# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/06/19/peak-motifs.2025-06-19.093456_2025-06-19.093456_nFlB6k/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/2025/06/19/peak-motifs.2025-06-19.093456_2025-06-19.093456_nFlB6k/results/discovered_vs_db/peak-motifs_motifs_vs_db_footprintDB-plants.tab

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m3_shift9 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m3_shift9 (oligos_6-8nt_m3) |  |  |  |
    ; oligos_6-8nt_m3; m=0 (reference); ncol1=11; shift=9; ncol=20; ---------ssACCGACCsc
    ; Alignment reference
    a	0	0	0	0	0	0	0	0	0	12	13	43	0	1	1	57	1	8	9	13
    c	0	0	0	0	0	0	0	0	0	16	22	6	61	54	3	1	57	47	24	21
    g	0	0	0	0	0	0	0	0	0	26	19	9	1	5	58	1	4	3	18	15
    t	0	0	0	0	0	0	0	0	0	8	8	4	0	2	0	3	0	4	11	13

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m2_shift3 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m2_shift3 (oligos_6-8nt_m2) |  |  |  |
    ; oligos_6-8nt_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---gkAGTACGyv
    ; Alignment reference
    a	0	0	0	6	6	29	0	0	31	0	1	5	8
    c	0	0	0	6	5	3	3	0	0	32	3	9	8
    g	0	0	0	16	8	0	28	0	0	0	26	6	12
    t	0	0	0	4	13	0	1	32	1	0	2	12	4

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m4_shift8 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m4_shift8 (oligos_6-8nt_m4) |  |  |  |
    ; oligos_6-8nt_m4; m=0 (reference); ncol1=10; shift=8; ncol=18; --------scCCCGCCsc
    ; Alignment reference
    a	0	0	0	0	0	0	0	0	9	9	0	0	0	0	0	0	11	9
    c	0	0	0	0	0	0	0	0	18	19	47	47	47	0	47	47	12	18
    g	0	0	0	0	0	0	0	0	15	8	0	0	0	47	0	0	14	11
    t	0	0	0	0	0	0	0	0	5	11	0	0	0	0	0	0	10	9

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m1_shift12 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m1_shift12 (oligos_6-8nt_m1) |  |  |  |
    ; oligos_6-8nt_m1; m=0 (reference); ncol1=12; shift=12; ncol=24; ------------wsGAAGGAACks
    ; Alignment reference
    a	0	0	0	0	0	0	0	0	0	0	0	0	9	4	0	22	23	1	1	20	21	2	5	5
    c	0	0	0	0	0	0	0	0	0	0	0	0	4	8	0	1	0	0	1	2	2	19	5	8
    g	0	0	0	0	0	0	0	0	0	0	0	0	4	7	24	1	0	23	22	2	1	2	7	6
    t	0	0	0	0	0	0	0	0	0	0	0	0	7	5	0	0	1	0	0	0	0	1	7	5

## One-to-n matrix alignment; reference matrix: oligos_6-8nt_m5_shift4 ; 1 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6-8nt_m5_shift4 (oligos_6-8nt_m5) |  |  |  |
    ; oligos_6-8nt_m5; m=0 (reference); ncol1=10; shift=4; ncol=14; ----scATGCAGsy
    ; Alignment reference
    a	0	0	0	0	8	8	42	0	0	0	42	0	3	9
    c	0	0	0	0	13	20	0	0	0	42	0	0	19	11
    g	0	0	0	0	14	7	0	0	42	0	0	42	12	10
    t	0	0	0	0	7	7	0	42	0	0	0	0	8	12