# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/oligos_8nt_mkv2_m21/peak-motifs_oligos_8nt_mkv2_m21.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_m21/peak-motifs_oligos_8nt_mkv2_m21_vs_db_jaspar_core_nonredundant_vertebrates

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m21_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m21_shift0 (oligos_8nt_mkv2_m21oligos_8nt_mkv2_m21) |  |  |  |
    ; oligos_8nt_mkv2_m21 (oligos_8nt_mkv2_m21oligos_8nt_mkv2_m21); m=0 (reference); ncol1=12; shift=0; ncol=14; yTGTAGAACAkw--
    ; Alignment reference
    a	1	0	0	0	32	0	32	32	0	32	2	14	0	0
    c	16	0	0	0	0	1	0	0	30	0	0	1	0	0
    g	4	1	32	0	0	31	0	0	0	0	10	1	0	0
    t	11	31	0	32	0	0	0	0	2	0	20	16	0	0
MA0868.2_shift4 (SOX8) |  |  |  |
    ; oligos_8nt_mkv2_m21 versus MA0868.2 (SOX8); m=1/1; ncol2=10; w=8; offset=4; strand=D; shift=4; score=0.416451; ----agAACAATrg
    ; cor=; Ncor=
    a	0	0	0	0	1827.0	740.0	1827.0	1827.0	3.0	1827.0	1827.0	273.0	1356.0	300.0
    c	0	0	0	0	1124.0	414.0	151.0	0.0	1827.0	0.0	43.0	36.0	208.0	421.0
    g	0	0	0	0	854.0	1827.0	263.0	0.0	35.0	0.0	0.0	20.0	1827.0	912.0
    t	0	0	0	0	724.0	571.0	222.0	45.0	70.0	16.0	36.0	1827.0	287.0	193.0