# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/oligos_8nt_mkv2_m28/peak-motifs_oligos_8nt_mkv2_m28.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.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 Myogenin_Rep3_motifs50/results/discovered_motifs/oligos_8nt_mkv2_m28/peak-motifs_oligos_8nt_mkv2_m28_vs_db_jaspar_core_nonredundant_vertebrates

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m28_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m28_shift0 (oligos_8nt_mkv2_m28oligos_8nt_mkv2_m28) |  |  |  |
    ; oligos_8nt_mkv2_m28 (oligos_8nt_mkv2_m28oligos_8nt_mkv2_m28); m=0 (reference); ncol1=12; shift=0; ncol=12; hsTCAAGTARvw
    ; Alignment reference
    a	2	0	0	0	7	7	0	0	7	5	3	2
    c	3	4	0	6	0	0	0	0	0	0	2	1
    g	0	3	0	0	0	0	7	0	0	2	2	1
    t	2	0	7	1	0	0	0	7	0	0	0	3
MA0673.1_rc_shift1 (NKX2-8_rc) |  |  |  |
    ; oligos_8nt_mkv2_m28 versus MA0673.1_rc (NKX2-8_rc); m=1/1; ncol2=9; w=9; offset=1; strand=R; shift=1; score=0.542685; -yTsRAGTGs--
    ; cor=; Ncor=
    a	0	811.0	2158.0	271.0	8562.0	8562.0	110.0	516.0	2155.0	249.0	0	0
    c	0	2593.0	696.0	4286.0	0.0	0.0	0.0	0.0	0.0	2843.0	0	0
    g	0	1964.0	908.0	2267.0	3197.0	91.0	8562.0	595.0	8562.0	3529.0	0	0
    t	0	3194.0	8562.0	1738.0	23.0	0.0	14.0	8562.0	70.0	1942.0	0	0