	7	16	2	0	1	1	3	2	24	14	6
    g	10	5	5	28	1	26	0	1	2	2	7	10
    t	4	9	8	1	0	3	0	0	27	2	5	2

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m2; m=0 (reference); ncol1=13; shift=0; ncol=13; rwyGAGAATCcrr
    ; Alignment reference
    a	12	10	2	0	30	1	30	27	0	3	5	13	10
    c	5	7	16	2	0	1	1	3	2	24	14	6	7
    g	10	5	5	28	1	26	0	1	2	2	7	10	8
    t	4	9	8	1	0	3	0	0	27	2	5	2	6
oligos_7nt_test_vs_ctrl_m2_shift0 (oligos_7nt_test_vs_ctrl_m2) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m2 versus oligos_7nt_test_vs_ctrl_m2; m=1/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score=      1; rwyGAGAATCcrr
    ; cor=; Ncor=
    a	12	10	2	0	30	1	30	27	0	3	5	13	10
    c	5	7	16	2	0	1	1	3	2	24	14	6	7
    g	10	5	5	28	1	26	0	1	2	2	7	10	8
    t	4	9	8	1	0	3	0	0	27	2	5	2	6
oligos_6nt_test_vs_ctrl_m5_shift1 (oligos_6nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m2 versus oligos_6nt_test_vs_ctrl_m5; m=2/2; ncol2=11; w=0; offset=1; strand=D; shift=1; score=0.815051; -wtgAGAATCgr-
    ; cor=; Ncor=
    a	0	17	9	3	48	0	48	44	2	1	11	17	0
    c	0	10	11	8	0	1	0	4	3	40	12	8	0
    g	0	8	11	33	1	46	1	1	2	5	14	15	0
    t	0	14	18	5	0	2	0	0	42	3	12	9	0

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; mgCAGGACAah
    ; Alignment reference
    a	16	9	4	51	3	1	52	5	54	18	14
    c	15	12	48	1	4	10	2	45	0	11	14
    g	11	25	1	0	47	41	0	1	0	13	10
    t	13	9	2	3	1	3	1	4	1	13	17
oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; mgCAGGACAah
    ; cor=; Ncor=
    a	16	9	4	51	3	1	52	5	54	18	14
    c	15	12	48	1	4	10	2	45	0	11	14
    g	11	25	1	0	47	41	0	1	0	13	10
    t	13	9	2	3	1	3	1	4	1	13	17

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=0; ncol=11; tkAGCTTTAyt
    ; Alignment reference
    a	14	7	55	3	7	2	2	2	48	14	15
    c	10	11	2	2	49	0	2	2	1	17	15
    g	11	25	2	54	1	2	1	1	6	12	15
    t	26	18	2	2	4	57	56	56	6	18	16
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; tkAGCTTTAyt
    ; cor=; Ncor=
    a	14	7	55	3	7	2	2	2	48	14	15
    c	10	11	2	2	49	0	2	2	1	17	15
    g	11	25	2	54	1	2	1	1	6	12	15
    t	26	18	2	2	4	57	56	56	6	18	16
oligos_6nt_test_vs_ctrl_m2_rc_shift0 (oligos_6nt_test_vs_ctrl_m2_rc) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m2_rc; m=2/2; ncol2=11; w=0; offset=0; strand=R; shift=0; score=0.773038; dtCGCTTTavh
    ; cor=; Ncor=
    a	15	11	3	2	4	0	2	2	36	15	15
    c	11	11	55	1	50	0	2	2	4	18	17
    g	16	11	1	55	4	4	1	0	6	16	10
    t	17	26	0	1	1	55	54	55	13	10	17

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=2; ncol=13; --rwTGGGAACrm
    ; Alignment reference
    a	0	0	33	24	2	1	4	8	80	79	9	27	22
    c	0	0	9	20	3	3	4	9	3	2	67	16	30
    g	0	0	23	15	3	74	73	66	2	0	3	22	17
    t	0	0	20	26	77	7	4	2	0	4	6	20	16
oligos_6nt_test_vs_ctrl_m3_shift2 (oligos_6nt_test_vs_ctrl_m3) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=2; score=      1; --rwTGGGAACrm
    ; cor=; Ncor=
    a	0	0	33	24	2	1	4	8	80	79	9	27	22
    c	0	0	9	20	3	3	4	9	3	2	67	16	30
    g	0	0	23	15	3	74	73	66	2	0	3	22	17
    t	0	0	20	26	77	7	4	2	0	4	6	20	16
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m5; m=2/2; ncol2=14; w=-2; offset=-2; strand=D; shift=0; score=0.654446; mrCATGGGAACAy
    ; cor=; Ncor=
    a	9	6	4	17	0	1	2	2	20	20	3	21	5
    c	6	4	15	1	3	3	0	1	1	0	18	0	8
    g	2	7	1	1	1	16	18	18	1	0	0	0	2
    t	5	5	2	3	18	2	2	1	0	2	1	1	7