# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.150947_2026-01-05.150947_WkkC55/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/2026/01/05/peak-motifs.2026-01-05.150947_2026-01-05.150947_WkkC55/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## 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=10; shift=2; ncol=12; --tcCTGGTAww
    ; Alignment reference
    a	0	0	6	7	2	0	2	0	1	28	9	9
    c	0	0	4	11	27	4	1	0	0	2	5	4
    g	0	0	5	7	1	4	27	30	0	0	6	6
    t	0	0	15	5	0	22	0	0	29	0	10	11
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=10; w=0; offset=0; strand=D; shift=2; score=      1; --tcCTGGTAww
    ; cor=; Ncor=
    a	0	0	6	7	2	0	2	0	1	28	9	9
    c	0	0	4	11	27	4	1	0	0	2	5	4
    g	0	0	5	7	1	4	27	30	0	0	6	6
    t	0	0	15	5	0	22	0	0	29	0	10	11
oligos_7nt_test_vs_ctrl_m4_rc_shift0 (oligos_7nt_test_vs_ctrl_m4_rc) |  |  |  |
    ; oligos_6nt_test_vs_ctrl_m3 versus oligos_7nt_test_vs_ctrl_m4_rc; m=2/2; ncol2=11; w=-2; offset=-2; strand=R; shift=0; score=0.62941; ksTCCTGGTkw-
    ; cor=; Ncor=
    a	5	10	1	4	1	1	3	1	4	13	21	0
    c	11	16	2	43	52	4	0	0	2	10	7	0
    g	19	15	1	2	1	3	47	51	0	17	8	0
    t	19	13	50	5	0	46	4	2	48	14	18	0

## 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=13; shift=0; ncol=13; wwCTTAAAATAyr
    ; Alignment reference
    a	8	13	4	3	6	27	26	29	28	2	29	3	10
    c	1	4	22	0	1	0	2	0	0	2	0	10	6
    g	6	5	2	6	2	0	1	0	0	1	1	2	9
    t	15	8	2	21	21	3	1	1	2	25	0	15	5
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=13; w=0; offset=0; strand=D; shift=0; score=      1; wwCTTAAAATAyr
    ; cor=; Ncor=
    a	8	13	4	3	6	27	26	29	28	2	29	3	10
    c	1	4	22	0	1	0	2	0	0	2	0	10	6
    g	6	5	2	6	2	0	1	0	0	1	1	2	9
    t	15	8	2	21	21	3	1	1	2	25	0	15	5
oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m5 versus oligos_7nt_test_vs_ctrl_m1; m=2/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=0.715855; wyCTTAAAAArt-
    ; cor=; Ncor=
    a	20	11	6	4	2	49	54	53	53	49	22	13	0
    c	8	15	40	0	3	0	0	3	1	1	8	12	0
    g	10	12	2	1	5	1	2	0	1	2	14	13	0
    t	18	18	8	51	46	6	0	0	1	4	12	18	0

## 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=14; shift=0; ncol=14; kdtargTAAGGAwa
    ; Alignment reference
    a	7	13	7	21	22	8	0	34	38	1	2	38	14	17
    c	6	2	7	8	2	2	1	4	0	0	4	1	8	9
    g	10	13	9	6	10	24	1	2	1	37	33	0	8	7
    t	17	12	17	5	6	6	38	0	1	2	1	1	10	7
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=14; w=0; offset=0; strand=D; shift=0; score=      1; kdtargTAAGGAwa
    ; cor=; Ncor=
    a	7	13	7	21	22	8	0	34	38	1	2	38	14	17
    c	6	2	7	8	2	2	1	4	0	0	4	1	8	9
    g	10	13	9	6	10	24	1	2	1	37	33	0	8	7
    t	17	12	17	5	6	6	38	0	1	2	1	1	10	7

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=11; shift=1; ncol=12; -wmACCAGGAsm
    ; Alignment reference
    a	0	18	14	48	2	4	46	0	5	50	13	19
    c	0	8	17	0	51	47	3	1	2	1	15	19
    g	0	7	10	2	0	0	4	52	43	2	16	11
    t	0	21	13	4	1	3	1	1	4	1	10	5
oligos_7nt_test_vs_ctrl_m4_shift1 (oligos_7nt_test_vs_ctrl_m4) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m4 versus oligos_7nt_test_vs_ctrl_m4; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=1; score=      1; -wmACCAGGAsm
    ; cor=; Ncor=
    a	0	18	14	48	2	4	46	0	5	50	13	19
    c	0	8	17	0	51	47	3	1	2	1	15	19
    g	0	7	10	2	0	0	4	52	43	2	16	11
    t	0	21	13	4	1	3	1	1	4	1	10	5
oligos_6nt_test_vs_ctrl_m3_rc_shift0 (oligos_6nt_test_vs_ctrl_m3_rc) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m4 versus oligos_6nt_test_vs_ctrl_m3_rc; m=2/2; ncol2=10; w=-1; offset=-1; strand=R; shift=0; score=0.62941; wwTACCAGga--
    ; cor=; Ncor=
    a	11	10	0	29	0	0	22	0	5	15	0	0
    c	6	6	0	0	30	27	4	1	7	5	0	0
    g	4	5	2	0	0	1	4	27	11	4	0	0
    t	9	9	28	1	0	2	0	2	7	6	0	0

## 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=14; shift=0; ncol=14; waAtAGCCTAgayk
    ; Alignment reference
    a	10	13	20	3	25	3	0	1	1	26	5	18	6	7
    c	5	4	1	3	0	0	28	25	3	0	3	2	9	3
    g	4	5	2	6	2	24	1	1	1	1	19	5	6	8
    t	10	7	6	17	2	2	0	2	24	2	2	4	8	11
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=14; w=0; offset=0; strand=D; shift=0; score=      1; waAtAGCCTAgayk
    ; cor=; Ncor=
    a	10	13	20	3	25	3	0	1	1	26	5	18	6	7
    c	5	4	1	3	0	0	28	25	3	0	3	2	9	3
    g	4	5	2	6	2	24	1	1	1	1	19	5	6	8
    t	10	7	6	17	2	2	0	2	24	2	2	4	8	11

## 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=11; shift=0; ncol=11; AATCAACCCra
    ; Alignment reference
    a	63	55	2	2	74	78	1	1	0	21	53
    c	7	10	4	76	5	1	79	78	79	6	9
    g	7	2	17	1	0	1	0	0	1	48	14
    t	3	13	57	1	1	0	0	1	0	5	4
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=11; w=0; offset=0; strand=D; shift=0; score=      1; AATCAACCCra
    ; cor=; Ncor=
    a	63	55	2	2	74	78	1	1	0	21	53
    c	7	10	4	76	5	1	79	78	79	6	9
    g	7	2	17	1	0	1	0	0	1	48	14
    t	3	13	57	1	1	0	0	1	0	5	4

## One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift0 ; 3 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=12; shift=0; ncol=12; wyCTTAAAAArt
    ; Alignment reference
    a	20	11	6	4	2	49	54	53	53	49	22	13
    c	8	15	40	0	3	0	0	3	1	1	8	12
    g	10	12	2	1	5	1	2	0	1	2	14	13
    t	18	18	8	51	46	6	0	0	1	4	12	18
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=1/2; ncol2=12; w=0; offset=0; strand=D; shift=0; score=      1; wyCTTAAAAArt
    ; cor=; Ncor=
    a	20	11	6	4	2	49	54	53	53	49	22	13
    c	8	15	40	0	3	0	0	3	1	1	8	12
    g	10	12	2	1	5	1	2	0	1	2	14	13
    t	18	18	8	51	46	6	0	0	1	4	12	18
oligos_7nt_test_vs_ctrl_m5_shift0 (oligos_7nt_test_vs_ctrl_m5) |  |  |  |
    ; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m5; m=2/2; ncol2=13; w=0; offset=0; strand=D; shift=0; score=0.715855; wwCTTAAAATAy
    ; cor=; Ncor=
    a	8	13	4	3	6	27	26	29	28	2	29	3
    c	1	4	22	0	1	0	2	0	0	2	0	10
    g	6	5	2	6	2	0	1	0	0	1	1	2
    t	15	8	2	21	21	3	1	1	2	25	0	15

## 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=13; shift=0; ncol=13; rraAGCAGCAtkt
    ; Alignment reference
    a	11	7	13	18	0	0	22	2	0	20	4	5	4
    c	2	4	2	1	0	23	0	1	22	1	4	2	5
    g	7	8	4	3	23	0	0	18	1	2	2	6	5
    t	3	4	4	1	0	0	1	2	0	0	13	10	9
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=13; w=0; offset=0; strand=D; shift=0; score=      1; rraAGCAGCAtkt
    ; cor=; Ncor=
    a	11	7	13	18	0	0	22	2	0	20	4	5	4
    c	2	4	2	1	0	23	0	1	22	1	4	2	5
    g	7	8	4	3	23	0	0	18	1	2	2	6	5
    t	3	4	4	1	0	0	1	2	0	0	13	10	9

## 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=18; shift=0; ncol=18; ymCTaATwAAAATwAkrw
    ; Alignment reference
    a	2	5	2	0	6	8	1	3	9	8	11	9	0	3	9	2	4	3
    c	4	4	8	0	2	1	2	0	0	2	0	0	1	0	1	0	2	1
    g	1	0	1	0	2	2	0	1	1	1	0	0	0	2	0	6	3	2
    t	4	2	0	11	1	0	8	7	1	0	0	2	10	6	1	3	2	5
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=18; w=0; offset=0; strand=D; shift=0; score=      1; ymCTaATwAAAATwAkrw
    ; cor=; Ncor=
    a	2	5	2	0	6	8	1	3	9	8	11	9	0	3	9	2	4	3
    c	4	4	8	0	2	1	2	0	0	2	0	0	1	0	1	0	2	1
    g	1	0	1	0	2	2	0	1	1	1	0	0	0	2	0	6	3	2
    t	4	2	0	11	1	0	8	7	1	0	0	2	10	6	1	3	2	5

## 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=12; shift=0; ncol=12; hdGATTAAAThh
    ; Alignment reference
    a	13	15	5	46	3	2	37	48	50	4	14	14
    c	13	4	6	2	0	0	5	0	0	2	16	16
    g	9	13	37	1	1	1	7	1	0	3	6	6
    t	15	18	2	1	46	47	1	1	0	41	14	14
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=12; w=0; offset=0; strand=D; shift=0; score=      1; hdGATTAAAThh
    ; cor=; Ncor=
    a	13	15	5	46	3	2	37	48	50	4	14	14
    c	13	4	6	2	0	0	5	0	0	2	16	16
    g	9	13	37	1	1	1	7	1	0	3	6	6
    t	15	18	2	1	46	47	1	1	0	41	14	14