# One-to-n alignments

    Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/www-data/2026/04/21/peak-motifs.2026-04-21.014834_2026-04-21.014834_X2uSrl/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/2026/04/21/peak-motifs.2026-04-21.014834_2026-04-21.014834_X2uSrl/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

## One-to-n matrix alignment; reference matrix: oligos_6nt_mkv2_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1; m=0 (reference); ncol1=10; shift=0; ncol=10; hwATACTAaw
    ; Alignment reference
    a	24	37	76	0	76	0	0	76	44	38
    c	21	11	0	0	0	76	0	0	6	1
    g	3	4	0	0	0	0	0	0	12	9
    t	28	24	0	76	0	0	76	0	14	28
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=1/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=      1; hwATACTAaw
    ; cor=; Ncor=
    a	24	37	76	0	76	0	0	76	44	38
    c	21	11	0	0	0	76	0	0	6	1
    g	3	4	0	0	0	0	0	0	12	9
    t	28	24	0	76	0	0	76	0	14	28
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_6nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=2/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.878154; wAATACTAAw
    ; cor=; Ncor=
    a	48	118	138	2	162	0	16	169	141	73
    c	37	17	0	0	0	173	2	2	6	6
    g	3	6	5	27	0	0	0	2	12	9
    t	85	32	30	144	11	0	155	0	14	85

## One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m1_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wAATACTAAwa
    ; Alignment reference
    a	48	118	138	2	162	0	16	169	141	73	86
    c	37	17	0	0	0	173	2	2	6	6	35
    g	3	6	5	27	0	0	0	2	12	9	25
    t	85	32	30	144	11	0	155	0	14	85	27
oligos_7nt_mkv2_m1_shift0 (oligos_7nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus oligos_7nt_mkv2_m1; m=1/2; ncol2=11; w=0; offset=0; strand=D; shift=0; score=      1; wAATACTAAwa
    ; cor=; Ncor=
    a	48	118	138	2	162	0	16	169	141	73	86
    c	37	17	0	0	0	173	2	2	6	6	35
    g	3	6	5	27	0	0	0	2	12	9	25
    t	85	32	30	144	11	0	155	0	14	85	27
oligos_6nt_mkv2_m1_shift0 (oligos_6nt_mkv2_m1) |  |  |  |
    ; oligos_7nt_mkv2_m1 versus oligos_6nt_mkv2_m1; m=2/2; ncol2=10; w=0; offset=0; strand=D; shift=0; score=0.878154; hwATACTAaw-
    ; cor=; Ncor=
    a	24	37	76	0	76	0	0	76	44	38	0
    c	21	11	0	0	0	76	0	0	6	1	0
    g	3	4	0	0	0	0	0	0	12	9	0
    t	28	24	0	76	0	0	76	0	14	28	0