# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m34/peak-motifs_dyads_m34.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/dyads_m34/peak-motifs_dyads_m34_vs_db_jaspar_core_nonredundant_vertebrates

## One-to-n matrix alignment; reference matrix: dyads_m34_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m34_shift0 (dyads_m34dyads_m34) |  |  |  |
    ; dyads_m34 (dyads_m34dyads_m34); m=0 (reference); ncol1=15; shift=0; ncol=15; ssACGcrsssCCGvs
    ; Alignment reference
    a	1	4	15	0	0	3	8	2	2	2	3	0	0	6	2
    c	6	7	3	21	1	11	4	7	7	7	15	19	0	6	8
    g	10	7	2	0	20	5	7	9	11	9	3	2	21	7	8
    t	4	3	1	0	0	2	2	3	1	3	0	0	0	2	3
MA0259.1_rc_shift0 (ARNT::HIF1A_rc) |  |  |  |
    ; dyads_m34 versus MA0259.1_rc (ARNT::HIF1A_rc); m=1/1; ncol2=8; w=8; offset=0; strand=R; shift=0; score=0.412867; gCACGTvb-------
    ; cor=; Ncor=
    a	15.0	0.0	104.0	0.0	1.0	1.0	31.0	0.0	0	0	0	0	0	0	0
    c	20.0	104.0	0.0	104.0	0.0	23.0	34.0	49.0	0	0	0	0	0	0	0
    g	51.0	0.0	0.0	0.0	103.0	2.0	29.0	28.0	0	0	0	0	0	0	0
    t	18.0	0.0	0.0	0.0	0.0	78.0	10.0	27.0	0	0	0	0	0	0	0