# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/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/2026/01/22/peak-motifs.2026-01-22.160303_2026-01-22.160303_u5bAOc/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## 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=18; shift=0; ncol=18; dwtATAAAAAAAgAtgma
    ; Alignment reference
    a	10	12	7	31	2	29	33	29	30	34	32	31	7	32	8	5	11	15
    c	3	2	4	2	0	3	1	4	0	1	0	0	4	2	0	1	11	9
    g	11	7	3	2	3	2	1	2	1	1	0	1	23	2	6	25	7	9
    t	13	16	23	2	32	3	2	2	6	1	5	5	3	1	23	6	8	4
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=18; w=0; offset=0; strand=D; shift=0; score=      1; dwtATAAAAAAAgAtgma
    ; cor=; Ncor=
    a	10	12	7	31	2	29	33	29	30	34	32	31	7	32	8	5	11	15
    c	3	2	4	2	0	3	1	4	0	1	0	0	4	2	0	1	11	9
    g	11	7	3	2	3	2	1	2	1	1	0	1	23	2	6	25	7	9
    t	13	16	23	2	32	3	2	2	6	1	5	5	3	1	23	6	8	4

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m2_shift0 ; 2 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=16; shift=0; ncol=16; hrgcTGAAAAACAtmw
    ; Alignment reference
    a	13	14	9	8	10	3	45	45	40	46	44	1	46	11	14	21
    c	13	12	6	34	2	3	2	0	1	2	4	44	2	7	16	9
    g	11	13	32	4	1	42	1	3	2	1	2	3	1	8	9	8
    t	14	12	4	5	38	3	3	3	8	2	1	3	2	25	12	13
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=1/1; ncol2=16; w=0; offset=0; strand=D; shift=0; score=      1; hrgcTGAAAAACAtmw
    ; cor=; Ncor=
    a	13	14	9	8	10	3	45	45	40	46	44	1	46	11	14	21
    c	13	12	6	34	2	3	2	0	1	2	4	44	2	7	16	9
    g	11	13	32	4	1	42	1	3	2	1	2	3	1	8	9	8
    t	14	12	4	5	38	3	3	3	8	2	1	3	2	25	12	13

## 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=23; shift=0; ncol=23; ArCTGAAyrTGTmyAAwkwwryk
    ; Alignment reference
    a	2	1	0	0	0	2	2	0	1	0	0	0	1	0	2	2	1	0	1	1	1	0	0
    c	0	0	2	0	0	0	0	1	0	0	0	0	1	1	0	0	0	0	0	0	0	1	0
    g	0	1	0	0	2	0	0	0	1	0	2	0	0	0	0	0	0	1	0	0	1	0	1
    t	0	0	0	2	0	0	0	1	0	2	0	2	0	1	0	0	1	1	1	1	0	1	1
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=23; w=0; offset=0; strand=D; shift=0; score=      1; ArCTGAAyrTGTmyAAwkwwryk
    ; cor=; Ncor=
    a	2	1	0	0	0	2	2	0	1	0	0	0	1	0	2	2	1	0	1	1	1	0	0
    c	0	0	2	0	0	0	0	1	0	0	0	0	1	1	0	0	0	0	0	0	0	1	0
    g	0	1	0	0	2	0	0	0	1	0	2	0	0	0	0	0	0	1	0	0	1	0	1
    t	0	0	0	2	0	0	0	1	0	2	0	2	0	1	0	0	1	1	1	1	0	1	1

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift0 ; 2 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; wwTAAAATATAAaa
    ; Alignment reference
    a	24	27	3	55	50	54	58	4	61	6	47	50	28	22
    c	10	11	1	0	4	4	1	1	0	5	4	1	10	12
    g	11	7	0	3	4	1	0	6	0	4	4	3	12	13
    t	16	16	57	3	3	2	2	50	0	46	6	7	11	14
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=1/1; ncol2=14; w=0; offset=0; strand=D; shift=0; score=      1; wwTAAAATATAAaa
    ; cor=; Ncor=
    a	24	27	3	55	50	54	58	4	61	6	47	50	28	22
    c	10	11	1	0	4	4	1	1	0	5	4	1	10	12
    g	11	7	0	3	4	1	0	6	0	4	4	3	12	13
    t	16	16	57	3	3	2	2	50	0	46	6	7	11	14

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; kkTaTTGTAAATGTTww
    ; Alignment reference
    a	5	6	2	18	3	3	2	2	20	23	24	1	3	0	1	15	13
    c	5	5	2	2	0	3	2	1	1	1	0	4	0	2	3	1	4
    g	7	9	1	4	3	0	22	0	3	3	1	1	23	1	3	5	3
    t	11	8	23	4	22	22	2	25	4	1	3	22	2	25	21	7	8
oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m5 versus oligos_6nt_test_vs_ctrl_m5; m=1/1; ncol2=17; w=0; offset=0; strand=D; shift=0; score=      1; kkTaTTGTAAATGTTww
    ; cor=; Ncor=
    a	5	6	2	18	3	3	2	2	20	23	24	1	3	0	1	15	13
    c	5	5	2	2	0	3	2	1	1	1	0	4	0	2	3	1	4
    g	7	9	1	4	3	0	22	0	3	3	1	1	23	1	3	5	3
    t	11	8	23	4	22	22	2	25	4	1	3	22	2	25	21	7	8

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=13; shift=0; ncol=13; gkCTGAATATAwh
    ; Alignment reference
    a	13	13	4	7	4	52	51	3	54	0	51	21	18
    c	14	9	50	3	3	0	1	4	0	1	1	10	18
    g	18	20	3	0	50	4	3	3	3	0	5	11	6
    t	13	16	1	48	1	2	3	48	1	57	1	16	16
oligos_6nt_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m3; m=1/1; ncol2=13; w=0; offset=0; strand=D; shift=0; score=      1; gkCTGAATATAwh
    ; cor=; Ncor=
    a	13	13	4	7	4	52	51	3	54	0	51	21	18
    c	14	9	50	3	3	0	1	4	0	1	1	10	18
    g	18	20	3	0	50	4	3	3	3	0	5	11	6
    t	13	16	1	48	1	2	3	48	1	57	1	16	16

## One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift0 ; 2 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=12; shift=0; ncol=12; wwTTAATTAAww
    ; Alignment reference
    a	84	84	12	11	199	206	22	30	221	217	73	81
    c	31	33	3	2	7	8	4	4	6	8	50	46
    g	46	50	8	5	4	4	8	6	2	3	33	31
    t	79	73	217	222	30	22	206	200	11	12	84	82
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=1/1; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; wwTTAATTAAww
    ; cor=; Ncor=
    a	84	84	12	11	199	206	22	30	221	217	73	81
    c	31	33	3	2	7	8	4	4	6	8	50	46
    g	46	50	8	5	4	4	8	6	2	3	33	31
    t	79	73	217	222	30	22	206	200	11	12	84	82

## 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=13; shift=0; ncol=13; wwATTTGATAAww
    ; Alignment reference
    a	25	25	59	5	7	2	5	71	4	72	70	29	25
    c	13	16	4	3	4	0	4	1	1	0	2	14	14
    g	17	14	4	4	5	0	63	1	1	3	1	13	18
    t	22	22	10	65	61	75	5	4	71	2	4	21	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=13; w=0; offset=0; strand=D; shift=0; score=      1; wwATTTGATAAww
    ; cor=; Ncor=
    a	25	25	59	5	7	2	5	71	4	72	70	29	25
    c	13	16	4	3	4	0	4	1	1	0	2	14	14
    g	17	14	4	4	5	0	63	1	1	3	1	13	18
    t	22	22	10	65	61	75	5	4	71	2	4	21	20

## 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; wrACAAAAAka
    ; Alignment reference
    a	39	31	106	0	98	93	93	96	104	26	48
    c	14	22	0	106	0	3	2	1	1	26	19
    g	21	29	0	0	1	5	3	5	1	27	16
    t	32	24	0	0	7	5	8	4	0	27	23
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; wrACAAAAAka
    ; cor=; Ncor=
    a	39	31	106	0	98	93	93	96	104	26	48
    c	14	22	0	106	0	3	2	1	1	26	19
    g	21	29	0	0	1	5	3	5	1	27	16
    t	32	24	0	0	7	5	8	4	0	27	23

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift0 ; 2 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=22; shift=0; ncol=22; wdsCTGAmWRdhYWkTCAGshw
    ; Alignment reference
    a	2	1	0	0	0	0	4	2	3	3	1	1	0	1	0	0	0	4	0	0	2	2
    c	0	0	2	4	0	0	0	2	0	0	0	2	1	0	0	0	4	0	0	2	1	0
    g	0	1	2	0	0	4	0	0	0	1	2	0	0	0	2	0	0	0	4	2	0	0
    t	2	2	0	0	4	0	0	0	1	0	1	1	3	3	2	4	0	0	0	0	1	2
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=1/1; ncol2=22; w=0; offset=0; strand=D; shift=0; score=      1; wdsCTGAmWRdhYWkTCAGshw
    ; cor=; Ncor=
    a	2	1	0	0	0	0	4	2	3	3	1	1	0	1	0	0	0	4	0	0	2	2
    c	0	0	2	4	0	0	0	2	0	0	0	2	1	0	0	0	4	0	0	2	1	0
    g	0	1	2	0	0	4	0	0	0	1	2	0	0	0	2	0	0	0	4	2	0	0
    t	2	2	0	0	4	0	0	0	1	0	1	1	3	3	2	4	0	0	0	0	1	2