# One-to-n alignments

    Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m39/peak-motifs_dyads_m39.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_m39/peak-motifs_dyads_m39_vs_db_jaspar_core_nonredundant_vertebrates

## One-to-n matrix alignment; reference matrix: dyads_m39_shift5 ; 2 matrices ; sort_field=Ncor

Matrix name | Aligned logos | cor | Ncor | Aligned matrices
--- | --- | --- | --- | ---
dyads_m39_shift5 (dyads_m39dyads_m39) |  |  |  |
    ; dyads_m39 (dyads_m39dyads_m39); m=0 (reference); ncol1=10; shift=5; ncol=15; -----GwGAAATAyr
    ; Alignment reference
    a	0	0	0	0	0	5	25	0	56	56	56	0	56	5	21
    c	0	0	0	0	0	7	1	0	0	0	0	0	0	20	6
    g	0	0	0	0	0	40	3	56	0	0	0	0	0	5	23
    t	0	0	0	0	0	4	27	0	0	0	0	56	0	26	6
MA0102.4_rc_shift0 (CEBPA_rc) |  |  |  |
    ; dyads_m39 versus MA0102.4_rc (CEBPA_rc); m=1/1; ncol2=14; w=9; offset=-5; strand=R; shift=0; score=0.442908; wwaTTGTGCAATmw-
    ; cor=; Ncor=
    a	24153.0	20623.0	50992.0	1411.0	1092.0	9787.0	6308.0	2053.0	10928.0	75354.0	76586.0	4573.0	28452.0	24323.0	0
    c	16045.0	12932.0	7312.0	1381.0	340.0	1583.0	6751.0	678.0	57887.0	2365.0	722.0	12772.0	20062.0	15847.0	0
    g	17147.0	17396.0	16193.0	1034.0	5655.0	61538.0	3535.0	75124.0	936.0	282.0	826.0	7284.0	12801.0	14823.0	0
    t	21658.0	28052.0	4506.0	75177.0	71916.0	6095.0	62409.0	1148.0	9252.0	1002.0	869.0	54374.0	17688.0	24010.0	0