# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -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/2025/05/21/peak-motifs.2025-05-21.033913_2025-05-21.033913_SwV7J2/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB-plants.tab

## One-to-n matrix alignment; reference matrix: dyads_m1_shift4 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m1_shift4 (dyads_m1) |  |  |  |
    ; dyads_m1; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wwAATGATtrw
    ; Alignment reference
    a	0	0	0	0	28	20	80	80	0	0	80	0	17	29	24
    c	0	0	0	0	15	18	0	0	3	0	0	0	8	13	16
    g	0	0	0	0	12	14	0	0	0	80	0	0	19	20	12
    t	0	0	0	0	25	28	0	0	77	0	0	80	36	18	28

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m2_shift5 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m2_shift5 (oligos_7nt_mkv2_m2) |  |  |  |
    ; oligos_7nt_mkv2_m2; m=0 (reference); ncol1=11; shift=5; ncol=16; -----wtCCTTTTCwt
    ; Alignment reference
    a	0	0	0	0	0	34	25	1	0	11	2	2	5	4	31	21
    c	0	0	0	0	0	7	15	94	93	2	15	10	5	97	13	19
    g	0	0	0	0	0	12	22	1	1	2	0	4	5	0	8	13
    t	0	0	0	0	0	48	39	5	7	86	84	85	86	0	49	48

## One-to-n matrix alignment; reference matrix: dyads_m4_shift7 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m4_shift7 (dyads_m4) |  |  |  |
    ; dyads_m4; m=0 (reference); ncol1=10; shift=7; ncol=17; -------whACCAAAww
    ; Alignment reference
    a	0	0	0	0	0	0	0	18	19	63	0	0	61	63	63	25	25
    c	0	0	0	0	0	0	0	12	16	0	63	62	0	0	0	9	12
    g	0	0	0	0	0	0	0	13	10	0	0	1	2	0	0	11	4
    t	0	0	0	0	0	0	0	20	18	0	0	0	0	0	0	18	22

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m3_shift2 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m3_shift2 (oligos_6nt_mkv2_m3) |  |  |  |
    ; oligos_6nt_mkv2_m3; m=0 (reference); ncol1=10; shift=2; ncol=12; --wrAGATAGwd
    ; Alignment reference
    a	0	0	16	19	48	0	52	0	46	0	21	15
    c	0	0	5	3	2	0	0	0	5	0	5	7
    g	0	0	12	18	2	52	0	1	0	52	10	15
    t	0	0	19	12	0	0	0	51	1	0	16	15

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m4_shift4 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m4_shift4 (oligos_8nt_mkv2_m4) |  |  |  |
    ; oligos_8nt_mkv2_m4; m=0 (reference); ncol1=12; shift=4; ncol=16; ----wwGTGACAGAkw
    ; Alignment reference
    a	0	0	0	0	18	13	3	1	1	34	4	35	3	36	9	13
    c	0	0	0	0	4	3	0	2	0	0	30	1	2	1	1	5
    g	0	0	0	0	5	6	35	2	37	2	3	2	34	0	15	9
    t	0	0	0	0	12	17	1	34	1	3	2	1	0	2	14	12

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m1_shift2 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m1_shift2 (oligos_8nt_mkv2_m1) |  |  |  |
    ; oligos_8nt_mkv2_m1; m=0 (reference); ncol1=12; shift=2; ncol=14; --wyCTTACTACww
    ; Alignment reference
    a	0	0	17	9	1	3	1	40	2	2	43	2	17	20
    c	0	0	6	12	43	1	3	1	38	1	1	40	8	4
    g	0	0	4	5	1	0	0	1	2	1	1	2	2	2
    t	0	0	19	20	1	42	42	4	4	42	1	2	19	20

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m2_shift6 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m2_shift6 (oligos_6nt_mkv2_m2) |  |  |  |
    ; oligos_6nt_mkv2_m2; m=0 (reference); ncol1=10; shift=6; ncol=16; ------wdTAGTAAdw
    ; Alignment reference
    a	0	0	0	0	0	0	22	16	0	55	0	0	55	55	17	20
    c	0	0	0	0	0	0	8	8	0	0	0	0	0	0	8	4
    g	0	0	0	0	0	0	9	14	0	0	55	0	0	0	16	12
    t	0	0	0	0	0	0	16	17	55	0	0	55	0	0	14	19

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m2_shift7 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m2_shift7 (oligos_8nt_mkv2_m2) |  |  |  |
    ; oligos_8nt_mkv2_m2; m=0 (reference); ncol1=12; shift=7; ncol=19; -------awGAAAAGGCww
    ; Alignment reference
    a	0	0	0	0	0	0	0	20	14	2	46	44	45	44	4	1	5	26	22
    c	0	0	0	0	0	0	0	9	5	1	0	3	0	0	1	1	38	5	6
    g	0	0	0	0	0	0	0	9	9	43	1	2	2	0	43	45	3	3	5
    t	0	0	0	0	0	0	0	11	21	3	2	0	2	5	1	2	3	15	16

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift4 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m1_shift4 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=12; shift=4; ncol=16; ----wdGGGACAgaaw
    ; Alignment reference
    a	0	0	0	0	21	21	3	3	1	54	4	50	10	32	24	22
    c	0	0	0	0	7	4	2	2	0	1	53	1	9	7	10	10
    g	0	0	0	0	9	15	52	49	57	2	1	7	34	6	11	9
    t	0	0	0	0	22	19	2	5	1	2	1	1	6	14	14	18

## One-to-n matrix alignment; reference matrix: dyads_m3_shift7 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m3_shift7 (dyads_m3) |  |  |  |
    ; dyads_m3; m=0 (reference); ncol1=18; shift=7; ncol=25; -------mmCTThtwthhwwTTCwt
    ; Alignment reference
    a	0	0	0	0	0	0	0	24	23	1	0	1	21	13	22	16	18	21	25	20	1	3	0	25	14
    c	0	0	0	0	0	0	0	17	18	64	1	1	19	16	11	15	17	20	14	14	0	0	66	15	13
    g	0	0	0	0	0	0	0	10	9	0	2	0	7	10	6	9	7	8	9	8	0	1	0	5	11
    t	0	0	0	0	0	0	0	15	16	1	63	64	19	27	27	26	24	17	18	24	65	62	0	21	28

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m3_shift4 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m3_shift4 (oligos_8nt_mkv2_m3) |  |  |  |
    ; oligos_8nt_mkv2_m3; m=0 (reference); ncol1=12; shift=4; ncol=16; ----rwGGAGGAGAwr
    ; Alignment reference
    a	0	0	0	0	12	16	3	3	36	0	5	35	3	35	16	18
    c	0	0	0	0	1	4	0	0	4	0	2	2	1	0	4	2
    g	0	0	0	0	21	6	36	38	0	41	35	3	36	6	10	13
    t	0	0	0	0	8	16	3	1	2	1	0	2	2	1	12	9

## One-to-n matrix alignment; reference matrix: dyads_m2_shift1 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m2_shift1 (dyads_m2) |  |  |  |
    ; dyads_m2; m=0 (reference); ncol1=14; shift=1; ncol=15; -adGGAGAGAAGGrd
    ; Alignment reference
    a	0	24	19	10	10	46	4	48	3	49	51	2	9	25	17
    c	0	5	5	2	5	1	3	1	3	1	0	1	3	7	6
    g	0	14	15	41	39	5	44	4	49	6	5	48	43	15	15
    t	0	14	18	4	3	5	6	4	2	1	1	6	2	10	19

## One-to-n matrix alignment; reference matrix: dyads_m5_shift2 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m5_shift2 (dyads_m5) |  |  |  |
    ; dyads_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --wwCGAwyACAha
    ; Alignment reference
    a	0	0	21	18	1	0	52	24	12	48	4	54	19	22
    c	0	0	10	13	58	0	3	13	15	3	49	2	15	14
    g	0	0	13	11	1	57	2	8	12	1	2	2	8	10
    t	0	0	16	18	0	3	3	15	21	8	5	2	18	14

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift4 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m1_shift4 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=4; ncol=15; ----wtCCTCTTCww
    ; Alignment reference
    a	0	0	0	0	32	29	6	14	6	2	8	0	7	46	36
    c	0	0	0	0	27	28	107	101	8	105	10	1	113	26	27
    g	0	0	0	0	12	16	1	1	0	0	3	0	1	7	15
    t	0	0	0	0	54	52	11	9	111	18	104	124	4	46	47

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m5_shift5 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m5_shift5 (oligos_8nt_mkv2_m5) |  |  |  |
    ; oligos_8nt_mkv2_m5; m=0 (reference); ncol1=12; shift=5; ncol=17; -----wrGTGGAGGArr
    ; Alignment reference
    a	0	0	0	0	0	15	15	1	9	0	3	35	8	2	40	15	21
    c	0	0	0	0	0	2	8	0	1	3	0	1	0	0	1	3	4
    g	0	0	0	0	0	8	15	42	1	37	39	1	34	40	0	16	12
    t	0	0	0	0	0	18	5	0	32	3	1	6	1	1	2	9	6