# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/oligos_8nt_mkv2_m18/peak-motifs_oligos_8nt_mkv2_m18.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_m18/peak-motifs_oligos_8nt_mkv2_m18_vs_db_jaspar_core_nonredundant_vertebrates

## One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m18_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
oligos_8nt_mkv2_m18_shift0 (oligos_8nt_mkv2_m18oligos_8nt_mkv2_m18) |  |  |  |
    ; oligos_8nt_mkv2_m18 (oligos_8nt_mkv2_m18oligos_8nt_mkv2_m18); m=0 (reference); ncol1=12; shift=0; ncol=14; rsATTTsTAAAw--
    ; Alignment reference
    a	16	3	28	0	1	0	0	0	28	23	24	7	0	0
    c	0	17	0	0	0	0	15	0	0	0	2	1	0	0
    g	10	7	0	0	0	0	12	0	0	5	1	2	0	0
    t	2	1	0	28	27	28	1	28	0	0	1	18	0	0
MA0845.1_shift3 (FOXB1) |  |  |  |
    ; oligos_8nt_mkv2_m18 versus MA0845.1 (FOXB1); m=1/1; ncol2=11; w=9; offset=3; strand=D; shift=3; score=0.460072; ---wAwGTMAAyAt
    ; cor=; Ncor=
    a	0	0	0	2393.0	5343.0	1983.0	1159.0	180.0	4891.0	6841.0	6841.0	28.0	6841.0	1704.0
    c	0	0	0	272.0	263.0	218.0	54.0	240.0	1950.0	213.0	47.0	2252.0	0.0	573.0
    g	0	0	0	190.0	1498.0	409.0	6841.0	113.0	75.0	0.0	47.0	104.0	157.0	556.0
    t	0	0	0	4448.0	561.0	4858.0	124.0	6841.0	73.0	381.0	216.0	4589.0	147.0	4008.0