# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/oligos_8nt_mkv2_m11/peak-motifs_oligos_8nt_mkv2_m11.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_m11/peak-motifs_oligos_8nt_mkv2_m11_vs_db_jaspar_core_nonredundant_vertebrates

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m11_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m11_shift0 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11) |  |  |  |
    ; oligos_8nt_mkv2_m11 (oligos_8nt_mkv2_m11oligos_8nt_mkv2_m11); m=0 (reference); ncol1=13; shift=0; ncol=13; AGAAATRCACACT
    ; Alignment reference
    a	59	4	71	72	71	0	18	0	68	0	72	1	3
    c	0	2	1	0	0	2	2	71	1	72	0	52	0
    g	3	63	0	0	0	1	50	0	1	0	0	9	3
    t	10	3	0	0	1	69	2	1	2	0	0	10	66
MA0479.1_shift0 (FOXH1) |  |  |  |
    ; oligos_8nt_mkv2_m11 versus MA0479.1 (FOXH1); m=1/1; ncol2=11; w=11; offset=0; strand=D; shift=0; score=0.622566; ybsAATMCACA--
    ; cor=; Ncor=
    a	939.0	1578.0	973.0	8211.0	7547.0	0.0	2374.0	1414.0	8211.0	0.0	7138.0	0	0
    c	2840.0	2333.0	3261.0	0.0	0.0	0.0	5773.0	6797.0	0.0	8211.0	0.0	0	0
    g	1490.0	2137.0	3156.0	0.0	229.0	0.0	0.0	0.0	0.0	0.0	0.0	0	0
    t	2942.0	2163.0	821.0	0.0	435.0	8211.0	64.0	0.0	0.0	0.0	1073.0	0	0